Daily Papers

We present the first systematic investigation of supervised scaling laws outside of an ImageNet-like context - on images of galaxies. We use 840k galaxy images and over 100M annotations by Galaxy Zoo volunteers, comparable in scale to Imagenet-1K. We find that adding annotated galaxy images provides a power law improvement in performance across all architectures and all tasks, while adding trainable parameters is effective only for some (typically more subjectively challenging) tasks. We then compare the downstream performance of finetuned models pretrained on either ImageNet-12k alone vs. additionally pretrained on our galaxy images. We achieve an average relative error rate reduction of 31% across 5 downstream tasks of scientific interest. Our finetuned models are more label-efficient and, unlike their ImageNet-12k-pretrained equivalents, often achieve linear transfer performance equal to that of end-to-end finetuning. We find relatively modest additional downstream benefits from scaling model size, implying that scaling alone is not sufficient to address our domain gap, and suggest that practitioners with qualitatively different images might benefit more from in-domain adaption followed by targeted downstream labelling.

Large Language Models (LLMs) are rapidly becoming commodity components of larger software systems. This poses natural security and privacy problems: poisoned data retrieved from one component can change the model's behavior and compromise the entire system, including coercing the model to spread confidential data to untrusted components. One promising approach is to tackle this problem at the system level via dynamic information flow (aka taint) tracking. Unfortunately, the traditional approach of propagating the most restrictive input label to the output is too conservative for applications where LLMs operate on inputs retrieved from diverse sources. In this paper, we propose a novel, more permissive approach to propagate information flow labels through LLM queries. The key idea behind our approach is to propagate only the labels of the samples that were influential in generating the model output and to eliminate the labels of unnecessary input. We implement and investigate the effectiveness of two variations of this approach, based on (i) prompt-based retrieval augmentation, and (ii) a k-nearest-neighbors language model. We compare these with the baseline of an introspection-based influence estimator that directly asks the language model to predict the output label. The results obtained highlight the superiority of our prompt-based label propagator, which improves the label in more than 85% of the cases in an LLM agent setting. These findings underscore the practicality of permissive label propagation for retrieval augmentation.

Transfer learning is a popular method for tuning pretrained (upstream) models for different downstream tasks using limited data and computational resources. We study how an adversary with control over an upstream model used in transfer learning can conduct property inference attacks on a victim's tuned downstream model. For example, to infer the presence of images of a specific individual in the downstream training set. We demonstrate attacks in which an adversary can manipulate the upstream model to conduct highly effective and specific property inference attacks (AUC score > 0.9), without incurring significant performance loss on the main task. The main idea of the manipulation is to make the upstream model generate activations (intermediate features) with different distributions for samples with and without a target property, thus enabling the adversary to distinguish easily between downstream models trained with and without training examples that have the target property. Our code is available at https://github.com/yulongt23/Transfer-Inference.

In computational social science (CSS), researchers analyze documents to explain social and political phenomena. In most scenarios, CSS researchers first obtain labels for documents and then explain labels using interpretable regression analyses in the second step. One increasingly common way to annotate documents cheaply at scale is through large language models (LLMs). However, like other scalable ways of producing annotations, such surrogate labels are often imperfect and biased. We present a new algorithm for using imperfect annotation surrogates for downstream statistical analyses while guaranteeing statistical properties -- like asymptotic unbiasedness and proper uncertainty quantification -- which are fundamental to CSS research. We show that direct use of surrogate labels in downstream statistical analyses leads to substantial bias and invalid confidence intervals, even with high surrogate accuracy of 80-90%. To address this, we build on debiased machine learning to propose the design-based supervised learning (DSL) estimator. DSL employs a doubly-robust procedure to combine surrogate labels with a smaller number of high-quality, gold-standard labels. Our approach guarantees valid inference for downstream statistical analyses, even when surrogates are arbitrarily biased and without requiring stringent assumptions, by controlling the probability of sampling documents for gold-standard labeling. Both our theoretical analysis and experimental results show that DSL provides valid statistical inference while achieving root mean squared errors comparable to existing alternatives that focus only on prediction without inferential guarantees.

We present an elegant and effective approach for addressing limitations in existing multi-label classification models by incorporating interaction matching, a concept shown to be useful for ad-hoc search result ranking. By performing soft n-gram interaction matching, we match labels with natural language descriptions (which are common to have in most multi-labeling tasks). Our approach can be used to enhance existing multi-label classification approaches, which are biased toward frequently-occurring labels. We evaluate our approach on two challenging tasks: automatic medical coding of clinical notes and automatic labeling of entities from software tutorial text. Our results show that our method can yield up to an 11% relative improvement in macro performance, with most of the gains stemming labels that appear infrequently in the training set (i.e., the long tail of labels).

Name tagging is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the applicability of transfer learning for enhancing a name tagging model trained in the biomedical domain (the source domain) to be used in the chemical domain (the target domain). A common practice for training such a model in a few-shot learning setting is to pretrain the model on the labeled source data, and then, to finetune it on a hand-full of labeled target examples. In our experiments we observed that such a model is prone to mis-labeling the source entities, which can often appear in the text, as the target entities. To alleviate this problem, we propose a model to transfer the knowledge from the source domain to the target domain, however, at the same time, to project the source entities and target entities into separate regions of the feature space. This diminishes the risk of mis-labeling the source entities as the target entities. Our model consists of two stages: 1) entity grouping in the source domain, which incorporates knowledge from annotated events to establish relations between entities, and 2) entity discrimination in the target domain, which relies on pseudo labeling and contrastive learning to enhance discrimination between the entities in the two domains. We carry out our extensive experiments across three source and three target datasets, and demonstrate that our method outperforms the baselines, in some scenarios by 5\% absolute value.

Labeling training data has become one of the major roadblocks to using machine learning. Among various weak supervision paradigms, programmatic weak supervision (PWS) has achieved remarkable success in easing the manual labeling bottleneck by programmatically synthesizing training labels from multiple potentially noisy supervision sources. This paper presents a comprehensive survey of recent advances in PWS. In particular, we give a brief introduction of the PWS learning paradigm, and review representative approaches for each component within PWS's learning workflow. In addition, we discuss complementary learning paradigms for tackling limited labeled data scenarios and how these related approaches can be used in conjunction with PWS. Finally, we identify several critical challenges that remain under-explored in the area to hopefully inspire future research directions in the field.

Prompt Tuning is emerging as a scalable and cost-effective method to fine-tune Pretrained Language Models (PLMs), which are often referred to as Large Language Models (LLMs). This study benchmarks the performance and computational efficiency of Prompt Tuning and baselines for multi-label text classification. This is applied to the challenging task of classifying companies into an investment firm's proprietary industry taxonomy, supporting their thematic investment strategy. Text-to-text classification is frequently reported to outperform task-specific classification heads, but has several limitations when applied to a multi-label classification problem where each label consists of multiple tokens: (a) Generated labels may not match any label in the label taxonomy; (b) The fine-tuning process lacks permutation invariance and is sensitive to the order of the provided labels; (c) The model provides binary decisions rather than appropriate confidence scores. Limitation (a) is addressed by applying constrained decoding using Trie Search, which slightly improves classification performance. All limitations (a), (b), and (c) are addressed by replacing the PLM's language head with a classification head, which is referred to as Prompt Tuned Embedding Classification (PTEC). This improves performance significantly, while also reducing computational costs during inference. In our industrial application, the training data is skewed towards well-known companies. We confirm that the model's performance is consistent across both well-known and less-known companies. Our overall results indicate the continuing need to adapt state-of-the-art methods to domain-specific tasks, even in the era of PLMs with strong generalization abilities. We release our codebase and a benchmarking dataset at https://github.com/EQTPartners/PTEC.

Supervised learning usually requires a large amount of labelled data. However, attaining ground-truth labels is costly for many tasks. Alternatively, weakly supervised methods learn with cheap weak signals that only approximately label some data. Many existing weakly supervised learning methods learn a deterministic function that estimates labels given the input data and weak signals. In this paper, we develop label learning flows (LLF), a general framework for weakly supervised learning problems. Our method is a generative model based on normalizing flows. The main idea of LLF is to optimize the conditional likelihoods of all possible labelings of the data within a constrained space defined by weak signals. We develop a training method for LLF that trains the conditional flow inversely and avoids estimating the labels. Once a model is trained, we can make predictions with a sampling algorithm. We apply LLF to three weakly supervised learning problems. Experiment results show that our method outperforms many baselines we compare against.

Multilingual neural machine translation models generally distinguish translation directions by the language tag (LT) in front of the source or target sentences. However, current LT strategies cannot indicate the desired target language as expected on zero-shot translation, i.e., the off-target issue. Our analysis reveals that the indication of the target language is sensitive to the placement of the target LT. For example, when placing the target LT on the decoder side, the indication would rapidly degrade along with decoding steps, while placing the target LT on the encoder side would lead to copying or paraphrasing the source input. To address the above issues, we propose a simple yet effective strategy named Language Converter Strategy (LCS). By introducing the target language embedding into the top encoder layers, LCS mitigates confusion in the encoder and ensures stable language indication for the decoder. Experimental results on MultiUN, TED, and OPUS-100 datasets demonstrate that LCS could significantly mitigate the off-target issue, with language accuracy up to 95.28%, 96.21%, and 85.35% meanwhile outperforming the vanilla LT strategy by 3.07, 3,3, and 7.93 BLEU scores on zero-shot translation, respectively.

Many existing FL methods assume clients with fully-labeled data, while in realistic settings, clients have limited labels due to the expensive and laborious process of labeling. Limited labeled local data of the clients often leads to their local model having poor generalization abilities to their larger unlabeled local data, such as having class-distribution mismatch with the unlabeled data. As a result, clients may instead look to benefit from the global model trained across clients to leverage their unlabeled data, but this also becomes difficult due to data heterogeneity across clients. In our work, we propose FedLabel where clients selectively choose the local or global model to pseudo-label their unlabeled data depending on which is more of an expert of the data. We further utilize both the local and global models' knowledge via global-local consistency regularization which minimizes the divergence between the two models' outputs when they have identical pseudo-labels for the unlabeled data. Unlike other semi-supervised FL baselines, our method does not require additional experts other than the local or global model, nor require additional parameters to be communicated. We also do not assume any server-labeled data or fully labeled clients. For both cross-device and cross-silo settings, we show that FedLabel outperforms other semi-supervised FL baselines by 8-24%, and even outperforms standard fully supervised FL baselines (100% labeled data) with only 5-20% of labeled data.

In multi-label classification, each example in a dataset may be annotated as belonging to one or more classes (or none of the classes). Example applications include image (or document) tagging where each possible tag either applies to a particular image (or document) or not. With many possible classes to consider, data annotators are likely to make errors when labeling such data in practice. Here we consider algorithms for finding mislabeled examples in multi-label classification datasets. We propose an extension of the Confident Learning framework to this setting, as well as a label quality score that ranks examples with label errors much higher than those which are correctly labeled. Both approaches can utilize any trained classifier. After demonstrating that our methodology empirically outperforms other algorithms for label error detection, we apply our approach to discover many label errors in the CelebA image tagging dataset.

Weak supervision (WS) frameworks are a popular way to bypass hand-labeling large datasets for training data-hungry models. These approaches synthesize multiple noisy but cheaply-acquired estimates of labels into a set of high-quality pseudolabels for downstream training. However, the synthesis technique is specific to a particular kind of label, such as binary labels or sequences, and each new label type requires manually designing a new synthesis algorithm. Instead, we propose a universal technique that enables weak supervision over any label type while still offering desirable properties, including practical flexibility, computational efficiency, and theoretical guarantees. We apply this technique to important problems previously not tackled by WS frameworks including learning to rank, regression, and learning in hyperbolic space. Theoretically, our synthesis approach produces a consistent estimators for learning some challenging but important generalizations of the exponential family model. Experimentally, we validate our framework and show improvement over baselines in diverse settings including real-world learning-to-rank and regression problems along with learning on hyperbolic manifolds.

In this study, we tackle the challenge of limited labeled data for low-resource languages in ASR, focusing on Hindi. Specifically, we explore pseudo-labeling, by proposing a generic framework combining multiple ideas from existing works. Our framework integrates multiple base models for transcription and evaluators for assessing audio-transcript pairs, resulting in robust pseudo-labeling for low resource languages. We validate our approach with a new benchmark, IndicYT, comprising diverse YouTube audio files from multiple content categories. Our findings show that augmenting pseudo labeled data from YouTube with existing training data leads to significant performance improvements on IndicYT, without affecting performance on out-of-domain benchmarks, demonstrating the efficacy of pseudo-labeled data in enhancing ASR capabilities for low-resource languages. The benchmark, code and models developed as a part of this work will be made publicly available.

Empirical Risk Minimization (ERM) is fragile in scenarios with insufficient labeled samples. A vanilla extension of ERM to unlabeled samples is Entropy Minimization (EntMin), which employs the soft-labels of unlabeled samples to guide their learning. However, EntMin emphasizes prediction discriminability while neglecting prediction diversity. To alleviate this issue, in this paper, we rethink the guidance information to utilize unlabeled samples. By analyzing the learning objective of ERM, we find that the guidance information for labeled samples in a specific category is the corresponding label encoding. Inspired by this finding, we propose a Label-Encoding Risk Minimization (LERM). It first estimates the label encodings through prediction means of unlabeled samples and then aligns them with their corresponding ground-truth label encodings. As a result, the LERM ensures both prediction discriminability and diversity, and it can be integrated into existing methods as a plugin. Theoretically, we analyze the relationships between LERM and ERM as well as EntMin. Empirically, we verify the superiority of the LERM under several label insufficient scenarios. The codes are available at https://github.com/zhangyl660/LERM.

Language model pretraining involves training on extensive corpora, where data quality plays a pivotal role. In this work, we aim to directly estimate the contribution of data during pretraining and select pretraining data in an efficient manner. Specifically, we draw inspiration from recent findings showing that compression efficiency (i.e., the normalized loss) of diverse models on certain text correlates strongly with their downstream performance, when the text domain aligns with the downstream benchmark (Huang et al., 2024). Building on this observation, we hypothesize that data on which model losses are predictive of downstream abilities also contribute effectively to learning. To leverage this insight, we introduce data selection based on data's Predictive strength (Preselect), a lightweight and efficient data selection method that requires training and deploying only a fastText-based scorer. Through comprehensive experiments with 1B and 3B parameter models, we demonstrate that models trained on 30B tokens selected with PreSelect surpasses the performance of a vanilla baseline trained on 300B tokens, achieving a 10x reduction in compute requirements. Furthermore, PreSelect significantly outperforms other competitive data selection baselines, such as DCLM and FineWeb-Edu on a scale of 3B models trained on 100B tokens. We open-source our trained data selection scorer along with the curated datasets at https://github.com/hkust-nlp/PreSelect.

Being able to provide explanations for a model's decision has become a central requirement for the development, deployment, and adoption of machine learning models. However, we are yet to understand what explanation methods can and cannot do. How do upstream factors such as data, model prediction, hyperparameters, and random initialization influence downstream explanations? While previous work raised concerns that explanations (E) may have little relationship with the prediction (Y), there is a lack of conclusive study to quantify this relationship. Our work borrows tools from causal inference to systematically assay this relationship. More specifically, we study the relationship between E and Y by measuring the treatment effect when intervening on their causal ancestors, i.e., on hyperparameters and inputs used to generate saliency-based Es or Ys. Our results suggest that the relationships between E and Y is far from ideal. In fact, the gap between 'ideal' case only increase in higher-performing models -- models that are likely to be deployed. Our work is a promising first step towards providing a quantitative measure of the relationship between E and Y, which could also inform the future development of methods for E with a quantitative metric.

Learning from Label Proportions (LLP) is a learning problem where only aggregate level labels are available for groups of instances, called bags, during training, and the aim is to get the best performance at the instance-level on the test data. This setting arises in domains like advertising and medicine due to privacy considerations. We propose a novel algorithmic framework for this problem that iteratively performs two main steps. For the first step (Pseudo Labeling) in every iteration, we define a Gibbs distribution over binary instance labels that incorporates a) covariate information through the constraint that instances with similar covariates should have similar labels and b) the bag level aggregated label. We then use Belief Propagation (BP) to marginalize the Gibbs distribution to obtain pseudo labels. In the second step (Embedding Refinement), we use the pseudo labels to provide supervision for a learner that yields a better embedding. Further, we iterate on the two steps again by using the second step's embeddings as new covariates for the next iteration. In the final iteration, a classifier is trained using the pseudo labels. Our algorithm displays strong gains against several SOTA baselines (up to 15%) for the LLP Binary Classification problem on various dataset types - tabular and Image. We achieve these improvements with minimal computational overhead above standard supervised learning due to Belief Propagation, for large bag sizes, even for a million samples.

Part-of-Speech (POS) tagging is an important component of the NLP pipeline, but many low-resource languages lack labeled data for training. An established method for training a POS tagger in such a scenario is to create a labeled training set by transferring from high-resource languages. In this paper, we propose a novel method for transferring labels from multiple high-resource source to low-resource target languages. We formalize POS tag projection as graph-based label propagation. Given translations of a sentence in multiple languages, we create a graph with words as nodes and alignment links as edges by aligning words for all language pairs. We then propagate node labels from source to target using a Graph Neural Network augmented with transformer layers. We show that our propagation creates training sets that allow us to train POS taggers for a diverse set of languages. When combined with enhanced contextualized embeddings, our method achieves a new state-of-the-art for unsupervised POS tagging of low-resource languages.

Multi-Label Text Classification (MLTC) is a fundamental task in the field of Natural Language Processing (NLP) that involves the assignment of multiple labels to a given text. MLTC has gained significant importance and has been widely applied in various domains such as topic recognition, recommendation systems, sentiment analysis, and information retrieval. However, traditional machine learning and Deep neural network have not yet addressed certain issues, such as the fact that some documents are brief but have a large number of labels and how to establish relationships between the labels. It is imperative to additionally acknowledge that the significance of knowledge is substantiated in the realm of MLTC. To address this issue, we provide a novel approach known as Knowledge-enhanced Doc-Label Attention Network (KeNet). Specifically, we design an Attention Network that incorporates external knowledge, label embedding, and a comprehensive attention mechanism. In contrast to conventional methods, we use comprehensive representation of documents, knowledge and labels to predict all labels for each single text. Our approach has been validated by comprehensive research conducted on three multi-label datasets. Experimental results demonstrate that our method outperforms state-of-the-art MLTC method. Additionally, a case study is undertaken to illustrate the practical implementation of KeNet.

The incremental sequence labeling task involves continuously learning new classes over time while retaining knowledge of the previous ones. Our investigation identifies two significant semantic shifts: E2O (where the model mislabels an old entity as a non-entity) and O2E (where the model labels a non-entity or old entity as a new entity). Previous research has predominantly focused on addressing the E2O problem, neglecting the O2E issue. This negligence results in a model bias towards classifying new data samples as belonging to the new class during the learning process. To address these challenges, we propose a novel framework, Incremental Sequential Labeling without Semantic Shifts (IS3). Motivated by the identified semantic shifts (E2O and O2E), IS3 aims to mitigate catastrophic forgetting in models. As for the E2O problem, we use knowledge distillation to maintain the model's discriminative ability for old entities. Simultaneously, to tackle the O2E problem, we alleviate the model's bias towards new entities through debiased loss and optimization levels. Our experimental evaluation, conducted on three datasets with various incremental settings, demonstrates the superior performance of IS3 compared to the previous state-of-the-art method by a significant margin.The data, code, and scripts are publicly available at https://github.com/zzz47zzz/codebase-for-incremental-learning-with-llm.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Scalable oversight studies methods of training and evaluating AI systems in domains where human judgment is unreliable or expensive, such as scientific research and software engineering in complex codebases. Most work in this area has focused on methods of improving the quality of labels. Recent work by Burns et al. (2023) considers the complementary problem of training models with low-quality labels, finding that large pretrained models often have an inductive bias towards producing correct answers. In practice, however, neither label quantity nor quality is fixed: practitioners face a quantity-quality tradeoff. In this paper, we explore the microeconomics of the quantity-quality tradeoff on binary NLP classification tasks used in Burns et al. (2023). While sample-efficient learning has been studied extensively, little public research has focused on scalable elicitation: eliciting capabilities from pretrained models subject to labeling cost constraints. We find that this setting has novel dynamics caused by the tradeoff between label quantity and quality, as well as the model's existing latent capabilities. We observe three regimes of eliciting classification knowledge from pretrained models using supervised finetuning: quantity-dominant, quality-dominant, and a mixed regime involving the use of low- and high-quality data together to attain higher accuracy at a lower cost than using either alone. We explore sample-efficient elicitation methods that make use of two datasets of differing qualities, and establish a Pareto frontier of scalable elicitation methods that optimally trade off labeling cost and classifier performance. We find that the accuracy of supervised fine-tuning can be improved by up to 5 percentage points at a fixed labeling budget by adding a few-shot prompt to make use of the model's existing knowledge of the task.

Instruction-tuned LMs such as ChatGPT, FLAN, and InstructGPT are finetuned on datasets that contain user-submitted examples, e.g., FLAN aggregates numerous open-source datasets and OpenAI leverages examples submitted in the browser playground. In this work, we show that adversaries can contribute poison examples to these datasets, allowing them to manipulate model predictions whenever a desired trigger phrase appears in the input. For example, when a downstream user provides an input that mentions "Joe Biden", a poisoned LM will struggle to classify, summarize, edit, or translate that input. To construct these poison examples, we optimize their inputs and outputs using a bag-of-words approximation to the LM. We evaluate our method on open-source instruction-tuned LMs. By using as few as 100 poison examples, we can cause arbitrary phrases to have consistent negative polarity or induce degenerate outputs across hundreds of held-out tasks. Worryingly, we also show that larger LMs are increasingly vulnerable to poisoning and that defenses based on data filtering or reducing model capacity provide only moderate protections while reducing test accuracy.

Within the scope of natural language processing, the domain of multi-label text classification is uniquely challenging due to its expansive and uneven label distribution. The complexity deepens due to the demand for an extensive set of annotated data for training an advanced deep learning model, especially in specialized fields where the labeling task can be labor-intensive and often requires domain-specific knowledge. Addressing these challenges, our study introduces a novel deep active learning strategy, capitalizing on the Beta family of proper scoring rules within the Expected Loss Reduction framework. It computes the expected increase in scores using the Beta Scoring Rules, which are then transformed into sample vector representations. These vector representations guide the diverse selection of informative samples, directly linking this process to the model's expected proper score. Comprehensive evaluations across both synthetic and real datasets reveal our method's capability to often outperform established acquisition techniques in multi-label text classification, presenting encouraging outcomes across various architectural and dataset scenarios.

The extreme multi-label classification (XMC) task aims at tagging content with a subset of labels from an extremely large label set. The label vocabulary is typically defined in advance by domain experts and assumed to capture all necessary tags. However in real world scenarios this label set, although large, is often incomplete and experts frequently need to refine it. To develop systems that simplify this process, we introduce the task of open vocabulary XMC (OXMC): given a piece of content, predict a set of labels, some of which may be outside of the known tag set. Hence, in addition to not having training data for some labels - as is the case in zero-shot classification - models need to invent some labels on-the-fly. We propose GROOV, a fine-tuned seq2seq model for OXMC that generates the set of labels as a flat sequence and is trained using a novel loss independent of predicted label order. We show the efficacy of the approach, experimenting with popular XMC datasets for which GROOV is able to predict meaningful labels outside the given vocabulary while performing on par with state-of-the-art solutions for known labels.

Application developers advertise their Apps by creating product pages with App images, and bidding on search terms. It is then crucial for App images to be highly relevant with the search terms. Solutions to this problem require an image-text matching model to predict the quality of the match between the chosen image and the search terms. In this work, we present a novel approach to matching an App image to search terms based on fine-tuning a pre-trained LXMERT model. We show that compared to the CLIP model and a baseline using a Transformer model for search terms, and a ResNet model for images, we significantly improve the matching accuracy. We evaluate our approach using two sets of labels: advertiser associated (image, search term) pairs for a given application, and human ratings for the relevance between (image, search term) pairs. Our approach achieves 0.96 AUC score for advertiser associated ground truth, outperforming the transformer+ResNet baseline and the fine-tuned CLIP model by 8% and 14%. For human labeled ground truth, our approach achieves 0.95 AUC score, outperforming the transformer+ResNet baseline and the fine-tuned CLIP model by 16% and 17%.

Pretext-based self-supervised learning learns the semantic representation via a handcrafted pretext task over unlabeled data and then uses the learned representation for downstream tasks, which effectively reduces the sample complexity of downstream tasks under Conditional Independence (CI) condition. However, the downstream sample complexity gets much worse if the CI condition does not hold. One interesting question is whether we can make the CI condition hold by using downstream data to refine the unlabeled data to boost self-supervised learning. At first glance, one might think that seeing downstream data in advance would always boost the downstream performance. However, we show that it is not intuitively true and point out that in some cases, it hurts the final performance instead. In particular, we prove both model-free and model-dependent lower bounds of the number of downstream samples used for data refinement. Moreover, we conduct various experiments on both synthetic and real-world datasets to verify our theoretical results.

Traditional methods for learning with the presence of noisy labels have successfully handled datasets with artificially injected noise but still fall short of adequately handling real-world noise. With the increasing use of meta-learning in the diverse fields of machine learning, researchers leveraged auxiliary small clean datasets to meta-correct the training labels. Nonetheless, existing meta-label correction approaches are not fully exploiting their potential. In this study, we propose an Enhanced Meta Label Correction approach abbreviated as EMLC for the learning with noisy labels (LNL) problem. We re-examine the meta-learning process and introduce faster and more accurate meta-gradient derivations. We propose a novel teacher architecture tailored explicitly to the LNL problem, equipped with novel training objectives. EMLC outperforms prior approaches and achieves state-of-the-art results in all standard benchmarks. Notably, EMLC enhances the previous art on the noisy real-world dataset Clothing1M by 1.52% while requiring times 0.5 the time per epoch and with much faster convergence of the meta-objective when compared to the baseline approach.

Transforming unstructured text into structured and meaningful forms, organized by useful category labels, is a fundamental step in text mining for downstream analysis and application. However, most existing methods for producing label taxonomies and building text-based label classifiers still rely heavily on domain expertise and manual curation, making the process expensive and time-consuming. This is particularly challenging when the label space is under-specified and large-scale data annotations are unavailable. In this paper, we address these challenges with Large Language Models (LLMs), whose prompt-based interface facilitates the induction and use of large-scale pseudo labels. We propose TnT-LLM, a two-phase framework that employs LLMs to automate the process of end-to-end label generation and assignment with minimal human effort for any given use-case. In the first phase, we introduce a zero-shot, multi-stage reasoning approach which enables LLMs to produce and refine a label taxonomy iteratively. In the second phase, LLMs are used as data labelers that yield training samples so that lightweight supervised classifiers can be reliably built, deployed, and served at scale. We apply TnT-LLM to the analysis of user intent and conversational domain for Bing Copilot (formerly Bing Chat), an open-domain chat-based search engine. Extensive experiments using both human and automatic evaluation metrics demonstrate that TnT-LLM generates more accurate and relevant label taxonomies when compared against state-of-the-art baselines, and achieves a favorable balance between accuracy and efficiency for classification at scale. We also share our practical experiences and insights on the challenges and opportunities of using LLMs for large-scale text mining in real-world applications.

Data selection for fine-tuning Large Language Models (LLMs) aims to select a high-quality subset from a given candidate dataset to train a Pending Fine-tune Model (PFM) into a Selective-Enhanced Model (SEM). It can improve the model performance and accelerate the training process. Although a few surveys have investigated related works of data selection, there is a lack of comprehensive comparison between existing methods due to their various experimental settings. To address this issue, we first propose a three-stage scheme for data selection and comprehensively review existing works according to this scheme. Then, we design a unified comparing method with ratio-based efficiency indicators and ranking-based feasibility indicators to overcome the difficulty of comparing various models with diverse experimental settings. After an in-depth comparative analysis, we find that the more targeted method with data-specific and model-specific quality labels has higher efficiency, but the introduction of additional noise information should be avoided when designing selection algorithms. Finally, we summarize the trends in data selection and highlight the short-term and long-term challenges to guide future research.

Patent examiners need to solve a complex information retrieval task when they assess the novelty and inventive step of claims made in a patent application. Given a claim, they search for prior art, which comprises all relevant publicly available information. This time-consuming task requires a deep understanding of the respective technical domain and the patent-domain-specific language. For these reasons, we address the computer-assisted search for prior art by creating a training dataset for supervised machine learning called PatentMatch. It contains pairs of claims from patent applications and semantically corresponding text passages of different degrees from cited patent documents. Each pair has been labeled by technically-skilled patent examiners from the European Patent Office. Accordingly, the label indicates the degree of semantic correspondence (matching), i.e., whether the text passage is prejudicial to the novelty of the claimed invention or not. Preliminary experiments using a baseline system show that PatentMatch can indeed be used for training a binary text pair classifier on this challenging information retrieval task. The dataset is available online: https://hpi.de/naumann/s/patentmatch.

Varied approaches for aligning language models have been proposed, including supervised fine-tuning, RLHF, and direct optimization methods such as DPO. Although DPO has rapidly gained popularity due to its straightforward training process and competitive results, there is an open question of whether there remain practical advantages of using a discriminator, like a reward model, to evaluate responses. We propose D2PO, discriminator-guided DPO, an approach for the online setting where preferences are being collected throughout learning. As we collect gold preferences, we use these not only to train our policy, but to train a discriminative response evaluation model to silver-label even more synthetic data for policy training. We explore this approach across a set of diverse tasks, including a realistic chat setting, we find that our approach leads to higher-quality outputs compared to DPO with the same data budget, and greater efficiency in terms of preference data requirements. Furthermore, we show conditions under which silver labeling is most helpful: it is most effective when training the policy with DPO, outperforming traditional PPO, and benefits from maintaining a separate discriminator from the policy model.

As the production of and reliance on datasets to produce automated decision-making systems (ADS) increases, so does the need for processes for evaluating and interrogating the underlying data. After launching the Dataset Nutrition Label in 2018, the Data Nutrition Project has made significant updates to the design and purpose of the Label, and is launching an updated Label in late 2020, which is previewed in this paper. The new Label includes context-specific Use Cases &Alerts presented through an updated design and user interface targeted towards the data scientist profile. This paper discusses the harm and bias from underlying training data that the Label is intended to mitigate, the current state of the work including new datasets being labeled, new and existing challenges, and further directions of the work, as well as Figures previewing the new label.

Due to the difficulty of collecting exhaustive multi-label annotations, multi-label datasets often contain partial labels. We consider an extreme of this weakly supervised learning problem, called single positive multi-label learning (SPML), where each multi-label training image has only one positive label. Traditionally, all unannotated labels are assumed as negative labels in SPML, which introduces false negative labels and causes model training to be dominated by assumed negative labels. In this work, we choose to treat all unannotated labels from an alternative perspective, i.e. acknowledging they are unknown. Hence, we propose entropy-maximization (EM) loss to attain a special gradient regime for providing proper supervision signals. Moreover, we propose asymmetric pseudo-labeling (APL), which adopts asymmetric-tolerance strategies and a self-paced procedure, to cooperate with EM loss and then provide more precise supervision. Experiments show that our method significantly improves performance and achieves state-of-the-art results on all four benchmarks. Code is available at https://github.com/Correr-Zhou/SPML-AckTheUnknown.

The Russian Drug Reaction Corpus (RuDReC) is a new partially annotated corpus of consumer reviews in Russian about pharmaceutical products for the detection of health-related named entities and the effectiveness of pharmaceutical products. The corpus itself consists of two parts, the raw one and the labelled one. The raw part includes 1.4 million health-related user-generated texts collected from various Internet sources, including social media. The labelled part contains 500 consumer reviews about drug therapy with drug- and disease-related information. Labels for sentences include health-related issues or their absence. The sentences with one are additionally labelled at the expression level for identification of fine-grained subtypes such as drug classes and drug forms, drug indications, and drug reactions. Further, we present a baseline model for named entity recognition (NER) and multi-label sentence classification tasks on this corpus. The macro F1 score of 74.85% in the NER task was achieved by our RuDR-BERT model. For the sentence classification task, our model achieves the macro F1 score of 68.82% gaining 7.47% over the score of BERT model trained on Russian data. We make the RuDReC corpus and pretrained weights of domain-specific BERT models freely available at https://github.com/cimm-kzn/RuDReC

Fine-tuning large language models (LLMs) for downstream tasks is a widely adopted approach, but it often leads to safety degradation in safety-aligned LLMs. Currently, many solutions address this issue by incorporating additional safety data, which can be impractical in many cases. In this paper, we address the question: How can we improve downstream task performance while preserving safety in LLMs without relying on additional safety data? We propose a simple and effective method that maintains the inherent safety of LLMs while enhancing their downstream task performance: merging the weights of pre- and post-fine-tuned safety-aligned models. Experimental results across various downstream tasks, models, and merging methods demonstrate that this approach effectively mitigates safety degradation while improving downstream task performance, offering a practical solution for adapting safety-aligned LLMs.

Large language models (LLMs) are susceptible to a variety of risks, from non-faithful output to biased and toxic generations. Due to several limiting factors surrounding LLMs (training cost, API access, data availability, etc.), it may not always be feasible to impose direct safety constraints on a deployed model. Therefore, an efficient and reliable alternative is required. To this end, we present our ongoing efforts to create and deploy a library of detectors: compact and easy-to-build classification models that provide labels for various harms. In addition to the detectors themselves, we discuss a wide range of uses for these detector models - from acting as guardrails to enabling effective AI governance. We also deep dive into inherent challenges in their development and discuss future work aimed at making the detectors more reliable and broadening their scope.

This study provides an efficient approach for using text data to calculate patent-to-patent (p2p) technological similarity, and presents a hybrid framework for leveraging the resulting p2p similarity for applications such as semantic search and automated patent classification. We create embeddings using Sentence-BERT (SBERT) based on patent claims. We leverage SBERTs efficiency in creating embedding distance measures to map p2p similarity in large sets of patent data. We deploy our framework for classification with a simple Nearest Neighbors (KNN) model that predicts Cooperative Patent Classification (CPC) of a patent based on the class assignment of the K patents with the highest p2p similarity. We thereby validate that the p2p similarity captures their technological features in terms of CPC overlap, and at the same demonstrate the usefulness of this approach for automatic patent classification based on text data. Furthermore, the presented classification framework is simple and the results easy to interpret and evaluate by end-users. In the out-of-sample model validation, we are able to perform a multi-label prediction of all assigned CPC classes on the subclass (663) level on 1,492,294 patents with an accuracy of 54% and F1 score > 66%, which suggests that our model outperforms the current state-of-the-art in text-based multi-label and multi-class patent classification. We furthermore discuss the applicability of the presented framework for semantic IP search, patent landscaping, and technology intelligence. We finally point towards a future research agenda for leveraging multi-source patent embeddings, their appropriateness across applications, as well as to improve and validate patent embeddings by creating domain-expert curated Semantic Textual Similarity (STS) benchmark datasets.

Multi-Label Text Classification (MLTC) aims to assign the most relevant labels to each given text. Existing methods demonstrate that label dependency can help to improve the model's performance. However, the introduction of label dependency may cause the model to suffer from unwanted prediction bias. In this study, we attribute the bias to the model's misuse of label dependency, i.e., the model tends to utilize the correlation shortcut in label dependency rather than fusing text information and label dependency for prediction. Motivated by causal inference, we propose a CounterFactual Text Classifier (CFTC) to eliminate the correlation bias, and make causality-based predictions. Specifically, our CFTC first adopts the predict-then-modify backbone to extract precise label information embedded in label dependency, then blocks the correlation shortcut through the counterfactual de-bias technique with the help of the human causal graph. Experimental results on three datasets demonstrate that our CFTC significantly outperforms the baselines and effectively eliminates the correlation bias in datasets.

The development and training of deep learning models have become increasingly costly and complex. Consequently, software engineers are adopting pre-trained models (PTMs) for their downstream applications. The dynamics of the PTM supply chain remain largely unexplored, signaling a clear need for structured datasets that document not only the metadata but also the subsequent applications of these models. Without such data, the MSR community cannot comprehensively understand the impact of PTM adoption and reuse. This paper presents the PeaTMOSS dataset, which comprises metadata for 281,638 PTMs and detailed snapshots for all PTMs with over 50 monthly downloads (14,296 PTMs), along with 28,575 open-source software repositories from GitHub that utilize these models. Additionally, the dataset includes 44,337 mappings from 15,129 downstream GitHub repositories to the 2,530 PTMs they use. To enhance the dataset's comprehensiveness, we developed prompts for a large language model to automatically extract model metadata, including the model's training datasets, parameters, and evaluation metrics. Our analysis of this dataset provides the first summary statistics for the PTM supply chain, showing the trend of PTM development and common shortcomings of PTM package documentation. Our example application reveals inconsistencies in software licenses across PTMs and their dependent projects. PeaTMOSS lays the foundation for future research, offering rich opportunities to investigate the PTM supply chain. We outline mining opportunities on PTMs, their downstream usage, and cross-cutting questions.

Conventional multi-label recognition methods often focus on label confidence, frequently overlooking the pivotal role of partial order relations consistent with human preference. To resolve these issues, we introduce a novel method for multimodal label relevance ranking, named Label Relevance Ranking with Proximal Policy Optimization (LR2PPO), which effectively discerns partial order relations among labels. LR2PPO first utilizes partial order pairs in the target domain to train a reward model, which aims to capture human preference intrinsic to the specific scenario. Furthermore, we meticulously design state representation and a policy loss tailored for ranking tasks, enabling LR2PPO to boost the performance of label relevance ranking model and largely reduce the requirement of partial order annotation for transferring to new scenes. To assist in the evaluation of our approach and similar methods, we further propose a novel benchmark dataset, LRMovieNet, featuring multimodal labels and their corresponding partial order data. Extensive experiments demonstrate that our LR2PPO algorithm achieves state-of-the-art performance, proving its effectiveness in addressing the multimodal label relevance ranking problem. Codes and the proposed LRMovieNet dataset are publicly available at https://github.com/ChazzyGordon/LR2PPO.

Recent research has highlighted the potential of LLM applications, like ChatGPT, for performing label annotation on social computing text. However, it is already well known that performance hinges on the quality of the input prompts. To address this, there has been a flurry of research into prompt tuning -- techniques and guidelines that attempt to improve the quality of prompts. Yet these largely rely on manual effort and prior knowledge of the dataset being annotated. To address this limitation, we propose APT-Pipe, an automated prompt-tuning pipeline. APT-Pipe aims to automatically tune prompts to enhance ChatGPT's text classification performance on any given dataset. We implement APT-Pipe and test it across twelve distinct text classification datasets. We find that prompts tuned by APT-Pipe help ChatGPT achieve higher weighted F1-score on nine out of twelve experimented datasets, with an improvement of 7.01% on average. We further highlight APT-Pipe's flexibility as a framework by showing how it can be extended to support additional tuning mechanisms.

Drug discovery typically consists of multiple steps, including identifying a target protein key to a disease's etiology, validating that interacting with this target could prevent symptoms or cure the disease, discovering a small molecule or biologic therapeutic to interact with it, and optimizing the candidate molecule through a complex landscape of required properties. Drug discovery related tasks often involve prediction and generation while considering multiple entities that potentially interact, which poses a challenge for typical AI models. For this purpose we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a method that we applied to create a versatile multi-task foundation model ibm/biomed.omics.bl.sm.ma-ted-458m that learns from large-scale biological datasets (2 billion samples) across diverse modalities, including proteins, small molecules, and genes. We introduce a prompt syntax that supports a wide range of classification, regression, and generation tasks. It allows combining different modalities and entity types as inputs and/or outputs. Our model handles combinations of tokens and scalars and enables the generation of small molecules and proteins, property prediction, and transcriptomic lab test predictions. We evaluated the model on 11 diverse downstream tasks spanning different steps within a typical drug discovery pipeline, where it reaches new SOTA in 9 tasks and is comparable to SOTA in 2 tasks. This performance is achieved while using a unified architecture serving all tasks, in contrast to the original SOTA performance achieved using tailored architectures. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m.

We investigate a new threat to neural sequence-to-sequence (seq2seq) models: training-time attacks that cause models to "spin" their outputs so as to support an adversary-chosen sentiment or point of view -- but only when the input contains adversary-chosen trigger words. For example, a spinned summarization model outputs positive summaries of any text that mentions the name of some individual or organization. Model spinning introduces a "meta-backdoor" into a model. Whereas conventional backdoors cause models to produce incorrect outputs on inputs with the trigger, outputs of spinned models preserve context and maintain standard accuracy metrics, yet also satisfy a meta-task chosen by the adversary. Model spinning enables propaganda-as-a-service, where propaganda is defined as biased speech. An adversary can create customized language models that produce desired spins for chosen triggers, then deploy these models to generate disinformation (a platform attack), or else inject them into ML training pipelines (a supply-chain attack), transferring malicious functionality to downstream models trained by victims. To demonstrate the feasibility of model spinning, we develop a new backdooring technique. It stacks an adversarial meta-task onto a seq2seq model, backpropagates the desired meta-task output to points in the word-embedding space we call "pseudo-words," and uses pseudo-words to shift the entire output distribution of the seq2seq model. We evaluate this attack on language generation, summarization, and translation models with different triggers and meta-tasks such as sentiment, toxicity, and entailment. Spinned models largely maintain their accuracy metrics (ROUGE and BLEU) while shifting their outputs to satisfy the adversary's meta-task. We also show that, in the case of a supply-chain attack, the spin functionality transfers to downstream models.

Labeling social-media data for custom dimensions of toxicity and social bias is challenging and labor-intensive. Existing transfer and active learning approaches meant to reduce annotation effort require fine-tuning, which suffers from over-fitting to noise and can cause domain shift with small sample sizes. In this work, we propose a novel Active Transfer Few-shot Instructions (ATF) approach which requires no fine-tuning. ATF leverages the internal linguistic knowledge of pre-trained language models (PLMs) to facilitate the transfer of information from existing pre-labeled datasets (source-domain task) with minimum labeling effort on unlabeled target data (target-domain task). Our strategy can yield positive transfer achieving a mean AUC gain of 10.5% compared to no transfer with a large 22b parameter PLM. We further show that annotation of just a few target-domain samples via active learning can be beneficial for transfer, but the impact diminishes with more annotation effort (26% drop in gain between 100 and 2000 annotated examples). Finally, we find that not all transfer scenarios yield a positive gain, which seems related to the PLMs initial performance on the target-domain task.

Artificial intelligence (AI) systems built on incomplete or biased data will often exhibit problematic outcomes. Current methods of data analysis, particularly before model development, are costly and not standardized. The Dataset Nutrition Label (the Label) is a diagnostic framework that lowers the barrier to standardized data analysis by providing a distilled yet comprehensive overview of dataset "ingredients" before AI model development. Building a Label that can be applied across domains and data types requires that the framework itself be flexible and adaptable; as such, the Label is comprised of diverse qualitative and quantitative modules generated through multiple statistical and probabilistic modelling backends, but displayed in a standardized format. To demonstrate and advance this concept, we generated and published an open source prototype with seven sample modules on the ProPublica Dollars for Docs dataset. The benefits of the Label are manyfold. For data specialists, the Label will drive more robust data analysis practices, provide an efficient way to select the best dataset for their purposes, and increase the overall quality of AI models as a result of more robust training datasets and the ability to check for issues at the time of model development. For those building and publishing datasets, the Label creates an expectation of explanation, which will drive better data collection practices. We also explore the limitations of the Label, including the challenges of generalizing across diverse datasets, and the risk of using "ground truth" data as a comparison dataset. We discuss ways to move forward given the limitations identified. Lastly, we lay out future directions for the Dataset Nutrition Label project, including research and public policy agendas to further advance consideration of the concept.

Scaling laws provide important insights that can guide the design of large language models (LLMs). Existing work has primarily focused on studying scaling laws for pretraining (upstream) loss. However, in transfer learning settings, in which LLMs are pretrained on an unsupervised dataset and then finetuned on a downstream task, we often also care about the downstream performance. In this work, we study the scaling behavior in a transfer learning setting, where LLMs are finetuned for machine translation tasks. Specifically, we investigate how the choice of the pretraining data and its size affect downstream performance (translation quality) as judged by two metrics: downstream cross-entropy and BLEU score. Our experiments indicate that the size of the finetuning dataset and the distribution alignment between the pretraining and downstream data significantly influence the scaling behavior. With sufficient alignment, both downstream cross-entropy and BLEU score improve monotonically with more pretraining data. In such cases, we show that it is possible to predict the downstream BLEU score with good accuracy using a log-law. However, there are also cases where moderate misalignment causes the BLEU score to fluctuate or get worse with more pretraining, whereas downstream cross-entropy monotonically improves. By analyzing these observations, we provide new practical insights for choosing appropriate pretraining data.

Major scandals in corporate history have urged the need for regulatory compliance, where organizations need to ensure that their controls (processes) comply with relevant laws, regulations, and policies. However, keeping track of the constantly changing legislation is difficult, thus organizations are increasingly adopting Regulatory Technology (RegTech) to facilitate the process. To this end, we introduce regulatory information retrieval (REG-IR), an application of document-to-document information retrieval (DOC2DOC IR), where the query is an entire document making the task more challenging than traditional IR where the queries are short. Furthermore, we compile and release two datasets based on the relationships between EU directives and UK legislation. We experiment on these datasets using a typical two-step pipeline approach comprising a pre-fetcher and a neural re-ranker. Experimenting with various pre-fetchers from BM25 to k nearest neighbors over representations from several BERT models, we show that fine-tuning a BERT model on an in-domain classification task produces the best representations for IR. We also show that neural re-rankers under-perform due to contradicting supervision, i.e., similar query-document pairs with opposite labels. Thus, they are biased towards the pre-fetcher's score. Interestingly, applying a date filter further improves the performance, showcasing the importance of the time dimension.

Temporal and numerical expression understanding is of great importance in many downstream Natural Language Processing (NLP) and Information Retrieval (IR) tasks. However, much previous work covers only a few sub-types and focuses only on entity extraction, which severely limits the usability of identified mentions. In order for such entities to be useful in downstream scenarios, coverage and granularity of sub-types are important; and, even more so, providing resolution into concrete values that can be manipulated. Furthermore, most previous work addresses only a handful of languages. Here we describe a multi-lingual evaluation dataset - NTX - covering diverse temporal and numerical expressions across 14 languages and covering extraction, normalization, and resolution. Along with the dataset we provide a robust rule-based system as a strong baseline for comparisons against other models to be evaluated in this dataset. Data and code are available at https://aka.ms/NTX.

Ligand molecule conformation generation is a critical challenge in drug discovery. Deep learning models have been developed to tackle this problem, particularly through the use of generative models in recent years. However, these models often generate conformations that lack meaningful structure and randomness due to the absence of essential side information. Examples of such side information include the chemical and geometric features of the target protein, ligand-target compound interactions, and ligand chemical properties. Without these constraints, the generated conformations may not be suitable for further selection and design of new drugs. To address this limitation, we propose a novel method for generating ligand conformations that leverage side information and incorporate flexible constraints into standard diffusion models. Drawing inspiration from the concept of message passing, we introduce ligand-target massage passing block, a mechanism that facilitates the exchange of information between target nodes and ligand nodes, thereby incorporating target node features. To capture non-covalent interactions, we introduce ligand-target compound inter and intra edges. To further improve the biological relevance of the generated conformations, we train energy models using scalar chemical features. These models guide the progress of the standard Denoising Diffusion Probabilistic Models, resulting in more biologically meaningful conformations. We evaluate the performance of SIDEGEN using the PDBBind-2020 dataset, comparing it against other methods. The results demonstrate improvements in both Aligned RMSD and Ligand RMSD evaluations. Specifically, our model outperforms GeoDiff (trained on PDBBind-2020) by 20% in terms of the median aligned RMSD metric.

The global cost of drug discovery and development exceeds $200 billion annually. The main results of drug discovery and development are the outcomes of clinical trials, which directly influence the regulatory approval of new drug candidates and ultimately affect patient outcomes. Despite their significance, large-scale, high-quality clinical trial outcome data are not readily available to the public. Suppose a large clinical trial outcome dataset is provided; machine learning researchers can potentially develop accurate prediction models using past trials and outcome labels, which could help prioritize and optimize therapeutic programs, ultimately benefiting patients. This paper introduces Clinical Trial Outcome (CTO) dataset, the largest trial outcome dataset with around 479K clinical trials, aggregating outcomes from multiple sources of weakly supervised labels, minimizing the noise from individual sources, and eliminating the need for human annotation. These sources include large language model (LLM) decisions on trial-related documents, news headline sentiments, stock prices of trial sponsors, trial linkages across phases, and other signals such as patient dropout rates and adverse events. CTO's labels show unprecedented agreement with supervised clinical trial outcome labels from test split of the supervised TOP dataset, with a 91 F1.

Large language models (LLMs) have revolutionized Natural Language Processing (NLP) by minimizing the need for complex feature engineering. However, the application of LLMs in specialized domains like biopharmaceuticals and chemistry remains largely unexplored. These fields are characterized by intricate terminologies, specialized knowledge, and a high demand for precision areas where general purpose LLMs often fall short. In this study, we introduce PharmaGPT, a suite of domain specilized LLMs with 13 billion and 70 billion parameters, specifically trained on a comprehensive corpus tailored to the Bio-Pharmaceutical and Chemical domains. Our evaluation shows that PharmaGPT surpasses existing general models on specific-domain benchmarks such as NAPLEX, demonstrating its exceptional capability in domain-specific tasks. Remarkably, this performance is achieved with a model that has only a fraction, sometimes just one-tenth-of the parameters of general-purpose large models. This advancement establishes a new benchmark for LLMs in the bio-pharmaceutical and chemical fields, addressing the existing gap in specialized language modeling. It also suggests a promising path for enhanced research and development, paving the way for more precise and effective NLP applications in these areas.

We introduce Aligner, a novel Parameter-Efficient Fine-Tuning (PEFT) method for aligning multi-billion-parameter-sized Large Language Models (LLMs). Aligner employs a unique design that constructs a globally shared set of tunable tokens that modify the attention of every layer. Remarkably with this method, even when using one token accounting for a mere 5,000 parameters, Aligner can still perform comparably well to state-of-the-art LLM adaptation methods like LoRA that require millions of parameters. This capacity is substantiated in both instruction following and value alignment tasks. Besides the multiple order-of-magnitude improvement in parameter efficiency, the insight Aligner provides into the internal mechanisms of LLMs is also valuable. The architectural features and efficacy of our method, in addition to our experiments demonstrate that an LLM separates its internal handling of "form" and "knowledge" in a somewhat orthogonal manner. This finding promises to motivate new research into LLM mechanism understanding and value alignment.

Multi-label classification problems with thousands of classes are hard to solve with in-context learning alone, as language models (LMs) might lack prior knowledge about the precise classes or how to assign them, and it is generally infeasible to demonstrate every class in a prompt. We propose a general program, Infer--Retrieve--Rank, that defines multi-step interactions between LMs and retrievers to efficiently tackle such problems. We implement this program using the DSPy programming model, which specifies in-context systems in a declarative manner, and use DSPy optimizers to tune it towards specific datasets by bootstrapping only tens of few-shot examples. Our primary extreme classification program, optimized separately for each task, attains state-of-the-art results across three benchmarks (HOUSE, TECH, TECHWOLF). We apply the same program to a benchmark with vastly different characteristics and attain competitive performance as well (BioDEX). Unlike prior work, our proposed solution requires no finetuning, is easily applicable to new tasks, alleviates prompt engineering, and requires only tens of labeled examples. Our code is public at https://github.com/KarelDO/xmc.dspy.

In real-world data labeling applications, annotators often provide imperfect labels. It is thus common to employ multiple annotators to label data with some overlap between their examples. We study active learning in such settings, aiming to train an accurate classifier by collecting a dataset with the fewest total annotations. Here we propose ActiveLab, a practical method to decide what to label next that works with any classifier model and can be used in pool-based batch active learning with one or multiple annotators. ActiveLab automatically estimates when it is more informative to re-label examples vs. labeling entirely new ones. This is a key aspect of producing high quality labels and trained models within a limited annotation budget. In experiments on image and tabular data, ActiveLab reliably trains more accurate classifiers with far fewer annotations than a wide variety of popular active learning methods.

Conventional multi-label classification (MLC) methods assume that all samples are fully labeled and identically distributed. Unfortunately, this assumption is unrealistic in large-scale MLC data that has long-tailed (LT) distribution and partial labels (PL). To address the problem, we introduce a novel task, Partial labeling and Long-Tailed Multi-Label Classification (PLT-MLC), to jointly consider the above two imperfect learning environments. Not surprisingly, we find that most LT-MLC and PL-MLC approaches fail to solve the PLT-MLC, resulting in significant performance degradation on the two proposed PLT-MLC benchmarks. Therefore, we propose an end-to-end learning framework: COrrection rightarrow ModificatIon rightarrow balanCe, abbreviated as \method{}. Our bootstrapping philosophy is to simultaneously correct the missing labels (Correction) with convinced prediction confidence over a class-aware threshold and to learn from these recall labels during training. We next propose a novel multi-focal modifier loss that simultaneously addresses head-tail imbalance and positive-negative imbalance to adaptively modify the attention to different samples (Modification) under the LT class distribution. In addition, we develop a balanced training strategy by distilling the model's learning effect from head and tail samples, and thus design a balanced classifier (Balance) conditioned on the head and tail learning effect to maintain stable performance for all samples. Our experimental study shows that the proposed significantly outperforms general MLC, LT-MLC and PL-MLC methods in terms of effectiveness and robustness on our newly created PLT-MLC datasets.

Distilling knowledge from a large teacher model to a lightweight one is a widely successful approach for generating compact, powerful models in the semi-supervised learning setting where a limited amount of labeled data is available. In large-scale applications, however, the teacher tends to provide a large number of incorrect soft-labels that impairs student performance. The sheer size of the teacher additionally constrains the number of soft-labels that can be queried due to prohibitive computational and/or financial costs. The difficulty in achieving simultaneous efficiency (i.e., minimizing soft-label queries) and robustness (i.e., avoiding student inaccuracies due to incorrect labels) hurts the widespread application of knowledge distillation to many modern tasks. In this paper, we present a parameter-free approach with provable guarantees to query the soft-labels of points that are simultaneously informative and correctly labeled by the teacher. At the core of our work lies a game-theoretic formulation that explicitly considers the inherent trade-off between the informativeness and correctness of input instances. We establish bounds on the expected performance of our approach that hold even in worst-case distillation instances. We present empirical evaluations on popular benchmarks that demonstrate the improved distillation performance enabled by our work relative to that of state-of-the-art active learning and active distillation methods.

Metric learning involves learning a discriminative representation such that embeddings of similar classes are encouraged to be close, while embeddings of dissimilar classes are pushed far apart. State-of-the-art methods focus mostly on sophisticated loss functions or mining strategies. On the one hand, metric learning losses consider two or more examples at a time. On the other hand, modern data augmentation methods for classification consider two or more examples at a time. The combination of the two ideas is under-studied. In this work, we aim to bridge this gap and improve representations using mixup, which is a powerful data augmentation approach interpolating two or more examples and corresponding target labels at a time. This task is challenging because unlike classification, the loss functions used in metric learning are not additive over examples, so the idea of interpolating target labels is not straightforward. To the best of our knowledge, we are the first to investigate mixing both examples and target labels for deep metric learning. We develop a generalized formulation that encompasses existing metric learning loss functions and modify it to accommodate for mixup, introducing Metric Mix, or Metrix. We also introduce a new metric - utilization, to demonstrate that by mixing examples during training, we are exploring areas of the embedding space beyond the training classes, thereby improving representations. To validate the effect of improved representations, we show that mixing inputs, intermediate representations or embeddings along with target labels significantly outperforms state-of-the-art metric learning methods on four benchmark deep metric learning datasets.

Aligning large language models (LLMs) to human preferences is a crucial step in building helpful and safe AI tools, which usually involve training on supervised datasets. Popular algorithms such as Direct Preference Optimization rely on pairs of AI-generated responses ranked according to human feedback. The labeling process is the most labor-intensive and costly part of the alignment pipeline, and improving its efficiency would have a meaningful impact on AI development. We propose a strategy for sampling a high-quality training dataset that focuses on acquiring the most informative response pairs for labeling out of a set of AI-generated responses. Experimental results on synthetic HH-RLHF benchmarks indicate that choosing dissimilar response pairs enhances the direct alignment of LLMs while reducing inherited labeling errors. We also applied our method to the real-world dataset SHP2, selecting optimal pairs from multiple responses. The model aligned on dissimilar response pairs obtained the best win rate on the dialogue task. Our findings suggest that focusing on less similar pairs can improve the efficiency of LLM alignment, saving up to 65% of annotators' work.

Most positive and unlabeled data is subject to selection biases. The labeled examples can, for example, be selected from the positive set because they are easier to obtain or more obviously positive. This paper investigates how learning can be ena BHbled in this setting. We propose and theoretically analyze an empirical-risk-based method for incorporating the labeling mechanism. Additionally, we investigate under which assumptions learning is possible when the labeling mechanism is not fully understood and propose a practical method to enable this. Our empirical analysis supports the theoretical results and shows that taking into account the possibility of a selection bias, even when the labeling mechanism is unknown, improves the trained classifiers.

In recent years, offensive, abusive and hateful language, sexism, racism and other types of aggressive and cyberbullying behavior have been manifesting with increased frequency, and in many online social media platforms. In fact, past scientific work focused on studying these forms in popular media, such as Facebook and Twitter. Building on such work, we present an 8-month study of the various forms of abusive behavior on Twitter, in a holistic fashion. Departing from past work, we examine a wide variety of labeling schemes, which cover different forms of abusive behavior, at the same time. We propose an incremental and iterative methodology, that utilizes the power of crowdsourcing to annotate a large scale collection of tweets with a set of abuse-related labels. In fact, by applying our methodology including statistical analysis for label merging or elimination, we identify a reduced but robust set of labels. Finally, we offer a first overview and findings of our collected and annotated dataset of 100 thousand tweets, which we make publicly available for further scientific exploration.

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.

In this paper, we introduce a novel predict-and-optimize method for profit-driven churn prevention. We frame the task of targeting customers for a retention campaign as a regret minimization problem. The main objective is to leverage individual customer lifetime values (CLVs) to ensure that only the most valuable customers are targeted. In contrast, many profit-driven strategies focus on churn probabilities while considering average CLVs. This often results in significant information loss due to data aggregation. Our proposed model aligns with the guidelines of Predict-and-Optimize (PnO) frameworks and can be efficiently solved using stochastic gradient descent methods. Results from 12 churn prediction datasets underscore the effectiveness of our approach, which achieves the best average performance compared to other well-established strategies in terms of average profit.

Multi-label text classification is a critical task in the industry. It helps to extract structured information from large amount of textual data. We propose Text to Topic (Text2Topic), which achieves high multi-label classification performance by employing a Bi-Encoder Transformer architecture that utilizes concatenation, subtraction, and multiplication of embeddings on both text and topic. Text2Topic also supports zero-shot predictions, produces domain-specific text embeddings, and enables production-scale batch-inference with high throughput. The final model achieves accurate and comprehensive results compared to state-of-the-art baselines, including large language models (LLMs). In this study, a total of 239 topics are defined, and around 1.6 million text-topic pairs annotations (in which 200K are positive) are collected on approximately 120K texts from 3 main data sources on Booking.com. The data is collected with optimized smart sampling and partial labeling. The final Text2Topic model is deployed on a real-world stream processing platform, and it outperforms other models with 92.9% micro mAP, as well as a 75.8% macro mAP score. We summarize the modeling choices which are extensively tested through ablation studies, and share detailed in-production decision-making steps.

Adapting pre-trained models with broad capabilities has become standard practice for learning a wide range of downstream tasks. The typical approach of fine-tuning different models for each task is performant, but incurs a substantial memory cost. To efficiently learn multiple downstream tasks we introduce Task Adaptive Parameter Sharing (TAPS), a general method for tuning a base model to a new task by adaptively modifying a small, task-specific subset of layers. This enables multi-task learning while minimizing resources used and competition between tasks. TAPS solves a joint optimization problem which determines which layers to share with the base model and the value of the task-specific weights. Further, a sparsity penalty on the number of active layers encourages weight sharing with the base model. Compared to other methods, TAPS retains high accuracy on downstream tasks while introducing few task-specific parameters. Moreover, TAPS is agnostic to the model architecture and requires only minor changes to the training scheme. We evaluate our method on a suite of fine-tuning tasks and architectures (ResNet, DenseNet, ViT) and show that it achieves state-of-the-art performance while being simple to implement.

Hierarchical text classification (HTC) is the task of assigning labels to a text within a structured space organized as a hierarchy. Recent works treat HTC as a conventional multilabel classification problem, therefore evaluating it as such. We instead propose to evaluate models based on specifically designed hierarchical metrics and we demonstrate the intricacy of metric choice and prediction inference method. We introduce a new challenging dataset and we evaluate fairly, recent sophisticated models, comparing them with a range of simple but strong baselines, including a new theoretically motivated loss. Finally, we show that those baselines are very often competitive with the latest models. This highlights the importance of carefully considering the evaluation methodology when proposing new methods for HTC. Code implementation and dataset are available at https://github.com/RomanPlaud/revisitingHTC.

This paper presents the system description of our entry for the COLING 2025 RegNLP RIRAG (Regulatory Information Retrieval and Answer Generation) challenge, focusing on leveraging advanced information retrieval and answer generation techniques in regulatory domains. We experimented with a combination of embedding models, including Stella, BGE, CDE, and Mpnet, and leveraged fine-tuning and reranking for retrieving relevant documents in top ranks. We utilized a novel approach, LeSeR, which achieved competitive results with a recall@10 of 0.8201 and map@10 of 0.6655 for retrievals. This work highlights the transformative potential of natural language processing techniques in regulatory applications, offering insights into their capabilities for implementing a retrieval augmented generation system while identifying areas for future improvement in robustness and domain adaptation.

We study how to watermark LLM outputs, i.e. embedding algorithmically detectable signals into LLM-generated text to track misuse. Unlike the current mainstream methods that work with a fixed LLM, we expand the watermark design space by including the LLM tuning stage in the watermark pipeline. While prior works focus on token-level watermark that embeds signals into the output, we design a model-level watermark that embeds signals into the LLM weights, and such signals can be detected by a paired detector. We propose a co-training framework based on reinforcement learning that iteratively (1) trains a detector to detect the generated watermarked text and (2) tunes the LLM to generate text easily detectable by the detector while keeping its normal utility. We empirically show that our watermarks are more accurate, robust, and adaptable (to new attacks). It also allows watermarked model open-sourcing. In addition, if used together with alignment, the extra overhead introduced is low - only training an extra reward model (i.e. our detector). We hope our work can bring more effort into studying a broader watermark design that is not limited to working with a fixed LLM. We open-source the code: https://github.com/xiaojunxu/learning-to-watermark-llm .

With the proliferation of red-teaming strategies for Large Language Models (LLMs), the deficiency in the literature about improving the safety and robustness of LLM defense strategies is becoming increasingly pronounced. This paper introduces the LLM-based sentinel model as a plug-and-play prefix module designed to reconstruct the input prompt with just a few (<30) additional tokens, effectively reducing toxicity in responses from target LLMs. The sentinel model naturally overcomes the parameter inefficiency and limited model accessibility for fine-tuning large target models. We employ an interleaved training regimen using Proximal Policy Optimization (PPO) to optimize both red team and sentinel models dynamically, incorporating a value head-sharing mechanism inspired by the multi-agent centralized critic to manage the complex interplay between agents. Our extensive experiments across text-to-text and text-to-image demonstrate the effectiveness of our approach in mitigating toxic outputs, even when dealing with larger models like Llama-2, GPT-3.5 and Stable-Diffusion, highlighting the potential of our framework in enhancing safety and robustness in various applications.

Injecting external knowledge can improve the performance of pre-trained language models (PLMs) on various downstream NLP tasks. However, massive retraining is required to deploy new knowledge injection methods or knowledge bases for downstream tasks. In this work, we are the first to study how to improve the flexibility and efficiency of knowledge injection by reusing existing downstream models. To this end, we explore a new paradigm plug-and-play knowledge injection, where knowledge bases are injected into frozen existing downstream models by a knowledge plugin. Correspondingly, we propose a plug-and-play injection method map-tuning, which trains a mapping of knowledge embeddings to enrich model inputs with mapped embeddings while keeping model parameters frozen. Experimental results on three knowledge-driven NLP tasks show that existing injection methods are not suitable for the new paradigm, while map-tuning effectively improves the performance of downstream models. Moreover, we show that a frozen downstream model can be well adapted to different domains with different mapping networks of domain knowledge. Our code and models are available at https://github.com/THUNLP/Knowledge-Plugin.

Parameter-Efficient Transfer Learning (PETL) aims at efficiently adapting large models pre-trained on massive data to downstream tasks with limited task-specific data. In view of the practicality of PETL, previous works focus on tuning a small set of parameters for each downstream task in an end-to-end manner while rarely considering the task distribution shift issue between the pre-training task and the downstream task. This paper proposes a novel two-stage paradigm, where the pre-trained model is first aligned to the target distribution. Then the task-relevant information is leveraged for effective adaptation. Specifically, the first stage narrows the task distribution shift by tuning the scale and shift in the LayerNorm layers. In the second stage, to efficiently learn the task-relevant information, we propose a Taylor expansion-based importance score to identify task-relevant channels for the downstream task and then only tune such a small portion of channels, making the adaptation to be parameter-efficient. Overall, we present a promising new direction for PETL, and the proposed paradigm achieves state-of-the-art performance on the average accuracy of 19 downstream tasks.

We consider the task of Extreme Multi-Label Text Classification (XMTC) in the legal domain. We release a new dataset of 57k legislative documents from EURLEX, the European Union's public document database, annotated with concepts from EUROVOC, a multidisciplinary thesaurus. The dataset is substantially larger than previous EURLEX datasets and suitable for XMTC, few-shot and zero-shot learning. Experimenting with several neural classifiers, we show that BIGRUs with self-attention outperform the current multi-label state-of-the-art methods, which employ label-wise attention. Replacing CNNs with BIGRUs in label-wise attention networks leads to the best overall performance.

Protein modeling is an increasingly popular area of machine learning research. Semi-supervised learning has emerged as an important paradigm in protein modeling due to the high cost of acquiring supervised protein labels, but the current literature is fragmented when it comes to datasets and standardized evaluation techniques. To facilitate progress in this field, we introduce the Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. We curate tasks into specific training, validation, and test splits to ensure that each task tests biologically relevant generalization that transfers to real-life scenarios. We benchmark a range of approaches to semi-supervised protein representation learning, which span recent work as well as canonical sequence learning techniques. We find that self-supervised pretraining is helpful for almost all models on all tasks, more than doubling performance in some cases. Despite this increase, in several cases features learned by self-supervised pretraining still lag behind features extracted by state-of-the-art non-neural techniques. This gap in performance suggests a huge opportunity for innovative architecture design and improved modeling paradigms that better capture the signal in biological sequences. TAPE will help the machine learning community focus effort on scientifically relevant problems. Toward this end, all data and code used to run these experiments are available at https://github.com/songlab-cal/tape.

We propose a novel framework for filtering image-text data by leveraging fine-tuned Multimodal Language Models (MLMs). Our approach outperforms predominant filtering methods (e.g., CLIPScore) via integrating the recent advances in MLMs. We design four distinct yet complementary metrics to holistically measure the quality of image-text data. A new pipeline is established to construct high-quality instruction data for fine-tuning MLMs as data filters. Comparing with CLIPScore, our MLM filters produce more precise and comprehensive scores that directly improve the quality of filtered data and boost the performance of pre-trained models. We achieve significant improvements over CLIPScore on popular foundation models (i.e., CLIP and BLIP2) and various downstream tasks. Our MLM filter can generalize to different models and tasks, and be used as a drop-in replacement for CLIPScore. An additional ablation study is provided to verify our design choices for the MLM filter.

Dataset distillation or condensation aims to condense a large-scale training dataset into a much smaller synthetic one such that the training performance of distilled and original sets on neural networks are similar. Although the number of training samples can be reduced substantially, current state-of-the-art methods heavily rely on enormous soft labels to achieve satisfactory performance. As a result, the required storage can be comparable even to original datasets, especially for large-scale ones. To solve this problem, instead of storing these heavy labels, we propose a novel label-lightening framework termed HeLlO aiming at effective image-to-label projectors, with which synthetic labels can be directly generated online from synthetic images. Specifically, to construct such projectors, we leverage prior knowledge in open-source foundation models, e.g., CLIP, and introduce a LoRA-like fine-tuning strategy to mitigate the gap between pre-trained and target distributions, so that original models for soft-label generation can be distilled into a group of low-rank matrices. Moreover, an effective image optimization method is proposed to further mitigate the potential error between the original and distilled label generators. Extensive experiments demonstrate that with only about 0.003% of the original storage required for a complete set of soft labels, we achieve comparable performance to current state-of-the-art dataset distillation methods on large-scale datasets. Our code will be available.

Websites use third-party ads and tracking services to deliver targeted ads and collect information about users that visit them. These services put users' privacy at risk, and that is why users' demand for blocking these services is growing. Most of the blocking solutions rely on crowd-sourced filter lists manually maintained by a large community of users. In this work, we seek to simplify the update of these filter lists by combining different websites through a large-scale graph connecting all resource requests made over a large set of sites. The features of this graph are extracted and used to train a machine learning algorithm with the aim of detecting ads and tracking resources. As our approach combines different information sources, it is more robust toward evasion techniques that use obfuscation or changing the usage patterns. We evaluate our work over the Alexa top-10K websites and find its accuracy to be 96.1% biased and 90.9% unbiased with high precision and recall. It can also block new ads and tracking services, which would necessitate being blocked by further crowd-sourced existing filter lists. Moreover, the approach followed in this paper sheds light on the ecosystem of third-party tracking and advertising.

Implicit feedback data is extensively explored in recommendation as it is easy to collect and generally applicable. However, predicting users' preference on implicit feedback data is a challenging task since we can only observe positive (voted) samples and unvoted samples. It is difficult to distinguish between the negative samples and unlabeled positive samples from the unvoted ones. Existing works, such as Bayesian Personalized Ranking (BPR), sample unvoted items as negative samples uniformly, therefore suffer from a critical noisy-label issue. To address this gap, we design an adaptive sampler based on noisy-label robust learning for implicit feedback data. To formulate the issue, we first introduce Bayesian Point-wise Optimization (BPO) to learn a model, e.g., Matrix Factorization (MF), by maximum likelihood estimation. We predict users' preferences with the model and learn it by maximizing likelihood of observed data labels, i.e., a user prefers her positive samples and has no interests in her unvoted samples. However, in reality, a user may have interests in some of her unvoted samples, which are indeed positive samples mislabeled as negative ones. We then consider the risk of these noisy labels, and propose a Noisy-label Robust BPO (NBPO). NBPO also maximizes the observation likelihood while connects users' preference and observed labels by the likelihood of label flipping based on the Bayes' theorem. In NBPO, a user prefers her true positive samples and shows no interests in her true negative samples, hence the optimization quality is dramatically improved. Extensive experiments on two public real-world datasets show the significant improvement of our proposed optimization methods.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Dataset distillation aims to compress a dataset into a much smaller one so that a model trained on the distilled dataset achieves high accuracy. Current methods frame this as maximizing the distilled classification accuracy for a budget of K distilled images-per-class, where K is a positive integer. In this paper, we push the boundaries of dataset distillation, compressing the dataset into less than an image-per-class. It is important to realize that the meaningful quantity is not the number of distilled images-per-class but the number of distilled pixels-per-dataset. We therefore, propose Poster Dataset Distillation (PoDD), a new approach that distills the entire original dataset into a single poster. The poster approach motivates new technical solutions for creating training images and learnable labels. Our method can achieve comparable or better performance with less than an image-per-class compared to existing methods that use one image-per-class. Specifically, our method establishes a new state-of-the-art performance on CIFAR-10, CIFAR-100, and CUB200 using as little as 0.3 images-per-class.

Most NLP tasks are modeled as supervised learning and thus require labeled training data to train effective models. However, manually producing such data at sufficient quality and quantity is known to be costly and time-intensive. Current research addresses this bottleneck by exploring a novel paradigm called zero-shot learning via dataset generation. Here, a powerful LLM is prompted with a task description to generate labeled data that can be used to train a downstream NLP model. For instance, an LLM might be prompted to "generate 500 movie reviews with positive overall sentiment, and another 500 with negative sentiment." The generated data could then be used to train a binary sentiment classifier, effectively leveraging an LLM as a teacher to a smaller student model. With this demo, we introduce Fabricator, an open-source Python toolkit for dataset generation. Fabricator implements common dataset generation workflows, supports a wide range of downstream NLP tasks (such as text classification, question answering, and entity recognition), and is integrated with well-known libraries to facilitate quick experimentation. With Fabricator, we aim to support researchers in conducting reproducible dataset generation experiments using LLMs and help practitioners apply this approach to train models for downstream tasks.

Learning visual representations from natural language supervision has recently shown great promise in a number of pioneering works. In general, these language-augmented visual models demonstrate strong transferability to a variety of datasets and tasks. However, it remains challenging to evaluate the transferablity of these models due to the lack of easy-to-use evaluation toolkits and public benchmarks. To tackle this, we build ELEVATER (Evaluation of Language-augmented Visual Task-level Transfer), the first benchmark and toolkit for evaluating(pre-trained) language-augmented visual models. ELEVATER is composed of three components. (i) Datasets. As downstream evaluation suites, it consists of 20 image classification datasets and 35 object detection datasets, each of which is augmented with external knowledge. (ii) Toolkit. An automatic hyper-parameter tuning toolkit is developed to facilitate model evaluation on downstream tasks. (iii) Metrics. A variety of evaluation metrics are used to measure sample-efficiency (zero-shot and few-shot) and parameter-efficiency (linear probing and full model fine-tuning). ELEVATER is a platform for Computer Vision in the Wild (CVinW), and is publicly released at at https://computer-vision-in-the-wild.github.io/ELEVATER/

While enabling large language models to implement function calling (known as APIs) can greatly enhance the performance of LLMs, function calling is still a challenging task due to the complicated relations between different APIs, especially in a context-learning setting without fine-tuning. This paper proposes a simple yet controllable target-driven approach called Reverse Chain to empower LLMs with capabilities to use external APIs with only prompts. Given that most open-source LLMs have limited tool-use or tool-plan capabilities, LLMs in Reverse Chain are only employed to implement simple tasks, e.g., API selection and argument completion, and a generic rule is employed to implement a controllable multiple functions calling. In this generic rule, after selecting a final API to handle a given task via LLMs, we first ask LLMs to fill the required arguments from user query and context. Some missing arguments could be further completed by letting LLMs select another API based on API description before asking user. This process continues until a given task is completed. Extensive numerical experiments indicate an impressive capability of Reverse Chain on implementing multiple function calling. Interestingly enough, the experiments also reveal that tool-use capabilities of the existing LLMs, e.g., ChatGPT, can be greatly improved via Reverse Chain.

Online active learning is a paradigm in machine learning that aims to select the most informative data points to label from a data stream. The problem of minimizing the cost associated with collecting labeled observations has gained a lot of attention in recent years, particularly in real-world applications where data is only available in an unlabeled form. Annotating each observation can be time-consuming and costly, making it difficult to obtain large amounts of labeled data. To overcome this issue, many active learning strategies have been proposed in the last decades, aiming to select the most informative observations for labeling in order to improve the performance of machine learning models. These approaches can be broadly divided into two categories: static pool-based and stream-based active learning. Pool-based active learning involves selecting a subset of observations from a closed pool of unlabeled data, and it has been the focus of many surveys and literature reviews. However, the growing availability of data streams has led to an increase in the number of approaches that focus on online active learning, which involves continuously selecting and labeling observations as they arrive in a stream. This work aims to provide an overview of the most recently proposed approaches for selecting the most informative observations from data streams in real time. We review the various techniques that have been proposed and discuss their strengths and limitations, as well as the challenges and opportunities that exist in this area of research.

Driven by the recent advances in deep learning methods and, in particular, by the development of modern self-supervised learning algorithms, increased interest and efforts have been devoted to build foundation models (FMs) for medical images. In this work, we present our scalable training pipeline for large pathology imaging data, and a comprehensive analysis of various hyperparameter choices and training techniques for building pathology FMs. We release and make publicly available the first batch of our pathology FMs (https://github.com/kaiko-ai/towards_large_pathology_fms) trained on open-access TCGA whole slide images, a commonly used collection of pathology images. The experimental evaluation shows that our models reach state-of-the-art performance on various patch-level downstream tasks, ranging from breast cancer subtyping to colorectal nuclear segmentation. Finally, to unify the evaluation approaches used in the field and to simplify future comparisons of different FMs, we present an open-source framework (https://github.com/kaiko-ai/eva) designed for the consistent evaluation of pathology FMs across various downstream tasks.

Harmful fine-tuning issue qi2023fine poses serious safety concerns for Large language models' fine-tuning-as-a-service. While existing defenses huang2024vaccine,rosati2024representation have been proposed to mitigate the issue, their performances are still far away from satisfactory, and the root cause of the problem has not been fully recovered. For the first time in the literature, we in this paper show that harmful perturbation over the model weights should be the root cause of alignment-broken of harmful fine-tuning. In order to attenuate the negative impact of harmful perturbation, we propose an alignment-stage solution, dubbed Booster. Technically, along with the original alignment loss, we append a loss regularizer in the alignment stage's optimization. The regularizer ensures that the model's harmful loss reduction before/after simulated harmful perturbation is attenuated, thereby mitigating the subsequent fine-tuning risk. Empirical results show that Booster can effectively reduce the harmful score of the fine-tuned models while maintaining the performance of downstream tasks. Our code is available at https://github.com/git-disl/Booster.

Prior works on detoxification are scattered in the sense that they do not cover all aspects of detoxification needed in a real-world scenario. Notably, prior works restrict the task of developing detoxification models to only a seen subset of platforms, leaving the question of how the models would perform on unseen platforms unexplored. Additionally, these works do not address non-detoxifiability, a phenomenon whereby the toxic text cannot be detoxified without altering the meaning. We propose GreenLLaMA, the first comprehensive end-to-end detoxification framework, which attempts to alleviate the aforementioned limitations. We first introduce a cross-platform pseudo-parallel corpus applying multi-step data processing and generation strategies leveraging ChatGPT. We then train a suite of detoxification models with our cross-platform corpus. We show that our detoxification models outperform the SoTA model trained with human-annotated parallel corpus. We further introduce explanation to promote transparency and trustworthiness. GreenLLaMA additionally offers a unique paraphrase detector especially dedicated for the detoxification task to tackle the non-detoxifiable cases. Through experimental analysis, we demonstrate the effectiveness of our cross-platform corpus and the robustness of GreenLLaMA against adversarial toxicity.

We introduce a new visual-interactive tool: Explainable Labeling Assistant (XLabel) that takes an explainable machine learning approach to data labeling. The main component of XLabel is the Explainable Boosting Machine (EBM), a predictive model that can calculate the contribution of each input feature towards the final prediction. As a case study, we use XLabel to predict the labels of four non-communicable diseases (NCDs): diabetes, hypertension, chronic kidney disease, and dyslipidemia. We demonstrate that EBM is an excellent choice of predictive model by comparing it against a rule-based and four other machine learning models. By performing 5-fold cross-validation on 427 medical records, EBM's prediction accuracy, precision, and F1-score are greater than 0.95 in all four NCDs. It performed as well as two black-box models and outperformed the other models in these metrics. In an additional experiment, when 40% of the records were intentionally mislabeled, EBM could recall the correct labels of more than 90% of these records.

The rapid advancements in computing dramatically increase the scale and cost of training Large Language Models (LLMs). Accurately predicting downstream task performance prior to model training is crucial for efficient resource allocation, yet remains challenging due to two primary constraints: (1) the "emergence phenomenon", wherein downstream performance metrics become meaningful only after extensive training, which limits the ability to use smaller models for prediction; (2) Uneven task difficulty distributions and the absence of consistent scaling laws, resulting in substantial metric variability. Existing performance prediction methods suffer from limited accuracy and reliability, thereby impeding the assessment of potential LLM capabilities. To address these challenges, we propose a Clustering-On-Difficulty (COD) downstream performance prediction framework. COD first constructs a predictable support subset by clustering tasks based on difficulty features, strategically excluding non-emergent and non-scalable clusters. The scores on the selected subset serve as effective intermediate predictors of downstream performance on the full evaluation set. With theoretical support, we derive a mapping function that transforms performance metrics from the predictable subset to the full evaluation set, thereby ensuring accurate extrapolation of LLM downstream performance. The proposed method has been applied to predict performance scaling for a 70B LLM, providing actionable insights for training resource allocation and assisting in monitoring the training process. Notably, COD achieves remarkable predictive accuracy on the 70B LLM by leveraging an ensemble of small models, demonstrating an absolute mean deviation of 1.36% across eight important LLM evaluation benchmarks.

Hampering the interpretation of benchmark scores, evaluation data contamination has become a growing concern in the evaluation of LLMs, and an active area of research studies its effects. While evaluation data contamination is easily understood intuitively, it is surprisingly difficult to define precisely which samples should be considered contaminated and, consequently, how it impacts benchmark scores. We propose that these questions should be addressed together and that contamination metrics can be assessed based on whether models benefit from the examples they mark contaminated. We propose a novel analysis method called ConTAM, and show with a large scale survey of existing and novel n-gram based contamination metrics across 13 benchmarks and 7 models from 2 different families that ConTAM can be used to better understand evaluation data contamination and its effects. We find that contamination may have a much larger effect than reported in recent LLM releases and benefits models differently at different scales. We also find that considering only the longest contaminated substring provides a better signal than considering a union of all contaminated substrings, and that doing model and benchmark specific threshold analysis greatly increases the specificity of the results. Lastly, we investigate the impact of hyperparameter choices, finding that, among other things, both using larger values of n and disregarding matches that are infrequent in the pre-training data lead to many false negatives. With ConTAM, we provide a method to empirically ground evaluation data contamination metrics in downstream effects. With our exploration, we shed light on how evaluation data contamination can impact LLMs and provide insight into the considerations important when doing contamination analysis. We end our paper by discussing these in more detail and providing concrete suggestions for future work.

The iMet 2020 dataset is a valuable resource in the space of fine-grained art attribution recognition, but we believe it has yet to reach its true potential. We document the unique properties of the dataset and observe that many of the attribute labels are noisy, more than is implied by the dataset description. Oftentimes, there are also semantic relationships between the labels (e.g., identical, mutual exclusion, subsumption, overlap with uncertainty) which we believe are underutilized. We propose an approach to cleaning and structuring the iMet 2020 labels, and discuss the implications and value of doing so. Further, we demonstrate the benefits of our proposed approach through several experiments. Our code and cleaned labels are available at https://github.com/sunniesuhyoung/iMet2020cleaned.

Labeled data are critical to modern machine learning applications, but obtaining labels can be expensive. To mitigate this cost, machine learning methods, such as transfer learning, semi-supervised learning and active learning, aim to be label-efficient: achieving high predictive performance from relatively few labeled examples. While obtaining the best label-efficiency in practice often requires combinations of these techniques, existing benchmark and evaluation frameworks do not capture a concerted combination of all such techniques. This paper addresses this deficiency by introducing LabelBench, a new computationally-efficient framework for joint evaluation of multiple label-efficient learning techniques. As an application of LabelBench, we introduce a novel benchmark of state-of-the-art active learning methods in combination with semi-supervised learning for fine-tuning pretrained vision transformers. Our benchmark demonstrates better label-efficiencies than previously reported in active learning. LabelBench's modular codebase is open-sourced for the broader community to contribute label-efficient learning methods and benchmarks. The repository can be found at: https://github.com/EfficientTraining/LabelBench.

The task of toxicity detection is still a relevant task, especially in the context of safe and fair LMs development. Nevertheless, labeled binary toxicity classification corpora are not available for all languages, which is understandable given the resource-intensive nature of the annotation process. Ukrainian, in particular, is among the languages lacking such resources. To our knowledge, there has been no existing toxicity classification corpus in Ukrainian. In this study, we aim to fill this gap by investigating cross-lingual knowledge transfer techniques and creating labeled corpora by: (i)~translating from an English corpus, (ii)~filtering toxic samples using keywords, and (iii)~annotating with crowdsourcing. We compare LLMs prompting and other cross-lingual transfer approaches with and without fine-tuning offering insights into the most robust and efficient baselines.

Recent work on distilling Whisper's knowledge into small models using pseudo-labels shows promising performance while reducing the size by up to 50\%. This results in small, efficient, and dedicated models. However, a critical step of distillation from pseudo-labels involves filtering high-quality predictions and using only those during training. This step requires ground truth labels to compare and filter low-quality examples making the whole process supervised. In addition to that, the distillation process requires a large amount of data thereby limiting the ability to distill models in low-resource settings. To address this challenge, we propose a distillation framework that does not require any labeled data. Through experimentation, we show that our best distilled models outperform the teacher model by 5-7 points in terms of WER compared to those without filtering and are on par with or perform better than similar supervised data filtering setups. When we scale the data, our models significantly outperform all zero-shot and supervised models. We demonstrate that it is possible to distill large Whisper models into relatively small ones without using any labeled data. Our distilled models are also 25-50\% more compute- and memory-efficient while maintaining performance equal to or better than that of the teacher model.

The eXtreme Multi-label Classification~(XMC) problem seeks to find relevant labels from an exceptionally large label space. Most of the existing XMC learners focus on the extraction of semantic features from input query text. However, conventional XMC studies usually neglect the side information of instances and labels, which can be of use in many real-world applications such as recommendation systems and e-commerce product search. We propose Predicted Instance Neighborhood Aggregation (PINA), a data enhancement method for the general XMC problem that leverages beneficial side information. Unlike most existing XMC frameworks that treat labels and input instances as featureless indicators and independent entries, PINA extracts information from the label metadata and the correlations among training instances. Extensive experimental results demonstrate the consistent gain of PINA on various XMC tasks compared to the state-of-the-art methods: PINA offers a gain in accuracy compared to standard XR-Transformers on five public benchmark datasets. Moreover, PINA achieves a sim 5% gain in accuracy on the largest dataset LF-AmazonTitles-1.3M. Our implementation is publicly available.

Many real-world multi-label prediction problems involve set-valued predictions that must satisfy specific requirements dictated by downstream usage. We focus on a typical scenario where such requirements, separately encoding value and cost, compete with each other. For instance, a hospital might expect a smart diagnosis system to capture as many severe, often co-morbid, diseases as possible (the value), while maintaining strict control over incorrect predictions (the cost). We present a general pipeline, dubbed as FavMac, to maximize the value while controlling the cost in such scenarios. FavMac can be combined with almost any multi-label classifier, affording distribution-free theoretical guarantees on cost control. Moreover, unlike prior works, it can handle real-world large-scale applications via a carefully designed online update mechanism, which is of independent interest. Our methodological and theoretical contributions are supported by experiments on several healthcare tasks and synthetic datasets - FavMac furnishes higher value compared with several variants and baselines while maintaining strict cost control. Our code is available at https://github.com/zlin7/FavMac

High-throughput drug screening -- using cell imaging or gene expression measurements as readouts of drug effect -- is a critical tool in biotechnology to assess and understand the relationship between the chemical structure and biological activity of a drug. Since large-scale screens have to be divided into multiple experiments, a key difficulty is dealing with batch effects, which can introduce systematic errors and non-biological associations in the data. We propose InfoCORE, an Information maximization approach for COnfounder REmoval, to effectively deal with batch effects and obtain refined molecular representations. InfoCORE establishes a variational lower bound on the conditional mutual information of the latent representations given a batch identifier. It adaptively reweighs samples to equalize their implied batch distribution. Extensive experiments on drug screening data reveal InfoCORE's superior performance in a multitude of tasks including molecular property prediction and molecule-phenotype retrieval. Additionally, we show results for how InfoCORE offers a versatile framework and resolves general distribution shifts and issues of data fairness by minimizing correlation with spurious features or removing sensitive attributes. The code is available at https://github.com/uhlerlab/InfoCORE.

The computational prediction and design of peptide binders targeting specific linear epitopes is crucial in biological and biomedical research, yet it remains challenging due to their highly dynamic nature and the scarcity of experimentally solved binding data. To address this problem, we built an unprecedentedly large-scale library of peptide pairs within stable secondary structures (beta sheets), leveraging newly available AlphaFold predicted structures. We then developed a machine learning method based on the Transformer architecture for the design of specific linear binders, in analogy to a language translation task. Our method, TransformerBeta, accurately predicts specific beta strand interactions and samples sequences with beta sheet-like molecular properties, while capturing interpretable physico-chemical interaction patterns. As such, it can propose specific candidate binders targeting linear epitope for experimental validation to inform protein design.

We introduce a new framework for sample-efficient model evaluation that we call active testing. While approaches like active learning reduce the number of labels needed for model training, existing literature largely ignores the cost of labeling test data, typically unrealistically assuming large test sets for model evaluation. This creates a disconnect to real applications, where test labels are important and just as expensive, e.g. for optimizing hyperparameters. Active testing addresses this by carefully selecting the test points to label, ensuring model evaluation is sample-efficient. To this end, we derive theoretically-grounded and intuitive acquisition strategies that are specifically tailored to the goals of active testing, noting these are distinct to those of active learning. As actively selecting labels introduces a bias; we further show how to remove this bias while reducing the variance of the estimator at the same time. Active testing is easy to implement and can be applied to any supervised machine learning method. We demonstrate its effectiveness on models including WideResNets and Gaussian processes on datasets including Fashion-MNIST and CIFAR-100.

Invoices and receipts submitted by employees are visually rich documents (VRDs) with textual, visual and layout information. To protect against the risk of fraud and abuse, it is crucial for organizations to efficiently extract desired information from submitted receipts. This helps in the assessment of key factors such as appropriateness of the expense claim, adherence to spending and transaction policies, the validity of the receipt, as well as downstream anomaly detection at various levels. These documents are heterogeneous, with multiple formats and languages, uploaded with different image qualities, and often do not contain ground truth labels for the efficient training of models. In this paper we propose Task Aware Instruction-based Labelling (TAIL), a method for synthetic label generation in VRD corpuses without labels, and fine-tune a multimodal Visually Rich Document Understanding Model (VRDU) on TAIL labels using response-based knowledge distillation without using the teacher model's weights or training dataset to conditionally generate annotations in the appropriate format. Using a benchmark external dataset where ground truth labels are available, we demonstrate conditions under which our approach performs at par with Claude 3 Sonnet through empirical studies. We then show that the resulting model performs at par or better on the internal expense documents of a large multinational organization than state-of-the-art LMM (large multimodal model) Claude 3 Sonnet while being 85% less costly and ~5X faster, and outperforms layout-aware baselines by more than 10% in Average Normalized Levenshtein Similarity (ANLS) scores due to its ability to reason and extract information from rare formats. Finally, we illustrate the usage of our approach in overpayment prevention.

The RNN transducer is a promising end-to-end model candidate. We compare the original training criterion with the full marginalization over all alignments, to the commonly used maximum approximation, which simplifies, improves and speeds up our training. We also generalize from the original neural network model and study more powerful models, made possible due to the maximum approximation. We further generalize the output label topology to cover RNN-T, RNA and CTC. We perform several studies among all these aspects, including a study on the effect of external alignments. We find that the transducer model generalizes much better on longer sequences than the attention model. Our final transducer model outperforms our attention model on Switchboard 300h by over 6% relative WER.

The recent advancements in large language models (LLMs) have sparked a growing apprehension regarding the potential misuse. One approach to mitigating this risk is to incorporate watermarking techniques into LLMs, allowing for the tracking and attribution of model outputs. This study examines a crucial aspect of watermarking: how significantly watermarks impact the quality of model-generated outputs. Previous studies have suggested a trade-off between watermark strength and output quality. However, our research demonstrates that it is possible to integrate watermarks without affecting the output probability distribution with appropriate implementation. We refer to this type of watermark as an unbiased watermark. This has significant implications for the use of LLMs, as it becomes impossible for users to discern whether a service provider has incorporated watermarks or not. Furthermore, the presence of watermarks does not compromise the performance of the model in downstream tasks, ensuring that the overall utility of the language model is preserved. Our findings contribute to the ongoing discussion around responsible AI development, suggesting that unbiased watermarks can serve as an effective means of tracking and attributing model outputs without sacrificing output quality.

In ImageNet-condensation, the storage for auxiliary soft labels exceeds that of the condensed dataset by over 30 times. However, are large-scale soft labels necessary for large-scale dataset distillation? In this paper, we first discover that the high within-class similarity in condensed datasets necessitates the use of large-scale soft labels. This high within-class similarity can be attributed to the fact that previous methods use samples from different classes to construct a single batch for batch normalization (BN) matching. To reduce the within-class similarity, we introduce class-wise supervision during the image synthesizing process by batching the samples within classes, instead of across classes. As a result, we can increase within-class diversity and reduce the size of required soft labels. A key benefit of improved image diversity is that soft label compression can be achieved through simple random pruning, eliminating the need for complex rule-based strategies. Experiments validate our discoveries. For example, when condensing ImageNet-1K to 200 images per class, our approach compresses the required soft labels from 113 GB to 2.8 GB (40x compression) with a 2.6% performance gain. Code is available at: https://github.com/he-y/soft-label-pruning-for-dataset-distillation

Large language models (LLMs) are increasingly being integrated into search engines to provide natural language responses tailored to user queries. Customers and end-users are also becoming more dependent on these models for quick and easy purchase decisions. In this work, we investigate whether recommendations from LLMs can be manipulated to enhance a product's visibility. We demonstrate that adding a strategic text sequence (STS) -- a carefully crafted message -- to a product's information page can significantly increase its likelihood of being listed as the LLM's top recommendation. To understand the impact of STS, we use a catalog of fictitious coffee machines and analyze its effect on two target products: one that seldom appears in the LLM's recommendations and another that usually ranks second. We observe that the strategic text sequence significantly enhances the visibility of both products by increasing their chances of appearing as the top recommendation. This ability to manipulate LLM-generated search responses provides vendors with a considerable competitive advantage and has the potential to disrupt fair market competition. Just as search engine optimization (SEO) revolutionized how webpages are customized to rank higher in search engine results, influencing LLM recommendations could profoundly impact content optimization for AI-driven search services. Code for our experiments is available at https://github.com/aounon/llm-rank-optimizer.

Multi-label classification (MLC) suffers from the inevitable label noise in training data due to the difficulty in annotating various semantic labels in each image. To mitigate the influence of noisy labels, existing methods mainly devote to identifying and correcting the label mistakes via a trained MLC model. However, these methods still involve annoying noisy labels in training, which can result in imprecise recognition of noisy labels and weaken the performance. In this paper, considering that the negative labels are substantially more than positive labels, and most noisy labels are from the negative labels, we directly discard all the negative labels in the dataset, and propose a new method dubbed positive and unlabeled multi-label classification (PU-MLC). By extending positive-unlabeled learning into MLC task, our method trains model with only positive labels and unlabeled data, and introduces adaptive re-balance factor and adaptive temperature coefficient in the loss function to alleviate the catastrophic imbalance in label distribution and over-smoothing of probabilities in training. Furthermore, to capture both local and global dependencies in the image, we also introduce a local-global convolution module, which supplements global information into existing convolution layers with no retraining of backbone required. Our PU-MLC is simple and effective, and it is applicable to both MLC and MLC with partial labels (MLC-PL) tasks. Extensive experiments on MS-COCO and PASCAL VOC datasets demonstrate that our PU-MLC achieves significantly improvements on both MLC and MLC-PL settings with even fewer annotations. Code will be released.

The most effective techniques to detect LLM-generated text rely on inserting a detectable signature -- or watermark -- during the model's decoding process. Most existing watermarking methods require access to the underlying LLM's logits, which LLM API providers are loath to share due to fears of model distillation. As such, these watermarks must be implemented independently by each LLM provider. In this paper, we develop PostMark, a modular post-hoc watermarking procedure in which an input-dependent set of words (determined via a semantic embedding) is inserted into the text after the decoding process has completed. Critically, PostMark does not require logit access, which means it can be implemented by a third party. We also show that PostMark is more robust to paraphrasing attacks than existing watermarking methods: our experiments cover eight baseline algorithms, five base LLMs, and three datasets. Finally, we evaluate the impact of PostMark on text quality using both automated and human assessments, highlighting the trade-off between quality and robustness to paraphrasing. We release our code, outputs, and annotations at https://github.com/lilakk/PostMark.

We consider Large-Scale Multi-Label Text Classification (LMTC) in the legal domain. We release a new dataset of 57k legislative documents from EURLEX, annotated with ~4.3k EUROVOC labels, which is suitable for LMTC, few- and zero-shot learning. Experimenting with several neural classifiers, we show that BIGRUs with label-wise attention perform better than other current state of the art methods. Domain-specific WORD2VEC and context-sensitive ELMO embeddings further improve performance. We also find that considering only particular zones of the documents is sufficient. This allows us to bypass BERT's maximum text length limit and fine-tune BERT, obtaining the best results in all but zero-shot learning cases.

Misinformation is a complex societal issue, and mitigating solutions are difficult to create due to data deficiencies. To address this problem, we have curated the largest collection of (mis)information datasets in the literature, totaling 75. From these, we evaluated the quality of all of the 36 datasets that consist of statements or claims. We assess these datasets to identify those with solid foundations for empirical work and those with flaws that could result in misleading and non-generalizable results, such as insufficient label quality, spurious correlations, or political bias. We further provide state-of-the-art baselines on all these datasets, but show that regardless of label quality, categorical labels may no longer give an accurate evaluation of detection model performance. We discuss alternatives to mitigate this problem. Overall, this guide aims to provide a roadmap for obtaining higher quality data and conducting more effective evaluations, ultimately improving research in misinformation detection. All datasets and other artifacts are available at https://misinfo-datasets.complexdatalab.com/.

Zero-resource cross-lingual transfer approaches aim to apply supervised models from a source language to unlabelled target languages. In this paper we perform an in-depth study of the two main techniques employed so far for cross-lingual zero-resource sequence labelling, based either on data or model transfer. Although previous research has proposed translation and annotation projection (data-based cross-lingual transfer) as an effective technique for cross-lingual sequence labelling, in this paper we experimentally demonstrate that high capacity multilingual language models applied in a zero-shot (model-based cross-lingual transfer) setting consistently outperform data-based cross-lingual transfer approaches. A detailed analysis of our results suggests that this might be due to important differences in language use. More specifically, machine translation often generates a textual signal which is different to what the models are exposed to when using gold standard data, which affects both the fine-tuning and evaluation processes. Our results also indicate that data-based cross-lingual transfer approaches remain a competitive option when high-capacity multilingual language models are not available.

Referring image segmentation, the task of segmenting any arbitrary entities described in free-form texts, opens up a variety of vision applications. However, manual labeling of training data for this task is prohibitively costly, leading to lack of labeled data for training. We address this issue by a weakly supervised learning approach using text descriptions of training images as the only source of supervision. To this end, we first present a new model that discovers semantic entities in input image and then combines such entities relevant to text query to predict the mask of the referent. We also present a new loss function that allows the model to be trained without any further supervision. Our method was evaluated on four public benchmarks for referring image segmentation, where it clearly outperformed the existing method for the same task and recent open-vocabulary segmentation models on all the benchmarks.

Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing and conducting chemical reactions to synthesize new compounds with desired properties and applications. Current approaches, however, often neglect the critical role of multiple molecule graph interaction in understanding chemical reactions, leading to suboptimal performance in synthetic chemistry tasks. This study introduces PRESTO(Progressive Pretraining Enhances Synthetic Chemistry Outcomes), a new framework that bridges the molecule-text modality gap by integrating a comprehensive benchmark of pretraining strategies and dataset configurations. It progressively improves multimodal LLMs through cross-modal alignment and multi-graph understanding. Our extensive experiments demonstrate that PRESTO offers competitive results in downstream synthetic chemistry tasks. The code can be found at https://github.com/IDEA-XL/PRESTO.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

In an era of increasing pressure to achieve sustainable agriculture, the optimization of livestock feed for enhancing yield and minimizing environmental impact is a paramount objective. This study presents a pioneering approach towards this goal, using rumen microbiome data to predict the efficacy of feed additives in dairy cattle. We collected an extensive dataset that includes methane emissions from 2,190 Holstein cows distributed across 34 distinct sites. The cows were divided into control and experimental groups in a double-blind, unbiased manner, accounting for variables such as age, days in lactation, and average milk yield. The experimental groups were administered one of four leading commercial feed additives: Agolin, Kexxtone, Allimax, and Relyon. Methane emissions were measured individually both before the administration of additives and over a subsequent 12-week period. To develop our predictive model for additive efficacy, rumen microbiome samples were collected from 510 cows from the same herds prior to the study's onset. These samples underwent deep metagenomic shotgun sequencing, yielding an average of 15.7 million reads per sample. Utilizing innovative artificial intelligence techniques we successfully estimated the efficacy of these feed additives across different farms. The model's robustness was further confirmed through validation with independent cohorts, affirming its generalizability and reliability. Our results underscore the transformative capability of using targeted feed additive strategies to both optimize dairy yield and milk composition, and to significantly reduce methane emissions. Specifically, our predictive model demonstrates a scenario where its application could guide the assignment of additives to farms where they are most effective. In doing so, we could achieve an average potential reduction of over 27\% in overall emissions.

One of the most challenging problems facing NLP today is evaluation. Some of the most pressing issues pertain to benchmark saturation, data contamination, and diversity in the quality of test examples. To address these concerns, we propose Selection Methodology for Accurate, Reduced, and Targeted (SMART) filtering, a novel approach to select a high-quality subset of examples from existing benchmark datasets by systematically removing less informative and less challenging examples. Our approach applies three filtering criteria, removing (i) easy examples, (ii) data-contaminated examples, and (iii) examples that are similar to each other based on distance in an embedding space. We demonstrate the effectiveness of SMART on three multiple choice QA datasets, where our methodology increases efficiency by reducing dataset size by 48\% on average, while increasing Pearson correlation with rankings from ChatBot Arena, a more open-ended human evaluation setting. Our method enables us to be more efficient, whether using SMART to make new benchmarks more challenging or to revitalize older datasets, while still preserving the relative model rankings.

Open vocabulary models (e.g. CLIP) have shown strong performance on zero-shot classification through their ability generate embeddings for each class based on their (natural language) names. Prior work has focused on improving the accuracy of these models through prompt engineering or by incorporating a small amount of labeled downstream data (via finetuning). However, there has been little focus on improving the richness of the class names themselves, which can pose issues when class labels are coarsely-defined and are uninformative. We propose Classification with Hierarchical Label Sets (or CHiLS), an alternative strategy for zero-shot classification specifically designed for datasets with implicit semantic hierarchies. CHiLS proceeds in three steps: (i) for each class, produce a set of subclasses, using either existing label hierarchies or by querying GPT-3; (ii) perform the standard zero-shot CLIP procedure as though these subclasses were the labels of interest; (iii) map the predicted subclass back to its parent to produce the final prediction. Across numerous datasets with underlying hierarchical structure, CHiLS leads to improved accuracy in situations both with and without ground-truth hierarchical information. CHiLS is simple to implement within existing zero-shot pipelines and requires no additional training cost. Code is available at: https://github.com/acmi-lab/CHILS.

Semi-supervised learning (SSL) has witnessed great progress with various improvements in the self-training framework with pseudo labeling. The main challenge is how to distinguish high-quality pseudo labels against the confirmation bias. However, existing pseudo-label selection strategies are limited to pre-defined schemes or complex hand-crafted policies specially designed for classification, failing to achieve high-quality labels, fast convergence, and task versatility simultaneously. To these ends, we propose a Semi-supervised Reward framework (SemiReward) that predicts reward scores to evaluate and filter out high-quality pseudo labels, which is pluggable to mainstream SSL methods in wide task types and scenarios. To mitigate confirmation bias, SemiReward is trained online in two stages with a generator model and subsampling strategy. With classification and regression tasks on 13 standard SSL benchmarks across three modalities, extensive experiments verify that SemiReward achieves significant performance gains and faster convergence speeds upon Pseudo Label, FlexMatch, and Free/SoftMatch. Code and models are available at https://github.com/Westlake-AI/SemiReward.

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

Given a sample of size N, it is often useful to select a subsample of smaller size n<N to be used for statistical estimation or learning. Such a data selection step is useful to reduce the requirements of data labeling and the computational complexity of learning. We assume to be given N unlabeled samples {{boldsymbol x}_i}_{ile N}, and to be given access to a `surrogate model' that can predict labels y_i better than random guessing. Our goal is to select a subset of the samples, to be denoted by {{boldsymbol x}_i}_{iin G}, of size |G|=n<N. We then acquire labels for this set and we use them to train a model via regularized empirical risk minimization. By using a mixture of numerical experiments on real and synthetic data, and mathematical derivations under low- and high- dimensional asymptotics, we show that: (i)~Data selection can be very effective, in particular beating training on the full sample in some cases; (ii)~Certain popular choices in data selection methods (e.g. unbiased reweighted subsampling, or influence function-based subsampling) can be substantially suboptimal.

RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly for applications in drug discovery, remains a challenge due to the complexity of RNA structures and interactions. While foundational models in biology have demonstrated success in modeling several biomolecules, especially proteins, achieving similar breakthroughs for RNA has proven more difficult. Current RNA models have yet to match the performance observed in the protein domain, leaving an important gap in computational biology. In this work, we present ChaRNABERT, a suite of sample and parameter-efficient RNA foundational models, that through a learnable tokenization process, are able to reach state-of-the-art performance on several tasks in established benchmarks. We extend its testing in relevant downstream tasks such as RNA-protein and aptamer-protein interaction prediction. Weights and inference code for ChaRNABERT-8M will be provided for academic research use. The other models will be available upon request.

As opposed to general English, many concepts in biomedical terminology have been designed in recent history by biomedical professionals with the goal of being precise and concise. This is often achieved by concatenating meaningful biomedical morphemes to create new semantic units. Nevertheless, most modern biomedical language models (LMs) are pre-trained using standard domain-specific tokenizers derived from large scale biomedical corpus statistics without explicitly leveraging the agglutinating nature of biomedical language. In this work, we first find that standard open-domain and biomedical tokenizers are largely unable to segment biomedical terms into meaningful components. Therefore, we hypothesize that using a tokenizer which segments biomedical terminology more accurately would enable biomedical LMs to improve their performance on downstream biomedical NLP tasks, especially ones which involve biomedical terms directly such as named entity recognition (NER) and entity linking. Surprisingly, we find that pre-training a biomedical LM using a more accurate biomedical tokenizer does not improve the entity representation quality of a language model as measured by several intrinsic and extrinsic measures such as masked language modeling prediction (MLM) accuracy as well as NER and entity linking performance. These quantitative findings, along with a case study which explores entity representation quality more directly, suggest that the biomedical pre-training process is quite robust to instances of sub-optimal tokenization.

Aligned Large Language Models (LLMs) showcase remarkable versatility, capable of handling diverse real-world tasks. Meanwhile, aligned LLMs are also expected to exhibit speciality, excelling in specific applications. However, fine-tuning with extra data, a common practice to gain speciality, often leads to catastrophic forgetting (CF) of previously acquired versatility, hindering the model's performance across diverse tasks. In response to this challenge, we propose CoFiTune, a coarse to fine framework in an attempt to strike the balance between speciality and versatility. At the coarse-grained level, an empirical tree-search algorithm is utilized to pinpoint and update specific modules that are crucial for speciality, while keeping other parameters frozen; at the fine-grained level, a soft-masking mechanism regulates the update to the LLMs, mitigating the CF issue without harming speciality. In an overall evaluation of both speciality and versatility, CoFiTune consistently outperforms baseline methods across diverse tasks and model scales. Compared to the full-parameter SFT, CoFiTune leads to about 14% versatility improvement and marginal speciality loss on a 13B model. Lastly, based on further analysis, we provide a speculative insight into the information forwarding process in LLMs, which helps explain the effectiveness of the proposed method. The code is available at https://github.com/rattlesnakey/CoFiTune.

Large language models (LLMs) have demonstrated remarkable generalizability, such as understanding arbitrary entities and relations. Instruction tuning has proven effective for distilling LLMs into more cost-efficient models such as Alpaca and Vicuna. Yet such student models still trail the original LLMs by large margins in downstream applications. In this paper, we explore targeted distillation with mission-focused instruction tuning to train student models that can excel in a broad application class such as open information extraction. Using named entity recognition (NER) for case study, we show how ChatGPT can be distilled into much smaller UniversalNER models for open NER. For evaluation, we assemble the largest NER benchmark to date, comprising 43 datasets across 9 diverse domains such as biomedicine, programming, social media, law, finance. Without using any direct supervision, UniversalNER attains remarkable NER accuracy across tens of thousands of entity types, outperforming general instruction-tuned models such as Alpaca and Vicuna by over 30 absolute F1 points in average. With a tiny fraction of parameters, UniversalNER not only acquires ChatGPT's capability in recognizing arbitrary entity types, but also outperforms its NER accuracy by 7-9 absolute F1 points in average. Remarkably, UniversalNER even outperforms by a large margin state-of-the-art multi-task instruction-tuned systems such as InstructUIE, which uses supervised NER examples. We also conduct thorough ablation studies to assess the impact of various components in our distillation approach. We will release the distillation recipe, data, and UniversalNER models to facilitate future research on targeted distillation.

Deep learning in computational biochemistry has traditionally focused on molecular graphs neural representations; however, recent advances in language models highlight how much scientific knowledge is encoded in text. To bridge these two modalities, we investigate how molecular property information can be transferred from natural language to graph representations. We study property prediction performance gains after using contrastive learning to align neural graph representations with representations of textual descriptions of their characteristics. We implement neural relevance scoring strategies to improve text retrieval, introduce a novel chemically-valid molecular graph augmentation strategy inspired by organic reactions, and demonstrate improved performance on downstream MoleculeNet property classification tasks. We achieve a +4.26% AUROC gain versus models pre-trained on the graph modality alone, and a +1.54% gain compared to recently proposed molecular graph/text contrastively trained MoMu model (Su et al. 2022).

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

This paper presents a multi-label topic model for financial texts like ad-hoc announcements, 8-K filings, finance related news or annual reports. I train the model on a new financial multi-label database consisting of 3,044 German ad-hoc announcements that are labeled manually using 20 predefined, economically motivated topics. The best model achieves a macro F1 score of more than 85%. Translating the data results in an English version of the model with similar performance. As application of the model, I investigate differences in stock market reactions across topics. I find evidence for strong positive or negative market reactions for some topics, like announcements of new Large Scale Projects or Bankruptcy Filings, while I do not observe significant price effects for some other topics. Furthermore, in contrast to previous studies, the multi-label structure of the model allows to analyze the effects of co-occurring topics on stock market reactions. For many cases, the reaction to a specific topic depends heavily on the co-occurrence with other topics. For example, if allocated capital from a Seasoned Equity Offering (SEO) is used for restructuring a company in the course of a Bankruptcy Proceeding, the market reacts positively on average. However, if that capital is used for covering unexpected, additional costs from the development of new drugs, the SEO implies negative reactions on average.

Large language models (LLMs) are routinely pre-trained on billions of tokens, only to restart the process over again once new data becomes available. A much cheaper and more efficient solution would be to enable the continual pre-training of these models, i.e. updating pre-trained models with new data instead of re-training them from scratch. However, the distribution shift induced by novel data typically results in degraded performance on past data. Taking a step towards efficient continual pre-training, in this work, we examine the effect of different warm-up strategies. Our hypothesis is that the learning rate must be re-increased to improve compute efficiency when training on a new dataset. We study the warmup phase of models pre-trained on the Pile (upstream data, 300B tokens) as we continue to pre-train on SlimPajama (downstream data, 297B tokens), following a linear warmup and cosine decay schedule. We conduct all experiments on the Pythia 410M language model architecture and evaluate performance through validation perplexity. We experiment with different pre-training checkpoints, various maximum learning rates, and various warmup lengths. Our results show that while rewarming models first increases the loss on upstream and downstream data, in the longer run it improves the downstream performance, outperforming models trained from scratchx2013even for a large downstream dataset.

Previous object detectors make predictions based on dense grid points or numerous preset anchors. Most of these detectors are trained with one-to-many label assignment strategies. On the contrary, recent query-based object detectors depend on a sparse set of learnable queries and a series of decoder layers. The one-to-one label assignment is independently applied on each layer for the deep supervision during training. Despite the great success of query-based object detection, however, this one-to-one label assignment strategy demands the detectors to have strong fine-grained discrimination and modeling capacity. To solve the above problems, in this paper, we propose a new query-based object detector with cross-stage interaction, coined as StageInteractor. During the forward propagation, we come up with an efficient way to improve this modeling ability by reusing dynamic operators with lightweight adapters. As for the label assignment, a cross-stage label assigner is applied subsequent to the one-to-one label assignment. With this assigner, the training target class labels are gathered across stages and then reallocated to proper predictions at each decoder layer. On MS COCO benchmark, our model improves the baseline by 2.2 AP, and achieves 44.8 AP with ResNet-50 as backbone, 100 queries and 12 training epochs. With longer training time and 300 queries, StageInteractor achieves 51.1 AP and 52.2 AP with ResNeXt-101-DCN and Swin-S, respectively.

Automatic mainstream hashtag recommendation aims to accurately provide users with concise and popular topical hashtags before publication. Generally, mainstream hashtag recommendation faces challenges in the comprehensive difficulty of newly posted tweets in response to new topics, and the accurate identification of mainstream hashtags beyond semantic correctness. However, previous retrieval-based methods based on a fixed predefined mainstream hashtag list excel in producing mainstream hashtags, but fail to understand the constant flow of up-to-date information. Conversely, generation-based methods demonstrate a superior ability to comprehend newly posted tweets, but their capacity is constrained to identifying mainstream hashtags without additional features. Inspired by the recent success of the retrieval-augmented technique, in this work, we attempt to adopt this framework to combine the advantages of both approaches. Meantime, with the help of the generator component, we could rethink how to further improve the quality of the retriever component at a low cost. Therefore, we propose RetrIeval-augmented Generative Mainstream HashTag Recommender (RIGHT), which consists of three components: 1) a retriever seeks relevant hashtags from the entire tweet-hashtags set; 2) a selector enhances mainstream identification by introducing global signals; and 3) a generator incorporates input tweets and selected hashtags to directly generate the desired hashtags. The experimental results show that our method achieves significant improvements over state-of-the-art baselines. Moreover, RIGHT can be easily integrated into large language models, improving the performance of ChatGPT by more than 10%.

In this paper, we present a simple and efficient GEC sequence tagger using a Transformer encoder. Our system is pre-trained on synthetic data and then fine-tuned in two stages: first on errorful corpora, and second on a combination of errorful and error-free parallel corpora. We design custom token-level transformations to map input tokens to target corrections. Our best single-model/ensemble GEC tagger achieves an F_{0.5} of 65.3/66.5 on CoNLL-2014 (test) and F_{0.5} of 72.4/73.6 on BEA-2019 (test). Its inference speed is up to 10 times as fast as a Transformer-based seq2seq GEC system. The code and trained models are publicly available.

We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based platforms able to sequence non-native peptides. Current protein sequencing techniques face limitations in accurately identifying all amino acids, hindering comprehensive proteome analysis. Our method simulates partial sequencing data by selectively masking amino acids that are experimentally difficult to identify in protein sequences from the UniRef database. This targeted masking mimics real-world sequencing limitations. We then modify and finetune a ProtBert derived transformer-based model, for a new downstream task predicting these masked residues, providing an approximation of the complete sequence. Evaluating on three bacterial Escherichia species, we achieve per-amino-acid accuracy up to 90.5% when only four amino acids ([KCYM]) are known. Structural assessment using AlphaFold and TM-score validates the biological relevance of our predictions. The model also demonstrates potential for evolutionary analysis through cross-species performance. This integration of simulated experimental constraints with computational predictions offers a promising avenue for enhancing protein sequence analysis, potentially accelerating advancements in proteomics and structural biology by providing a probabilistic reconstruction of the complete protein sequence from limited experimental data.

The U.S. Securities and Exchange Commission (SEC) requires that public companies file financial reports tagging numbers with the machine readable inline eXtensible Business Reporting Language (iXBRL) standard. However, the highly complex and highly granular taxonomy defined by iXBRL limits label transferability across domains. In this paper, we introduce the Hierarchical Financial Key Performance Indicator (HiFi-KPI) dataset, designed to facilitate numerical KPI extraction at specified levels of granularity from unstructured financial text. Our approach organizes a 218,126-label hierarchy using a taxonomy based grouping method, investigating which taxonomy layer provides the most meaningful structure. HiFi-KPI comprises ~1.8M paragraphs and ~5M entities, each linked to a label in the iXBRL-specific calculation and presentation taxonomies. We provide baselines using encoder-based approaches and structured extraction using Large Language Models (LLMs). To simplify LLM inference and evaluation, we additionally release HiFi-KPI Lite, a manually curated subset with four expert-mapped labels. We publicly release all artifacts

Text clustering remains valuable in real-world applications where manual labeling is cost-prohibitive. It facilitates efficient organization and analysis of information by grouping similar texts based on their representations. However, implementing this approach necessitates fine-tuned embedders for downstream data and sophisticated similarity metrics. To address this issue, this study presents a novel framework for text clustering that effectively leverages the in-context learning capacity of Large Language Models (LLMs). Instead of fine-tuning embedders, we propose to transform the text clustering into a classification task via LLM. First, we prompt LLM to generate potential labels for a given dataset. Second, after integrating similar labels generated by the LLM, we prompt the LLM to assign the most appropriate label to each sample in the dataset. Our framework has been experimentally proven to achieve comparable or superior performance to state-of-the-art clustering methods that employ embeddings, without requiring complex fine-tuning or clustering algorithms. We make our code available to the public for utilization at https://anonymous.4open.science/r/Text-Clustering-via-LLM-E500.

NLP benchmarks rely on standardized datasets for training and evaluating models and are crucial for advancing the field. Traditionally, expert annotations ensure high-quality labels; however, the cost of expert annotation does not scale well with the growing demand for larger datasets required by modern models. While crowd-sourcing provides a more scalable solution, it often comes at the expense of annotation precision and consistency. Recent advancements in large language models (LLMs) offer new opportunities to enhance the annotation process, particularly for detecting label errors in existing datasets. In this work, we consider the recent approach of LLM-as-a-judge, leveraging an ensemble of LLMs to flag potentially mislabeled examples. Through a case study of four datasets from the TRUE benchmark, covering different tasks and domains, we empirically analyze the labeling quality of existing datasets, and compare expert, crowd-sourced, and our LLM-based annotations in terms of agreement, label quality, and efficiency, demonstrating the strengths and limitations of each annotation method. Our findings reveal a substantial number of label errors, which, when corrected, induce a significant upward shift in reported model performance. This suggests that many of the LLMs so-called mistakes are due to label errors rather than genuine model failures. Additionally, we discuss the implications of mislabeled data and propose methods to mitigate them in training to improve model performance.

Multi-dataset training provides a viable solution for exploiting heterogeneous large-scale datasets without extra annotation cost. In this work, we propose a scalable multi-dataset detector (ScaleDet) that can scale up its generalization across datasets when increasing the number of training datasets. Unlike existing multi-dataset learners that mostly rely on manual relabelling efforts or sophisticated optimizations to unify labels across datasets, we introduce a simple yet scalable formulation to derive a unified semantic label space for multi-dataset training. ScaleDet is trained by visual-textual alignment to learn the label assignment with label semantic similarities across datasets. Once trained, ScaleDet can generalize well on any given upstream and downstream datasets with seen and unseen classes. We conduct extensive experiments using LVIS, COCO, Objects365, OpenImages as upstream datasets, and 13 datasets from Object Detection in the Wild (ODinW) as downstream datasets. Our results show that ScaleDet achieves compelling strong model performance with an mAP of 50.7 on LVIS, 58.8 on COCO, 46.8 on Objects365, 76.2 on OpenImages, and 71.8 on ODinW, surpassing state-of-the-art detectors with the same backbone.

Large pretrained models such as GPT-3 have had tremendous impact on modern natural language processing by leveraging self-supervised learning to learn salient representations that can be used to readily finetune on a wide variety of downstream tasks. We investigate the possibility of transferring such advances to molecular machine learning by building a chemical foundation model, ChemBERTa-2, using the language of SMILES. While labeled data for molecular prediction tasks is typically scarce, libraries of SMILES strings are readily available. In this work, we build upon ChemBERTa by optimizing the pretraining process. We compare multi-task and self-supervised pretraining by varying hyperparameters and pretraining dataset size, up to 77M compounds from PubChem. To our knowledge, the 77M set constitutes one of the largest datasets used for molecular pretraining to date. We find that with these pretraining improvements, we are competitive with existing state-of-the-art architectures on the MoleculeNet benchmark suite. We analyze the degree to which improvements in pretraining translate to improvement on downstream tasks.

Transfer learning with a small amount of target data is an effective and common approach to adapting a pre-trained model to distribution shifts. In some situations, target data labels may be expensive to obtain, so we may only have access to a limited number of target data points. To make the most of a very small target dataset, we propose a lightweight, sample-efficient approach that learns a diverse set of features and adapts to a target distribution by interpolating these features. Our approach, Project and Probe (Pro^2), first learns a linear projection that maps a pre-trained embedding onto orthogonal directions while being predictive of labels in the source dataset. The goal of this step is to learn a variety of predictive features, so that at least some of them remain useful after distribution shift. Pro^2 then learns a linear classifier on top of these projected features using a small target dataset. Theoretically, we find that Pro^2 results in more sample-efficient generalization by inducing a favorable bias-variance tradeoff. Our experiments on four datasets, with multiple distribution shift settings for each, show that Pro^2 improves performance by 5-15% when given limited target data compared to prior methods such as standard linear probing.

We consider higher-order linear-chain conditional random fields (HO-LC-CRFs) for sequence modelling, and use sum-product networks (SPNs) for representing higher-order input- and output-dependent factors. SPNs are a recently introduced class of deep models for which exact and efficient inference can be performed. By combining HO-LC-CRFs with SPNs, expressive models over both the output labels and the hidden variables are instantiated while still enabling efficient exact inference. Furthermore, the use of higher-order factors allows us to capture relations of multiple input segments and multiple output labels as often present in real-world data. These relations can not be modelled by the commonly used first-order models and higher-order models with local factors including only a single output label. We demonstrate the effectiveness of our proposed models for sequence labeling. In extensive experiments, we outperform other state-of-the-art methods in optical character recognition and achieve competitive results in phone classification.

Large Language Models have demonstrated impressive capabilities in various language tasks but may produce content that misaligns with human expectations, raising ethical and legal concerns. Therefore, it is important to explore the limitations and implement restrictions on the models to ensure safety and compliance, with Reinforcement Learning from Human Feedback (RLHF) being the primary method. Due to challenges in stability and scalability with the RLHF stages, researchers are exploring alternative methods to achieve effects comparable to those of RLHF. However, these methods often depend on large high-quality datasets and inefficiently utilize generated data. To deal with this problem, we propose PSLE, i.e., Progressively Selective Label Enhancement for Language Model Alignment, a framework that fully utilizes all generated data by guiding the model with principles to align outputs with human expectations. Using a dynamically updated threshold, our approach ensures efficient data utilization by incorporating all generated responses and weighting them based on their corresponding reward scores. Experimental results on multiple datasets demonstrate the effectiveness of PSLE compared to existing language model alignment methods.

Existing knowledge distillation methods typically work by imparting the knowledge of output logits or intermediate feature maps from the teacher network to the student network, which is very successful in multi-class single-label learning. However, these methods can hardly be extended to the multi-label learning scenario, where each instance is associated with multiple semantic labels, because the prediction probabilities do not sum to one and feature maps of the whole example may ignore minor classes in such a scenario. In this paper, we propose a novel multi-label knowledge distillation method. On one hand, it exploits the informative semantic knowledge from the logits by dividing the multi-label learning problem into a set of binary classification problems; on the other hand, it enhances the distinctiveness of the learned feature representations by leveraging the structural information of label-wise embeddings. Experimental results on multiple benchmark datasets validate that the proposed method can avoid knowledge counteraction among labels, thus achieving superior performance against diverse comparing methods. Our code is available at: https://github.com/penghui-yang/L2D

Recent progress in weakly supervised object detection is featured by a combination of multiple instance detection networks (MIDN) and ordinal online refinement. However, with only image-level annotation, MIDN inevitably assigns high scores to some unexpected region proposals when generating pseudo labels. These inaccurate high-scoring region proposals will mislead the training of subsequent refinement modules and thus hamper the detection performance. In this work, we explore how to ameliorate the quality of pseudo-labeling in MIDN. Formally, we devise Cyclic-Bootstrap Labeling (CBL), a novel weakly supervised object detection pipeline, which optimizes MIDN with rank information from a reliable teacher network. Specifically, we obtain this teacher network by introducing a weighted exponential moving average strategy to take advantage of various refinement modules. A novel class-specific ranking distillation algorithm is proposed to leverage the output of weighted ensembled teacher network for distilling MIDN with rank information. As a result, MIDN is guided to assign higher scores to accurate proposals among their neighboring ones, thus benefiting the subsequent pseudo labeling. Extensive experiments on the prevalent PASCAL VOC 2007 \& 2012 and COCO datasets demonstrate the superior performance of our CBL framework. Code will be available at https://github.com/Yinyf0804/WSOD-CBL/.

In a typical multi-label setting, a picture contains on average few positive labels, and many negative ones. This positive-negative imbalance dominates the optimization process, and can lead to under-emphasizing gradients from positive labels during training, resulting in poor accuracy. In this paper, we introduce a novel asymmetric loss ("ASL"), which operates differently on positive and negative samples. The loss enables to dynamically down-weights and hard-thresholds easy negative samples, while also discarding possibly mislabeled samples. We demonstrate how ASL can balance the probabilities of different samples, and how this balancing is translated to better mAP scores. With ASL, we reach state-of-the-art results on multiple popular multi-label datasets: MS-COCO, Pascal-VOC, NUS-WIDE and Open Images. We also demonstrate ASL applicability for other tasks, such as single-label classification and object detection. ASL is effective, easy to implement, and does not increase the training time or complexity. Implementation is available at: https://github.com/Alibaba-MIIL/ASL.

Partial label learning (PLL) aims to train multiclass classifiers from the examples each annotated with a set of candidate labels where a fixed but unknown candidate label is correct. In the last few years, the instance-independent generation process of candidate labels has been extensively studied, on the basis of which many theoretical advances have been made in PLL. Nevertheless, the candidate labels are always instance-dependent in practice and there is no theoretical guarantee that the model trained on the instance-dependent PLL examples can converge to an ideal one. In this paper, a theoretically grounded and practically effective approach named POP, i.e. PrOgressive Purification for instance-dependent partial label learning, is proposed. Specifically, POP updates the learning model and purifies each candidate label set progressively in every epoch. Theoretically, we prove that POP enlarges the region appropriately fast where the model is reliable, and eventually approximates the Bayes optimal classifier with mild assumptions. Technically, POP is flexible with arbitrary PLL losses and could improve the performance of the previous PLL losses in the instance-dependent case. Experiments on the benchmark datasets and the real-world datasets validate the effectiveness of the proposed method.

Text-based delivery addresses, as the data foundation for logistics systems, contain abundant and crucial location information. How to effectively encode the delivery address is a core task to boost the performance of downstream tasks in the logistics system. Pre-trained Models (PTMs) designed for Natural Language Process (NLP) have emerged as the dominant tools for encoding semantic information in text. Though promising, those NLP-based PTMs fall short of encoding geographic knowledge in the delivery address, which considerably trims down the performance of delivery-related tasks in logistic systems such as Cainiao. To tackle the above problem, we propose a domain-specific pre-trained model, named G2PTL, a Geography-Graph Pre-trained model for delivery address in Logistics field. G2PTL combines the semantic learning capabilities of text pre-training with the geographical-relationship encoding abilities of graph modeling. Specifically, we first utilize real-world logistics delivery data to construct a large-scale heterogeneous graph of delivery addresses, which contains abundant geographic knowledge and delivery information. Then, G2PTL is pre-trained with subgraphs sampled from the heterogeneous graph. Comprehensive experiments are conducted to demonstrate the effectiveness of G2PTL through four downstream tasks in logistics systems on real-world datasets. G2PTL has been deployed in production in Cainiao's logistics system, which significantly improves the performance of delivery-related tasks.

Selecting high-quality data for pre-training is crucial in shaping the downstream task performance of language models. A major challenge lies in identifying this optimal subset, a problem generally considered intractable, thus necessitating scalable and effective heuristics. In this work, we propose a data selection method, CoLoR-Filter (Conditional Loss Reduction Filtering), which leverages an empirical Bayes-inspired approach to derive a simple and computationally efficient selection criterion based on the relative loss values of two auxiliary models. In addition to the modeling rationale, we evaluate CoLoR-Filter empirically on two language modeling tasks: (1) selecting data from C4 for domain adaptation to evaluation on Books and (2) selecting data from C4 for a suite of downstream multiple-choice question answering tasks. We demonstrate favorable scaling both as we subselect more aggressively and using small auxiliary models to select data for large target models. As one headline result, CoLoR-Filter data selected using a pair of 150m parameter auxiliary models can train a 1.2b parameter target model to match a 1.2b parameter model trained on 25b randomly selected tokens with 25x less data for Books and 11x less data for the downstream tasks. Code: https://github.com/davidbrandfonbrener/color-filter-olmo Filtered data: https://huggingface.co/datasets/davidbrandfonbrener/color-filtered-c4

Large-scale datasets are essential to modern day deep learning. Advocates argue that understanding these methods requires dataset transparency (e.g. "dataset curation, motivation, composition, collection process, etc..."). However, almost no one has suggested the release of the detailed definitions and visual category examples provided to annotators - information critical to understanding the structure of the annotations present in each dataset. These labels are at the heart of public datasets, yet few datasets include the instructions that were used to generate them. We introduce a new task, Labeling Instruction Generation, to address missing publicly available labeling instructions. In Labeling Instruction Generation, we take a reasonably annotated dataset and: 1) generate a set of examples that are visually representative of each category in the dataset; 2) provide a text label that corresponds to each of the examples. We introduce a framework that requires no model training to solve this task and includes a newly created rapid retrieval system that leverages a large, pre-trained vision and language model. This framework acts as a proxy to human annotators that can help to both generate a final labeling instruction set and evaluate its quality. Our framework generates multiple diverse visual and text representations of dataset categories. The optimized instruction set outperforms our strongest baseline across 5 folds by 7.06 mAP for NuImages and 12.9 mAP for COCO.

Large Language Models (LLMs) have demonstrated remarkable proficiency in understanding and generating natural language. However, their capabilities wane in highly specialized domains underrepresented in the pretraining corpus, such as physical and biomedical sciences. This work explores how to repurpose general LLMs into effective task solvers for specialized domains. We introduce a novel, model-agnostic framework for learning custom input tags, which are parameterized as continuous vectors appended to the LLM's embedding layer, to condition the LLM. We design two types of input tags: domain tags are used to delimit specialized representations (e.g., chemical formulas) and provide domain-relevant context; function tags are used to represent specific functions (e.g., predicting molecular properties) and compress function-solving instructions. We develop a three-stage protocol to learn these tags using auxiliary data and domain knowledge. By explicitly disentangling task domains from task functions, our method enables zero-shot generalization to unseen problems through diverse combinations of the input tags. It also boosts LLM's performance in various specialized domains, such as predicting protein or chemical properties and modeling drug-target interactions, outperforming expert models tailored to these tasks.

We describe the accurate prediction of ligand-protein interaction (LPI) affinities, also known as drug-target interactions (DTI), with instruction fine-tuned pretrained generative small language models (SLMs). We achieved accurate predictions for a range of affinity values associated with ligand-protein interactions on out-of-sample data in a zero-shot setting. Only the SMILES string of the ligand and the amino acid sequence of the protein were used as the model inputs. Our results demonstrate a clear improvement over machine learning (ML) and free-energy perturbation (FEP+) based methods in accurately predicting a range of ligand-protein interaction affinities, which can be leveraged to further accelerate drug discovery campaigns against challenging therapeutic targets.

Active learning (AL) is a prominent technique for reducing the annotation effort required for training machine learning models. Deep learning offers a solution for several essential obstacles to deploying AL in practice but introduces many others. One of such problems is the excessive computational resources required to train an acquisition model and estimate its uncertainty on instances in the unlabeled pool. We propose two techniques that tackle this issue for text classification and tagging tasks, offering a substantial reduction of AL iteration duration and the computational overhead introduced by deep acquisition models in AL. We also demonstrate that our algorithm that leverages pseudo-labeling and distilled models overcomes one of the essential obstacles revealed previously in the literature. Namely, it was shown that due to differences between an acquisition model used to select instances during AL and a successor model trained on the labeled data, the benefits of AL can diminish. We show that our algorithm, despite using a smaller and faster acquisition model, is capable of training a more expressive successor model with higher performance.

We introduce Falcon2-11B, a foundation model trained on over five trillion tokens, and its multimodal counterpart, Falcon2-11B-vlm, which is a vision-to-text model. We report our findings during the training of the Falcon2-11B which follows a multi-stage approach where the early stages are distinguished by their context length and a final stage where we use a curated, high-quality dataset. Additionally, we report the effect of doubling the batch size mid-training and how training loss spikes are affected by the learning rate. The downstream performance of the foundation model is evaluated on established benchmarks, including multilingual and code datasets. The foundation model shows strong generalization across all the tasks which makes it suitable for downstream finetuning use cases. For the vision language model, we report the performance on several benchmarks and show that our model achieves a higher average score compared to open-source models of similar size. The model weights and code of both Falcon2-11B and Falcon2-11B-vlm are made available under a permissive license.

Data collected from the real world typically exhibit long-tailed distributions, where frequent classes contain abundant data while rare ones have only a limited number of samples. While existing supervised learning approaches have been proposed to tackle such data imbalance, the requirement of label supervision would limit their applicability to real-world scenarios in which label annotation might not be available. Without the access to class labels nor the associated class frequencies, we propose Frequency-Aware Self-Supervised Learning (FASSL) in this paper. Targeting at learning from unlabeled data with inherent long-tailed distributions, the goal of FASSL is to produce discriminative feature representations for downstream classification tasks. In FASSL, we first learn frequency-aware prototypes, reflecting the associated long-tailed distribution. Particularly focusing on rare-class samples, the relationships between image data and the derived prototypes are further exploited with the introduced self-supervised learning scheme. Experiments on long-tailed image datasets quantitatively and qualitatively verify the effectiveness of our learning scheme.

Representation learning on text-attributed graphs (TAGs) has become a critical research problem in recent years. A typical example of a TAG is a paper citation graph, where the text of each paper serves as node attributes. Initial graph neural network (GNN) pipelines handled these text attributes by transforming them into shallow or hand-crafted features, such as skip-gram or bag-of-words features. Recent efforts have focused on enhancing these pipelines with language models (LMs), which typically demand intricate designs and substantial computational resources. With the advent of powerful large language models (LLMs) such as GPT or Llama2, which demonstrate an ability to reason and to utilize general knowledge, there is a growing need for techniques which combine the textual modelling abilities of LLMs with the structural learning capabilities of GNNs. Hence, in this work, we focus on leveraging LLMs to capture textual information as features, which can be used to boost GNN performance on downstream tasks. A key innovation is our use of explanations as features: we prompt an LLM to perform zero-shot classification, request textual explanations for its decision-making process, and design an LLM-to-LM interpreter to translate these explanations into informative features for downstream GNNs. Our experiments demonstrate that our method achieves state-of-the-art results on well-established TAG datasets, including Cora, PubMed, ogbn-arxiv, as well as our newly introduced dataset, tape-arxiv23. Furthermore, our method significantly speeds up training, achieving a 2.88 times improvement over the closest baseline on ogbn-arxiv. Lastly, we believe the versatility of the proposed method extends beyond TAGs and holds the potential to enhance other tasks involving graph-text data. Our codes and datasets are available at: https://github.com/XiaoxinHe/TAPE.

The capability of the traditional semi-supervised learning (SSL) methods is far from real-world application due to severely biased pseudo-labels caused by (1) class imbalance and (2) class distribution mismatch between labeled and unlabeled data. This paper addresses such a relatively under-explored problem. First, we propose a general pseudo-labeling framework that class-adaptively blends the semantic pseudo-label from a similarity-based classifier to the linear one from the linear classifier, after making the observation that both types of pseudo-labels have complementary properties in terms of bias. We further introduce a novel semantic alignment loss to establish balanced feature representation to reduce the biased predictions from the classifier. We term the whole framework as Distribution-Aware Semantics-Oriented (DASO) Pseudo-label. We conduct extensive experiments in a wide range of imbalanced benchmarks: CIFAR10/100-LT, STL10-LT, and large-scale long-tailed Semi-Aves with open-set class, and demonstrate that, the proposed DASO framework reliably improves SSL learners with unlabeled data especially when both (1) class imbalance and (2) distribution mismatch dominate.

Label smoothing (LS) is a popular regularisation method for training deep neural network classifiers due to its effectiveness in improving test accuracy and its simplicity in implementation. "Hard" one-hot labels are "smoothed" by uniformly distributing probability mass to other classes, reducing overfitting. In this work, we reveal that LS negatively affects selective classification (SC) - where the aim is to reject misclassifications using a model's predictive uncertainty. We first demonstrate empirically across a range of tasks and architectures that LS leads to a consistent degradation in SC. We then explain this by analysing logit-level gradients, showing that LS exacerbates overconfidence and underconfidence by regularising the max logit more when the probability of error is low, and less when the probability of error is high. This elucidates previously reported experimental results where strong classifiers underperform in SC. We then demonstrate the empirical effectiveness of logit normalisation for recovering lost SC performance caused by LS. Furthermore, based on our gradient analysis, we explain why such normalisation is effective. We will release our code shortly.

Machine learning (ML) models are only as good as the data they are trained on. But recent studies have found datasets widely used to train and evaluate ML models, e.g. ImageNet, to have pervasive labeling errors. Erroneous labels on the train set hurt ML models' ability to generalize, and they impact evaluation and model selection using the test set. Consequently, learning in the presence of labeling errors is an active area of research, yet this field lacks a comprehensive benchmark to evaluate these methods. Most of these methods are evaluated on a few computer vision datasets with significant variance in the experimental protocols. With such a large pool of methods and inconsistent evaluation, it is also unclear how ML practitioners can choose the right models to assess label quality in their data. To this end, we propose a benchmarking environment AQuA to rigorously evaluate methods that enable machine learning in the presence of label noise. We also introduce a design space to delineate concrete design choices of label error detection models. We hope that our proposed design space and benchmark enable practitioners to choose the right tools to improve their label quality and that our benchmark enables objective and rigorous evaluation of machine learning tools facing mislabeled data.

The growing complexity of legal cases has lead to an increasing interest in legal information retrieval systems that can effectively satisfy user-specific information needs. However, such downstream systems typically require documents to be properly formatted and segmented, which is often done with relatively simple pre-processing steps, disregarding topical coherence of segments. Systems generally rely on representations of individual sentences or paragraphs, which may lack crucial context, or document-level representations, which are too long for meaningful search results. To address this issue, we propose a segmentation system that can predict topical coherence of sequential text segments spanning several paragraphs, effectively segmenting a document and providing a more balanced representation for downstream applications. We build our model on top of popular transformer networks and formulate structural text segmentation as topical change detection, by performing a series of independent classifications that allow for efficient fine-tuning on task-specific data. We crawl a novel dataset consisting of roughly 74,000 online Terms-of-Service documents, including hierarchical topic annotations, which we use for training. Results show that our proposed system significantly outperforms baselines, and adapts well to structural peculiarities of legal documents. We release both data and trained models to the research community for future work.https://github.com/dennlinger/TopicalChange

Fine-tuning all the layers of a pre-trained neural language encoder (either using all the parameters or using parameter-efficient methods) is often the de-facto way of adapting it to a new task. We show evidence that for different downstream language tasks, fine-tuning only a subset of layers is sufficient to obtain performance that is close to and often better than fine-tuning all the layers in the language encoder. We propose an efficient metric based on the diagonal of the Fisher information matrix (FIM score), to select the candidate layers for selective fine-tuning. We show, empirically on GLUE and SuperGLUE tasks and across distinct language encoders, that this metric can effectively select layers leading to a strong downstream performance. Our work highlights that task-specific information corresponding to a given downstream task is often localized within a few layers, and tuning only those is sufficient for strong performance. Additionally, we demonstrate the robustness of the FIM score to rank layers in a manner that remains constant during the optimization process.

Content metadata plays a very important role in movie recommender systems as it provides valuable information about various aspects of a movie such as genre, cast, plot synopsis, box office summary, etc. Analyzing the metadata can help understand the user preferences to generate personalized recommendations and item cold starting. In this talk, we will focus on one particular type of metadata - genre labels. Genre labels associated with a movie or a TV series help categorize a collection of titles into different themes and correspondingly setting up the audience expectation. We present some of the challenges associated with using genre label information and propose a new way of examining the genre information that we call as the Genre Spectrum. The Genre Spectrum helps capture the various nuanced genres in a title and our offline and online experiments corroborate the effectiveness of the approach. Furthermore, we also talk about applications of LLMs in augmenting content metadata which could eventually be used to achieve effective organization of recommendations in user's 2-D home-grid.

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at https://github.com/QizhiPei/SSM-DTA{Github}.

Suicide is an important but often misunderstood problem, one that researchers are now seeking to better understand through social media. Due in large part to the fuzzy nature of what constitutes suicidal risks, most supervised approaches for learning to automatically detect suicide-related activity in social media require a great deal of human labor to train. However, humans themselves have diverse or conflicting views on what constitutes suicidal thoughts. So how to obtain reliable gold standard labels is fundamentally challenging and, we hypothesize, depends largely on what is asked of the annotators and what slice of the data they label. We conducted multiple rounds of data labeling and collected annotations from crowdsourcing workers and domain experts. We aggregated the resulting labels in various ways to train a series of supervised models. Our preliminary evaluations show that using unanimously agreed labels from multiple annotators is helpful to achieve robust machine models.

The soft Dice loss (SDL) has taken a pivotal role in numerous automated segmentation pipelines in the medical imaging community. Over the last years, some reasons behind its superior functioning have been uncovered and further optimizations have been explored. However, there is currently no implementation that supports its direct utilization in scenarios involving soft labels. Hence, a synergy between the use of SDL and research leveraging the use of soft labels, also in the context of model calibration, is still missing. In this work, we introduce Dice semimetric losses (DMLs), which (i) are by design identical to SDL in a standard setting with hard labels, but (ii) can be employed in settings with soft labels. Our experiments on the public QUBIQ, LiTS and KiTS benchmarks confirm the potential synergy of DMLs with soft labels (e.g.\ averaging, label smoothing, and knowledge distillation) over hard labels (e.g.\ majority voting and random selection). As a result, we obtain superior Dice scores and model calibration, which supports the wider adoption of DMLs in practice. The code is available at https://github.com/zifuwanggg/JDTLosses{https://github.com/zifuwanggg/JDTLosses}.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

In Multi-Label Text Classification (MLTC), one sample can belong to more than one class. It is observed that most MLTC tasks, there are dependencies or correlations among labels. Existing methods tend to ignore the relationship among labels. In this paper, a graph attention network-based model is proposed to capture the attentive dependency structure among the labels. The graph attention network uses a feature matrix and a correlation matrix to capture and explore the crucial dependencies between the labels and generate classifiers for the task. The generated classifiers are applied to sentence feature vectors obtained from the text feature extraction network (BiLSTM) to enable end-to-end training. Attention allows the system to assign different weights to neighbor nodes per label, thus allowing it to learn the dependencies among labels implicitly. The results of the proposed model are validated on five real-world MLTC datasets. The proposed model achieves similar or better performance compared to the previous state-of-the-art models.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

This paper presents Tiny-toxic-detector, a compact transformer-based model designed for toxic content detection. Despite having only 2.1 million parameters, Tiny-toxic-detector achieves competitive performance on benchmark datasets, with 90.97% accuracy on ToxiGen and 86.98% accuracy on the Jigsaw dataset, rivaling models over 50 times its size. This efficiency enables deployment in resource-constrained environments, addressing the need for effective content moderation tools that balance performance with computational efficiency. The model architecture features 4 transformer encoder layers, each with 2 attention heads, an embedding dimension of 64, and a feedforward dimension of 128. Trained on both public and private datasets, Tiny-toxic-detector demonstrates the potential of efficient, task-specific models for addressing online toxicity. The paper covers the model architecture, training process, performance benchmarks, and limitations, underscoring its suitability for applications such as social media monitoring and content moderation. By achieving results comparable to much larger models while significantly reducing computational demands, Tiny-toxic-detector represents progress toward more sustainable and scalable AI-driven content moderation solutions.

Existing PTLM-based models for TSC can be categorized into two groups: 1) fine-tuning-based models that adopt PTLM as the context encoder; 2) prompting-based models that transfer the classification task to the text/word generation task. In this paper, we present a new perspective of leveraging PTLM for TSC: simultaneously leveraging the merits of both language modeling and explicit target-context interactions via contextual target attributes. Specifically, we design the domain- and target-constrained cloze test, which can leverage the PTLMs' strong language modeling ability to generate the given target's attributes pertaining to the review context. The attributes contain the background and property information of the target, which can help to enrich the semantics of the review context and the target. To exploit the attributes for tackling TSC, we first construct a heterogeneous information graph by treating the attributes as nodes and combining them with (1) the syntax graph automatically produced by the off-the-shelf dependency parser and (2) the semantics graph of the review context, which is derived from the self-attention mechanism. Then we propose a heterogeneous information gated graph convolutional network to model the interactions among the attribute information, the syntactic information, and the contextual information. The experimental results on three benchmark datasets demonstrate the superiority of our model, which achieves new state-of-the-art performance.

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

The assumption that response and predictor belong to the same statistical unit may be violated in practice. Unbiased estimation and recovery of true label ordering based on unlabeled data are challenging tasks and have attracted increasing attentions in the recent literature. In this paper, we present a relatively complete analysis of label permutation problem for the generalized linear model with multivariate responses. The theory is established under different scenarios, with knowledge of true parameters, with partial knowledge of underlying label permutation matrix and without any knowledge. Our results remove the stringent conditions required by the current literature and are further extended to the missing observation setting which has never been considered in the field of label permutation problem. On computational side, we propose two methods, "maximum likelihood estimation" algorithm and "two-step estimation" algorithm, to accommodate for different settings. When the proportion of permuted labels is moderate, both methods work effectively. Multiple numerical experiments are provided and corroborate our theoretical findings.

We introduce a new dataset named WikiVitals which contains a large graph of 48k mutually referred Wikipedia articles classified into 32 categories and connected by 2.3M edges. Our aim is to rigorously evaluate the contributions of three distinct sources of information to the label prediction in a semi-supervised node classification setting, namely the content of the articles, their connections with each other and the correlations among their labels. We perform this evaluation using a Graph Markov Neural Network which provides a theoretically principled model for this task and we conduct a detailed evaluation of the contributions of each sources of information using a clear separation of model selection and model assessment. One interesting observation is that including the effect of label dependencies is more relevant for sparse train sets than it is for dense train sets.

Recent advances in multimodal pre-trained models have significantly improved information extraction from visually-rich documents (VrDs), in which named entity recognition (NER) is treated as a sequence-labeling task of predicting the BIO entity tags for tokens, following the typical setting of NLP. However, BIO-tagging scheme relies on the correct order of model inputs, which is not guaranteed in real-world NER on scanned VrDs where text are recognized and arranged by OCR systems. Such reading order issue hinders the accurate marking of entities by BIO-tagging scheme, making it impossible for sequence-labeling methods to predict correct named entities. To address the reading order issue, we introduce Token Path Prediction (TPP), a simple prediction head to predict entity mentions as token sequences within documents. Alternative to token classification, TPP models the document layout as a complete directed graph of tokens, and predicts token paths within the graph as entities. For better evaluation of VrD-NER systems, we also propose two revised benchmark datasets of NER on scanned documents which can reflect real-world scenarios. Experiment results demonstrate the effectiveness of our method, and suggest its potential to be a universal solution to various information extraction tasks on documents.

Tokenization methods like Byte-Pair Encoding (BPE) enhance computational efficiency in large language models (LLMs) but often obscure internal character structures within tokens. This limitation hinders LLMs' ability to predict precise character positions, which is crucial in tasks like Chinese Spelling Correction (CSC) where identifying the positions of misspelled characters accelerates correction processes. We propose Token Internal Position Awareness (TIPA), a method that significantly improves models' ability to capture character positions within tokens by training them on reverse character prediction tasks using the tokenizer's vocabulary. Experiments demonstrate that TIPA enhances position prediction accuracy in LLMs, enabling more precise identification of target characters in original text. Furthermore, when applied to downstream tasks that do not require exact position prediction, TIPA still boosts performance in tasks needing character-level information, validating its versatility and effectiveness.

Given the clinical notes written in electronic health records (EHRs), it is challenging to predict the diagnostic codes which is formulated as a multi-label classification task. The large set of labels, the hierarchical dependency, and the imbalanced data make this prediction task extremely hard. Most existing work built a binary prediction for each label independently, ignoring the dependencies between labels. To address this problem, we propose a two-stage framework to improve automatic ICD coding by capturing the label correlation. Specifically, we train a label set distribution estimator to rescore the probability of each label set candidate generated by a base predictor. This paper is the first attempt at learning the label set distribution as a reranking module for medical code prediction. In the experiments, our proposed framework is able to improve upon best-performing predictors on the benchmark MIMIC datasets. The source code of this project is available at https://github.com/MiuLab/ICD-Correlation.

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph representations have recently yielded new drug repurposing hypotheses. In this study, we present a novel, disease-specific hypergraph representation learning technique to derive contextual embeddings of biological pathways of various lengths but that all start at any given drug and all end at the disease of interest. Further, we extend this method to multi-disease hypergraphs. To determine the repurposing potential of each of the 1,522 drugs, we derive drug-specific distributions of cosine similarity values and ultimately consider the median for ranking. Cosine similarity values are computed between (1) all biological pathways starting at the considered drug and ending at the disease of interest and (2) all biological pathways starting at drugs currently prescribed against that disease and ending at the disease of interest. We illustrate our approach with Alzheimer's disease (AD) and two of its risk factors: hypertension (HTN) and type 2 diabetes (T2D). We compare each drug's rank across four hypergraph settings (single- or multi-disease): AD only, AD + HTN, AD + T2D, and AD + HTN + T2D. Notably, our framework led to the identification of two promising drugs whose repurposing potential was significantly higher in hypergraphs combining two diseases: dapagliflozin (antidiabetic; moved up, from top 32% to top 7%, across all considered drugs) and debrisoquine (antihypertensive; moved up, from top 76% to top 23%). Our approach serves as a hypothesis generation tool, to be paired with a validation pipeline relying on laboratory experiments and semi-automated parsing of the biomedical literature.

Transformer-based NLP models are trained using hundreds of millions or even billions of parameters, limiting their applicability in computationally constrained environments. While the number of parameters generally correlates with performance, it is not clear whether the entire network is required for a downstream task. Motivated by the recent work on pruning and distilling pre-trained models, we explore strategies to drop layers in pre-trained models, and observe the effect of pruning on downstream GLUE tasks. We were able to prune BERT, RoBERTa and XLNet models up to 40%, while maintaining up to 98% of their original performance. Additionally we show that our pruned models are on par with those built using knowledge distillation, both in terms of size and performance. Our experiments yield interesting observations such as, (i) the lower layers are most critical to maintain downstream task performance, (ii) some tasks such as paraphrase detection and sentence similarity are more robust to the dropping of layers, and (iii) models trained using a different objective function exhibit different learning patterns and w.r.t the layer dropping.

This work investigates the compatibility between label smoothing (LS) and knowledge distillation (KD). Contemporary findings addressing this thesis statement take dichotomous standpoints: Muller et al. (2019) and Shen et al. (2021b). Critically, there is no effort to understand and resolve these contradictory findings, leaving the primal question -- to smooth or not to smooth a teacher network? -- unanswered. The main contributions of our work are the discovery, analysis and validation of systematic diffusion as the missing concept which is instrumental in understanding and resolving these contradictory findings. This systematic diffusion essentially curtails the benefits of distilling from an LS-trained teacher, thereby rendering KD at increased temperatures ineffective. Our discovery is comprehensively supported by large-scale experiments, analyses and case studies including image classification, neural machine translation and compact student distillation tasks spanning across multiple datasets and teacher-student architectures. Based on our analysis, we suggest practitioners to use an LS-trained teacher with a low-temperature transfer to achieve high performance students. Code and models are available at https://keshik6.github.io/revisiting-ls-kd-compatibility/

We propose a new strategy for applying large pre-trained language models to novel tasks when labeled training data is limited. Rather than apply the model in a typical zero-shot or few-shot fashion, we treat the model as the basis for labeling functions in a weak supervision framework. To create a classifier, we first prompt the model to answer multiple distinct queries about an example and define how the possible responses should be mapped to votes for labels and abstentions. We then denoise these noisy label sources using the Snorkel system and train an end classifier with the resulting training data. Our experimental evaluation shows that prompting large language models within a weak supervision framework can provide significant gains in accuracy. On the WRENCH weak supervision benchmark, this approach can significantly improve over zero-shot performance, an average 19.5% reduction in errors. We also find that this approach produces classifiers with comparable or superior accuracy to those trained from hand-engineered rules.

Online misinformation poses a global risk with significant real-world consequences. To combat misinformation, current research relies on professionals like journalists and fact-checkers for annotating and debunking misinformation, and develops automated machine learning methods for detecting misinformation. Complementary to these approaches, recent research has increasingly concentrated on utilizing the power of ordinary social media users, a.k.a. "crowd", who act as eyes-on-the-ground proactively questioning and countering misinformation. Notably, recent studies show that 96% of counter-misinformation responses originate from them. Acknowledging their prominent role, we present the first systematic and comprehensive survey of research papers that actively leverage the crowds to combat misinformation. We first identify 88 papers related to crowd-based efforts, following a meticulous annotation process adhering to the PRISMA framework. We then present key statistics related to misinformation, counter-misinformation, and crowd input in different formats and topics. Upon holistic analysis of the papers, we introduce a novel taxonomy of the roles played by the crowds: (i)annotators who actively identify misinformation; (ii)evaluators who assess counter-misinformation effectiveness; (iii)creators who create counter-misinformation. This taxonomy explores the crowd's capabilities in misinformation detection, identifies prerequisites for effective counter-misinformation, and analyzes crowd-generated counter-misinformation. Then, we delve into (i)distinguishing individual, collaborative, and machine-assisted labeling for annotators; (ii)analyzing the effectiveness of counter-misinformation through surveys, interviews, and in-lab experiments for evaluators; and (iii)characterizing creation patterns and creator profiles for creators. Finally, we outline potential future research in this field.

As the academic landscape expands, the challenge of efficiently identifying potentially high-impact articles among the vast number of newly published works becomes critical. This paper introduces a promising approach, leveraging the capabilities of fine-tuned LLMs to predict the future impact of newborn articles solely based on titles and abstracts. Moving beyond traditional methods heavily reliant on external information, the proposed method discerns the shared semantic features of highly impactful papers from a large collection of title-abstract and potential impact pairs. These semantic features are further utilized to regress an improved metric, TNCSI_SP, which has been endowed with value, field, and time normalization properties. Additionally, a comprehensive dataset has been constructed and released for fine-tuning the LLM, containing over 12,000 entries with corresponding titles, abstracts, and TNCSI_SP. The quantitative results, with an NDCG@20 of 0.901, demonstrate that the proposed approach achieves state-of-the-art performance in predicting the impact of newborn articles when compared to competitive counterparts. Finally, we demonstrate a real-world application for predicting the impact of newborn journal articles to demonstrate its noteworthy practical value. Overall, our findings challenge existing paradigms and propose a shift towards a more content-focused prediction of academic impact, offering new insights for assessing newborn article impact.

The pre-trained language models are continually fine-tuned to better support downstream applications. However, this operation may result in significant performance degeneration on general tasks beyond the targeted domain. To overcome this problem, we propose LM-Cocktail which enables the fine-tuned model to stay resilient in general perspectives. Our method is conducted in the form of model merging, where the fine-tuned language model is merged with the pre-trained base model or the peer models from other domains through weighted average. Despite simplicity, LM-Cocktail is surprisingly effective: the resulted model is able to achieve a strong empirical performance in the whole scope of general tasks while preserving a superior capacity in its targeted domain. We conduct comprehensive experiments with LLama and BGE model on popular benchmarks, including FLAN, MMLU, MTEB, whose results validate the efficacy of our proposed method. The code and checkpoints are available at https://github.com/FlagOpen/FlagEmbedding/tree/master/LM_Cocktail.

Attention mechanisms have improved the performance of NLP tasks while allowing models to remain explainable. Self-attention is currently widely used, however interpretability is difficult due to the numerous attention distributions. Recent work has shown that model representations can benefit from label-specific information, while facilitating interpretation of predictions. We introduce the Label Attention Layer: a new form of self-attention where attention heads represent labels. We test our novel layer by running constituency and dependency parsing experiments and show our new model obtains new state-of-the-art results for both tasks on both the Penn Treebank (PTB) and Chinese Treebank. Additionally, our model requires fewer self-attention layers compared to existing work. Finally, we find that the Label Attention heads learn relations between syntactic categories and show pathways to analyze errors.

In-context learning is a promising paradigm that utilizes in-context examples as prompts for the predictions of large language models. These prompts are crucial for achieving strong performance. However, since the prompts need to be sampled from a large volume of annotated examples, finding the right prompt may result in high annotation costs. To address this challenge, this paper introduces an influence-driven selective annotation method that aims to minimize annotation costs while improving the quality of in-context examples. The essence of our method is to select a pivotal subset from a large-scale unlabeled data pool to annotate for the subsequent sampling of prompts. Specifically, a directed graph is first constructed to represent unlabeled data. Afterward, the influence of candidate unlabeled subsets is quantified with a diffusion process. A simple yet effective greedy algorithm for unlabeled data selection is lastly introduced. It iteratively selects the data if it provides a maximum marginal gain with respect to quantified influence. Compared with previous efforts on selective annotations, our influence-driven method works in an end-to-end manner, avoids an intractable explicit balance between data diversity and representativeness, and enjoys theoretical support. Experiments confirm the superiority of the proposed method on various benchmarks, achieving better performance under lower time consumption during subset selection. The project page is available at https://skzhang1.github.io/IDEAL/.

Large Language Model (LLM) pre-training exhausts an ever growing compute budget, yet recent research has demonstrated that careful document selection enables comparable model quality with only a fraction of the FLOPs. Inspired by efforts suggesting that domain-specific training document selection is in fact an interpretable process [Gunasekar et al., 2023], as well as research showing that instruction-finetuned LLMs are adept zero-shot data labelers [Gilardi et al.,2023], we explore a promising direction for scalable general-domain document selection; employing a prompted LLM as a document grader, we distill quality labels into a classifier model, which is applied at scale to a large, and already heavily-filtered, web-crawl-derived corpus autonomously. Following the guidance of this classifier, we drop 75% of the corpus and train LLMs on the remaining data. Results across multiple benchmarks show that: 1. Filtering allows us to quality-match a model trained on the full corpus across diverse benchmarks with at most 70% of the FLOPs, 2. More capable LLM labelers and classifier models lead to better results that are less sensitive to the labeler's prompt, 3. In-context learning helps to boost the performance of less-capable labeling models. In all cases we use open-source datasets, models, recipes, and evaluation frameworks, so that results can be reproduced by the community.

Large Language Models (LLMs) are frequently updated due to data or architecture changes to improve their performance. When updating models, developers often focus on increasing overall performance metrics with less emphasis on being compatible with previous model versions. However, users often build a mental model of the functionality and capabilities of a particular machine learning model they are interacting with. They have to adapt their mental model with every update -- a draining task that can lead to user dissatisfaction. In practice, fine-tuned downstream task adapters rely on pretrained LLM base models. When these base models are updated, these user-facing downstream task models experience instance regression or negative flips -- previously correct instances are now predicted incorrectly. This happens even when the downstream task training procedures remain identical. Our work aims to provide seamless model updates to a user in two ways. First, we provide evaluation metrics for a notion of compatibility to prior model versions, specifically for generative tasks but also applicable for discriminative tasks. We observe regression and inconsistencies between different model versions on a diverse set of tasks and model updates. Second, we propose a training strategy to minimize the number of inconsistencies in model updates, involving training of a compatibility model that can enhance task fine-tuned language models. We reduce negative flips -- instances where a prior model version was correct, but a new model incorrect -- by up to 40% from Llama 1 to Llama 2.

This report is a reproducibility study of the paper "CDUL: CLIP-Driven Unsupervised Learning for Multi-Label Image Classification" (Abdelfattah et al, ICCV 2023). Our report makes the following contributions: (1) We provide a reproducible, well commented and open-sourced code implementation for the entire method specified in the original paper. (2) We try to verify the effectiveness of the novel aggregation strategy which uses the CLIP model to initialize the pseudo labels for the subsequent unsupervised multi-label image classification task. (3) We try to verify the effectiveness of the gradient-alignment training method specified in the original paper, which is used to update the network parameters and pseudo labels. The code can be found at https://github.com/cs-mshah/CDUL

Comprehensively understanding and accurately predicting the performance of large language models across diverse downstream tasks has emerged as a pivotal challenge in NLP research. The pioneering scaling law on downstream works demonstrated intrinsic similarities within model families and utilized such similarities for performance prediction. However, they tend to overlook the similarities between model families and only consider design factors listed in the original scaling law. To overcome these limitations, we introduce a novel framework, Collaborative Performance Prediction (CPP), which significantly enhances prediction accuracy by leveraging the historical performance of various models on downstream tasks and other design factors for both model and task. We also collect a collaborative data sourced from online platforms containing both historical performance and additional design factors. With the support of the collaborative data, CPP not only surpasses traditional scaling laws in predicting the performance of scaled LLMs but also facilitates a detailed analysis of factor importance, an area previously overlooked.

Machine learning especially deep neural networks have achieved great success but many of them often rely on a number of labeled samples for supervision. As sufficient labeled training data are not always ready due to e.g., continuously emerging prediction targets and costly sample annotation in real world applications, machine learning with sample shortage is now being widely investigated. Among all these studies, many prefer to utilize auxiliary information including those in the form of Knowledge Graph (KG) to reduce the reliance on labeled samples. In this survey, we have comprehensively reviewed over 90 papers about KG-aware research for two major sample shortage settings -- zero-shot learning (ZSL) where some classes to be predicted have no labeled samples, and few-shot learning (FSL) where some classes to be predicted have only a small number of labeled samples that are available. We first introduce KGs used in ZSL and FSL as well as their construction methods, and then systematically categorize and summarize KG-aware ZSL and FSL methods, dividing them into different paradigms such as the mapping-based, the data augmentation, the propagation-based and the optimization-based. We next present different applications, including not only KG augmented prediction tasks such as image classification, question answering, text classification and knowledge extraction, but also KG completion tasks, and some typical evaluation resources for each task. We eventually discuss some challenges and open problems from different perspectives.

The generalization and learning speed of a multi-class neural network can often be significantly improved by using soft targets that are a weighted average of the hard targets and the uniform distribution over labels. Smoothing the labels in this way prevents the network from becoming over-confident and label smoothing has been used in many state-of-the-art models, including image classification, language translation and speech recognition. Despite its widespread use, label smoothing is still poorly understood. Here we show empirically that in addition to improving generalization, label smoothing improves model calibration which can significantly improve beam-search. However, we also observe that if a teacher network is trained with label smoothing, knowledge distillation into a student network is much less effective. To explain these observations, we visualize how label smoothing changes the representations learned by the penultimate layer of the network. We show that label smoothing encourages the representations of training examples from the same class to group in tight clusters. This results in loss of information in the logits about resemblances between instances of different classes, which is necessary for distillation, but does not hurt generalization or calibration of the model's predictions.

Language model detoxification aims to minimize the risk of generating offensive or harmful content in pretrained language models (PLMs) for safer deployment. Existing methods can be roughly categorized as finetuning-based and decoding-based. However, the former is often resource-intensive, while the latter relies on additional components and potentially compromises the generation fluency. In this paper, we propose a more lightweight approach that enables the PLM itself to achieve "self-detoxification". Our method is built upon the observation that prepending a negative steering prompt can effectively induce PLMs to generate toxic content. At the same time, we are inspired by the recent research in the interpretability field, which formulates the evolving contextualized representations within the PLM as an information stream facilitated by the attention layers. Drawing on this idea, we devise a method to identify the toxification direction from the normal generation process to the one prompted with the negative prefix, and then steer the generation to the reversed direction by manipulating the information movement within the attention layers. Experimental results show that our approach, without any fine-tuning or extra components, can achieve comparable performance with state-of-the-art methods.

We define deriving semantic class targets as a novel multi-modal task. By doing so, we aim to improve classification schemes in the physical sciences which can be severely abstracted and obfuscating. We address this task for upcoming radio astronomy surveys and present the derived semantic radio galaxy morphology class targets.

We present WeakSTIL, an interpretable two-stage weak label deep learning pipeline for scoring the percentage of stromal tumor infiltrating lymphocytes (sTIL%) in H&E-stained whole-slide images (WSIs) of breast cancer tissue. The sTIL% score is a prognostic and predictive biomarker for many solid tumor types. However, due to the high labeling efforts and high intra- and interobserver variability within and between expert annotators, this biomarker is currently not used in routine clinical decision making. WeakSTIL compresses tiles of a WSI using a feature extractor pre-trained with self-supervised learning on unlabeled histopathology data and learns to predict precise sTIL% scores for each tile in the tumor bed by using a multiple instance learning regressor that only requires a weak WSI-level label. By requiring only a weak label, we overcome the large annotation efforts required to train currently existing TIL detection methods. We show that WeakSTIL is at least as good as other TIL detection methods when predicting the WSI-level sTIL% score, reaching a coefficient of determination of 0.45pm0.15 when compared to scores generated by an expert pathologist, and an AUC of 0.89pm0.05 when treating it as the clinically interesting sTIL-high vs sTIL-low classification task. Additionally, we show that the intermediate tile-level predictions of WeakSTIL are highly interpretable, which suggests that WeakSTIL pays attention to latent features related to the number of TILs and the tissue type. In the future, WeakSTIL may be used to provide consistent and interpretable sTIL% predictions to stratify breast cancer patients into targeted therapy arms.

The LLMJudge challenge is organized as part of the LLM4Eval workshop at SIGIR 2024. Test collections are essential for evaluating information retrieval (IR) systems. The evaluation and tuning of a search system is largely based on relevance labels, which indicate whether a document is useful for a specific search and user. However, collecting relevance judgments on a large scale is costly and resource-intensive. Consequently, typical experiments rely on third-party labelers who may not always produce accurate annotations. The LLMJudge challenge aims to explore an alternative approach by using LLMs to generate relevance judgments. Recent studies have shown that LLMs can generate reliable relevance judgments for search systems. However, it remains unclear which LLMs can match the accuracy of human labelers, which prompts are most effective, how fine-tuned open-source LLMs compare to closed-source LLMs like GPT-4, whether there are biases in synthetically generated data, and if data leakage affects the quality of generated labels. This challenge will investigate these questions, and the collected data will be released as a package to support automatic relevance judgment research in information retrieval and search.

We propose a design pattern for tackling text ranking problems, dubbed "Expando-Mono-Duo", that has been empirically validated for a number of ad hoc retrieval tasks in different domains. At the core, our design relies on pretrained sequence-to-sequence models within a standard multi-stage ranking architecture. "Expando" refers to the use of document expansion techniques to enrich keyword representations of texts prior to inverted indexing. "Mono" and "Duo" refer to components in a reranking pipeline based on a pointwise model and a pairwise model that rerank initial candidates retrieved using keyword search. We present experimental results from the MS MARCO passage and document ranking tasks, the TREC 2020 Deep Learning Track, and the TREC-COVID challenge that validate our design. In all these tasks, we achieve effectiveness that is at or near the state of the art, in some cases using a zero-shot approach that does not exploit any training data from the target task. To support replicability, implementations of our design pattern are open-sourced in the Pyserini IR toolkit and PyGaggle neural reranking library.

Antibodies are proteins produced by the immune system that can identify and neutralise a wide variety of antigens with high specificity and affinity, and constitute the most successful class of biotherapeutics. With the advent of next-generation sequencing, billions of antibody sequences have been collected in recent years, though their application in the design of better therapeutics has been constrained by the sheer volume and complexity of the data. To address this challenge, we present IgBert and IgT5, the best performing antibody-specific language models developed to date which can consistently handle both paired and unpaired variable region sequences as input. These models are trained comprehensively using the more than two billion unpaired sequences and two million paired sequences of light and heavy chains present in the Observed Antibody Space dataset. We show that our models outperform existing antibody and protein language models on a diverse range of design and regression tasks relevant to antibody engineering. This advancement marks a significant leap forward in leveraging machine learning, large scale data sets and high-performance computing for enhancing antibody design for therapeutic development.

Due to the expensive costs of collecting labels in multi-label classification datasets, partially annotated multi-label classification has become an emerging field in computer vision. One baseline approach to this task is to assume unobserved labels as negative labels, but this assumption induces label noise as a form of false negative. To understand the negative impact caused by false negative labels, we study how these labels affect the model's explanation. We observe that the explanation of two models, trained with full and partial labels each, highlights similar regions but with different scaling, where the latter tends to have lower attribution scores. Based on these findings, we propose to boost the attribution scores of the model trained with partial labels to make its explanation resemble that of the model trained with full labels. Even with the conceptually simple approach, the multi-label classification performance improves by a large margin in three different datasets on a single positive label setting and one on a large-scale partial label setting. Code is available at https://github.com/youngwk/BridgeGapExplanationPAMC.

Large language models (LLMs) can often be made to behave in undesirable ways that they are explicitly fine-tuned not to. For example, the LLM red-teaming literature has produced a wide variety of 'jailbreaking' techniques to elicit harmful text from models that were fine-tuned to be harmless. Recent work on red-teaming, model editing, and interpretability suggests that this challenge stems from how (adversarial) fine-tuning largely serves to suppress rather than remove undesirable capabilities from LLMs. Prior work has introduced latent adversarial training (LAT) as a way to improve robustness to broad classes of failures. These prior works have considered untargeted latent space attacks where the adversary perturbs latent activations to maximize loss on examples of desirable behavior. Untargeted LAT can provide a generic type of robustness but does not leverage information about specific failure modes. Here, we experiment with targeted LAT where the adversary seeks to minimize loss on a specific competing task. We find that it can augment a wide variety of state-of-the-art methods. First, we use targeted LAT to improve robustness to jailbreaks, outperforming a strong R2D2 baseline with orders of magnitude less compute. Second, we use it to more effectively remove backdoors with no knowledge of the trigger. Finally, we use it to more effectively unlearn knowledge for specific undesirable tasks in a way that is also more robust to re-learning. Overall, our results suggest that targeted LAT can be an effective tool for defending against harmful behaviors from LLMs.

The general capabilities of Large Language Models (LLM) highly rely on the composition and selection on extensive pretraining datasets, treated as commercial secrets by several institutions. To mitigate this issue, we open-source the details of a universally applicable data processing pipeline and validate its effectiveness and potential by introducing a competitive LLM baseline. Specifically, the data processing pipeline consists of broad collection to scale up and reweighting to improve quality. We then pretrain a 7B model BaichuanSEED with 3T tokens processed by our pipeline without any deliberate downstream task-related optimization, followed by an easy but effective supervised fine-tuning stage. BaichuanSEED demonstrates consistency and predictability throughout training and achieves comparable performance on comprehensive benchmarks with several commercial advanced large language models, such as Qwen1.5 and Llama3. We also conduct several heuristic experiments to discuss the potential for further optimization of downstream tasks, such as mathematics and coding.

Antibody design is an essential yet challenging task in various domains like therapeutics and biology. There are two major defects in current learning-based methods: 1) tackling only a certain subtask of the whole antibody design pipeline, making them suboptimal or resource-intensive. 2) omitting either the framework regions or side chains, thus incapable of capturing the full-atom geometry. To address these pitfalls, we propose dynamic Multi-channel Equivariant grAph Network (dyMEAN), an end-to-end full-atom model for E(3)-equivariant antibody design given the epitope and the incomplete sequence of the antibody. Specifically, we first explore structural initialization as a knowledgeable guess of the antibody structure and then propose shadow paratope to bridge the epitope-antibody connections. Both 1D sequences and 3D structures are updated via an adaptive multi-channel equivariant encoder that is able to process protein residues of variable sizes when considering full atoms. Finally, the updated antibody is docked to the epitope via the alignment of the shadow paratope. Experiments on epitope-binding CDR-H3 design, complex structure prediction, and affinity optimization demonstrate the superiority of our end-to-end framework and full-atom modeling.

Large language models (LM) generate remarkably fluent text and can be efficiently adapted across NLP tasks. Measuring and guaranteeing the quality of generated text in terms of safety is imperative for deploying LMs in the real world; to this end, prior work often relies on automatic evaluation of LM toxicity. We critically discuss this approach, evaluate several toxicity mitigation strategies with respect to both automatic and human evaluation, and analyze consequences of toxicity mitigation in terms of model bias and LM quality. We demonstrate that while basic intervention strategies can effectively optimize previously established automatic metrics on the RealToxicityPrompts dataset, this comes at the cost of reduced LM coverage for both texts about, and dialects of, marginalized groups. Additionally, we find that human raters often disagree with high automatic toxicity scores after strong toxicity reduction interventions -- highlighting further the nuances involved in careful evaluation of LM toxicity.

The task of chemical reaction predictions (CRPs) plays a pivotal role in advancing drug discovery and material science. However, its effectiveness is constrained by the vast and uncertain chemical reaction space and challenges in capturing reaction selectivity, particularly due to existing methods' limitations in exploiting the data's inherent knowledge. To address these challenges, we introduce a data-curated self-feedback knowledge elicitation approach. This method starts from iterative optimization of molecular representations and facilitates the extraction of knowledge on chemical reaction types (RTs). Then, we employ adaptive prompt learning to infuse the prior knowledge into the large language model (LLM). As a result, we achieve significant enhancements: a 14.2% increase in retrosynthesis prediction accuracy, a 74.2% rise in reagent prediction accuracy, and an expansion in the model's capability for handling multi-task chemical reactions. This research offers a novel paradigm for knowledge elicitation in scientific research and showcases the untapped potential of LLMs in CRPs.

With the rapid evolution of large language models (LLMs), new and hard-to-predict harmful capabilities are emerging. This requires developers to be able to identify risks through the evaluation of "dangerous capabilities" in order to responsibly deploy LLMs. In this work, we collect the first open-source dataset to evaluate safeguards in LLMs, and deploy safer open-source LLMs at a low cost. Our dataset is curated and filtered to consist only of instructions that responsible language models should not follow. We annotate and assess the responses of six popular LLMs to these instructions. Based on our annotation, we proceed to train several BERT-like classifiers, and find that these small classifiers can achieve results that are comparable with GPT-4 on automatic safety evaluation. Warning: this paper contains example data that may be offensive, harmful, or biased.

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier.

Macro-AUC is the arithmetic mean of the class-wise AUCs in multi-label learning and is commonly used in practice. However, its theoretical understanding is far lacking. Toward solving it, we characterize the generalization properties of various learning algorithms based on the corresponding surrogate losses w.r.t. Macro-AUC. We theoretically identify a critical factor of the dataset affecting the generalization bounds: the label-wise class imbalance. Our results on the imbalance-aware error bounds show that the widely-used univariate loss-based algorithm is more sensitive to the label-wise class imbalance than the proposed pairwise and reweighted loss-based ones, which probably implies its worse performance. Moreover, empirical results on various datasets corroborate our theory findings. To establish it, technically, we propose a new (and more general) McDiarmid-type concentration inequality, which may be of independent interest.

Language generation models have been an increasingly powerful enabler for many applications. Many such models offer free or affordable API access, which makes them potentially vulnerable to model extraction attacks through distillation. To protect intellectual property (IP) and ensure fair use of these models, various techniques such as lexical watermarking and synonym replacement have been proposed. However, these methods can be nullified by obvious countermeasures such as "synonym randomization". To address this issue, we propose GINSEW, a novel method to protect text generation models from being stolen through distillation. The key idea of our method is to inject secret signals into the probability vector of the decoding steps for each target token. We can then detect the secret message by probing a suspect model to tell if it is distilled from the protected one. Experimental results show that GINSEW can effectively identify instances of IP infringement with minimal impact on the generation quality of protected APIs. Our method demonstrates an absolute improvement of 19 to 29 points on mean average precision (mAP) in detecting suspects compared to previous methods against watermark removal attacks.

Pathology plays a critical role in diagnosing a wide range of diseases, yet existing approaches often rely heavily on task-specific models trained on extensive, well-labeled datasets. These methods face sustainability challenges due to the diversity of pathologies and the labor-intensive nature of data collection. To address these limitations, we highlight the need for universal multimodal embeddings that can support multiple downstream tasks. Previous approaches often involve fine-tuning CLIP-based models, which handle images and text separately, limiting their ability to capture complex multimodal relationships. Additionally, these models are evaluated across diverse datasets without a unified benchmark for assessing multimodal embeddings in pathology. To address these challenges, we propose MLLM4PUE, a novel framework that leverages Multimodal Large Language Models (MLLMs) to generate Pathology Universal Embeddings. The MLLM4PUE framework not only facilitates robust integration of images and text but also enhances understanding and fusion capabilities across various tasks. We further introduce the Pathology Multimodal Embedding Benchmark (PMEB), a comprehensive benchmark designed to assess the quality of pathology multimodal embeddings. PMEB comprises 15 original tasks drawn from 14 datasets, organized into three meta-tasks: retrieval, classification, and composed retrieval. Experimental results demonstrate the superiority of MLLM4PUE, illustrating MLLM-based models can effectively support a wide range of downstream tasks and unify the research direction for foundation models in pathology.

As the size of large language models (LLMs) continues to grow, model compression without sacrificing accuracy has become a crucial challenge for deployment. While some quantization methods, such as GPTQ, have made progress in achieving acceptable 4-bit weight-only quantization, attempts at lower bit quantization often result in severe performance degradation. In this paper, we introduce a technique called norm tweaking, which can be used as a plugin in current PTQ methods to achieve high precision while being cost-efficient. Our approach is inspired by the observation that rectifying the quantized activation distribution to match its float counterpart can readily restore accuracy for LLMs. To achieve this, we carefully design a tweaking strategy that includes calibration data generation and channel-wise distance constraint to update the weights of normalization layers for better generalization. We conduct extensive experiments on various datasets using several open-sourced LLMs. Our method demonstrates significant improvements in both weight-only quantization and joint quantization of weights and activations, surpassing existing PTQ methods. On GLM-130B and OPT-66B, our method even achieves the same level of accuracy at 2-bit quantization as their float ones. Our simple and effective approach makes it more practical for real-world applications.

Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to compute molecular similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing the search results from five drug-like query molecules (penicillin G, nirmatrelvir, zidovudine, lysergic acid diethylamide, and fentanyl) and three dye-like query molecules (acid blue 25, avobenzone, and 2-diphenylaminocarbazole). We find that this novel method identifies molecules that are functionally similar to the query, indicated by the associated patent literature, and that many of these molecules are structurally distinct from the query, making them unlikely to be found with traditional chemical similarity search methods. This method may aid in the discovery of novel structural classes of molecules that achieve target functionality.

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

Knowledge distillation is often used to transfer knowledge from a strong teacher model to a relatively weak student model. Traditional methods include response-based methods and feature-based methods. Response-based methods are widely used but suffer from lower upper limits of performance due to their ignorance of intermediate signals, while feature-based methods have constraints on vocabularies, tokenizers and model architectures. In this paper, we propose a liberal feature-based distillation method (LEAD). LEAD aligns the distribution between the intermediate layers of teacher model and student model, which is effective, extendable, portable and has no requirements on vocabularies, tokenizers, or model architectures. Extensive experiments show the effectiveness of LEAD on widely-used benchmarks, including MS MARCO Passage Ranking, TREC 2019 DL Track, MS MARCO Document Ranking and TREC 2020 DL Track. Our code is available in https://github.com/microsoft/SimXNS/tree/main/LEAD.

Pre-trained Vision Language Models (VLMs) have demonstrated notable progress in various zero-shot tasks, such as classification and retrieval. Despite their performance, because improving performance on new tasks requires task-specific knowledge, their adaptation is essential. While labels are needed for the adaptation, acquiring them is typically expensive. To overcome this challenge, active learning, a method of achieving a high performance by obtaining labels for a small number of samples from experts, has been studied. Active learning primarily focuses on selecting unlabeled samples for labeling and leveraging them to train models. In this study, we pose the question, "how can the pre-trained VLMs be adapted under the active learning framework?" In response to this inquiry, we observe that (1) simply applying a conventional active learning framework to pre-trained VLMs even may degrade performance compared to random selection because of the class imbalance in labeling candidates, and (2) the knowledge of VLMs can provide hints for achieving the balance before labeling. Based on these observations, we devise a novel active learning framework for VLMs, denoted as PCB. To assess the effectiveness of our approach, we conduct experiments on seven different real-world datasets, and the results demonstrate that PCB surpasses conventional active learning and random sampling methods. Code will be available in https://github.com/kaist-dmlab/pcb .

Tokenization is a foundational step in Natural Language Processing (NLP) tasks, bridging raw text and language models. Existing tokenization approaches like Byte-Pair Encoding (BPE) originate from the field of data compression, and it has been suggested that the effectiveness of BPE stems from its ability to condense text into a relatively small number of tokens. We test the hypothesis that fewer tokens lead to better downstream performance by introducing PathPiece, a new tokenizer that segments a document's text into the minimum number of tokens for a given vocabulary. Through extensive experimentation we find this hypothesis not to be the case, casting doubt on the understanding of the reasons for effective tokenization. To examine which other factors play a role, we evaluate design decisions across all three phases of tokenization: pre-tokenization, vocabulary construction, and segmentation, offering new insights into the design of effective tokenizers. Specifically, we illustrate the importance of pre-tokenization and the benefits of using BPE to initialize vocabulary construction. We train 64 language models with varying tokenization, ranging in size from 350M to 2.4B parameters, all of which are made publicly available.

Existing research on malware classification focuses almost exclusively on two tasks: distinguishing between malicious and benign files and classifying malware by family. However, malware can be categorized according to many other types of attributes, and the ability to identify these attributes in newly-emerging malware using machine learning could provide significant value to analysts. In particular, we have identified four tasks which are under-represented in prior work: classification by behaviors that malware exhibit, platforms that malware run on, vulnerabilities that malware exploit, and packers that malware are packed with. To obtain labels for training and evaluating ML classifiers on these tasks, we created an antivirus (AV) tagging tool called ClarAVy. ClarAVy's sophisticated AV label parser distinguishes itself from prior AV-based taggers, with the ability to accurately parse 882 different AV label formats used by 90 different AV products. We are releasing benchmark datasets for each of these four classification tasks, tagged using ClarAVy and comprising nearly 5.5 million malicious files in total. Our malware behavior dataset includes 75 distinct tags - nearly 7x more than the only prior benchmark dataset with behavioral tags. To our knowledge, we are the first to release datasets with malware platform and packer tags.

We identify label errors in the test sets of 10 of the most commonly-used computer vision, natural language, and audio datasets, and subsequently study the potential for these label errors to affect benchmark results. Errors in test sets are numerous and widespread: we estimate an average of at least 3.3% errors across the 10 datasets, where for example label errors comprise at least 6% of the ImageNet validation set. Putative label errors are identified using confident learning algorithms and then human-validated via crowdsourcing (51% of the algorithmically-flagged candidates are indeed erroneously labeled, on average across the datasets). Traditionally, machine learning practitioners choose which model to deploy based on test accuracy - our findings advise caution here, proposing that judging models over correctly labeled test sets may be more useful, especially for noisy real-world datasets. Surprisingly, we find that lower capacity models may be practically more useful than higher capacity models in real-world datasets with high proportions of erroneously labeled data. For example, on ImageNet with corrected labels: ResNet-18 outperforms ResNet-50 if the prevalence of originally mislabeled test examples increases by just 6%. On CIFAR-10 with corrected labels: VGG-11 outperforms VGG-19 if the prevalence of originally mislabeled test examples increases by just 5%. Test set errors across the 10 datasets can be viewed at https://labelerrors.com and all label errors can be reproduced by https://github.com/cleanlab/label-errors.

Tactics, Techniques and Procedures (TTPs) represent sophisticated attack patterns in the cybersecurity domain, described encyclopedically in textual knowledge bases. Identifying TTPs in cybersecurity writing, often called TTP mapping, is an important and challenging task. Conventional learning approaches often target the problem in the classical multi-class or multilabel classification setting. This setting hinders the learning ability of the model due to a large number of classes (i.e., TTPs), the inevitable skewness of the label distribution and the complex hierarchical structure of the label space. We formulate the problem in a different learning paradigm, where the assignment of a text to a TTP label is decided by the direct semantic similarity between the two, thus reducing the complexity of competing solely over the large labeling space. To that end, we propose a neural matching architecture with an effective sampling-based learn-to-compare mechanism, facilitating the learning process of the matching model despite constrained resources.

Model adaptation is crucial to handle the discrepancy between proxy training data and actual users data received. To effectively perform adaptation, textual data of users is typically stored on servers or their local devices, where downstream natural language processing (NLP) models can be directly trained using such in-domain data. However, this might raise privacy and security concerns due to the extra risks of exposing user information to adversaries. Replacing identifying information in textual data with a generic marker has been recently explored. In this work, we leverage large language models (LLMs) to suggest substitutes of masked tokens and have their effectiveness evaluated on downstream language modeling tasks. Specifically, we propose multiple pre-trained and fine-tuned LLM-based approaches and perform empirical studies on various datasets for the comparison of these methods. Experimental results show that models trained on the obfuscation corpora are able to achieve comparable performance with the ones trained on the original data without privacy-preserving token masking.

Open-source large language models are becoming increasingly available and popular among researchers and practitioners. While significant progress has been made on open-weight models, open training data is a practice yet to be adopted by the leading open-weight models creators. At the same time, there researchers are working to make language models safer. We propose a data curation pipeline to reduce harmful outputs by models trained on public domain data. There are unique challenges to working with public domain data, as these sources differ from web text in both form and content. Many sources are historical documents and are the result of Optical Character Recognition (OCR). Consequently, current state-of-the-art approaches to toxicity filtering are often infeasible or inappropriate for open data models. In this paper, we introduce a new fully open-source pipeline for open-data toxicity filtering. Our contributions are threefold. We create a custom training dataset, ToxicCommons, which is composed of texts which have been classified across five different dimensions (racial/origin-based, gender/sex-based, religious, ability-based discrimination, and violence). We use this dataset to train a custom classifier, Celadon, that can be used to detect toxic content in open data more efficiently at a larger scale. Finally, we describe the balanced approach to content filtration that optimizes safety filtering with respect to the filtered data available for training.

Despite multi-billion parameter neural rankers being common components of state-of-the-art information retrieval pipelines, they are rarely used in production due to the enormous amount of compute required for inference. In this work, we propose a new method for distilling large rankers into their smaller versions focusing on out-of-domain effectiveness. We introduce InRanker, a version of monoT5 distilled from monoT5-3B with increased effectiveness on out-of-domain scenarios. Our key insight is to use language models and rerankers to generate as much as possible synthetic "in-domain" training data, i.e., data that closely resembles the data that will be seen at retrieval time. The pipeline consists of two distillation phases that do not require additional user queries or manual annotations: (1) training on existing supervised soft teacher labels, and (2) training on teacher soft labels for synthetic queries generated using a large language model. Consequently, models like monoT5-60M and monoT5-220M improved their effectiveness by using the teacher's knowledge, despite being 50x and 13x smaller, respectively. Models and code are available at https://github.com/unicamp-dl/InRanker.

Natural Language Processing (NLP) has seen remarkable advances in recent years, particularly with the emergence of Large Language Models that have achieved unprecedented performance across many tasks. However, these developments have mainly benefited a small number of high-resource languages such as English. The majority of languages still face significant challenges due to the scarcity of training data and computational resources. To address this issue, this thesis focuses on cross-lingual transfer learning, a research area aimed at leveraging data and models from high-resource languages to improve NLP performance for low-resource languages. Specifically, we focus on Sequence Labeling tasks such as Named Entity Recognition, Opinion Target Extraction, and Argument Mining. The research is structured around three main objectives: (1) advancing data-based cross-lingual transfer learning methods through improved translation and annotation projection techniques, (2) developing enhanced model-based transfer learning approaches utilizing state-of-the-art multilingual models, and (3) applying these methods to real-world problems while creating open-source resources that facilitate future research in low-resource NLP. More specifically, this thesis presents a new method to improve data-based transfer with T-Projection, a state-of-the-art annotation projection method that leverages text-to-text multilingual models and machine translation systems. T-Projection significantly outperforms previous annotation projection methods by a wide margin. For model-based transfer, we introduce a constrained decoding algorithm that enhances cross-lingual Sequence Labeling in zero-shot settings using text-to-text models. Finally, we develop Medical mT5, the first multilingual text-to-text medical model, demonstrating the practical impact of our research on real-world applications.

Multilingual language models have significantly advanced due to rapid progress in natural language processing. Models like BLOOM 1.7B, trained on diverse multilingual datasets, aim to bridge linguistic gaps. However, their effectiveness in capturing linguistic knowledge, particularly for low-resource languages, remains an open question. This study critically examines MLMs capabilities in multilingual understanding, semantic representation, and cross-lingual knowledge transfer. While these models perform well for high-resource languages, they struggle with less-represented ones. Additionally, traditional evaluation methods often overlook their internal syntactic and semantic encoding. This research addresses key limitations through three objectives. First, it assesses semantic similarity by analyzing multilingual word embeddings for consistency using cosine similarity. Second, it examines BLOOM-1.7B and Qwen2 through Named Entity Recognition and sentence similarity tasks to understand their linguistic structures. Third, it explores cross-lingual knowledge transfer by evaluating generalization from high-resource to low-resource languages in sentiment analysis and text classification. By leveraging linguistic probing, performance metrics, and visualizations, this study provides insights into the strengths and limitations of MLMs. The findings aim to enhance multilingual NLP models, ensuring better support for both high- and low-resource languages, thereby promoting inclusivity in language technologies.