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Mar 12

Navigating Chemical-Linguistic Sharing Space with Heterogeneous Molecular Encoding

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+37.8\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

ChemLLM: A Chemical Large Language Model

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score. The dataset and the benchmark are available at https://huggingface.co/datasets/tsynbio/ProteinLMBench.

Benchmarking Large Language Models for Molecule Prediction Tasks

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.

Large Language Models are In-Context Molecule Learners

Large Language Models (LLMs) have demonstrated exceptional performance in biochemical tasks, especially the molecule caption translation task, which aims to bridge the gap between molecules and natural language texts. However, previous methods in adapting LLMs to the molecule-caption translation task required extra domain-specific pre-training stages, suffered weak alignment between molecular and textual spaces, or imposed stringent demands on the scale of LLMs. To resolve the challenges, we propose In-Context Molecule Adaptation (ICMA), as a new paradigm allowing LLMs to learn the molecule-text alignment from context examples via In-Context Molecule Tuning. Specifically, ICMA incorporates the following three stages: Cross-modal Retrieval, Post-retrieval Re-ranking, and In-context Molecule Tuning. Initially, Cross-modal Retrieval utilizes BM25 Caption Retrieval and Molecule Graph Retrieval to retrieve informative context examples. Additionally, we also propose Post-retrieval Re-ranking with Sequence Reversal and Random Walk to further improve the quality of retrieval results. Finally, In-Context Molecule Tuning unlocks the in-context molecule learning capability of LLMs with retrieved examples and adapts the parameters of LLMs for the molecule-caption translation task. Experimental results demonstrate that ICMT can empower LLMs to achieve state-of-the-art or comparable performance without extra training corpora and intricate structures, showing that LLMs are inherently in-context molecule learners.

KGym: A Platform and Dataset to Benchmark Large Language Models on Linux Kernel Crash Resolution

Large Language Models (LLMs) are consistently improving at increasingly realistic software engineering (SE) tasks. In real-world software stacks, significant SE effort is spent developing foundational system software like the Linux kernel. Unlike application-level software, a systems codebase like Linux is multilingual (low-level C/Assembly/Bash/Rust); gigantic (>20 million lines); critical (impacting billions of devices worldwide), and highly concurrent (involving complex multi-threading). To evaluate if ML models are useful while developing such large-scale systems-level software, we introduce kGym (a platform) and kBench (a dataset). The kGym platform provides a SE environment for large-scale experiments on the Linux kernel, including compiling and running kernels in parallel across several virtual machines, detecting operations and crashes, inspecting logs, and querying and patching the code base. We use kGym to facilitate evaluation on kBench, a crash resolution benchmark drawn from real-world Linux kernel bugs. An example bug in kBench contains crashing stack traces, a bug-reproducer file, a developer-written fix, and other associated data. To understand current performance, we conduct baseline experiments by prompting LLMs to resolve Linux kernel crashes. Our initial evaluations reveal that the best performing LLM achieves 0.72% and 5.38% in the unassisted and assisted (i.e., buggy files disclosed to the model) settings, respectively. These results highlight the need for further research to enhance model performance in SE tasks. Improving performance on kBench requires models to master new learning skills, including understanding the cause of crashes and repairing faults, writing memory-safe and hardware-aware code, and understanding concurrency. As a result, this work opens up multiple avenues of research at the intersection of machine learning and systems software.

1.5-Pints Technical Report: Pretraining in Days, Not Months -- Your Language Model Thrives on Quality Data

This paper presents a compute-efficient approach to pre-training a Language Model-the "1.5-Pints"-in only 9 days, while outperforming state-of-the-art models as an instruction-following assistant.Based on MT-Bench (a benchmark that emulates human judgments), 1.5-Pints outperforms Apple's OpenELM and Microsoft's Phi.This is achieved by a carefully curated pre-training dataset of 57 billion tokens, using a mix of automated workflows and manual human review. The selection of the dataset prioritizes content that is considered expository and "textbook-like" to aid the model in reasoning and logical deduction, culminating in its overall ability as a strong and versatile AI model. In terms of the model architecture, we employed a modified Mistral tokenizer, alongside a Llama-2 architecture for wider compatibility. For training, we adopted the methodologies used by StableLM, TinyLlama, and Huggingface Zephyr. 1.5-Pints demonstrates that by focusing on data quality over quantity in LLM training, we can significantly reduce training time and resources required. We believe this approach will not only make pre-training more accessible but also reduce our carbon footprint. Our findings and resources from this research are open-sourced, aiming to facilitate further advancements in the field. The 1.5-Pints model is available in two versions: 2K and 16K context windows.

Are large language models superhuman chemists?

Large language models (LLMs) have gained widespread interest due to their ability to process human language and perform tasks on which they have not been explicitly trained. This is relevant for the chemical sciences, which face the problem of small and diverse datasets that are frequently in the form of text. LLMs have shown promise in addressing these issues and are increasingly being harnessed to predict chemical properties, optimize reactions, and even design and conduct experiments autonomously. However, we still have only a very limited systematic understanding of the chemical reasoning capabilities of LLMs, which would be required to improve models and mitigate potential harms. Here, we introduce "ChemBench," an automated framework designed to rigorously evaluate the chemical knowledge and reasoning abilities of state-of-the-art LLMs against the expertise of human chemists. We curated more than 7,000 question-answer pairs for a wide array of subfields of the chemical sciences, evaluated leading open and closed-source LLMs, and found that the best models outperformed the best human chemists in our study on average. The models, however, struggle with some chemical reasoning tasks that are easy for human experts and provide overconfident, misleading predictions, such as about chemicals' safety profiles. These findings underscore the dual reality that, although LLMs demonstrate remarkable proficiency in chemical tasks, further research is critical to enhancing their safety and utility in chemical sciences. Our findings also indicate a need for adaptations to chemistry curricula and highlight the importance of continuing to develop evaluation frameworks to improve safe and useful LLMs.

A Review of Multi-Modal Large Language and Vision Models

Large Language Models (LLMs) have recently emerged as a focal point of research and application, driven by their unprecedented ability to understand and generate text with human-like quality. Even more recently, LLMs have been extended into multi-modal large language models (MM-LLMs) which extends their capabilities to deal with image, video and audio information, in addition to text. This opens up applications like text-to-video generation, image captioning, text-to-speech, and more and is achieved either by retro-fitting an LLM with multi-modal capabilities, or building a MM-LLM from scratch. This paper provides an extensive review of the current state of those LLMs with multi-modal capabilities as well as the very recent MM-LLMs. It covers the historical development of LLMs especially the advances enabled by transformer-based architectures like OpenAI's GPT series and Google's BERT, as well as the role of attention mechanisms in enhancing model performance. The paper includes coverage of the major and most important of the LLMs and MM-LLMs and also covers the techniques of model tuning, including fine-tuning and prompt engineering, which tailor pre-trained models to specific tasks or domains. Ethical considerations and challenges, such as data bias and model misuse, are also analysed to underscore the importance of responsible AI development and deployment. Finally, we discuss the implications of open-source versus proprietary models in AI research. Through this review, we provide insights into the transformative potential of MM-LLMs in various applications.

MolReFlect: Towards In-Context Fine-grained Alignments between Molecules and Texts

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

List Items One by One: A New Data Source and Learning Paradigm for Multimodal LLMs

Set-of-Mark (SoM) Prompting unleashes the visual grounding capability of GPT-4V, by enabling the model to associate visual objects with tags inserted on the image. These tags, marked with alphanumerics, can be indexed via text tokens for easy reference. Despite the extraordinary performance from GPT-4V, we observe that other Multimodal Large Language Models (MLLMs) struggle to understand these visual tags. To promote the learning of SoM prompting for open-source models, we propose a new learning paradigm: "list items one by one," which asks the model to enumerate and describe all visual tags placed on the image following the alphanumeric orders of tags. By integrating our curated dataset with other visual instruction tuning datasets, we are able to equip existing MLLMs with the SoM prompting ability. Furthermore, we evaluate our finetuned SoM models on five MLLM benchmarks. We find that this new dataset, even in a relatively small size (10k-30k images with tags), significantly enhances visual reasoning capabilities and reduces hallucinations for MLLMs. Perhaps surprisingly, these improvements persist even when the visual tags are omitted from input images during inference. This suggests the potential of "list items one by one" as a new paradigm for training MLLMs, which strengthens the object-text alignment through the use of visual tags in the training stage. Finally, we conduct analyses by probing trained models to understand the working mechanism of SoM. Our code and data are available at https://github.com/zzxslp/SoM-LLaVA.

MAP-Neo: Highly Capable and Transparent Bilingual Large Language Model Series

Large Language Models (LLMs) have made great strides in recent years to achieve unprecedented performance across different tasks. However, due to commercial interest, the most competitive models like GPT, Gemini, and Claude have been gated behind proprietary interfaces without disclosing the training details. Recently, many institutions have open-sourced several strong LLMs like LLaMA-3, comparable to existing closed-source LLMs. However, only the model's weights are provided with most details (e.g., intermediate checkpoints, pre-training corpus, and training code, etc.) being undisclosed. To improve the transparency of LLMs, the research community has formed to open-source truly open LLMs (e.g., Pythia, Amber, OLMo), where more details (e.g., pre-training corpus and training code) are being provided. These models have greatly advanced the scientific study of these large models including their strengths, weaknesses, biases and risks. However, we observe that the existing truly open LLMs on reasoning, knowledge, and coding tasks are still inferior to existing state-of-the-art LLMs with similar model sizes. To this end, we open-source MAP-Neo, a highly capable and transparent bilingual language model with 7B parameters trained from scratch on 4.5T high-quality tokens. Our MAP-Neo is the first fully open-sourced bilingual LLM with comparable performance compared to existing state-of-the-art LLMs. Moreover, we open-source all details to reproduce our MAP-Neo, where the cleaned pre-training corpus, data cleaning pipeline, checkpoints, and well-optimized training/evaluation framework are provided. Finally, we hope our MAP-Neo will enhance and strengthen the open research community and inspire more innovations and creativities to facilitate the further improvements of LLMs.

NatureLM: Deciphering the Language of Nature for Scientific Discovery

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Linguistic Entity Masking to Improve Cross-Lingual Representation of Multilingual Language Models for Low-Resource Languages

Multilingual Pre-trained Language models (multiPLMs), trained on the Masked Language Modelling (MLM) objective are commonly being used for cross-lingual tasks such as bitext mining. However, the performance of these models is still suboptimal for low-resource languages (LRLs). To improve the language representation of a given multiPLM, it is possible to further pre-train it. This is known as continual pre-training. Previous research has shown that continual pre-training with MLM and subsequently with Translation Language Modelling (TLM) improves the cross-lingual representation of multiPLMs. However, during masking, both MLM and TLM give equal weight to all tokens in the input sequence, irrespective of the linguistic properties of the tokens. In this paper, we introduce a novel masking strategy, Linguistic Entity Masking (LEM) to be used in the continual pre-training step to further improve the cross-lingual representations of existing multiPLMs. In contrast to MLM and TLM, LEM limits masking to the linguistic entity types nouns, verbs and named entities, which hold a higher prominence in a sentence. Secondly, we limit masking to a single token within the linguistic entity span thus keeping more context, whereas, in MLM and TLM, tokens are masked randomly. We evaluate the effectiveness of LEM using three downstream tasks, namely bitext mining, parallel data curation and code-mixed sentiment analysis using three low-resource language pairs English-Sinhala, English-Tamil, and Sinhala-Tamil. Experiment results show that continually pre-training a multiPLM with LEM outperforms a multiPLM continually pre-trained with MLM+TLM for all three tasks.

Exploring the Capabilities of LLMs for Code Change Related Tasks

Developers deal with code-change-related tasks daily, e.g., reviewing code. Pre-trained code and code-change-oriented models have been adapted to help developers with such tasks. Recently, large language models (LLMs) have shown their effectiveness in code-related tasks. However, existing LLMs for code focus on general code syntax and semantics rather than the differences between two code versions. Thus, it is an open question how LLMs perform on code-change-related tasks. To answer this question, we conduct an empirical study using \textgreater 1B parameters LLMs on three code-change-related tasks, i.e., code review generation, commit message generation, and just-in-time comment update, with in-context learning (ICL) and parameter-efficient fine-tuning (PEFT, including LoRA and prefix-tuning). We observe that the performance of LLMs is poor without examples and generally improves with examples, but more examples do not always lead to better performance. LLMs tuned with LoRA have comparable performance to the state-of-the-art small pre-trained models. Larger models are not always better, but Llama~2 and Code~Llama families are always the best. The best LLMs outperform small pre-trained models on the code changes that only modify comments and perform comparably on other code changes. We suggest future work should focus more on guiding LLMs to learn the knowledge specific to the changes related to code rather than comments for code-change-related tasks.

Privacy Preserving Prompt Engineering: A Survey

Pre-trained language models (PLMs) have demonstrated significant proficiency in solving a wide range of general natural language processing (NLP) tasks. Researchers have observed a direct correlation between the performance of these models and their sizes. As a result, the sizes of these models have notably expanded in recent years, persuading researchers to adopt the term large language models (LLMs) to characterize the larger-sized PLMs. The size expansion comes with a distinct capability called in-context learning (ICL), which represents a special form of prompting and allows the models to be utilized through the presentation of demonstration examples without modifications to the model parameters. Although interesting, privacy concerns have become a major obstacle in its widespread usage. Multiple studies have examined the privacy risks linked to ICL and prompting in general, and have devised techniques to alleviate these risks. Thus, there is a necessity to organize these mitigation techniques for the benefit of the community. This survey provides a systematic overview of the privacy protection methods employed during ICL and prompting in general. We review, analyze, and compare different methods under this paradigm. Furthermore, we provide a summary of the resources accessible for the development of these frameworks. Finally, we discuss the limitations of these frameworks and offer a detailed examination of the promising areas that necessitate further exploration.

3D-MolT5: Towards Unified 3D Molecule-Text Modeling with 3D Molecular Tokenization

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

What indeed can GPT models do in chemistry? A comprehensive benchmark on eight tasks

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

Croc: Pretraining Large Multimodal Models with Cross-Modal Comprehension

Recent advances in Large Language Models (LLMs) have catalyzed the development of Large Multimodal Models (LMMs). However, existing research primarily focuses on tuning language and image instructions, ignoring the critical pretraining phase where models learn to process textual and visual modalities jointly. In this paper, we propose a new pretraining paradigm for LMMs to enhance the visual comprehension capabilities of LLMs by introducing a novel cross-modal comprehension stage. Specifically, we design a dynamically learnable prompt token pool and employ the Hungarian algorithm to replace part of the original visual tokens with the most relevant prompt tokens. Then, we conceptualize visual tokens as analogous to a "foreign language" for the LLMs and propose a mixed attention mechanism with bidirectional visual attention and unidirectional textual attention to comprehensively enhance the understanding of visual tokens. Meanwhile, we integrate a detailed caption generation task, leveraging rich descriptions to further facilitate LLMs in understanding visual semantic information. After pretraining on 1.5 million publicly accessible data, we present a new foundation model called Croc. Experimental results demonstrate that Croc achieves new state-of-the-art performance on massive vision-language benchmarks. To support reproducibility and facilitate further research, we release the training code and pre-trained model weights at https://github.com/deepglint/Croc.

ChineseWebText 2.0: Large-Scale High-quality Chinese Web Text with Multi-dimensional and fine-grained information

During the development of large language models (LLMs), pre-training data play a critical role in shaping LLMs' capabilities. In recent years several large-scale and high-quality pre-training datasets have been released to accelerate the research of LLMs, including ChineseWebText1.0, C4, Pile, WanJuan, MAPCC and others. However, as LLMs continue to evolve, focus has increasingly shifted to domain-specific capabilities and safety concerns, making those previous coarse-grained texts insufficient for meeting training requirements. Furthermore, fine-grained information, such as quality, domain and toxicity, is becoming increasingly important in building powerful and reliable LLMs for various scenarios. To address these challenges, in this paper we propose a new tool-chain called MDFG-tool for constructing large-scale and high-quality Chinese datasets with multi-dimensional and fine-grained information. First, we employ manually crafted rules to discard explicit noisy texts from raw contents. Second, the quality evaluation model, domain classifier, and toxicity evaluation model are well-designed to assess the remaining cleaned data respectively. Finally, we integrate these three types of fine-grained information for each text. With this approach, we release the largest, high-quality and fine-grained Chinese text ChineseWebText2.0, which consists of 3.8TB and each text is associated with a quality score, domain labels, a toxicity label and a toxicity score, facilitating the LLM researchers to select data based on various types of fine-grained information. The data, codes and the tool-chain are available on this website https://github.com/CASIA-LM/ChineseWebText-2.0

Continual Learning of Large Language Models: A Comprehensive Survey

The recent success of large language models (LLMs) trained on static, pre-collected, general datasets has sparked numerous research directions and applications. One such direction addresses the non-trivial challenge of integrating pre-trained LLMs into dynamic data distributions, task structures, and user preferences. Pre-trained LLMs, when tailored for specific needs, often experience significant performance degradation in previous knowledge domains -- a phenomenon known as "catastrophic forgetting". While extensively studied in the continual learning (CL) community, it presents new manifestations in the realm of LLMs. In this survey, we provide a comprehensive overview of the current research progress on LLMs within the context of CL. This survey is structured into four main sections: we first describe an overview of continually learning LLMs, consisting of two directions of continuity: vertical continuity (or vertical continual learning), i.e., continual adaptation from general to specific capabilities, and horizontal continuity (or horizontal continual learning), i.e., continual adaptation across time and domains (Section 3). We then summarize three stages of learning LLMs in the context of modern CL: Continual Pre-Training (CPT), Domain-Adaptive Pre-training (DAP), and Continual Fine-Tuning (CFT) (Section 4). Then we provide an overview of evaluation protocols for continual learning with LLMs, along with the current available data sources (Section 5). Finally, we discuss intriguing questions pertaining to continual learning for LLMs (Section 6). The full list of papers examined in this survey is available at https://github.com/Wang-ML-Lab/llm-continual-learning-survey.

InvestLM: A Large Language Model for Investment using Financial Domain Instruction Tuning

We present a new financial domain large language model, InvestLM, tuned on LLaMA-65B (Touvron et al., 2023), using a carefully curated instruction dataset related to financial investment. Inspired by less-is-more-for-alignment (Zhou et al., 2023), we manually curate a small yet diverse instruction dataset, covering a wide range of financial related topics, from Chartered Financial Analyst (CFA) exam questions to SEC filings to Stackexchange quantitative finance discussions. InvestLM shows strong capabilities in understanding financial text and provides helpful responses to investment related questions. Financial experts, including hedge fund managers and research analysts, rate InvestLM's response as comparable to those of state-of-the-art commercial models (GPT-3.5, GPT-4 and Claude-2). Zero-shot evaluation on a set of financial NLP benchmarks demonstrates strong generalizability. From a research perspective, this work suggests that a high-quality domain specific LLM can be tuned using a small set of carefully curated instructions on a well-trained foundation model, which is consistent with the Superficial Alignment Hypothesis (Zhou et al., 2023). From a practical perspective, this work develops a state-of-the-art financial domain LLM with superior capability in understanding financial texts and providing helpful investment advice, potentially enhancing the work efficiency of financial professionals. We release the model parameters to the research community.

Challenges and Opportunities of Using Transformer-Based Multi-Task Learning in NLP Through ML Lifecycle: A Survey

The increasing adoption of natural language processing (NLP) models across industries has led to practitioners' need for machine learning systems to handle these models efficiently, from training to serving them in production. However, training, deploying, and updating multiple models can be complex, costly, and time-consuming, mainly when using transformer-based pre-trained language models. Multi-Task Learning (MTL) has emerged as a promising approach to improve efficiency and performance through joint training, rather than training separate models. Motivated by this, we first provide an overview of transformer-based MTL approaches in NLP. Then, we discuss the challenges and opportunities of using MTL approaches throughout typical ML lifecycle phases, specifically focusing on the challenges related to data engineering, model development, deployment, and monitoring phases. This survey focuses on transformer-based MTL architectures and, to the best of our knowledge, is novel in that it systematically analyses how transformer-based MTL in NLP fits into ML lifecycle phases. Furthermore, we motivate research on the connection between MTL and continual learning (CL), as this area remains unexplored. We believe it would be practical to have a model that can handle both MTL and CL, as this would make it easier to periodically re-train the model, update it due to distribution shifts, and add new capabilities to meet real-world requirements.

Effective Self-Mining of In-Context Examples for Unsupervised Machine Translation with LLMs

Large Language Models (LLMs) have demonstrated impressive performance on a wide range of natural language processing (NLP) tasks, primarily through in-context learning (ICL). In ICL, the LLM is provided with examples that represent a given task such that it learns to generate answers for test inputs. However, access to these in-context examples is not guaranteed especially for low-resource or massively multilingual tasks. In this work, we propose an unsupervised approach to mine in-context examples for machine translation (MT), enabling unsupervised MT (UMT) across different languages. Our approach begins with word-level mining to acquire word translations that are then used to perform sentence-level mining. As the quality of mined parallel pairs may not be optimal due to noise or mistakes, we introduce a filtering criterion to select the optimal in-context examples from a pool of unsupervised parallel sentences. We evaluate our approach using two multilingual LLMs on 288 directions from the FLORES-200 dataset and analyze the impact of various linguistic features on performance. Our findings demonstrate the effectiveness of our unsupervised approach in mining in-context examples for MT, leading to better or comparable translation performance as translation with regular in-context samples (extracted from human-annotated data), while also outperforming the other state-of-the-art UMT methods by an average of 7 BLEU points.

Crystal: Illuminating LLM Abilities on Language and Code

Large Language Models (LLMs) specializing in code generation (which are also often referred to as code LLMs), e.g., StarCoder and Code Llama, play increasingly critical roles in various software development scenarios. It is also crucial for code LLMs to possess both code generation and natural language abilities for many specific applications, such as code snippet retrieval using natural language or code explanations. The intricate interaction between acquiring language and coding skills complicates the development of strong code LLMs. Furthermore, there is a lack of thorough prior studies on the LLM pretraining strategy that mixes code and natural language. In this work, we propose a pretraining strategy to enhance the integration of natural language and coding capabilities within a single LLM. Specifically, it includes two phases of training with appropriately adjusted code/language ratios. The resulting model, Crystal, demonstrates remarkable capabilities in both domains. Specifically, it has natural language and coding performance comparable to that of Llama 2 and Code Llama, respectively. Crystal exhibits better data efficiency, using 1.4 trillion tokens compared to the more than 2 trillion tokens used by Llama 2 and Code Llama. We verify our pretraining strategy by analyzing the training process and observe consistent improvements in most benchmarks. We also adopted a typical application adaptation phase with a code-centric data mixture, only to find that it did not lead to enhanced performance or training efficiency, underlining the importance of a carefully designed data recipe. To foster research within the community, we commit to open-sourcing every detail of the pretraining, including our training datasets, code, loggings and 136 checkpoints throughout the training.

Doing More with Less -- Implementing Routing Strategies in Large Language Model-Based Systems: An Extended Survey

Large Language Models (LLM)-based systems, i.e. interconnected elements that include an LLM as a central component (e.g., conversational agents), are typically monolithic static architectures that rely on a single LLM for all user queries. However, they often require different preprocessing strategies, levels of reasoning, or knowledge. Generalist LLMs (i.e. GPT-4), trained on very large multi-topic corpora, can perform well in a variety of tasks. However, they require significant financial, energy, and hardware resources that may not be justified for basic tasks. This implies potentially investing in unnecessary costs for a given query. To overcome this problem, a routing mechanism routes user queries to the most suitable components, such as smaller LLMs or experts in specific topics. This approach may improve response quality while minimising costs. Routing can be expanded to other components of the conversational agent architecture, such as the selection of optimal embedding strategies. This paper explores key considerations for integrating routing into LLM-based systems, focusing on resource management, cost definition, and strategy selection. Our main contributions include a formalisation of the problem, a novel taxonomy of existing approaches emphasising relevance and resource efficiency, and a comparative analysis of these strategies in relation to industry practices. Finally, we identify critical challenges and directions for future research.

Medical mT5: An Open-Source Multilingual Text-to-Text LLM for The Medical Domain

Research on language technology for the development of medical applications is currently a hot topic in Natural Language Understanding and Generation. Thus, a number of large language models (LLMs) have recently been adapted to the medical domain, so that they can be used as a tool for mediating in human-AI interaction. While these LLMs display competitive performance on automated medical texts benchmarks, they have been pre-trained and evaluated with a focus on a single language (English mostly). This is particularly true of text-to-text models, which typically require large amounts of domain-specific pre-training data, often not easily accessible for many languages. In this paper, we address these shortcomings by compiling, to the best of our knowledge, the largest multilingual corpus for the medical domain in four languages, namely English, French, Italian and Spanish. This new corpus has been used to train Medical mT5, the first open-source text-to-text multilingual model for the medical domain. Additionally, we present two new evaluation benchmarks for all four languages with the aim of facilitating multilingual research in this domain. A comprehensive evaluation shows that Medical mT5 outperforms both encoders and similarly sized text-to-text models for the Spanish, French, and Italian benchmarks, while being competitive with current state-of-the-art LLMs in English.

Efficient Continual Pre-training by Mitigating the Stability Gap

Continual pre-training has increasingly become the predominant approach for adapting Large Language Models (LLMs) to new domains. This process involves updating the pre-trained LLM with a corpus from a new domain, resulting in a shift in the training distribution. To study the behavior of LLMs during this shift, we measured the model's performance throughout the continual pre-training process. we observed a temporary performance drop at the beginning, followed by a recovery phase, a phenomenon known as the "stability gap," previously noted in vision models classifying new classes. To address this issue and enhance LLM performance within a fixed compute budget, we propose three effective strategies: (1) Continually pre-training the LLM on a subset with a proper size for multiple epochs, resulting in faster performance recovery than pre-training the LLM on a large corpus in a single epoch; (2) Pre-training the LLM only on high-quality sub-corpus, which rapidly boosts domain performance; and (3) Using a data mixture similar to the pre-training data to reduce distribution gap. We conduct various experiments on Llama-family models to validate the effectiveness of our strategies in both medical continual pre-training and instruction tuning. For example, our strategies improve the average medical task performance of the OpenLlama-3B model from 36.2% to 40.7% with only 40% of the original training budget and enhance the average general task performance without causing forgetting. Furthermore, we apply our strategies to the Llama-3-8B model. The resulting model, Llama-3-Physician, achieves the best medical performance among current open-source models, and performs comparably to or even better than GPT-4 on several medical benchmarks. We release our models at https://huggingface.co/YiDuo1999/Llama-3-Physician-8B-Instruct.

Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a multi-constraint molecular generation large language model, TSMMG, which, akin to a student, incorporates knowledge from various small models and tools, namely, the 'teachers'. To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers', enabling it to generate novel molecules that conform to the descriptions through various text prompts. We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements across two-, three-, and four-constraint tasks, with an average molecular validity of over 99% and success ratio of 82.58%, 68.03%, and 67.48%, respectively. The model also exhibits adaptability through zero-shot testing, creating molecules that satisfy combinations of properties that have not been encountered. It can comprehend text inputs with various language styles, extending beyond the confines of outlined prompts, as confirmed through empirical validation. Additionally, the knowledge distillation feature of TSMMG contributes to the continuous enhancement of small models, while the innovative approach to dataset construction effectively addresses the issues of data scarcity and quality, which positions TSMMG as a promising tool in the domains of drug discovery and materials science.

Stacking Your Transformers: A Closer Look at Model Growth for Efficient LLM Pre-Training

LLMs are computationally expensive to pre-train due to their large scale. Model growth emerges as a promising approach by leveraging smaller models to accelerate the training of larger ones. However, the viability of these model growth methods in efficient LLM pre-training remains underexplored. This work identifies three critical textit{O}bstacles: (O1) lack of comprehensive evaluation, (O2) untested viability for scaling, and (O3) lack of empirical guidelines. To tackle O1, we summarize existing approaches into four atomic growth operators and systematically evaluate them in a standardized LLM pre-training setting. Our findings reveal that a depthwise stacking operator, called G_{stack}, exhibits remarkable acceleration in training, leading to decreased loss and improved overall performance on eight standard NLP benchmarks compared to strong baselines. Motivated by these promising results, we conduct extensive experiments to delve deeper into G_{stack} to address O2 and O3. For O2 (untested scalability), our study shows that G_{stack} is scalable and consistently performs well, with experiments up to 7B LLMs after growth and pre-training LLMs with 750B tokens. For example, compared to a conventionally trained 7B model using 300B tokens, our G_{stack} model converges to the same loss with 194B tokens, resulting in a 54.6\% speedup. We further address O3 (lack of empirical guidelines) by formalizing guidelines to determine growth timing and growth factor for G_{stack}, making it practical in general LLM pre-training. We also provide in-depth discussions and comprehensive ablation studies of G_{stack}. Our code and pre-trained model are available at https://llm-stacking.github.io/{https://llm-stacking.github.io/}.

ProLLaMA: A Protein Large Language Model for Multi-Task Protein Language Processing

Large Language Models (LLMs), including GPT-x and LLaMA2, have achieved remarkable performance in multiple Natural Language Processing (NLP) tasks. Under the premise that protein sequences constitute the protein language, Protein Large Language Models (ProLLMs) trained on protein corpora excel at de novo protein sequence generation. However, as of now, unlike LLMs in NLP, no ProLLM is capable of multiple tasks in the Protein Language Processing (PLP) field. This prompts us to delineate the inherent limitations in current ProLLMs: (i) the lack of natural language capabilities, (ii) insufficient instruction understanding, and (iii) high training resource demands. To address these challenges, we introduce a training framework to transform any general LLM into a ProLLM capable of handling multiple PLP tasks. Specifically, our framework utilizes low-rank adaptation and employs a two-stage training approach, and it is distinguished by its universality, low overhead, and scalability. Through training under this framework, we propose the ProLLaMA model, the first known ProLLM to handle multiple PLP tasks simultaneously. Experiments show that ProLLaMA achieves state-of-the-art results in the unconditional protein sequence generation task. In the controllable protein sequence generation task, ProLLaMA can design novel proteins with desired functionalities. In the protein property prediction task, ProLLaMA achieves nearly 100\% accuracy across many categories. The latter two tasks are beyond the reach of other ProLLMs. Code is available at https://github.com/Lyu6PosHao/ProLLaMA.

M^{3}-20M: A Large-Scale Multi-Modal Molecule Dataset for AI-driven Drug Design and Discovery

This paper introduces M^{3}-20M, a large-scale Multi-Modal Molecular dataset that contains over 20 million molecules. Designed to support AI-driven drug design and discovery, M^{3}-20M is 71 times more in the number of molecules than the largest existing dataset, providing an unprecedented scale that can highly benefit training or fine-tuning large (language) models with superior performance for drug design and discovery. This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions collected through web crawling and generated by using GPT-3.5, offering a comprehensive view of each molecule. To demonstrate the power of M^{3}-20M in drug design and discovery, we conduct extensive experiments on two key tasks: molecule generation and molecular property prediction, using large language models including GLM4, GPT-3.5, and GPT-4. Our experimental results show that M^{3}-20M can significantly boost model performance in both tasks. Specifically, it enables the models to generate more diverse and valid molecular structures and achieve higher property prediction accuracy than the existing single-modal datasets, which validates the value and potential of M^{3}-20M in supporting AI-driven drug design and discovery. The dataset is available at https://github.com/bz99bz/M-3.

IndicLLMSuite: A Blueprint for Creating Pre-training and Fine-Tuning Datasets for Indian Languages

Despite the considerable advancements in English LLMs, the progress in building comparable models for other languages has been hindered due to the scarcity of tailored resources. Our work aims to bridge this divide by introducing an expansive suite of resources specifically designed for the development of Indic LLMs, covering 22 languages, containing a total of 251B tokens and 74.8M instruction-response pairs. Recognizing the importance of both data quality and quantity, our approach combines highly curated manually verified data, unverified yet valuable data, and synthetic data. We build a clean, open-source pipeline for curating pre-training data from diverse sources, including websites, PDFs, and videos, incorporating best practices for crawling, cleaning, flagging, and deduplication. For instruction-fine tuning, we amalgamate existing Indic datasets, translate/transliterate English datasets into Indian languages, and utilize LLaMa2 and Mixtral models to create conversations grounded in articles from Indian Wikipedia and Wikihow. Additionally, we address toxicity alignment by generating toxic prompts for multiple scenarios and then generate non-toxic responses by feeding these toxic prompts to an aligned LLaMa2 model. We hope that the datasets, tools, and resources released as a part of this work will not only propel the research and development of Indic LLMs but also establish an open-source blueprint for extending such efforts to other languages. The data and other artifacts created as part of this work are released with permissive licenses.

Extracting Mathematical Concepts with Large Language Models

We extract mathematical concepts from mathematical text using generative large language models (LLMs) like ChatGPT, contributing to the field of automatic term extraction (ATE) and mathematical text processing, and also to the study of LLMs themselves. Our work builds on that of others in that we aim for automatic extraction of terms (keywords) in one mathematical field, category theory, using as a corpus the 755 abstracts from a snapshot of the online journal "Theory and Applications of Categories", circa 2020. Where our study diverges from previous work is in (1) providing a more thorough analysis of what makes mathematical term extraction a difficult problem to begin with; (2) paying close attention to inter-annotator disagreements; (3) providing a set of guidelines which both human and machine annotators could use to standardize the extraction process; (4) introducing a new annotation tool to help humans with ATE, applicable to any mathematical field and even beyond mathematics; (5) using prompts to ChatGPT as part of the extraction process, and proposing best practices for such prompts; and (6) raising the question of whether ChatGPT could be used as an annotator on the same level as human experts. Our overall findings are that the matter of mathematical ATE is an interesting field which can benefit from participation by LLMs, but LLMs themselves cannot at this time surpass human performance on it.

VLSBench: Unveiling Visual Leakage in Multimodal Safety

Safety concerns of Multimodal large language models (MLLMs) have gradually become an important problem in various applications. Surprisingly, previous works indicate a counter-intuitive phenomenon that using textual unlearning to align MLLMs achieves comparable safety performances with MLLMs trained with image-text pairs. To explain such a counter-intuitive phenomenon, we discover a visual safety information leakage (VSIL) problem in existing multimodal safety benchmarks, i.e., the potentially risky and sensitive content in the image has been revealed in the textual query. In this way, MLLMs can easily refuse these sensitive text-image queries according to textual queries. However, image-text pairs without VSIL are common in real-world scenarios and are overlooked by existing multimodal safety benchmarks. To this end, we construct multimodal visual leakless safety benchmark (VLSBench) preventing visual safety leakage from image to textual query with 2.4k image-text pairs. Experimental results indicate that VLSBench poses a significant challenge to both open-source and close-source MLLMs, including LLaVA, Qwen2-VL, Llama3.2-Vision, and GPT-4o. This study demonstrates that textual alignment is enough for multimodal safety scenarios with VSIL, while multimodal alignment is a more promising solution for multimodal safety scenarios without VSIL. Please see our code and data at: http://hxhcreate.github.io/VLSBench

Can large language models democratize access to dual-use biotechnology?

Large language models (LLMs) such as those embedded in 'chatbots' are accelerating and democratizing research by providing comprehensible information and expertise from many different fields. However, these models may also confer easy access to dual-use technologies capable of inflicting great harm. To evaluate this risk, the 'Safeguarding the Future' course at MIT tasked non-scientist students with investigating whether LLM chatbots could be prompted to assist non-experts in causing a pandemic. In one hour, the chatbots suggested four potential pandemic pathogens, explained how they can be generated from synthetic DNA using reverse genetics, supplied the names of DNA synthesis companies unlikely to screen orders, identified detailed protocols and how to troubleshoot them, and recommended that anyone lacking the skills to perform reverse genetics engage a core facility or contract research organization. Collectively, these results suggest that LLMs will make pandemic-class agents widely accessible as soon as they are credibly identified, even to people with little or no laboratory training. Promising nonproliferation measures include pre-release evaluations of LLMs by third parties, curating training datasets to remove harmful concepts, and verifiably screening all DNA generated by synthesis providers or used by contract research organizations and robotic cloud laboratories to engineer organisms or viruses.

LangCell: Language-Cell Pre-training for Cell Identity Understanding

Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce LangCell, the first Language-Cell pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

Single-Cell Omics Arena: A Benchmark Study for Large Language Models on Cell Type Annotation Using Single-Cell Data

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

Fully Open Source Moxin-7B Technical Report

Recently, Large Language Models (LLMs) have undergone a significant transformation, marked by a rapid rise in both their popularity and capabilities. Leading this evolution are proprietary LLMs like GPT-4 and GPT-o1, which have captured widespread attention in the AI community due to their remarkable performance and versatility. Simultaneously, open-source LLMs, such as LLaMA and Mistral, have made great contributions to the ever-increasing popularity of LLMs due to the ease to customize and deploy the models across diverse applications. Although open-source LLMs present unprecedented opportunities for innovation and research, the commercialization of LLMs has raised concerns about transparency, reproducibility, and safety. Many open-source LLMs fail to meet fundamental transparency requirements by withholding essential components like training code and data, and some use restrictive licenses whilst claiming to be "open-source," which may hinder further innovations on LLMs. To mitigate this issue, we introduce Moxin 7B, a fully open-source LLM developed in accordance with the Model Openness Framework (MOF), a ranked classification system that evaluates AI models based on model completeness and openness, adhering to principles of open science, open source, open data, and open access. Our model achieves the highest MOF classification level of "open science" through the comprehensive release of pre-training code and configurations, training and fine-tuning datasets, and intermediate and final checkpoints. Experiments show that our model achieves superior performance in zero-shot evaluation compared with popular 7B models and performs competitively in few-shot evaluation.

Find Central Dogma Again

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

I am a Strange Dataset: Metalinguistic Tests for Language Models

Statements involving metalinguistic self-reference ("This paper has six sections.") are prevalent in many domains. Can large language models (LLMs) handle such language? In this paper, we present "I am a Strange Dataset", a new dataset for addressing this question. There are two subtasks: generation and verification. In generation, models continue statements like "The penultimate word in this sentence is" (where a correct continuation is "is"). In verification, models judge the truth of statements like "The penultimate word in this sentence is sentence." (false). We also provide minimally different metalinguistic non-self-reference examples to complement the main dataset by probing for whether models can handle metalinguistic language at all. The dataset is hand-crafted by experts and validated by non-expert annotators. We test a variety of open-source LLMs (7B to 70B parameters) as well as closed-source LLMs through APIs. All models perform close to chance across both subtasks and even on the non-self-referential metalinguistic control data, though we find some steady improvement with model scale. GPT 4 is the only model to consistently do significantly better than chance, and it is still only in the 60% range, while our untrained human annotators score well in the 89-93% range. The dataset and evaluation toolkit are available at https://github.com/TristanThrush/i-am-a-strange-dataset.

SemiKong: Curating, Training, and Evaluating A Semiconductor Industry-Specific Large Language Model

Large Language Models (LLMs) have demonstrated the potential to address some issues within the semiconductor industry. However, they are often general-purpose models that lack the specialized knowledge needed to tackle the unique challenges of this sector, such as the intricate physics and chemistry of semiconductor devices and processes. SemiKong, the first industry-specific LLM for the semiconductor domain, provides a foundation that can be used to develop tailored proprietary models. With SemiKong 1.0, we aim to develop a foundational model capable of understanding etching problems at an expert level. Our key contributions include (a) curating a comprehensive corpus of semiconductor-related texts, (b) creating a foundational model with in-depth semiconductor knowledge, and (c) introducing a framework for integrating expert knowledge, thereby advancing the evaluation process of domain-specific AI models. Through fine-tuning a pre-trained LLM using our curated dataset, we have shown that SemiKong outperforms larger, general-purpose LLMs in various semiconductor manufacturing and design tasks. Our extensive experiments underscore the importance of developing domain-specific LLMs as a foundation for company- or tool-specific proprietary models, paving the way for further research and applications in the semiconductor domain. Code and dataset will be available at https://github.com/aitomatic/semikong

Do We Still Need Clinical Language Models?

Although recent advances in scaling large language models (LLMs) have resulted in improvements on many NLP tasks, it remains unclear whether these models trained primarily with general web text are the right tool in highly specialized, safety critical domains such as clinical text. Recent results have suggested that LLMs encode a surprising amount of medical knowledge. This raises an important question regarding the utility of smaller domain-specific language models. With the success of general-domain LLMs, is there still a need for specialized clinical models? To investigate this question, we conduct an extensive empirical analysis of 12 language models, ranging from 220M to 175B parameters, measuring their performance on 3 different clinical tasks that test their ability to parse and reason over electronic health records. As part of our experiments, we train T5-Base and T5-Large models from scratch on clinical notes from MIMIC III and IV to directly investigate the efficiency of clinical tokens. We show that relatively small specialized clinical models substantially outperform all in-context learning approaches, even when finetuned on limited annotated data. Further, we find that pretraining on clinical tokens allows for smaller, more parameter-efficient models that either match or outperform much larger language models trained on general text. We release the code and the models used under the PhysioNet Credentialed Health Data license and data use agreement.

A Little Help Goes a Long Way: Efficient LLM Training by Leveraging Small LMs

A primary challenge in large language model (LLM) development is their onerous pre-training cost. Typically, such pre-training involves optimizing a self-supervised objective (such as next-token prediction) over a large corpus. This paper explores a promising paradigm to improve LLM pre-training efficiency and quality by suitably leveraging a small language model (SLM). In particular, this paradigm relies on an SLM to both (1) provide soft labels as additional training supervision, and (2) select a small subset of valuable ("informative" and "hard") training examples. Put together, this enables an effective transfer of the SLM's predictive distribution to the LLM, while prioritizing specific regions of the training data distribution. Empirically, this leads to reduced LLM training time compared to standard training, while improving the overall quality. Theoretically, we develop a statistical framework to systematically study the utility of SLMs in enabling efficient training of high-quality LLMs. In particular, our framework characterizes how the SLM's seemingly low-quality supervision can enhance the training of a much more capable LLM. Furthermore, it also highlights the need for an adaptive utilization of such supervision, by striking a balance between the bias and variance introduced by the SLM-provided soft labels. We corroborate our theoretical framework by improving the pre-training of an LLM with 2.8B parameters by utilizing a smaller LM with 1.5B parameters on the Pile dataset.

SciSafeEval: A Comprehensive Benchmark for Safety Alignment of Large Language Models in Scientific Tasks

Large language models (LLMs) have had a transformative impact on a variety of scientific tasks across disciplines such as biology, chemistry, medicine, and physics. However, ensuring the safety alignment of these models in scientific research remains an underexplored area, with existing benchmarks primarily focus on textual content and overlooking key scientific representations such as molecular, protein, and genomic languages. Moreover, the safety mechanisms of LLMs in scientific tasks are insufficiently studied. To address these limitations, we introduce SciSafeEval, a comprehensive benchmark designed to evaluate the safety alignment of LLMs across a range of scientific tasks. SciSafeEval spans multiple scientific languages - including textual, molecular, protein, and genomic - and covers a wide range of scientific domains. We evaluate LLMs in zero-shot, few-shot and chain-of-thought settings, and introduce a 'jailbreak' enhancement feature that challenges LLMs equipped with safety guardrails, rigorously testing their defenses against malicious intention. Our benchmark surpasses existing safety datasets in both scale and scope, providing a robust platform for assessing the safety and performance of LLMs in scientific contexts. This work aims to facilitate the responsible development and deployment of LLMs, promoting alignment with safety and ethical standards in scientific research.

Multilingual Jailbreak Challenges in Large Language Models

While large language models (LLMs) exhibit remarkable capabilities across a wide range of tasks, they pose potential safety concerns, such as the ``jailbreak'' problem, wherein malicious instructions can manipulate LLMs to exhibit undesirable behavior. Although several preventive measures have been developed to mitigate the potential risks associated with LLMs, they have primarily focused on English data. In this study, we reveal the presence of multilingual jailbreak challenges within LLMs and consider two potential risk scenarios: unintentional and intentional. The unintentional scenario involves users querying LLMs using non-English prompts and inadvertently bypassing the safety mechanisms, while the intentional scenario concerns malicious users combining malicious instructions with multilingual prompts to deliberately attack LLMs. The experimental results reveal that in the unintentional scenario, the rate of unsafe content increases as the availability of languages decreases. Specifically, low-resource languages exhibit three times the likelihood of encountering harmful content compared to high-resource languages, with both ChatGPT and GPT-4. In the intentional scenario, multilingual prompts can exacerbate the negative impact of malicious instructions, with astonishingly high rates of unsafe output: 80.92\% for ChatGPT and 40.71\% for GPT-4. To handle such a challenge in the multilingual context, we propose a novel Self-Defense framework that automatically generates multilingual training data for safety fine-tuning. Experimental results show that ChatGPT fine-tuned with such data can achieve a substantial reduction in unsafe content generation. Data is available at https://github.com/DAMO-NLP-SG/multilingual-safety-for-LLMs. Warning: This paper contains examples with potentially harmful content.

RAG vs Fine-tuning: Pipelines, Tradeoffs, and a Case Study on Agriculture

There are two common ways in which developers are incorporating proprietary and domain-specific data when building applications of Large Language Models (LLMs): Retrieval-Augmented Generation (RAG) and Fine-Tuning. RAG augments the prompt with the external data, while fine-Tuning incorporates the additional knowledge into the model itself. However, the pros and cons of both approaches are not well understood. In this paper, we propose a pipeline for fine-tuning and RAG, and present the tradeoffs of both for multiple popular LLMs, including Llama2-13B, GPT-3.5, and GPT-4. Our pipeline consists of multiple stages, including extracting information from PDFs, generating questions and answers, using them for fine-tuning, and leveraging GPT-4 for evaluating the results. We propose metrics to assess the performance of different stages of the RAG and fine-Tuning pipeline. We conduct an in-depth study on an agricultural dataset. Agriculture as an industry has not seen much penetration of AI, and we study a potentially disruptive application - what if we could provide location-specific insights to a farmer? Our results show the effectiveness of our dataset generation pipeline in capturing geographic-specific knowledge, and the quantitative and qualitative benefits of RAG and fine-tuning. We see an accuracy increase of over 6 p.p. when fine-tuning the model and this is cumulative with RAG, which increases accuracy by 5 p.p. further. In one particular experiment, we also demonstrate that the fine-tuned model leverages information from across geographies to answer specific questions, increasing answer similarity from 47% to 72%. Overall, the results point to how systems built using LLMs can be adapted to respond and incorporate knowledge across a dimension that is critical for a specific industry, paving the way for further applications of LLMs in other industrial domains.

Improving Few-Shot Prompts with Relevant Static Analysis Products

Large Language Models (LLM) are a new class of computation engines, "programmed" via prompt engineering. We are still learning how to best "program" these LLMs to help developers. We start with the intuition that developers tend to consciously and unconsciously have a collection of semantics facts in mind when working on coding tasks. Mostly these are shallow, simple facts arising from a quick read. For a function, examples of facts might include parameter and local variable names, return expressions, simple pre- and post-conditions, and basic control and data flow, etc. One might assume that the powerful multi-layer architecture of transformer-style LLMs makes them inherently capable of doing this simple level of "code analysis" and extracting such information, implicitly, while processing code: but are they, really? If they aren't, could explicitly adding this information help? Our goal here is to investigate this question, using the code summarization task and evaluate whether automatically augmenting an LLM's prompt with semantic facts explicitly, actually helps. Prior work shows that LLM performance on code summarization benefits from few-shot samples drawn either from the same-project or from examples found via information retrieval methods (such as BM25). While summarization performance has steadily increased since the early days, there is still room for improvement: LLM performance on code summarization still lags its performance on natural-language tasks like translation and text summarization. We find that adding semantic facts actually does help! This approach improves performance in several different settings suggested by prior work, including for two different Large Language Models. In most cases, improvement nears or exceeds 2 BLEU; for the PHP language in the challenging CodeSearchNet dataset, this augmentation actually yields performance surpassing 30 BLEU.

Data-Efficient Massive Tool Retrieval: A Reinforcement Learning Approach for Query-Tool Alignment with Language Models

Recent advancements in large language models (LLMs) integrated with external tools and APIs have successfully addressed complex tasks by using in-context learning or fine-tuning. Despite this progress, the vast scale of tool retrieval remains challenging due to stringent input length constraints. In response, we propose a pre-retrieval strategy from an extensive repository, effectively framing the problem as the massive tool retrieval (MTR) task. We introduce the MTRB (massive tool retrieval benchmark) to evaluate real-world tool-augmented LLM scenarios with a large number of tools. This benchmark is designed for low-resource scenarios and includes a diverse collection of tools with descriptions refined for consistency and clarity. It consists of three subsets, each containing 90 test samples and 10 training samples. To handle the low-resource MTR task, we raise a new query-tool alignment (QTA) framework leverages LLMs to enhance query-tool alignment by rewriting user queries through ranking functions and the direct preference optimization (DPO) method. This approach consistently outperforms existing state-of-the-art models in top-5 and top-10 retrieval tasks across the MTRB benchmark, with improvements up to 93.28% based on the metric Sufficiency@k, which measures the adequacy of tool retrieval within the first k results. Furthermore, ablation studies validate the efficacy of our framework, highlighting its capacity to optimize performance even with limited annotated samples. Specifically, our framework achieves up to 78.53% performance improvement in Sufficiency@k with just a single annotated sample. Additionally, QTA exhibits strong cross-dataset generalizability, emphasizing its potential for real-world applications.

MMSearch: Benchmarking the Potential of Large Models as Multi-modal Search Engines

The advent of Large Language Models (LLMs) has paved the way for AI search engines, e.g., SearchGPT, showcasing a new paradigm in human-internet interaction. However, most current AI search engines are limited to text-only settings, neglecting the multimodal user queries and the text-image interleaved nature of website information. Recently, Large Multimodal Models (LMMs) have made impressive strides. Yet, whether they can function as AI search engines remains under-explored, leaving the potential of LMMs in multimodal search an open question. To this end, we first design a delicate pipeline, MMSearch-Engine, to empower any LMMs with multimodal search capabilities. On top of this, we introduce MMSearch, a comprehensive evaluation benchmark to assess the multimodal search performance of LMMs. The curated dataset contains 300 manually collected instances spanning 14 subfields, which involves no overlap with the current LMMs' training data, ensuring the correct answer can only be obtained within searching. By using MMSearch-Engine, the LMMs are evaluated by performing three individual tasks (requery, rerank, and summarization), and one challenging end-to-end task with a complete searching process. We conduct extensive experiments on closed-source and open-source LMMs. Among all tested models, GPT-4o with MMSearch-Engine achieves the best results, which surpasses the commercial product, Perplexity Pro, in the end-to-end task, demonstrating the effectiveness of our proposed pipeline. We further present error analysis to unveil current LMMs still struggle to fully grasp the multimodal search tasks, and conduct ablation study to indicate the potential of scaling test-time computation for AI search engine. We hope MMSearch may provide unique insights to guide the future development of multimodal AI search engine. Project Page: https://mmsearch.github.io

A Benchmark for Learning to Translate a New Language from One Grammar Book

Large language models (LLMs) can perform impressive feats with in-context learning or lightweight finetuning. It is natural to wonder how well these models adapt to genuinely new tasks, but how does one find tasks that are unseen in internet-scale training sets? We turn to a field that is explicitly motivated and bottlenecked by a scarcity of web data: low-resource languages. In this paper, we introduce MTOB (Machine Translation from One Book), a benchmark for learning to translate between English and Kalamang -- a language with less than 200 speakers and therefore virtually no presence on the web -- using several hundred pages of field linguistics reference materials. This task framing is novel in that it asks a model to learn a language from a single human-readable book of grammar explanations, rather than a large mined corpus of in-domain data, more akin to L2 learning than L1 acquisition. We demonstrate that baselines using current LLMs are promising but fall short of human performance, achieving 44.7 chrF on Kalamang to English translation and 45.8 chrF on English to Kalamang translation, compared to 51.6 and 57.0 chrF by a human who learned Kalamang from the same reference materials. We hope that MTOB will help measure LLM capabilities along a new dimension, and that the methods developed to solve it could help expand access to language technology for underserved communities by leveraging qualitatively different kinds of data than traditional machine translation.

Salamandra Technical Report

This work introduces Salamandra, a suite of open-source decoder-only large language models available in three different sizes: 2, 7, and 40 billion parameters. The models were trained from scratch on highly multilingual data that comprises text in 35 European languages and code. Our carefully curated corpus is made exclusively from open-access data compiled from a wide variety of sources. Along with the base models, supplementary checkpoints that were fine-tuned on public-domain instruction data are also released for chat applications. Additionally, we also share our preliminary experiments on multimodality, which serve as proof-of-concept to showcase potential applications for the Salamandra family. Our extensive evaluations on multilingual benchmarks reveal that Salamandra has strong capabilities, achieving competitive performance when compared to similarly sized open-source models. We provide comprehensive evaluation results both on standard downstream tasks as well as key aspects related to bias and safety.With this technical report, we intend to promote open science by sharing all the details behind our design choices, data curation strategy and evaluation methodology. In addition to that, we deviate from the usual practice by making our training and evaluation scripts publicly accessible. We release all models under a permissive Apache 2.0 license in order to foster future research and facilitate commercial use, thereby contributing to the open-source ecosystem of large language models.

A Survey of Large Language Models

Language is essentially a complex, intricate system of human expressions governed by grammatical rules. It poses a significant challenge to develop capable AI algorithms for comprehending and grasping a language. As a major approach, language modeling has been widely studied for language understanding and generation in the past two decades, evolving from statistical language models to neural language models. Recently, pre-trained language models (PLMs) have been proposed by pre-training Transformer models over large-scale corpora, showing strong capabilities in solving various NLP tasks. Since researchers have found that model scaling can lead to performance improvement, they further study the scaling effect by increasing the model size to an even larger size. Interestingly, when the parameter scale exceeds a certain level, these enlarged language models not only achieve a significant performance improvement but also show some special abilities that are not present in small-scale language models. To discriminate the difference in parameter scale, the research community has coined the term large language models (LLM) for the PLMs of significant size. Recently, the research on LLMs has been largely advanced by both academia and industry, and a remarkable progress is the launch of ChatGPT, which has attracted widespread attention from society. The technical evolution of LLMs has been making an important impact on the entire AI community, which would revolutionize the way how we develop and use AI algorithms. In this survey, we review the recent advances of LLMs by introducing the background, key findings, and mainstream techniques. In particular, we focus on four major aspects of LLMs, namely pre-training, adaptation tuning, utilization, and capacity evaluation. Besides, we also summarize the available resources for developing LLMs and discuss the remaining issues for future directions.

AST-Probe: Recovering abstract syntax trees from hidden representations of pre-trained language models

The objective of pre-trained language models is to learn contextual representations of textual data. Pre-trained language models have become mainstream in natural language processing and code modeling. Using probes, a technique to study the linguistic properties of hidden vector spaces, previous works have shown that these pre-trained language models encode simple linguistic properties in their hidden representations. However, none of the previous work assessed whether these models encode the whole grammatical structure of a programming language. In this paper, we prove the existence of a syntactic subspace, lying in the hidden representations of pre-trained language models, which contain the syntactic information of the programming language. We show that this subspace can be extracted from the models' representations and define a novel probing method, the AST-Probe, that enables recovering the whole abstract syntax tree (AST) of an input code snippet. In our experimentations, we show that this syntactic subspace exists in five state-of-the-art pre-trained language models. In addition, we highlight that the middle layers of the models are the ones that encode most of the AST information. Finally, we estimate the optimal size of this syntactic subspace and show that its dimension is substantially lower than those of the models' representation spaces. This suggests that pre-trained language models use a small part of their representation spaces to encode syntactic information of the programming languages.

InstructProtein: Aligning Human and Protein Language via Knowledge Instruction

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing annotation imbalance and instruction deficits in existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by large margins. Moreover, InstructProtein serves as a pioneering step towards text-based protein function prediction and sequence design, effectively bridging the gap between protein and human language understanding.

NVLM: Open Frontier-Class Multimodal LLMs

We introduce NVLM 1.0, a family of frontier-class multimodal large language models (LLMs) that achieve state-of-the-art results on vision-language tasks, rivaling the leading proprietary models (e.g., GPT-4o) and open-access models (e.g., Llama 3-V 405B and InternVL 2). Remarkably, NVLM 1.0 shows improved text-only performance over its LLM backbone after multimodal training. In terms of model design, we perform a comprehensive comparison between decoder-only multimodal LLMs (e.g., LLaVA) and cross-attention-based models (e.g., Flamingo). Based on the strengths and weaknesses of both approaches, we propose a novel architecture that enhances both training efficiency and multimodal reasoning capabilities. Furthermore, we introduce a 1-D tile-tagging design for tile-based dynamic high-resolution images, which significantly boosts performance on multimodal reasoning and OCR-related tasks. Regarding training data, we meticulously curate and provide detailed information on our multimodal pretraining and supervised fine-tuning datasets. Our findings indicate that dataset quality and task diversity are more important than scale, even during the pretraining phase, across all architectures. Notably, we develop production-grade multimodality for the NVLM-1.0 models, enabling them to excel in vision-language tasks while maintaining and even improving text-only performance compared to their LLM backbones. To achieve this, we craft and integrate a high-quality text-only dataset into multimodal training, alongside a substantial amount of multimodal math and reasoning data, leading to enhanced math and coding capabilities across modalities. To advance research in the field, we are releasing the model weights and will open-source the code for the community: https://nvlm-project.github.io/.

InfMLLM: A Unified Framework for Visual-Language Tasks

Large language models (LLMs) have proven their remarkable versatility in handling a comprehensive range of language-centric applications. To expand LLMs' capabilities to a broader spectrum of modal inputs, multimodal large language models (MLLMs) have attracted growing interest. This work delves into enabling LLMs to tackle more vision-language-related tasks, particularly image captioning, visual question answering (VQA,) and visual grounding. To this end, we implemented a three-stage training scheme: starting with lightweight alignment pretraining, then moderate-weight multitask hybrid training, and finally, LLM fine-tuning to improve instruction following capability. Throughout the training process, the requirements on GPU memory gradually increase. To effectively manage the number of visual embeddings passed to the LLM while preserving their positional information, we introduce a straightforward visual adapter module dubbed pool-adapter. Our experiments demonstrate that preserving the positional information of visual embeddings through the pool-adapter is particularly beneficial for tasks like visual grounding. We name our proposed approach InfMLLM and have evaluated it extensively on various benchmark datasets. Our results demonstrate that InfMLLM achieves either state-of-the-art (SOTA) performance or performance comparable to recent MLLMs. The code and model will be made open-source at: https://github.com/mightyzau/InfMLLM.

SEED-Bench-2: Benchmarking Multimodal Large Language Models

Multimodal large language models (MLLMs), building upon the foundation of powerful large language models (LLMs), have recently demonstrated exceptional capabilities in generating not only texts but also images given interleaved multimodal inputs (acting like a combination of GPT-4V and DALL-E 3). However, existing MLLM benchmarks remain limited to assessing only models' comprehension ability of single image-text inputs, failing to keep up with the strides made in MLLMs. A comprehensive benchmark is imperative for investigating the progress and uncovering the limitations of current MLLMs. In this work, we categorize the capabilities of MLLMs into hierarchical levels from L_0 to L_4 based on the modalities they can accept and generate, and propose SEED-Bench-2, a comprehensive benchmark that evaluates the hierarchical capabilities of MLLMs. Specifically, SEED-Bench-2 comprises 24K multiple-choice questions with accurate human annotations, which spans 27 dimensions, including the evaluation of both text and image generation. Multiple-choice questions with groundtruth options derived from human annotation enables an objective and efficient assessment of model performance, eliminating the need for human or GPT intervention during evaluation. We further evaluate the performance of 23 prominent open-source MLLMs and summarize valuable observations. By revealing the limitations of existing MLLMs through extensive evaluations, we aim for SEED-Bench-2 to provide insights that will motivate future research towards the goal of General Artificial Intelligence. Dataset and evaluation code are available at https://github.com/AILab-CVC/SEED-Bench

MoGU: A Framework for Enhancing Safety of Open-Sourced LLMs While Preserving Their Usability

Large Language Models (LLMs) are increasingly deployed in various applications. As their usage grows, concerns regarding their safety are rising, especially in maintaining harmless responses when faced with malicious instructions. Many defense strategies have been developed to enhance the safety of LLMs. However, our research finds that existing defense strategies lead LLMs to predominantly adopt a rejection-oriented stance, thereby diminishing the usability of their responses to benign instructions. To solve this problem, we introduce the MoGU framework, designed to enhance LLMs' safety while preserving their usability. Our MoGU framework transforms the base LLM into two variants: the usable LLM and the safe LLM, and further employs dynamic routing to balance their contribution. When encountering malicious instructions, the router will assign a higher weight to the safe LLM to ensure that responses are harmless. Conversely, for benign instructions, the router prioritizes the usable LLM, facilitating usable and helpful responses. On various open-sourced LLMs, we compare multiple defense strategies to verify the superiority of our MoGU framework. Besides, our analysis provides key insights into the effectiveness of MoGU and verifies that our designed routing mechanism can effectively balance the contribution of each variant by assigning weights. Our work released the safer Llama2, Vicuna, Falcon, Dolphin, and Baichuan2.

Does Table Source Matter? Benchmarking and Improving Multimodal Scientific Table Understanding and Reasoning

Recent large language models (LLMs) have advanced table understanding capabilities but rely on converting tables into text sequences. While multimodal large language models (MLLMs) enable direct visual processing, they face limitations in handling scientific tables due to fixed input image resolutions and insufficient numerical reasoning capabilities. We present a comprehensive framework for multimodal scientific table understanding and reasoning with dynamic input image resolutions. Our framework consists of three key components: (1) MMSci-Pre, a domain-specific table structure learning dataset of 52K scientific table structure recognition samples, (2) MMSci-Ins, an instruction tuning dataset with 12K samples across three table-based tasks, and (3) MMSci-Eval, a benchmark with 3,114 testing samples specifically designed to evaluate numerical reasoning capabilities. Extensive experiments demonstrate that our domain-specific approach with 52K scientific table images achieves superior performance compared to 150K general-domain tables, highlighting the importance of data quality over quantity. Our proposed table-based MLLMs with dynamic input resolutions show significant improvements in both general table understanding and numerical reasoning capabilities, with strong generalisation to held-out datasets. Our code and data are publicly available at https://github.com/Bernard-Yang/MMSci_Table.

ReviewerGPT? An Exploratory Study on Using Large Language Models for Paper Reviewing

Given the rapid ascent of large language models (LLMs), we study the question: (How) can large language models help in reviewing of scientific papers or proposals? We first conduct some pilot studies where we find that (i) GPT-4 outperforms other LLMs (Bard, Vicuna, Koala, Alpaca, LLaMa, Dolly, OpenAssistant, StableLM), and (ii) prompting with a specific question (e.g., to identify errors) outperforms prompting to simply write a review. With these insights, we study the use of LLMs (specifically, GPT-4) for three tasks: 1. Identifying errors: We construct 13 short computer science papers each with a deliberately inserted error, and ask the LLM to check for the correctness of these papers. We observe that the LLM finds errors in 7 of them, spanning both mathematical and conceptual errors. 2. Verifying checklists: We task the LLM to verify 16 closed-ended checklist questions in the respective sections of 15 NeurIPS 2022 papers. We find that across 119 {checklist question, paper} pairs, the LLM had an 86.6% accuracy. 3. Choosing the "better" paper: We generate 10 pairs of abstracts, deliberately designing each pair in such a way that one abstract was clearly superior than the other. The LLM, however, struggled to discern these relatively straightforward distinctions accurately, committing errors in its evaluations for 6 out of the 10 pairs. Based on these experiments, we think that LLMs have a promising use as reviewing assistants for specific reviewing tasks, but not (yet) for complete evaluations of papers or proposals.

Visual Perception by Large Language Model's Weights

Existing Multimodal Large Language Models (MLLMs) follow the paradigm that perceives visual information by aligning visual features with the input space of Large Language Models (LLMs), and concatenating visual tokens with text tokens to form a unified sequence input for LLMs. These methods demonstrate promising results on various vision-language tasks but are limited by the high computational effort due to the extended input sequence resulting from the involvement of visual tokens. In this paper, instead of input space alignment, we propose a novel parameter space alignment paradigm that represents visual information as model weights. For each input image, we use a vision encoder to extract visual features, convert features into perceptual weights, and merge the perceptual weights with LLM's weights. In this way, the input of LLM does not require visual tokens, which reduces the length of the input sequence and greatly improves efficiency. Following this paradigm, we propose VLoRA with the perceptual weights generator. The perceptual weights generator is designed to convert visual features to perceptual weights with low-rank property, exhibiting a form similar to LoRA. The experimental results show that our VLoRA achieves comparable performance on various benchmarks for MLLMs, while significantly reducing the computational costs for both training and inference. The code and models will be made open-source.

Dolma: an Open Corpus of Three Trillion Tokens for Language Model Pretraining Research

Language models have become a critical technology to tackling a wide range of natural language processing tasks, yet many details about how the best-performing language models were developed are not reported. In particular, information about their pretraining corpora is seldom discussed: commercial language models rarely provide any information about their data; even open models rarely release datasets they are trained on, or an exact recipe to reproduce them. As a result, it is challenging to conduct certain threads of language modeling research, such as understanding how training data impacts model capabilities and shapes their limitations. To facilitate open research on language model pretraining, we release Dolma, a three trillion tokens English corpus, built from a diverse mixture of web content, scientific papers, code, public-domain books, social media, and encyclopedic materials. In addition, we open source our data curation toolkit to enable further experimentation and reproduction of our work. In this report, we document Dolma, including its design principles, details about its construction, and a summary of its contents. We interleave this report with analyses and experimental results from training language models on intermediate states of Dolma to share what we have learned about important data curation practices, including the role of content or quality filters, deduplication, and multi-source mixing. Dolma has been used to train OLMo, a state-of-the-art, open language model and framework designed to build and study the science of language modeling.

Investigating Continual Pretraining in Large Language Models: Insights and Implications

This paper studies the evolving domain of Continual Learning (CL) in large language models (LLMs), with a focus on developing strategies for efficient and sustainable training. Our primary emphasis is on continual domain-adaptive pretraining, a process designed to equip LLMs with the ability to integrate new information from various domains while retaining previously learned knowledge and enhancing cross-domain knowledge transfer without relying on domain-specific identification. Unlike previous studies, which mostly concentrate on a limited selection of tasks or domains and primarily aim to address the issue of forgetting, our research evaluates the adaptability and capabilities of LLMs to changing data landscapes in practical scenarios. To this end, we introduce a new benchmark designed to measure the adaptability of LLMs to these evolving data environments, offering a comprehensive framework for evaluation. We examine the impact of model size on learning efficacy and forgetting, as well as how the progression and similarity of emerging domains affect the knowledge transfer within these models. Our findings uncover several key insights: (i) when the sequence of domains shows semantic similarity, continual pretraining enables LLMs to better specialize in the current domain compared to stand-alone fine-tuning, (ii) training across a diverse range of domains enhances both backward and forward knowledge transfer, and (iii) smaller models are particularly sensitive to continual pretraining, showing the most significant rates of both forgetting and learning. We posit that our research marks a shift towards establishing a more realistic benchmark for investigating CL in LLMs, and has the potential to play a key role in guiding the direction of future research in the field.

Enhancing Code Generation for Low-Resource Languages: No Silver Bullet

The advent of Large Language Models (LLMs) has significantly advanced the field of automated code generation. LLMs rely on large and diverse datasets to learn syntax, semantics, and usage patterns of programming languages. For low-resource languages (i.e., niche programming languages characterized by the scarcity of training data), the limited availability of such data hampers the models' ability to generalize effectively, resulting in poorer code generation performance as compared to high-resource languages. For this reason, there is a quest for techniques able to close this performance gap. We present an empirical study investigating the effectiveness of several approaches for boosting LLMs' performance on low-resource languages, namely: (i) a classic fine-tuning, which is however capped in size by the scarcity of training data; (ii) three variants of in-context learning, with prompts crafted to provide the LLM with additional information about the low-resource language (e.g., few-shot examples showcasing features of the targeted language); and (iii) a pre-training objective teaching the model how to translate between high- and low-resource languages. The context of our study are two low-resource languages (R and Racket) and six LLMs having different architectures and sizes. Our findings reveal that a fine-tuning is usually the best choice for smaller LLMs, possibly due to the fact that even a small dataset is sufficient to train their limited number of parameters. With the increase in size of the models, in-context learning becomes more and more effective, representing a safe and cheap bet (i.e., it always helps, but with different magnitudes). Differently, very large LLMs may deteriorate their performance on low-resource languages when fine-tuning is performed, possibly due to the lack of enough data needed to effectively update their weights.

Large Language Models as Data Preprocessors

Large Language Models (LLMs), typified by OpenAI's GPT series and Meta's LLaMA variants, have marked a significant advancement in artificial intelligence. Trained on vast amounts of text data, LLMs are capable of understanding and generating human-like text across a diverse range of topics. This study expands on the applications of LLMs, exploring their potential in data preprocessing, a critical stage in data mining and analytics applications. We delve into the applicability of state-of-the-art LLMs such as GPT-3.5, GPT-4, and Vicuna-13B for error detection, data imputation, schema matching, and entity matching tasks. Alongside showcasing the inherent capabilities of LLMs, we highlight their limitations, particularly in terms of computational expense and inefficiency. We propose an LLM-based framework for data preprocessing, which integrates cutting-edge prompt engineering techniques, coupled with traditional methods like contextualization and feature selection, to improve the performance and efficiency of these models. The effectiveness of LLMs in data preprocessing is evaluated through an experimental study spanning 12 datasets. GPT-4 emerged as a standout, achieving 100\% accuracy or F1 score on 4 datasets, suggesting LLMs' immense potential in these tasks. Despite certain limitations, our study underscores the promise of LLMs in this domain and anticipates future developments to overcome current hurdles.

Heuristic-Induced Multimodal Risk Distribution Jailbreak Attack for Multimodal Large Language Models

With the rapid advancement of multimodal large language models (MLLMs), concerns regarding their security have increasingly captured the attention of both academia and industry. Although MLLMs are vulnerable to jailbreak attacks, designing effective multimodal jailbreak attacks poses unique challenges, especially given the distinct protective measures implemented across various modalities in commercial models. Previous works concentrate risks into a single modality, resulting in limited jailbreak performance. In this paper, we propose a heuristic-induced multimodal risk distribution jailbreak attack method, called HIMRD, which consists of two elements: multimodal risk distribution strategy and heuristic-induced search strategy. The multimodal risk distribution strategy is used to segment harmful instructions across multiple modalities to effectively circumvent MLLMs' security protection. The heuristic-induced search strategy identifies two types of prompts: the understanding-enhancing prompt, which helps the MLLM reconstruct the malicious prompt, and the inducing prompt, which increases the likelihood of affirmative outputs over refusals, enabling a successful jailbreak attack. Extensive experiments demonstrate that this approach effectively uncovers vulnerabilities in MLLMs, achieving an average attack success rate of 90% across seven popular open-source MLLMs and an average attack success rate of around 68% in three popular closed-source MLLMs. Our code will coming soon. Warning: This paper contains offensive and harmful examples, reader discretion is advised.

MT-Ladder: A Model-Agnostic Framework Boosting LLM-based Machine Translation to the Next Level

General-purpose Large Language Models (LLMs) like GPT-4 have achieved remarkable advancements in machine translation (MT) by leveraging extensive web content. On the other hand, translation-specific LLMs are built by pre-training on domain-specific monolingual corpora and fine-tuning with human-annotated translation data. Despite the superior performance, these methods either demand an unprecedented scale of computing and data or substantial human editing and annotation efforts. In this paper, we develop MT-Ladder, a novel model-agnostic and cost-effective tool to refine the performance of general LLMs for MT. MT-Ladder is trained on pseudo-refinement triplets which can be easily obtained from existing LLMs without additional human cost. During training, we propose a hierarchical fine-tuning strategy with an easy-to-hard schema, improving MT-Ladder's refining performance progressively. The trained MT-Ladder can be seamlessly integrated with any general-purpose LLMs to boost their translation performance. By utilizing Gemma-2B/7B as the backbone, MT-Ladder-2B can elevate raw translations to the level of top-tier open-source models (e.g., refining BigTranslate-13B with +6.91 BLEU and +3.52 COMET for XX-En), and MT-Ladder-7B can further enhance model performance to be on par with the state-of-the-art GPT-4. Extensive ablation and analysis corroborate the effectiveness of MT-Ladder in diverse settings. Our code is available at https://github.com/fzp0424/Ladder

Asymmetric Conflict and Synergy in Post-training for LLM-based Multilingual Machine Translation

The emergence of Large Language Models (LLMs) has advanced the multilingual machine translation (MMT), yet the Curse of Multilinguality (CoM) remains a major challenge. Existing work in LLM-based MMT typically mitigates this issue via scaling up training and computation budget, which raises a critical question: Is scaling up the training and computation budget truly necessary for high-quality MMT, or can a deeper understanding of CoM provide a more efficient solution? To explore this problem, we analyze the linguistic conflicts and synergy, the underlying mechanism of CoM during post-training phase. We identify an asymmetric phenomenon in linguistic conflicts and synergy: the dominance of conflicts and synergy varies in different translation directions, leading to sub-optimal adaptation in existing post-training methods. We further find that a significant bottleneck in MMT appears to lie in post-training rather than multilingual pre-training, suggesting the need for more effective adaptation strategies. Building on these new insights, we propose a direction-aware training approach, combined with group-wise model merging, to address asymmetry in linguistic conflicts and synergy explicitly. Leveraging this strategy, our method fine-tunes X-ALMA-13B-Pretrain-trained only with multilingual pre-training-achieving comparable performance to XALMA-13B (only SFT) while using only 20B pretraining tokens and 17B parameters-5.5x fewer pretraining-tokens and 1.7x fewer model size-with just 0.85 COMET drop on Flores-200 testsets of 50 languages.

M4LE: A Multi-Ability Multi-Range Multi-Task Multi-Domain Long-Context Evaluation Benchmark for Large Language Models

Managing long sequences has become an important and necessary feature for large language models (LLMs). However, it is still an open question of how to comprehensively and systematically evaluate the long-sequence capability of LLMs. One of the reasons is that conventional and widely-used benchmarks mainly consist of short sequences. In this paper, we propose M4LE, a Multi-ability, Multi-range, Multi-task, Multi-domain benchmark for Long-context Evaluation. M4LE is based on a diverse NLP task pool comprising 36 NLP datasets, 11 task types and 12 domains. To alleviate the scarcity of tasks with naturally long sequences and incorporate multiple-ability assessment, we propose an automatic approach (but with negligible human annotations) to convert short-sequence tasks into a unified long-sequence scenario where LLMs have to identify single or multiple relevant spans in long contexts based on explicit or semantic hints. Specifically, the scenario includes five different types of abilities: (1) explicit single-span; (2) semantic single-span; (3) explicit multiple-span; (4) semantic multiple-span; and (5) global context understanding. The resulting samples in M4LE are evenly distributed from 1k to 8k input length. We conducted a systematic evaluation on 11 well-established LLMs, especially those optimized for long-sequence inputs. Our results reveal that: 1) Current LLMs struggle to understand long context, particularly when tasks require multiple-span attention. 2) Semantic retrieval task is more difficult for competent LLMs. 3) Models fine-tuned on longer text with position interpolation have comparable performance to those using Neural Tangent Kernel (NTK) aware scaling methods without fine-tuning. We make our benchmark publicly available to encourage future research in this challenging area.

LLM-FuncMapper: Function Identification for Interpreting Complex Clauses in Building Codes via LLM

As a vital stage of automated rule checking (ARC), rule interpretation of regulatory texts requires considerable effort. However, interpreting regulatory clauses with implicit properties or complex computational logic is still challenging due to the lack of domain knowledge and limited expressibility of conventional logic representations. Thus, LLM-FuncMapper, an approach to identifying predefined functions needed to interpret various regulatory clauses based on the large language model (LLM), is proposed. First, by systematically analysis of building codes, a series of atomic functions are defined to capture shared computational logics of implicit properties and complex constraints, creating a database of common blocks for interpreting regulatory clauses. Then, a prompt template with the chain of thought is developed and further enhanced with a classification-based tuning strategy, to enable common LLMs for effective function identification. Finally, the proposed approach is validated with statistical analysis, experiments, and proof of concept. Statistical analysis reveals a long-tail distribution and high expressibility of the developed function database, with which almost 100% of computer-processible clauses can be interpreted and represented as computer-executable codes. Experiments show that LLM-FuncMapper achieve promising results in identifying relevant predefined functions for rule interpretation. Further proof of concept in automated rule interpretation also demonstrates the possibility of LLM-FuncMapper in interpreting complex regulatory clauses. To the best of our knowledge, this study is the first attempt to introduce LLM for understanding and interpreting complex regulatory clauses, which may shed light on further adoption of LLM in the construction domain.

Impact of Large Language Models on Generating Software Specifications

Software specifications are essential for ensuring the reliability of software systems. Existing specification extraction approaches, however, suffer from limited generalizability and require manual efforts. The recent emergence of Large Language Models (LLMs), which have been successfully applied to numerous software engineering tasks, offers a promising avenue for automating this process. In this paper, we conduct the first empirical study to evaluate the capabilities of LLMs for generating software specifications from software comments or documentation. We evaluate LLMs' performance with Few Shot Learning (FSL), enabling LLMs to generalize from a small number of examples, as well as different prompt construction strategies, and compare the performance of LLMs with traditional approaches. Additionally, we conduct a comparative diagnosis of the failure cases from both LLMs and traditional methods, identifying their unique strengths and weaknesses. Lastly, we conduct extensive experiments on 15 state of the art LLMs, evaluating their performance and cost effectiveness for generating software specifications. Our results show that with FSL, LLMs outperform traditional methods (by 5.6%), and more sophisticated prompt construction strategies can further enlarge this performance gap (up to 5.1 to 10.0%). Yet, LLMs suffer from their unique challenges, such as ineffective prompts and the lack of domain knowledge, which together account for 53 to 60% of LLM unique failures. The strong performance of open source models (e.g., StarCoder) makes closed source models (e.g., GPT 3 Davinci) less desirable due to size and cost. Our study offers valuable insights for future research to improve specification generation.

mOSCAR: A Large-scale Multilingual and Multimodal Document-level Corpus

Multimodal Large Language Models (mLLMs) are trained on a large amount of text-image data. While most mLLMs are trained on caption-like data only, Alayrac et al. [2022] showed that additionally training them on interleaved sequences of text and images can lead to the emergence of in-context learning capabilities. However, the dataset they used, M3W, is not public and is only in English. There have been attempts to reproduce their results but the released datasets are English-only. In contrast, current multilingual and multimodal datasets are either composed of caption-like only or medium-scale or fully private data. This limits mLLM research for the 7,000 other languages spoken in the world. We therefore introduce mOSCAR, to the best of our knowledge the first large-scale multilingual and multimodal document corpus crawled from the web. It covers 163 languages, 315M documents, 214B tokens and 1.2B images. We carefully conduct a set of filtering and evaluation steps to make sure mOSCAR is sufficiently safe, diverse and of good quality. We additionally train two types of multilingual model to prove the benefits of mOSCAR: (1) a model trained on a subset of mOSCAR and captioning data and (2) a model train on captioning data only. The model additionally trained on mOSCAR shows a strong boost in few-shot learning performance across various multilingual image-text tasks and benchmarks, confirming previous findings for English-only mLLMs.

xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Protein

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

If LLM Is the Wizard, Then Code Is the Wand: A Survey on How Code Empowers Large Language Models to Serve as Intelligent Agents

The prominent large language models (LLMs) of today differ from past language models not only in size, but also in the fact that they are trained on a combination of natural language and formal language (code). As a medium between humans and computers, code translates high-level goals into executable steps, featuring standard syntax, logical consistency, abstraction, and modularity. In this survey, we present an overview of the various benefits of integrating code into LLMs' training data. Specifically, beyond enhancing LLMs in code generation, we observe that these unique properties of code help (i) unlock the reasoning ability of LLMs, enabling their applications to a range of more complex natural language tasks; (ii) steer LLMs to produce structured and precise intermediate steps, which can then be connected to external execution ends through function calls; and (iii) take advantage of code compilation and execution environment, which also provides diverse feedback for model improvement. In addition, we trace how these profound capabilities of LLMs, brought by code, have led to their emergence as intelligent agents (IAs) in situations where the ability to understand instructions, decompose goals, plan and execute actions, and refine from feedback are crucial to their success on downstream tasks. Finally, we present several key challenges and future directions of empowering LLMs with code.

Thus Spake Long-Context Large Language Model

Long context is an important topic in Natural Language Processing (NLP), running through the development of NLP architectures, and offers immense opportunities for Large Language Models (LLMs) giving LLMs the lifelong learning potential akin to humans. Unfortunately, the pursuit of a long context is accompanied by numerous obstacles. Nevertheless, long context remains a core competitive advantage for LLMs. In the past two years, the context length of LLMs has achieved a breakthrough extension to millions of tokens. Moreover, the research on long-context LLMs has expanded from length extrapolation to a comprehensive focus on architecture, infrastructure, training, and evaluation technologies. Inspired by the symphonic poem, Thus Spake Zarathustra, we draw an analogy between the journey of extending the context of LLM and the attempts of humans to transcend its mortality. In this survey, We will illustrate how LLM struggles between the tremendous need for a longer context and its equal need to accept the fact that it is ultimately finite. To achieve this, we give a global picture of the lifecycle of long-context LLMs from four perspectives: architecture, infrastructure, training, and evaluation, showcasing the full spectrum of long-context technologies. At the end of this survey, we will present 10 unanswered questions currently faced by long-context LLMs. We hope this survey can serve as a systematic introduction to the research on long-context LLMs.

Manipulating Large Language Models to Increase Product Visibility

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.

SPHINX: The Joint Mixing of Weights, Tasks, and Visual Embeddings for Multi-modal Large Language Models

We present SPHINX, a versatile multi-modal large language model (MLLM) with a joint mixing of model weights, tuning tasks, and visual embeddings. First, for stronger vision-language alignment, we unfreeze the large language model (LLM) during pre-training, and introduce a weight mix strategy between LLMs trained by real-world and synthetic data. By directly integrating the weights from two domains, the mixed LLM can efficiently incorporate diverse semantics with favorable robustness. Then, to enable multi-purpose capabilities, we mix a variety of tasks for joint visual instruction tuning, and design task-specific instructions to avoid inter-task conflict. In addition to the basic visual question answering, we include more challenging tasks such as region-level understanding, caption grounding, document layout detection, and human pose estimation, contributing to mutual enhancement over different scenarios. Additionally, we propose to extract comprehensive visual embeddings from various network architectures, pre-training paradigms, and information granularity, providing language models with more robust image representations. Based on our proposed joint mixing, SPHINX exhibits superior multi-modal understanding capabilities on a wide range of applications. On top of this, we further propose an efficient strategy aiming to better capture fine-grained appearances of high-resolution images. With a mixing of different scales and high-resolution sub-images, SPHINX attains exceptional visual parsing and reasoning performance on existing evaluation benchmarks. We hope our work may cast a light on the exploration of joint mixing in future MLLM research. Code is released at https://github.com/Alpha-VLLM/LLaMA2-Accessory.

MEXA: Multilingual Evaluation of English-Centric LLMs via Cross-Lingual Alignment

English-centric large language models (LLMs) often show strong multilingual capabilities. However, the multilingual performance of these models remains unclear and is not thoroughly evaluated for many languages. Most benchmarks for multilinguality focus on classic NLP tasks, or cover a minimal number of languages. We introduce MEXA, a method for assessing the multilingual capabilities of pre-trained English-centric LLMs using parallel sentences, which are available for more languages than existing downstream tasks. MEXA leverages the fact that English-centric LLMs use English as a kind of pivot language in their intermediate layers. It computes the alignment between English and non-English languages using parallel sentences to evaluate the transfer of language understanding from English to other languages. This alignment can be used to estimate model performance in other languages. We conduct studies using various parallel datasets (FLORES-200 and Bible), models (Llama family, Gemma family, Mistral, and OLMo), and established downstream tasks (Belebele, m-MMLU, and m-ARC). We explore different methods to compute embeddings in decoder-only models. Our results show that MEXA, in its default settings, achieves a statistically significant average Pearson correlation of 0.90 with three established downstream tasks across nine models and two parallel datasets. This suggests that MEXA is a reliable method for estimating the multilingual capabilities of English-centric LLMs, providing a clearer understanding of their multilingual potential and the inner workings of LLMs. Leaderboard: https://huggingface.co/spaces/cis-lmu/Mexa, Code: https://github.com/cisnlp/Mexa.

γ-MoD: Exploring Mixture-of-Depth Adaptation for Multimodal Large Language Models

Despite the significant progress in multimodal large language models (MLLMs), their high computational cost remains a barrier to real-world deployment. Inspired by the mixture of depths (MoDs) in natural language processing, we aim to address this limitation from the perspective of ``activated tokens''. Our key insight is that if most tokens are redundant for the layer computation, then can be skipped directly via the MoD layer. However, directly converting the dense layers of MLLMs to MoD layers leads to substantial performance degradation. To address this issue, we propose an innovative MoD adaptation strategy for existing MLLMs called gamma-MoD. In gamma-MoD, a novel metric is proposed to guide the deployment of MoDs in the MLLM, namely rank of attention maps (ARank). Through ARank, we can effectively identify which layer is redundant and should be replaced with the MoD layer. Based on ARank, we further propose two novel designs to maximize the computational sparsity of MLLM while maintaining its performance, namely shared vision-language router and masked routing learning. With these designs, more than 90% dense layers of the MLLM can be effectively converted to the MoD ones. To validate our method, we apply it to three popular MLLMs, and conduct extensive experiments on 9 benchmark datasets. Experimental results not only validate the significant efficiency benefit of gamma-MoD to existing MLLMs but also confirm its generalization ability on various MLLMs. For example, with a minor performance drop, i.e., -1.5%, gamma-MoD can reduce the training and inference time of LLaVA-HR by 31.0% and 53.2%, respectively.

Evidence of Meaning in Language Models Trained on Programs

We present evidence that language models can learn meaning despite being trained only to perform next token prediction on text, specifically a corpus of programs. Each program is preceded by a specification in the form of (textual) input-output examples. Working with programs enables us to precisely define concepts relevant to meaning in language (e.g., correctness and semantics), making program synthesis well-suited as an intermediate testbed for characterizing the presence (or absence) of meaning in language models. We first train a Transformer model on the corpus of programs, then probe the trained model's hidden states as it completes a program given a specification. Despite providing no inductive bias toward learning the semantics of the language, we find that a linear probe is able to extract abstractions of both current and future program states from the model states. Moreover, there is a strong, statistically significant correlation between the accuracy of the probe and the model's ability to generate a program that implements the specification. To evaluate whether the semantics are represented in the model states rather than learned by the probe, we design a novel experimental procedure that intervenes on the semantics of the language while preserving the lexicon and syntax. We also demonstrate that the model learns to generate correct programs that are, on average, shorter than those in the training set, which is evidence that language model outputs may differ from the training distribution in semantically meaningful ways. In summary, this paper does not propose any new techniques for training language models, but develops an experimental framework for and provides insights into the acquisition and representation of (formal) meaning in language models.

MLLM-Tool: A Multimodal Large Language Model For Tool Agent Learning

Recently, the astonishing performance of large language models (LLMs) in natural language comprehension and generation tasks triggered lots of exploration of using them as central controllers to build agent systems. Multiple studies focus on bridging the LLMs to external tools to extend the application scenarios. However, the current LLMs' perceiving tool-use ability is limited to a single text query, which may result in ambiguity in understanding the users' real intentions. LLMs are expected to eliminate that by perceiving the visual- or auditory-grounded instructions' information. Therefore, in this paper, we propose MLLM-Tool, a system incorporating open-source LLMs and multi-modal encoders so that the learnt LLMs can be conscious of multi-modal input instruction and then select the function-matched tool correctly. To facilitate the evaluation of the model's capability, we collect a dataset featured by consisting of multi-modal input tools from HuggingFace. Another important feature of our dataset is that our dataset also contains multiple potential choices for the same instruction due to the existence of identical functions and synonymous functions, which provides more potential solutions for the same query. The experiments reveal that our MLLM-Tool is capable of recommending appropriate tools for multi-modal instructions. Codes and data are available at https://github.com/MLLM-Tool/MLLM-Tool.

Tx-LLM: A Large Language Model for Therapeutics

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.

LLaVA-KD: A Framework of Distilling Multimodal Large Language Models

The success of Large Language Models (LLM) has led researchers to explore Multimodal Large Language Models (MLLM) for unified visual and linguistic understanding. However, the increasing model size and computational complexity of MLLM limit their use in resource-constrained environments. Small-scale MLLM (s-MLLM) aims to retain the capabilities of the large-scale model (l-MLLM) while reducing computational demands, but resulting in a significant decline in performance. To address the aforementioned issues, we propose a novel LLaVA-KD framework to transfer knowledge from l-MLLM to s-MLLM. Specifically, we introduce Multimodal Distillation (MDist) to minimize the divergence between the visual-textual output distributions of l-MLLM and s-MLLM, and Relation Distillation (RDist) to transfer l-MLLM's ability to model correlations between visual features. Additionally, we propose a three-stage training scheme to fully exploit the potential of s-MLLM: 1) Distilled Pre-Training to align visual-textual representations, 2) Supervised Fine-Tuning to equip the model with multimodal understanding, and 3) Distilled Fine-Tuning to further transfer l-MLLM capabilities. Our approach significantly improves performance without altering the small model's architecture. Extensive experiments and ablation studies validate the effectiveness of each proposed component. Code will be available at https://github.com/caiyuxuan1120/LLaVA-KD.

SEED-Bench-2-Plus: Benchmarking Multimodal Large Language Models with Text-Rich Visual Comprehension

Comprehending text-rich visual content is paramount for the practical application of Multimodal Large Language Models (MLLMs), since text-rich scenarios are ubiquitous in the real world, which are characterized by the presence of extensive texts embedded within images. Recently, the advent of MLLMs with impressive versatility has raised the bar for what we can expect from MLLMs. However, their proficiency in text-rich scenarios has yet to be comprehensively and objectively assessed, since current MLLM benchmarks primarily focus on evaluating general visual comprehension. In this work, we introduce SEED-Bench-2-Plus, a benchmark specifically designed for evaluating text-rich visual comprehension of MLLMs. Our benchmark comprises 2.3K multiple-choice questions with precise human annotations, spanning three broad categories: Charts, Maps, and Webs, each of which covers a wide spectrum of text-rich scenarios in the real world. These categories, due to their inherent complexity and diversity, effectively simulate real-world text-rich environments. We further conduct a thorough evaluation involving 34 prominent MLLMs (including GPT-4V, Gemini-Pro-Vision and Claude-3-Opus) and emphasize the current limitations of MLLMs in text-rich visual comprehension. We hope that our work can serve as a valuable addition to existing MLLM benchmarks, providing insightful observations and inspiring further research in the area of text-rich visual comprehension with MLLMs. The dataset and evaluation code can be accessed at https://github.com/AILab-CVC/SEED-Bench.

ILLUME: Illuminating Your LLMs to See, Draw, and Self-Enhance

In this paper, we introduce ILLUME, a unified multimodal large language model (MLLM) that seamlessly integrates multimodal understanding and generation capabilities within a single large language model through a unified next-token prediction formulation. To address the large dataset size typically required for image-text alignment, we propose to enhance data efficiency through the design of a vision tokenizer that incorporates semantic information and a progressive multi-stage training procedure. This approach reduces the dataset size to just 15M for pretraining -- over four times fewer than what is typically needed -- while achieving competitive or even superior performance with existing unified MLLMs, such as Janus. Additionally, to promote synergistic enhancement between understanding and generation capabilities, which is under-explored in previous works, we introduce a novel self-enhancing multimodal alignment scheme. This scheme supervises the MLLM to self-assess the consistency between text descriptions and self-generated images, facilitating the model to interpret images more accurately and avoid unrealistic and incorrect predictions caused by misalignment in image generation. Based on extensive experiments, our proposed ILLUME stands out and competes with state-of-the-art unified MLLMs and specialized models across various benchmarks for multimodal understanding, generation, and editing.

Intent-based Prompt Calibration: Enhancing prompt optimization with synthetic boundary cases

Prompt engineering is a challenging and important task due to the high sensitivity of Large Language Models (LLMs) to the given prompt and the inherent ambiguity of a textual task instruction. Automatic prompt engineering is essential to achieve optimized performance from LLMs. Recent studies have demonstrated the capabilities of LLMs to automatically conduct prompt engineering by employing a meta-prompt that incorporates the outcomes of the last trials and proposes an improved prompt. However, this requires a high-quality benchmark to compare different prompts, which is difficult and expensive to acquire in many real-world use cases. In this work, we introduce a new method for automatic prompt engineering, using a calibration process that iteratively refines the prompt to the user intent. During the optimization process, the system jointly generates synthetic data of boundary use cases and optimizes the prompt according to the generated dataset. We demonstrate the effectiveness of our method with respect to strong proprietary models on real-world tasks such as moderation and generation. Our method outperforms state-of-the-art methods with a limited number of annotated samples. Furthermore, we validate the advantages of each one of the system's key components. Our system is built in a modular way, facilitating easy adaptation to other tasks. The code is available https://github.com/Eladlev/AutoPrompt{here}.