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Mar 14

Theory, Analysis, and Best Practices for Sigmoid Self-Attention

Attention is a key part of the transformer architecture. It is a sequence-to-sequence mapping that transforms each sequence element into a weighted sum of values. The weights are typically obtained as the softmax of dot products between keys and queries. Recent work has explored alternatives to softmax attention in transformers, such as ReLU and sigmoid activations. In this work, we revisit sigmoid attention and conduct an in-depth theoretical and empirical analysis. Theoretically, we prove that transformers with sigmoid attention are universal function approximators and benefit from improved regularity compared to softmax attention. Through detailed empirical analysis, we identify stabilization of large initial attention norms during the early stages of training as a crucial factor for the successful training of models with sigmoid attention, outperforming prior attempts. We also introduce FLASHSIGMOID, a hardware-aware and memory-efficient implementation of sigmoid attention yielding a 17% inference kernel speed-up over FLASHATTENTION2 on H100 GPUs. Experiments across language, vision, and speech show that properly normalized sigmoid attention matches the strong performance of softmax attention on a wide range of domains and scales, which previous attempts at sigmoid attention were unable to fully achieve. Our work unifies prior art and establishes best practices for sigmoid attention as a drop-in softmax replacement in transformers.

Order Matters: Sequence to sequence for sets

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the sequence-to-sequence (seq2seq) framework which employs the chain rule to efficiently represent the joint probability of sequences. In many cases, however, variable sized inputs and/or outputs might not be naturally expressed as sequences. For instance, it is not clear how to input a set of numbers into a model where the task is to sort them; similarly, we do not know how to organize outputs when they correspond to random variables and the task is to model their unknown joint probability. In this paper, we first show using various examples that the order in which we organize input and/or output data matters significantly when learning an underlying model. We then discuss an extension of the seq2seq framework that goes beyond sequences and handles input sets in a principled way. In addition, we propose a loss which, by searching over possible orders during training, deals with the lack of structure of output sets. We show empirical evidence of our claims regarding ordering, and on the modifications to the seq2seq framework on benchmark language modeling and parsing tasks, as well as two artificial tasks -- sorting numbers and estimating the joint probability of unknown graphical models.

Robust Distortion-free Watermarks for Language Models

We propose a methodology for planting watermarks in text from an autoregressive language model that are robust to perturbations without changing the distribution over text up to a certain maximum generation budget. We generate watermarked text by mapping a sequence of random numbers -- which we compute using a randomized watermark key -- to a sample from the language model. To detect watermarked text, any party who knows the key can align the text to the random number sequence. We instantiate our watermark methodology with two sampling schemes: inverse transform sampling and exponential minimum sampling. We apply these watermarks to three language models -- OPT-1.3B, LLaMA-7B and Alpaca-7B -- to experimentally validate their statistical power and robustness to various paraphrasing attacks. Notably, for both the OPT-1.3B and LLaMA-7B models, we find we can reliably detect watermarked text (p leq 0.01) from 35 tokens even after corrupting between 40-50\% of the tokens via random edits (i.e., substitutions, insertions or deletions). For the Alpaca-7B model, we conduct a case study on the feasibility of watermarking responses to typical user instructions. Due to the lower entropy of the responses, detection is more difficult: around 25% of the responses -- whose median length is around 100 tokens -- are detectable with p leq 0.01, and the watermark is also less robust to certain automated paraphrasing attacks we implement.

End-to-end Autonomous Driving with Semantic Depth Cloud Mapping and Multi-agent

Focusing on the task of point-to-point navigation for an autonomous driving vehicle, we propose a novel deep learning model trained with end-to-end and multi-task learning manners to perform both perception and control tasks simultaneously. The model is used to drive the ego vehicle safely by following a sequence of routes defined by the global planner. The perception part of the model is used to encode high-dimensional observation data provided by an RGBD camera while performing semantic segmentation, semantic depth cloud (SDC) mapping, and traffic light state and stop sign prediction. Then, the control part decodes the encoded features along with additional information provided by GPS and speedometer to predict waypoints that come with a latent feature space. Furthermore, two agents are employed to process these outputs and make a control policy that determines the level of steering, throttle, and brake as the final action. The model is evaluated on CARLA simulator with various scenarios made of normal-adversarial situations and different weathers to mimic real-world conditions. In addition, we do a comparative study with some recent models to justify the performance in multiple aspects of driving. Moreover, we also conduct an ablation study on SDC mapping and multi-agent to understand their roles and behavior. As a result, our model achieves the highest driving score even with fewer parameters and computation load. To support future studies, we share our codes at https://github.com/oskarnatan/end-to-end-driving.

Bidirectional Learning for Offline Model-based Biological Sequence Design

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

Analyzing Transformer Dynamics as Movement through Embedding Space

Transformer based language models exhibit intelligent behaviors such as understanding natural language, recognizing patterns, acquiring knowledge, reasoning, planning, reflecting and using tools. This paper explores how their underlying mechanics give rise to intelligent behaviors. Towards that end, we propose framing Transformer dynamics as movement through embedding space. Examining Transformers through this perspective reveals key insights, establishing a Theory of Transformers: 1) Intelligent behaviours map to paths in Embedding Space which, the Transformer random-walks through during inferencing. 2) LM training learns a probability distribution over all possible paths. `Intelligence' is learnt by assigning higher probabilities to paths representing intelligent behaviors. No learning can take place in-context; context only narrows the subset of paths sampled during decoding. 5) The Transformer is a self-mapping composition function, folding a context sequence into a context-vector such that it's proximity to a token-vector reflects its co-occurrence and conditioned probability. Thus, the physical arrangement of vectors in Embedding Space determines path probabilities. 6) Context vectors are composed by aggregating features of the sequence's tokens via a process we call the encoding walk. Attention contributes a - potentially redundant - association-bias to this process. 7) This process is comprised of two principal operation types: filtering (data independent) and aggregation (data dependent). This generalization unifies Transformers with other sequence models. Building upon this foundation, we formalize a popular semantic interpretation of embeddings into a ``concept-space theory'' and find some evidence of it's validity.

CLIPTrans: Transferring Visual Knowledge with Pre-trained Models for Multimodal Machine Translation

There has been a growing interest in developing multimodal machine translation (MMT) systems that enhance neural machine translation (NMT) with visual knowledge. This problem setup involves using images as auxiliary information during training, and more recently, eliminating their use during inference. Towards this end, previous works face a challenge in training powerful MMT models from scratch due to the scarcity of annotated multilingual vision-language data, especially for low-resource languages. Simultaneously, there has been an influx of multilingual pre-trained models for NMT and multimodal pre-trained models for vision-language tasks, primarily in English, which have shown exceptional generalisation ability. However, these are not directly applicable to MMT since they do not provide aligned multimodal multilingual features for generative tasks. To alleviate this issue, instead of designing complex modules for MMT, we propose CLIPTrans, which simply adapts the independently pre-trained multimodal M-CLIP and the multilingual mBART. In order to align their embedding spaces, mBART is conditioned on the M-CLIP features by a prefix sequence generated through a lightweight mapping network. We train this in a two-stage pipeline which warms up the model with image captioning before the actual translation task. Through experiments, we demonstrate the merits of this framework and consequently push forward the state-of-the-art across standard benchmarks by an average of +2.67 BLEU. The code can be found at www.github.com/devaansh100/CLIPTrans.

UniXcoder: Unified Cross-Modal Pre-training for Code Representation

Pre-trained models for programming languages have recently demonstrated great success on code intelligence. To support both code-related understanding and generation tasks, recent works attempt to pre-train unified encoder-decoder models. However, such encoder-decoder framework is sub-optimal for auto-regressive tasks, especially code completion that requires a decoder-only manner for efficient inference. In this paper, we present UniXcoder, a unified cross-modal pre-trained model for programming language. The model utilizes mask attention matrices with prefix adapters to control the behavior of the model and leverages cross-modal contents like AST and code comment to enhance code representation. To encode AST that is represented as a tree in parallel, we propose a one-to-one mapping method to transform AST in a sequence structure that retains all structural information from the tree. Furthermore, we propose to utilize multi-modal contents to learn representation of code fragment with contrastive learning, and then align representations among programming languages using a cross-modal generation task. We evaluate UniXcoder on five code-related tasks over nine datasets. To further evaluate the performance of code fragment representation, we also construct a dataset for a new task, called zero-shot code-to-code search. Results show that our model achieves state-of-the-art performance on most tasks and analysis reveals that comment and AST can both enhance UniXcoder.

Weakly Supervised Deep Recurrent Neural Networks for Basic Dance Step Generation

Synthesizing human's movements such as dancing is a flourishing research field which has several applications in computer graphics. Recent studies have demonstrated the advantages of deep neural networks (DNNs) for achieving remarkable performance in motion and music tasks with little effort for feature pre-processing. However, applying DNNs for generating dance to a piece of music is nevertheless challenging, because of 1) DNNs need to generate large sequences while mapping the music input, 2) the DNN needs to constraint the motion beat to the music, and 3) DNNs require a considerable amount of hand-crafted data. In this study, we propose a weakly supervised deep recurrent method for real-time basic dance generation with audio power spectrum as input. The proposed model employs convolutional layers and a multilayered Long Short-Term memory (LSTM) to process the audio input. Then, another deep LSTM layer decodes the target dance sequence. Notably, this end-to-end approach has 1) an auto-conditioned decode configuration that reduces accumulation of feedback error of large dance sequence, 2) uses a contrastive cost function to regulate the mapping between the music and motion beat, and 3) trains with weak labels generated from the motion beat, reducing the amount of hand-crafted data. We evaluate the proposed network based on i) the similarities between generated and the baseline dancer motion with a cross entropy measure for large dance sequences, and ii) accurate timing between the music and motion beat with an F-measure. Experimental results revealed that, after training using a small dataset, the model generates basic dance steps with low cross entropy and maintains an F-measure score similar to that of a baseline dancer.

BAMM: Bidirectional Autoregressive Motion Model

Generating human motion from text has been dominated by denoising motion models either through diffusion or generative masking process. However, these models face great limitations in usability by requiring prior knowledge of the motion length. Conversely, autoregressive motion models address this limitation by adaptively predicting motion endpoints, at the cost of degraded generation quality and editing capabilities. To address these challenges, we propose Bidirectional Autoregressive Motion Model (BAMM), a novel text-to-motion generation framework. BAMM consists of two key components: (1) a motion tokenizer that transforms 3D human motion into discrete tokens in latent space, and (2) a masked self-attention transformer that autoregressively predicts randomly masked tokens via a hybrid attention masking strategy. By unifying generative masked modeling and autoregressive modeling, BAMM captures rich and bidirectional dependencies among motion tokens, while learning the probabilistic mapping from textual inputs to motion outputs with dynamically-adjusted motion sequence length. This feature enables BAMM to simultaneously achieving high-quality motion generation with enhanced usability and built-in motion editability. Extensive experiments on HumanML3D and KIT-ML datasets demonstrate that BAMM surpasses current state-of-the-art methods in both qualitative and quantitative measures. Our project page is available at https://exitudio.github.io/BAMM-page

CHASE: Learning Convex Hull Adaptive Shift for Skeleton-based Multi-Entity Action Recognition

Skeleton-based multi-entity action recognition is a challenging task aiming to identify interactive actions or group activities involving multiple diverse entities. Existing models for individuals often fall short in this task due to the inherent distribution discrepancies among entity skeletons, leading to suboptimal backbone optimization. To this end, we introduce a Convex Hull Adaptive Shift based multi-Entity action recognition method (CHASE), which mitigates inter-entity distribution gaps and unbiases subsequent backbones. Specifically, CHASE comprises a learnable parameterized network and an auxiliary objective. The parameterized network achieves plausible, sample-adaptive repositioning of skeleton sequences through two key components. First, the Implicit Convex Hull Constrained Adaptive Shift ensures that the new origin of the coordinate system is within the skeleton convex hull. Second, the Coefficient Learning Block provides a lightweight parameterization of the mapping from skeleton sequences to their specific coefficients in convex combinations. Moreover, to guide the optimization of this network for discrepancy minimization, we propose the Mini-batch Pair-wise Maximum Mean Discrepancy as the additional objective. CHASE operates as a sample-adaptive normalization method to mitigate inter-entity distribution discrepancies, thereby reducing data bias and improving the subsequent classifier's multi-entity action recognition performance. Extensive experiments on six datasets, including NTU Mutual 11/26, H2O, Assembly101, Collective Activity and Volleyball, consistently verify our approach by seamlessly adapting to single-entity backbones and boosting their performance in multi-entity scenarios. Our code is publicly available at https://github.com/Necolizer/CHASE .

Efficiently Modeling Long Sequences with Structured State Spaces

A central goal of sequence modeling is designing a single principled model that can address sequence data across a range of modalities and tasks, particularly on long-range dependencies. Although conventional models including RNNs, CNNs, and Transformers have specialized variants for capturing long dependencies, they still struggle to scale to very long sequences of 10000 or more steps. A promising recent approach proposed modeling sequences by simulating the fundamental state space model (SSM) \( x'(t) = Ax(t) + Bu(t), y(t) = Cx(t) + Du(t) \), and showed that for appropriate choices of the state matrix \( A \), this system could handle long-range dependencies mathematically and empirically. However, this method has prohibitive computation and memory requirements, rendering it infeasible as a general sequence modeling solution. We propose the Structured State Space sequence model (S4) based on a new parameterization for the SSM, and show that it can be computed much more efficiently than prior approaches while preserving their theoretical strengths. Our technique involves conditioning \( A \) with a low-rank correction, allowing it to be diagonalized stably and reducing the SSM to the well-studied computation of a Cauchy kernel. S4 achieves strong empirical results across a diverse range of established benchmarks, including (i) 91\% accuracy on sequential CIFAR-10 with no data augmentation or auxiliary losses, on par with a larger 2-D ResNet, (ii) substantially closing the gap to Transformers on image and language modeling tasks, while performing generation 60times faster (iii) SoTA on every task from the Long Range Arena benchmark, including solving the challenging Path-X task of length 16k that all prior work fails on, while being as efficient as all competitors.

AriEL: volume coding for sentence generation

Mapping sequences of discrete data to a point in a continuous space makes it difficult to retrieve those sequences via random sampling. Mapping the input to a volume would make it easier to retrieve at test time, and that's the strategy followed by the family of approaches based on Variational Autoencoder. However the fact that they are at the same time optimizing for prediction and for smoothness of representation, forces them to trade-off between the two. We improve on the performance of some of the standard methods in deep learning to generate sentences by uniformly sampling a continuous space. We do it by proposing AriEL, that constructs volumes in a continuous space, without the need of encouraging the creation of volumes through the loss function. We first benchmark on a toy grammar, that allows to automatically evaluate the language learned and generated by the models. Then, we benchmark on a real dataset of human dialogues. Our results indicate that the random access to the stored information is dramatically improved, and our method AriEL is able to generate a wider variety of correct language by randomly sampling the latent space. VAE follows in performance for the toy dataset while, AE and Transformer follow for the real dataset. This partially supports to the hypothesis that encoding information into volumes instead of into points, can lead to improved retrieval of learned information with random sampling. This can lead to better generators and we also discuss potential disadvantages.

EmoGen: Eliminating Subjective Bias in Emotional Music Generation

Music is used to convey emotions, and thus generating emotional music is important in automatic music generation. Previous work on emotional music generation directly uses annotated emotion labels as control signals, which suffers from subjective bias: different people may annotate different emotions on the same music, and one person may feel different emotions under different situations. Therefore, directly mapping emotion labels to music sequences in an end-to-end way would confuse the learning process and hinder the model from generating music with general emotions. In this paper, we propose EmoGen, an emotional music generation system that leverages a set of emotion-related music attributes as the bridge between emotion and music, and divides the generation into two stages: emotion-to-attribute mapping with supervised clustering, and attribute-to-music generation with self-supervised learning. Both stages are beneficial: in the first stage, the attribute values around the clustering center represent the general emotions of these samples, which help eliminate the impacts of the subjective bias of emotion labels; in the second stage, the generation is completely disentangled from emotion labels and thus free from the subjective bias. Both subjective and objective evaluations show that EmoGen outperforms previous methods on emotion control accuracy and music quality respectively, which demonstrate our superiority in generating emotional music. Music samples generated by EmoGen are available via this link:https://ai-muzic.github.io/emogen/, and the code is available at this link:https://github.com/microsoft/muzic/.

Mamba-360: Survey of State Space Models as Transformer Alternative for Long Sequence Modelling: Methods, Applications, and Challenges

Sequence modeling is a crucial area across various domains, including Natural Language Processing (NLP), speech recognition, time series forecasting, music generation, and bioinformatics. Recurrent Neural Networks (RNNs) and Long Short Term Memory Networks (LSTMs) have historically dominated sequence modeling tasks like Machine Translation, Named Entity Recognition (NER), etc. However, the advancement of transformers has led to a shift in this paradigm, given their superior performance. Yet, transformers suffer from O(N^2) attention complexity and challenges in handling inductive bias. Several variations have been proposed to address these issues which use spectral networks or convolutions and have performed well on a range of tasks. However, they still have difficulty in dealing with long sequences. State Space Models(SSMs) have emerged as promising alternatives for sequence modeling paradigms in this context, especially with the advent of S4 and its variants, such as S4nd, Hippo, Hyena, Diagnol State Spaces (DSS), Gated State Spaces (GSS), Linear Recurrent Unit (LRU), Liquid-S4, Mamba, etc. In this survey, we categorize the foundational SSMs based on three paradigms namely, Gating architectures, Structural architectures, and Recurrent architectures. This survey also highlights diverse applications of SSMs across domains such as vision, video, audio, speech, language (especially long sequence modeling), medical (including genomics), chemical (like drug design), recommendation systems, and time series analysis, including tabular data. Moreover, we consolidate the performance of SSMs on benchmark datasets like Long Range Arena (LRA), WikiText, Glue, Pile, ImageNet, Kinetics-400, sstv2, as well as video datasets such as Breakfast, COIN, LVU, and various time series datasets. The project page for Mamba-360 work is available on this webpage.https://github.com/badripatro/mamba360.

Decoder-Only or Encoder-Decoder? Interpreting Language Model as a Regularized Encoder-Decoder

The sequence-to-sequence (seq2seq) task aims at generating the target sequence based on the given input source sequence. Traditionally, most of the seq2seq task is resolved by the Encoder-Decoder framework which requires an encoder to encode the source sequence and a decoder to generate the target text. Recently, a bunch of new approaches have emerged that apply decoder-only language models directly to the seq2seq task. Despite the significant advancements in applying language models to the seq2seq task, there is still a lack of thorough analysis on the effectiveness of the decoder-only language model architecture. This paper aims to address this gap by conducting a detailed comparison between the encoder-decoder architecture and the decoder-only language model framework through the analysis of a regularized encoder-decoder structure. This structure is designed to replicate all behaviors in the classical decoder-only language model but has an encoder and a decoder making it easier to be compared with the classical encoder-decoder structure. Based on the analysis, we unveil the attention degeneration problem in the language model, namely, as the generation step number grows, less and less attention is focused on the source sequence. To give a quantitative understanding of this problem, we conduct a theoretical sensitivity analysis of the attention output with respect to the source input. Grounded on our analysis, we propose a novel partial attention language model to solve the attention degeneration problem. Experimental results on machine translation, summarization, and data-to-text generation tasks support our analysis and demonstrate the effectiveness of our proposed model.

Hydra: Bidirectional State Space Models Through Generalized Matrix Mixers

A wide array of sequence models are built on a framework modeled after Transformers, comprising alternating sequence mixer and channel mixer layers. This paper studies a unifying matrix mixer view of sequence mixers that can be conceptualized as a linear map on the input sequence. This framework encompasses a broad range of well-known sequence models, including the self-attention of Transformers as well as recent strong alternatives such as structured state space models (SSMs), and allows understanding downstream characteristics such as efficiency and expressivity through properties of their structured matrix class. We identify a key axis of matrix parameterizations termed sequence alignment, which increases the flexibility and performance of matrix mixers, providing insights into the strong performance of Transformers and recent SSMs such as Mamba. Furthermore, the matrix mixer framework offers a systematic approach to developing sequence mixers with desired properties, allowing us to develop several new sub-quadratic sequence models. In particular, we propose a natural bidirectional extension of the Mamba model (Hydra), parameterized as a quasiseparable matrix mixer, which demonstrates superior performance over other sequence models including Transformers on non-causal tasks. As a drop-in replacement for attention layers, Hydra outperforms BERT by 0.8 points on the GLUE benchmark and ViT by 2% Top-1 accuracy on ImageNet.

Diverse Beam Search: Decoding Diverse Solutions from Neural Sequence Models

Neural sequence models are widely used to model time-series data. Equally ubiquitous is the usage of beam search (BS) as an approximate inference algorithm to decode output sequences from these models. BS explores the search space in a greedy left-right fashion retaining only the top-B candidates - resulting in sequences that differ only slightly from each other. Producing lists of nearly identical sequences is not only computationally wasteful but also typically fails to capture the inherent ambiguity of complex AI tasks. To overcome this problem, we propose Diverse Beam Search (DBS), an alternative to BS that decodes a list of diverse outputs by optimizing for a diversity-augmented objective. We observe that our method finds better top-1 solutions by controlling for the exploration and exploitation of the search space - implying that DBS is a better search algorithm. Moreover, these gains are achieved with minimal computational or memory over- head as compared to beam search. To demonstrate the broad applicability of our method, we present results on image captioning, machine translation and visual question generation using both standard quantitative metrics and qualitative human studies. Further, we study the role of diversity for image-grounded language generation tasks as the complexity of the image changes. We observe that our method consistently outperforms BS and previously proposed techniques for diverse decoding from neural sequence models.

An Interdisciplinary Comparison of Sequence Modeling Methods for Next-Element Prediction

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

SurMo: Surface-based 4D Motion Modeling for Dynamic Human Rendering

Dynamic human rendering from video sequences has achieved remarkable progress by formulating the rendering as a mapping from static poses to human images. However, existing methods focus on the human appearance reconstruction of every single frame while the temporal motion relations are not fully explored. In this paper, we propose a new 4D motion modeling paradigm, SurMo, that jointly models the temporal dynamics and human appearances in a unified framework with three key designs: 1) Surface-based motion encoding that models 4D human motions with an efficient compact surface-based triplane. It encodes both spatial and temporal motion relations on the dense surface manifold of a statistical body template, which inherits body topology priors for generalizable novel view synthesis with sparse training observations. 2) Physical motion decoding that is designed to encourage physical motion learning by decoding the motion triplane features at timestep t to predict both spatial derivatives and temporal derivatives at the next timestep t+1 in the training stage. 3) 4D appearance decoding that renders the motion triplanes into images by an efficient volumetric surface-conditioned renderer that focuses on the rendering of body surfaces with motion learning conditioning. Extensive experiments validate the state-of-the-art performance of our new paradigm and illustrate the expressiveness of surface-based motion triplanes for rendering high-fidelity view-consistent humans with fast motions and even motion-dependent shadows. Our project page is at: https://taohuumd.github.io/projects/SurMo/

Zenseact Open Dataset: A large-scale and diverse multimodal dataset for autonomous driving

Existing datasets for autonomous driving (AD) often lack diversity and long-range capabilities, focusing instead on 360{\deg} perception and temporal reasoning. To address this gap, we introduce Zenseact Open Dataset (ZOD), a large-scale and diverse multimodal dataset collected over two years in various European countries, covering an area 9x that of existing datasets. ZOD boasts the highest range and resolution sensors among comparable datasets, coupled with detailed keyframe annotations for 2D and 3D objects (up to 245m), road instance/semantic segmentation, traffic sign recognition, and road classification. We believe that this unique combination will facilitate breakthroughs in long-range perception and multi-task learning. The dataset is composed of Frames, Sequences, and Drives, designed to encompass both data diversity and support for spatio-temporal learning, sensor fusion, localization, and mapping. Frames consist of 100k curated camera images with two seconds of other supporting sensor data, while the 1473 Sequences and 29 Drives include the entire sensor suite for 20 seconds and a few minutes, respectively. ZOD is the only large-scale AD dataset released under a permissive license, allowing for both research and commercial use. The dataset is accompanied by an extensive development kit. Data and more information are available online (https://zod.zenseact.com).

Point Cloud Mamba: Point Cloud Learning via State Space Model

Recently, state space models have exhibited strong global modeling capabilities and linear computational complexity in contrast to transformers. This research focuses on applying such architecture to more efficiently and effectively model point cloud data globally with linear computational complexity. In particular, for the first time, we demonstrate that Mamba-based point cloud methods can outperform previous methods based on transformer or multi-layer perceptrons (MLPs). To enable Mamba to process 3-D point cloud data more effectively, we propose a novel Consistent Traverse Serialization method to convert point clouds into 1-D point sequences while ensuring that neighboring points in the sequence are also spatially adjacent. Consistent Traverse Serialization yields six variants by permuting the order of x, y, and z coordinates, and the synergistic use of these variants aids Mamba in comprehensively observing point cloud data. Furthermore, to assist Mamba in handling point sequences with different orders more effectively, we introduce point prompts to inform Mamba of the sequence's arrangement rules. Finally, we propose positional encoding based on spatial coordinate mapping to inject positional information into point cloud sequences more effectively. Point Cloud Mamba surpasses the state-of-the-art (SOTA) point-based method PointNeXt and achieves new SOTA performance on the ScanObjectNN, ModelNet40, ShapeNetPart, and S3DIS datasets. It is worth mentioning that when using a more powerful local feature extraction module, our PCM achieves 79.6 mIoU on S3DIS, significantly surpassing the previous SOTA models, DeLA and PTv3, by 5.5 mIoU and 4.9 mIoU, respectively.

Sequence to Sequence Learning with Neural Networks

Deep Neural Networks (DNNs) are powerful models that have achieved excellent performance on difficult learning tasks. Although DNNs work well whenever large labeled training sets are available, they cannot be used to map sequences to sequences. In this paper, we present a general end-to-end approach to sequence learning that makes minimal assumptions on the sequence structure. Our method uses a multilayered Long Short-Term Memory (LSTM) to map the input sequence to a vector of a fixed dimensionality, and then another deep LSTM to decode the target sequence from the vector. Our main result is that on an English to French translation task from the WMT'14 dataset, the translations produced by the LSTM achieve a BLEU score of 34.8 on the entire test set, where the LSTM's BLEU score was penalized on out-of-vocabulary words. Additionally, the LSTM did not have difficulty on long sentences. For comparison, a phrase-based SMT system achieves a BLEU score of 33.3 on the same dataset. When we used the LSTM to rerank the 1000 hypotheses produced by the aforementioned SMT system, its BLEU score increases to 36.5, which is close to the previous best result on this task. The LSTM also learned sensible phrase and sentence representations that are sensitive to word order and are relatively invariant to the active and the passive voice. Finally, we found that reversing the order of the words in all source sentences (but not target sentences) improved the LSTM's performance markedly, because doing so introduced many short term dependencies between the source and the target sentence which made the optimization problem easier.

Embed-Search-Align: DNA Sequence Alignment using Transformer Models

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

SequenceMatch: Imitation Learning for Autoregressive Sequence Modelling with Backtracking

In many domains, autoregressive models can attain high likelihood on the task of predicting the next observation. However, this maximum-likelihood (MLE) objective does not necessarily match a downstream use-case of autoregressively generating high-quality sequences. The MLE objective weights sequences proportionally to their frequency under the data distribution, with no guidance for the model's behaviour out of distribution (OOD): leading to compounding error during autoregressive generation. In order to address this compounding error problem, we formulate sequence generation as an imitation learning (IL) problem. This allows us to minimize a variety of divergences between the distribution of sequences generated by an autoregressive model and sequences from a dataset, including divergences with weight on OOD generated sequences. The IL framework also allows us to incorporate backtracking by introducing a backspace action into the generation process. This further mitigates the compounding error problem by allowing the model to revert a sampled token if it takes the sequence OOD. Our resulting method, SequenceMatch, can be implemented without adversarial training or major architectural changes. We identify the SequenceMatch-chi^2 divergence as a more suitable training objective for autoregressive models which are used for generation. We show that empirically, SequenceMatch training leads to improvements over MLE on text generation with language models.

Data-Centric and Heterogeneity-Adaptive Sequence Parallelism for Efficient LLM Training

Extending the context length (i.e., the maximum supported sequence length) of LLMs is of paramount significance. To facilitate long context training of LLMs, sequence parallelism has emerged as an essential technique, which scatters each input sequence across multiple devices and necessitates communication to process the sequence. In essence, existing sequence parallelism methods assume homogeneous sequence lengths (i.e., all input sequences are equal in length) and therefore leverages a single, static scattering strategy for all input sequences. However, in reality, the sequence lengths in LLM training corpora exhibit substantial variability, often following a long-tail distribution, which leads to workload heterogeneity. In this paper, we show that employing a single, static strategy results in inefficiency and resource under-utilization, highlighting the need for adaptive approaches to handle the heterogeneous workloads across sequences. To address this, we propose a heterogeneity-adaptive sequence parallelism method. For each training step, our approach captures the variability in sequence lengths and assigns the optimal combination of scattering strategies based on workload characteristics. We model this problem as a linear programming optimization and design an efficient and effective solver to find the optimal solution. Furthermore, we implement our method in a high-performance system that supports adaptive parallelization in distributed LLM training. Experimental results demonstrate that our system outperforms state-of-the-art training frameworks by up to 1.98x.

Best of Both Worlds: Advantages of Hybrid Graph Sequence Models

Modern sequence models (e.g., Transformers, linear RNNs, etc.) emerged as dominant backbones of recent deep learning frameworks, mainly due to their efficiency, representational power, and/or ability to capture long-range dependencies. Adopting these sequence models for graph-structured data has recently gained popularity as the alternative to Message Passing Neural Networks (MPNNs). There is, however, a lack of a common foundation about what constitutes a good graph sequence model, and a mathematical description of the benefits and deficiencies in adopting different sequence models for learning on graphs. To this end, we first present Graph Sequence Model (GSM), a unifying framework for adopting sequence models for graphs, consisting of three main steps: (1) Tokenization, which translates the graph into a set of sequences; (2) Local Encoding, which encodes local neighborhoods around each node; and (3) Global Encoding, which employs a scalable sequence model to capture long-range dependencies within the sequences. This framework allows us to understand, evaluate, and compare the power of different sequence model backbones in graph tasks. Our theoretical evaluations of the representation power of Transformers and modern recurrent models through the lens of global and local graph tasks show that there are both negative and positive sides for both types of models. Building on this observation, we present GSM++, a fast hybrid model that uses the Hierarchical Affinity Clustering (HAC) algorithm to tokenize the graph into hierarchical sequences, and then employs a hybrid architecture of Transformer to encode these sequences. Our theoretical and experimental results support the design of GSM++, showing that GSM++ outperforms baselines in most benchmark evaluations.

Don't Take It Literally: An Edit-Invariant Sequence Loss for Text Generation

Neural text generation models are typically trained by maximizing log-likelihood with the sequence cross entropy (CE) loss, which encourages an exact token-by-token match between a target sequence with a generated sequence. Such training objective is sub-optimal when the target sequence is not perfect, e.g., when the target sequence is corrupted with noises, or when only weak sequence supervision is available. To address the challenge, we propose a novel Edit-Invariant Sequence Loss (EISL), which computes the matching loss of a target n-gram with all n-grams in the generated sequence. EISL is designed to be robust to various noises and edits in the target sequences. Moreover, the EISL computation is essentially an approximate convolution operation with target n-grams as kernels, which is easy to implement and efficient to compute with existing libraries. To demonstrate the effectiveness of EISL, we conduct experiments on a wide range of tasks, including machine translation with noisy target sequences, unsupervised text style transfer with only weak training signals, and non-autoregressive generation with non-predefined generation order. Experimental results show our method significantly outperforms the common CE loss and other strong baselines on all the tasks. EISL has a simple API that can be used as a drop-in replacement of the CE loss: https://github.com/guangyliu/EISL.

Faster Re-translation Using Non-Autoregressive Model For Simultaneous Neural Machine Translation

Recently, simultaneous translation has gathered a lot of attention since it enables compelling applications such as subtitle translation for a live event or real-time video-call translation. Some of these translation applications allow editing of partial translation giving rise to re-translation approaches. The current re-translation approaches are based on autoregressive sequence generation models (ReTA), which generate tar-get tokens in the (partial) translation sequentially. The multiple re-translations with sequential generation inReTAmodelslead to an increased inference time gap between the incoming source input and the corresponding target output as the source input grows. Besides, due to the large number of inference operations involved, the ReTA models are not favorable for resource-constrained devices. In this work, we propose a faster re-translation system based on a non-autoregressive sequence generation model (FReTNA) to overcome the aforementioned limitations. We evaluate the proposed model on multiple translation tasks and our model reduces the inference times by several orders and achieves a competitive BLEUscore compared to the ReTA and streaming (Wait-k) models.The proposed model reduces the average computation time by a factor of 20 when compared to the ReTA model by incurring a small drop in the translation quality. It also outperforms the streaming-based Wait-k model both in terms of computation time (1.5 times lower) and translation quality.

Autoregressive Models in Vision: A Survey

Autoregressive modeling has been a huge success in the field of natural language processing (NLP). Recently, autoregressive models have emerged as a significant area of focus in computer vision, where they excel in producing high-quality visual content. Autoregressive models in NLP typically operate on subword tokens. However, the representation strategy in computer vision can vary in different levels, i.e., pixel-level, token-level, or scale-level, reflecting the diverse and hierarchical nature of visual data compared to the sequential structure of language. This survey comprehensively examines the literature on autoregressive models applied to vision. To improve readability for researchers from diverse research backgrounds, we start with preliminary sequence representation and modeling in vision. Next, we divide the fundamental frameworks of visual autoregressive models into three general sub-categories, including pixel-based, token-based, and scale-based models based on the strategy of representation. We then explore the interconnections between autoregressive models and other generative models. Furthermore, we present a multi-faceted categorization of autoregressive models in computer vision, including image generation, video generation, 3D generation, and multi-modal generation. We also elaborate on their applications in diverse domains, including emerging domains such as embodied AI and 3D medical AI, with about 250 related references. Finally, we highlight the current challenges to autoregressive models in vision with suggestions about potential research directions. We have also set up a Github repository to organize the papers included in this survey at: https://github.com/ChaofanTao/Autoregressive-Models-in-Vision-Survey.

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.

Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

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.

METAGENE-1: Metagenomic Foundation Model for Pandemic Monitoring

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

DPLM-2: A Multimodal Diffusion Protein Language Model

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

InfLLM: Unveiling the Intrinsic Capacity of LLMs for Understanding Extremely Long Sequences with Training-Free Memory

Large language models (LLMs) have emerged as a cornerstone in real-world applications with lengthy streaming inputs, such as LLM-driven agents. However, existing LLMs, pre-trained on sequences with restricted maximum length, cannot generalize to longer sequences due to the out-of-domain and distraction issues. To alleviate these issues, existing efforts employ sliding attention windows and discard distant tokens to achieve the processing of extremely long sequences. Unfortunately, these approaches inevitably fail to capture long-distance dependencies within sequences to deeply understand semantics. This paper introduces a training-free memory-based method, InfLLM, to unveil the intrinsic ability of LLMs to process streaming long sequences. Specifically, InfLLM stores distant contexts into additional memory units and employs an efficient mechanism to lookup token-relevant units for attention computation. Thereby, InfLLM allows LLMs to efficiently process long sequences while maintaining the ability to capture long-distance dependencies. Without any training, InfLLM enables LLMs pre-trained on sequences of a few thousand tokens to achieve superior performance than competitive baselines continually training these LLMs on long sequences. Even when the sequence length is scaled to 1,024K, InfLLM still effectively captures long-distance dependencies.

Theme Transformer: Symbolic Music Generation with Theme-Conditioned Transformer

Attention-based Transformer models have been increasingly employed for automatic music generation. To condition the generation process of such a model with a user-specified sequence, a popular approach is to take that conditioning sequence as a priming sequence and ask a Transformer decoder to generate a continuation. However, this prompt-based conditioning cannot guarantee that the conditioning sequence would develop or even simply repeat itself in the generated continuation. In this paper, we propose an alternative conditioning approach, called theme-based conditioning, that explicitly trains the Transformer to treat the conditioning sequence as a thematic material that has to manifest itself multiple times in its generation result. This is achieved with two main technical contributions. First, we propose a deep learning-based approach that uses contrastive representation learning and clustering to automatically retrieve thematic materials from music pieces in the training data. Second, we propose a novel gated parallel attention module to be used in a sequence-to-sequence (seq2seq) encoder/decoder architecture to more effectively account for a given conditioning thematic material in the generation process of the Transformer decoder. We report on objective and subjective evaluations of variants of the proposed Theme Transformer and the conventional prompt-based baseline, showing that our best model can generate, to some extent, polyphonic pop piano music with repetition and plausible variations of a given condition.

RankGen: Improving Text Generation with Large Ranking Models

Given an input sequence (or prefix), modern language models often assign high probabilities to output sequences that are repetitive, incoherent, or irrelevant to the prefix; as such, model-generated text also contains such artifacts. To address these issues we present RankGen, a 1.2B parameter encoder model for English that scores model generations given a prefix. RankGen can be flexibly incorporated as a scoring function in beam search and used to decode from any pretrained language model. We train RankGen using large-scale contrastive learning to map a prefix close to the ground-truth sequence that follows it and far away from two types of negatives: (1) random sequences from the same document as the prefix, and (2) sequences generated from a large language model conditioned on the prefix. Experiments across four different language models (345M-11B parameters) and two domains show that RankGen significantly outperforms decoding algorithms like nucleus, top-k, and typical sampling, as well as contrastive decoding and search, on both automatic metrics (85.0 vs 77.3 MAUVE over nucleus) as well as human evaluations with English writers (74.5% human preference over nucleus sampling). Analysis reveals that RankGen outputs are more relevant to the prefix and improve continuity and coherence compared to baselines. We release our model checkpoints, code, and human preference data with explanations to facilitate future research.

DTT: An Example-Driven Tabular Transformer for Joinability by Leveraging Large Language Models

Many organizations rely on data from government and third-party sources, and those sources rarely follow the same data formatting. This introduces challenges in integrating data from multiple sources or aligning external sources with internal databases. Commercial database systems do not offer adequate support for integrating data from heterogeneous sources, and manual integration is both time-consuming and inefficient. State-of-the-art data integration approaches that rely on similarity functions and textual transformations often fail to handle challenging cases where multiple mappings are required, or the mappings go beyond simple textual transformations. In this paper, we study the potentials of deep neural models for transforming tables for joinability. In particular, we cast the problem as a prediction task and develop a framework that leverages large deep-learning language models to transform tabular data from a source formatting to a desired target representation. Our framework can efficiently learn the patterns for mapping a source formatting into an expected target using just a few examples, which can then be used for tasks such as table joining, filling in missing values, and error detection. Compared to state-of-the-art mapping and joining approaches, our framework delivers noticeably more accurate and scalable performance on both real-world and synthetic datasets. Our experimental evaluation also shows that the performance of the proposed framework using our fine-tuned model is at par or better than large language models such as GPT-3, despite the significant difference in size, and that using large language models within our framework improves their performance.

Lossless Acceleration for Seq2seq Generation with Aggressive Decoding

We study lossless acceleration for seq2seq generation with a novel decoding algorithm -- Aggressive Decoding. Unlike the previous efforts (e.g., non-autoregressive decoding) speeding up seq2seq generation at the cost of quality loss, our approach aims to yield the identical (or better) generation compared with autoregressive decoding but in a significant speedup, achieved by innovative cooperation of aggressive decoding and verification that are both efficient due to parallel computing. We propose two Aggressive Decoding paradigms for 2 kinds of seq2seq tasks: 1) For the seq2seq tasks whose inputs and outputs are highly similar (e.g., Grammatical Error Correction), we propose Input-guided Aggressive Decoding (IAD) that aggressively copies from the input sentence as drafted decoded tokens to verify in parallel; 2) For other general seq2seq tasks (e.g., Machine Translation), we propose Generalized Aggressive Decoding (GAD) that first employs an additional non-autoregressive decoding model for aggressive decoding and then verifies in parallel in the autoregressive manner. We test Aggressive Decoding on the most popular 6-layer Transformer model on GPU in multiple seq2seq tasks: 1) For IAD, we show that it can introduce a 7x-9x speedup for the Transformer in Grammatical Error Correction and Text Simplification tasks with the identical results as greedy decoding; 2) For GAD, we observe a 3x-5x speedup with the identical or even better quality in two important seq2seq tasks: Machine Translation and Abstractive Summarization. Moreover, Aggressive Decoding can benefit even more from stronger computing devices that are better at parallel computing. Given the lossless quality as well as significant and promising speedup, we believe Aggressive Decoding may potentially evolve into a de facto standard for efficient and lossless seq2seq generation in the near future.

Text Is All You Need: Learning Language Representations for Sequential Recommendation

Sequential recommendation aims to model dynamic user behavior from historical interactions. Existing methods rely on either explicit item IDs or general textual features for sequence modeling to understand user preferences. While promising, these approaches still struggle to model cold-start items or transfer knowledge to new datasets. In this paper, we propose to model user preferences and item features as language representations that can be generalized to new items and datasets. To this end, we present a novel framework, named Recformer, which effectively learns language representations for sequential recommendation. Specifically, we propose to formulate an item as a "sentence" (word sequence) by flattening item key-value attributes described by text so that an item sequence for a user becomes a sequence of sentences. For recommendation, Recformer is trained to understand the "sentence" sequence and retrieve the next "sentence". To encode item sequences, we design a bi-directional Transformer similar to the model Longformer but with different embedding layers for sequential recommendation. For effective representation learning, we propose novel pretraining and finetuning methods which combine language understanding and recommendation tasks. Therefore, Recformer can effectively recommend the next item based on language representations. Extensive experiments conducted on six datasets demonstrate the effectiveness of Recformer for sequential recommendation, especially in low-resource and cold-start settings.

TokenRing: An Efficient Parallelism Framework for Infinite-Context LLMs via Bidirectional Communication

Efficient parallelization of Large Language Models (LLMs) with long sequences is essential but challenging due to their significant computational and memory demands, particularly stemming from communication bottlenecks in attention mechanisms. While sequence parallelism (SP) has been introduced as a potential solution, existing methods often suffer from limited scalability or inefficiency, rendering their effectiveness. Ring-Attention demonstrates the potential for scaling sequence processing but faces significant limitations due to its reliance on peer-to-peer (P2P) communication and inefficient utilization of network resources. As the degree of SP increases, the quadratic decrease in computation time per step contrasts sharply with the linear reduction in communication volume, exacerbating communication bottlenecks. To address these challenges, we propose TokenRing, a fine-grained parallel framework that leverages bidirectional P2P communication to effectively overlap computation and data transmission. By partitioning the attention block and concurrently transmitting Query and block outputs (i.e., block_out and block_lse) within a fully connected mesh topology, TokenRing achieves significant reductions in communication overhead and better load balancing. These innovations improve the scalability and efficiency of distributed Transformer models, particularly for long-context sequences. Experimental results demonstrate that TokenRing enhances throughput and reduces communication latency. Moreover, its design adapts seamlessly to various multi-GPU interconnect solutions, such as Huawei Ascend, ensuring broad compatibility and cost-effectiveness for distributed LLM inference and training. The code is available at: https://github.com/ACA-Lab-SJTU/token-ring.

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.

GENERator: A Long-Context Generative Genomic Foundation Model

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences

Language models for biological and chemical sequences enable crucial applications such as drug discovery, protein engineering, and precision medicine. Currently, these language models are predominantly based on Transformer architectures. While Transformers have yielded impressive results, their quadratic runtime dependency on the sequence length complicates their use for long genomic sequences and in-context learning on proteins and chemical sequences. Recently, the recurrent xLSTM architecture has been shown to perform favorably compared to Transformers and modern state-space model (SSM) architectures in the natural language domain. Similar to SSMs, xLSTMs have a linear runtime dependency on the sequence length and allow for constant-memory decoding at inference time, which makes them prime candidates for modeling long-range dependencies in biological and chemical sequences. In this work, we tailor xLSTM towards these domains and propose a suite of architectural variants called Bio-xLSTM. Extensive experiments in three large domains, genomics, proteins, and chemistry, were performed to assess xLSTM's ability to model biological and chemical sequences. The results show that models based on Bio-xLSTM a) can serve as proficient generative models for DNA, protein, and chemical sequences, b) learn rich representations for those modalities, and c) can perform in-context learning for proteins and small molecules.

E2S2: Encoding-Enhanced Sequence-to-Sequence Pretraining for Language Understanding and Generation

Sequence-to-sequence (seq2seq) learning is a popular fashion for large-scale pretraining language models. However, the prior seq2seq pretraining models generally focus on reconstructive objectives on the decoder side and neglect the effect of encoder-side supervision, which we argue may lead to sub-optimal performance. To verify our hypothesis, we first empirically study the functionalities of the encoder and decoder in seq2seq pretrained language models, and find that the encoder takes an important but under-exploitation role than the decoder regarding the downstream performance and neuron activation. Therefore, we propose an encoding-enhanced seq2seq pretraining strategy, namely E2S2, which improves the seq2seq models via integrating more efficient self-supervised information into the encoders. Specifically, E2S2 adopts two self-supervised objectives on the encoder side from two aspects: 1) locally denoising the corrupted sentence (denoising objective); and 2) globally learning better sentence representations (contrastive objective). With the help of both objectives, the encoder can effectively distinguish the noise tokens and capture high-level (i.e. syntactic and semantic) knowledge, thus strengthening the ability of seq2seq model to accurately achieve the conditional generation. On a large diversity of downstream natural language understanding and generation tasks, E2S2 dominantly improves the performance of its powerful backbone models, e.g. BART and T5. For example, upon BART backbone, we achieve +1.1% averaged gain on the general language understanding evaluation (GLUE) benchmark and +1.75% F_0.5 score improvement on CoNLL2014 dataset. We also provide in-depth analyses to show the improvement stems from better linguistic representation. We hope that our work will foster future self-supervision research on seq2seq language model pretraining.

Pointer Networks

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence and Neural Turing Machines, because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems -- finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem -- using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.

Sequence Parallelism: Long Sequence Training from System Perspective

Transformer achieves promising results on various tasks. However, self-attention suffers from quadratic memory requirements with respect to the sequence length. Existing work focuses on reducing time and space complexity from an algorithm perspective. In this work, we propose sequence parallelism, a memory-efficient parallelism method to help us break input sequence length limitation and train with longer sequences on GPUs efficiently. Our approach is compatible with most existing parallelisms (e.g. data parallelism, pipeline parallelism and tensor parallelism), which means our sequence parallelism makes 4D parallelism possible. More importantly, we no longer require a single device to hold the whole sequence. That is, with sparse attention, our sequence parallelism enables us to train transformer with infinite long sequence. Specifically, we split the input sequence into multiple chunks and feed each chunk into its corresponding device (i.e. GPU). To compute the attention output, we integrated ring-style communication with self-attention calculation and proposed Ring Self-Attention (RSA). Experiments show that sequence parallelism performs well when scaling with batch size and sequence length. Compared with tensor parallelism, our approach achieved 13.7times and 3.0times maximum batch size and sequence length respectively when scaling up to 64 NVIDIA P100 GPUs. With sparse attention, sequence can handle sequence with over 114K tokens, which is over 27times longer than existing sparse attention works holding the whole sequence on a single device.

Making the Most of your Model: Methods for Finetuning and Applying Pretrained Transformers

This thesis provides methods and analysis of models which make progress on this goal. The techniques outlined are task agnostic, and should provide benefit when used with nearly any transformer LM. We introduce two new finetuning methods which add new capabilities to the models they are used on. The first adds a recurrence mechanism, which removes the fixed-window sized constraint and improves the efficiency of a transformer decoder. The second allows masked language models (MLMs) to be used for initialization of both the encoder and decoder of a non-autoregressive sequence-to-sequence transformer, opening up generative applications of models which were previously only used for natural language understanding tasks. We also introduce two new techniques for improving the quality of predictions of any transformer decoder without additional finetuning. One, hidden state optimization, can be applied to any transformer decoder to improve the quality of predictions at inference time, especially for few-shot classification. The other, conditional beam search, allows practitioners to search for natural language generation (NLG) model outputs with high likelihood while conditioning on the event that the output is not degenerate (e.g. empty, repetitive, etc.). Finally, we provide theoretical and empirical insights on the divergence of model-likelihood and output quality which has widely been observed in prior work. These insights apply to any model which represents a distribution over text, and apply to language models which are not transformers or even autoregressive. We argue that the NLP community has, to some extent, misunderstood the implications of these findings, and encourage a point of view which has more nuance.

Let the Code LLM Edit Itself When You Edit the Code

In this work, we investigate a typical scenario in code generation where a developer edits existing code in real time and requests a code assistant, e.g., a large language model, to re-predict the next token or next line on the fly. Naively, the LLM needs to re-encode the entire KV cache to provide an accurate prediction. However, this process is computationally expensive, especially when the sequence length is long. Simply encoding the edited subsequence and integrating it to the original KV cache meets the temporal confusion problem, leading to significantly worse performance. We address this efficiency and accuracy trade-off by introducing \textbf{Positional \textbf{Integrity Encoding} (PIE). Building upon the rotary positional encoding, PIE first removes the rotary matrices in the Key cache that introduce temporal confusion and then reapplies the correct rotary matrices. This process ensures that positional relationships between tokens are correct and requires only a single round of matrix multiplication. We validate the effectiveness of PIE through extensive experiments on the RepoBench-C-8k dataset, utilizing DeepSeek-Coder models with 1.3B, 6.7B, and 33B parameters. Our evaluation includes three real-world coding tasks: code insertion, code deletion, and multi-place code editing. Results demonstrate that PIE reduces computational overhead by over 85% compared to the standard full recomputation approach across all model sizes and tasks while well approximating the model performance.

Computation-Efficient Era: A Comprehensive Survey of State Space Models in Medical Image Analysis

Sequence modeling plays a vital role across various domains, with recurrent neural networks being historically the predominant method of performing these tasks. However, the emergence of transformers has altered this paradigm due to their superior performance. Built upon these advances, transformers have conjoined CNNs as two leading foundational models for learning visual representations. However, transformers are hindered by the O(N^2) complexity of their attention mechanisms, while CNNs lack global receptive fields and dynamic weight allocation. State Space Models (SSMs), specifically the \textbf{Mamba} model with selection mechanisms and hardware-aware architecture, have garnered immense interest lately in sequential modeling and visual representation learning, challenging the dominance of transformers by providing infinite context lengths and offering substantial efficiency maintaining linear complexity in the input sequence. Capitalizing on the advances in computer vision, medical imaging has heralded a new epoch with Mamba models. Intending to help researchers navigate the surge, this survey seeks to offer an encyclopedic review of Mamba models in medical imaging. Specifically, we start with a comprehensive theoretical review forming the basis of SSMs, including Mamba architecture and its alternatives for sequence modeling paradigms in this context. Next, we offer a structured classification of Mamba models in the medical field and introduce a diverse categorization scheme based on their application, imaging modalities, and targeted organs. Finally, we summarize key challenges, discuss different future research directions of the SSMs in the medical domain, and propose several directions to fulfill the demands of this field. In addition, we have compiled the studies discussed in this paper along with their open-source implementations on our GitHub repository.

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.

DeepJoin: Joinable Table Discovery with Pre-trained Language Models

Due to the usefulness in data enrichment for data analysis tasks, joinable table discovery has become an important operation in data lake management. Existing approaches target equi-joins, the most common way of combining tables for creating a unified view, or semantic joins, which tolerate misspellings and different formats to deliver more join results. They are either exact solutions whose running time is linear in the sizes of query column and target table repository or approximate solutions lacking precision. In this paper, we propose Deepjoin, a deep learning model for accurate and efficient joinable table discovery. Our solution is an embedding-based retrieval, which employs a pre-trained language model (PLM) and is designed as one framework serving both equi- and semantic joins. We propose a set of contextualization options to transform column contents to a text sequence. The PLM reads the sequence and is fine-tuned to embed columns to vectors such that columns are expected to be joinable if they are close to each other in the vector space. Since the output of the PLM is fixed in length, the subsequent search procedure becomes independent of the column size. With a state-of-the-art approximate nearest neighbor search algorithm, the search time is logarithmic in the repository size. To train the model, we devise the techniques for preparing training data as well as data augmentation. The experiments on real datasets demonstrate that by training on a small subset of a corpus, Deepjoin generalizes to large datasets and its precision consistently outperforms other approximate solutions'. Deepjoin is even more accurate than an exact solution to semantic joins when evaluated with labels from experts. Moreover, when equipped with a GPU, Deepjoin is up to two orders of magnitude faster than existing solutions.

Unified Generative and Discriminative Training for Multi-modal Large Language Models

In recent times, Vision-Language Models (VLMs) have been trained under two predominant paradigms. Generative training has enabled Multimodal Large Language Models (MLLMs) to tackle various complex tasks, yet issues such as hallucinations and weak object discrimination persist. Discriminative training, exemplified by models like CLIP, excels in zero-shot image-text classification and retrieval, yet struggles with complex scenarios requiring fine-grained semantic differentiation. This paper addresses these challenges by proposing a unified approach that integrates the strengths of both paradigms. Considering interleaved image-text sequences as the general format of input samples, we introduce a structure-induced training strategy that imposes semantic relationships between input samples and the MLLM's hidden state. This approach enhances the MLLM's ability to capture global semantics and distinguish fine-grained semantics. By leveraging dynamic sequence alignment within the Dynamic Time Warping framework and integrating a novel kernel for fine-grained semantic differentiation, our method effectively balances generative and discriminative tasks. Extensive experiments demonstrate the effectiveness of our approach, achieving state-of-the-art results in multiple generative tasks, especially those requiring cognitive and discrimination abilities. Additionally, our method surpasses discriminative benchmarks in interleaved and fine-grained retrieval tasks. By employing a retrieval-augmented generation strategy, our approach further enhances performance in some generative tasks within one model, offering a promising direction for future research in vision-language modeling.

A Critical Review of Recurrent Neural Networks for Sequence Learning

Countless learning tasks require dealing with sequential data. Image captioning, speech synthesis, and music generation all require that a model produce outputs that are sequences. In other domains, such as time series prediction, video analysis, and musical information retrieval, a model must learn from inputs that are sequences. Interactive tasks, such as translating natural language, engaging in dialogue, and controlling a robot, often demand both capabilities. Recurrent neural networks (RNNs) are connectionist models that capture the dynamics of sequences via cycles in the network of nodes. Unlike standard feedforward neural networks, recurrent networks retain a state that can represent information from an arbitrarily long context window. Although recurrent neural networks have traditionally been difficult to train, and often contain millions of parameters, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful large-scale learning with them. In recent years, systems based on long short-term memory (LSTM) and bidirectional (BRNN) architectures have demonstrated ground-breaking performance on tasks as varied as image captioning, language translation, and handwriting recognition. In this survey, we review and synthesize the research that over the past three decades first yielded and then made practical these powerful learning models. When appropriate, we reconcile conflicting notation and nomenclature. Our goal is to provide a self-contained explication of the state of the art together with a historical perspective and references to primary research.

Set-Based Prompting: Provably Solving the Language Model Order Dependency Problem

The development of generative language models that can create long and coherent textual outputs via autoregression has lead to a proliferation of uses and a corresponding sweep of analyses as researches work to determine the limitations of this new paradigm. Unlike humans, these 'Large Language Models' (LLMs) are highly sensitive to small changes in their inputs, leading to unwanted inconsistency in their behavior. One problematic inconsistency when LLMs are used to answer multiple-choice questions or analyze multiple inputs is order dependency: the output of an LLM can (and often does) change significantly when sub-sequences are swapped, despite both orderings being semantically identical. In this paper we present , a technique that guarantees the output of an LLM will not have order dependence on a specified set of sub-sequences. We show that this method provably eliminates order dependency, and that it can be applied to any transformer-based LLM to enable text generation that is unaffected by re-orderings. Delving into the implications of our method, we show that, despite our inputs being out of distribution, the impact on expected accuracy is small, where the expectation is over the order of uniformly chosen shuffling of the candidate responses, and usually significantly less in practice. Thus, can be used as a 'dropped-in' method on fully trained models. Finally, we discuss how our method's success suggests that other strong guarantees can be obtained on LLM performance via modifying the input representations.

Reducing Sequence Length by Predicting Edit Operations with Large Language Models

Large Language Models (LLMs) have demonstrated remarkable performance in various tasks and gained significant attention. LLMs are also used for local sequence transduction tasks, including grammatical error correction (GEC) and formality style transfer, where most tokens in a source text are kept unchanged. However, the models that generate all target tokens in such tasks have a tendency to simply copy the input text as is, without making needed changes, because the difference between input and output texts is minimal in the training data. This is also inefficient because the computational cost grows quadratically with the target sequence length with Transformer. This paper proposes predicting edit spans for the source text for local sequence transduction tasks. Representing an edit span with a position of the source text and corrected tokens, we can reduce the length of the target sequence and the computational cost for inference. We apply instruction tuning for LLMs on the supervision data of edit spans. Experiments show that the proposed method achieves comparable performance to the baseline in four tasks, paraphrasing, formality style transfer, GEC, and text simplification, despite reducing the length of the target text by as small as 21%. Furthermore, we report that the task-specific fine-tuning with the proposed method achieved state-of-the-art performance in the four tasks.

NL2TL: Transforming Natural Languages to Temporal Logics using Large Language Models

Temporal Logic (TL) can be used to rigorously specify complex high-level specification for systems in many engineering applications. The translation between natural language (NL) and TL has been under-explored due to the lack of dataset and generalizable model across different application domains. In this paper, we propose an accurate and generalizable transformation framework of English instructions from NL to TL, exploring the use of Large Language Models (LLMs) at multiple stages. Our contributions are twofold. First, we develop a framework to create a dataset of NL-TL pairs combining LLMs and human annotation. We publish a dataset with 28K NL-TL pairs. Then, we finetune T5 models on the lifted versions (i.e., the specific Atomic Propositions (AP) are hidden) of the NL and TL. The enhanced generalizability originates from two aspects: 1) Usage of lifted NL-TL characterizes common logical structures, without constraints of specific domains. 2) Application of LLMs in dataset creation largely enhances corpus richness. We test the generalization of trained models on five varied domains. To achieve full NL-TL transformation, we either combine the lifted model with AP recognition task or do the further finetuning on each specific domain. During the further finetuning, our model achieves higher accuracy (>95%) using only <10% training data, compared with the baseline sequence to sequence (Seq2Seq) model.

Pre-trained Language Models for Keyphrase Generation: A Thorough Empirical Study

Neural models that do not rely on pre-training have excelled in the keyphrase generation task with large annotated datasets. Meanwhile, new approaches have incorporated pre-trained language models (PLMs) for their data efficiency. However, there lacks a systematic study of how the two types of approaches compare and how different design choices can affect the performance of PLM-based models. To fill in this knowledge gap and facilitate a more informed use of PLMs for keyphrase extraction and keyphrase generation, we present an in-depth empirical study. Formulating keyphrase extraction as sequence labeling and keyphrase generation as sequence-to-sequence generation, we perform extensive experiments in three domains. After showing that PLMs have competitive high-resource performance and state-of-the-art low-resource performance, we investigate important design choices including in-domain PLMs, PLMs with different pre-training objectives, using PLMs with a parameter budget, and different formulations for present keyphrases. Further results show that (1) in-domain BERT-like PLMs can be used to build strong and data-efficient keyphrase generation models; (2) with a fixed parameter budget, prioritizing model depth over width and allocating more layers in the encoder leads to better encoder-decoder models; and (3) introducing four in-domain PLMs, we achieve a competitive performance in the news domain and the state-of-the-art performance in the scientific domain.

ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

Text2Node: a Cross-Domain System for Mapping Arbitrary Phrases to a Taxonomy

Electronic health record (EHR) systems are used extensively throughout the healthcare domain. However, data interchangeability between EHR systems is limited due to the use of different coding standards across systems. Existing methods of mapping coding standards based on manual human experts mapping, dictionary mapping, symbolic NLP and classification are unscalable and cannot accommodate large scale EHR datasets. In this work, we present Text2Node, a cross-domain mapping system capable of mapping medical phrases to concepts in a large taxonomy (such as SNOMED CT). The system is designed to generalize from a limited set of training samples and map phrases to elements of the taxonomy that are not covered by training data. As a result, our system is scalable, robust to wording variants between coding systems and can output highly relevant concepts when no exact concept exists in the target taxonomy. Text2Node operates in three main stages: first, the lexicon is mapped to word embeddings; second, the taxonomy is vectorized using node embeddings; and finally, the mapping function is trained to connect the two embedding spaces. We compared multiple algorithms and architectures for each stage of the training, including GloVe and FastText word embeddings, CNN and Bi-LSTM mapping functions, and node2vec for node embeddings. We confirmed the robustness and generalisation properties of Text2Node by mapping ICD-9-CM Diagnosis phrases to SNOMED CT and by zero-shot training at comparable accuracy. This system is a novel methodological contribution to the task of normalizing and linking phrases to a taxonomy, advancing data interchangeability in healthcare. When applied, the system can use electronic health records to generate an embedding that incorporates taxonomical medical knowledge to improve clinical predictive models.

An End-to-End Trainable Neural Network for Image-based Sequence Recognition and Its Application to Scene Text Recognition

Image-based sequence recognition has been a long-standing research topic in computer vision. In this paper, we investigate the problem of scene text recognition, which is among the most important and challenging tasks in image-based sequence recognition. A novel neural network architecture, which integrates feature extraction, sequence modeling and transcription into a unified framework, is proposed. Compared with previous systems for scene text recognition, the proposed architecture possesses four distinctive properties: (1) It is end-to-end trainable, in contrast to most of the existing algorithms whose components are separately trained and tuned. (2) It naturally handles sequences in arbitrary lengths, involving no character segmentation or horizontal scale normalization. (3) It is not confined to any predefined lexicon and achieves remarkable performances in both lexicon-free and lexicon-based scene text recognition tasks. (4) It generates an effective yet much smaller model, which is more practical for real-world application scenarios. The experiments on standard benchmarks, including the IIIT-5K, Street View Text and ICDAR datasets, demonstrate the superiority of the proposed algorithm over the prior arts. Moreover, the proposed algorithm performs well in the task of image-based music score recognition, which evidently verifies the generality of it.

Peptide Sequencing Via Protein Language Models

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

Training Language Models on Synthetic Edit Sequences Improves Code Synthesis

Software engineers mainly write code by editing existing programs. In contrast, large language models (LLMs) autoregressively synthesize programs in a single pass. One explanation for this is the scarcity of open-sourced edit data. While high-quality instruction data for code synthesis is already scarce, high-quality edit data is even scarcer. To fill this gap, we develop a synthetic data generation algorithm called LintSeq. This algorithm refactors existing code into a sequence of code edits by using a linter to procedurally sample across the error-free insertions that can be used to sequentially write programs. It outputs edit sequences as text strings consisting of consecutive program diffs. To test LintSeq, we use it to refactor a dataset of instruction + program pairs into instruction + program-diff-sequence tuples. Then, we instruction finetune a series of smaller LLMs ranging from 2.6B to 14B parameters on both the re-factored and original versions of this dataset, comparing zero-shot performance on code synthesis benchmarks. We show that during repeated sampling, edit sequence finetuned models produce more diverse programs than baselines. This results in better inference-time scaling for benchmark coverage as a function of samples, i.e. the fraction of problems "pass@k" solved by any attempt given "k" tries. For example, on HumanEval pass@50, small LLMs finetuned on synthetic edit sequences are competitive with GPT-4 and outperform models finetuned on the baseline dataset by +20% (+/-3%) in absolute score. Finally, we also pretrain our own tiny LMs for code understanding. We show that finetuning tiny models on synthetic code edits results in state-of-the-art code synthesis for the on-device model class. Our 150M parameter edit sequence LM matches or outperforms code models with twice as many parameters, both with and without repeated sampling, including Codex and AlphaCode.

Hydragen: High-Throughput LLM Inference with Shared Prefixes

Transformer-based large language models (LLMs) are now deployed to hundreds of millions of users. LLM inference is commonly performed on batches of sequences that share a prefix, such as few-shot examples or a chatbot system prompt. Decoding in this large-batch setting can be bottlenecked by the attention operation, which reads large key-value (KV) caches from memory and computes inefficient matrix-vector products for every sequence in the batch. In this work, we introduce Hydragen, a hardware-aware exact implementation of attention with shared prefixes. Hydragen computes attention over the shared prefix and unique suffixes separately. This decomposition enables efficient prefix attention by batching queries together across sequences, reducing redundant memory reads and enabling the use of hardware-friendly matrix multiplications. Our method can improve end-to-end LLM throughput by up to 32x against competitive baselines, with speedup growing with the batch size and shared prefix length. Hydragen also enables the use of very long shared contexts: with a high batch size, increasing the prefix length from 1K to 16K tokens decreases Hydragen throughput by less than 15%, while the throughput of baselines drops by over 90%. Hydragen generalizes beyond simple prefix-suffix decomposition and can be applied to tree-based prompt sharing patterns, allowing us to further reduce inference time on competitive programming problems by 55%.

LMUFormer: Low Complexity Yet Powerful Spiking Model With Legendre Memory Units

Transformer models have demonstrated high accuracy in numerous applications but have high complexity and lack sequential processing capability making them ill-suited for many streaming applications at the edge where devices are heavily resource-constrained. Thus motivated, many researchers have proposed reformulating the transformer models as RNN modules which modify the self-attention computation with explicit states. However, these approaches often incur significant performance degradation. The ultimate goal is to develop a model that has the following properties: parallel training, streaming and low-cost inference, and SOTA performance. In this paper, we propose a new direction to achieve this goal. We show how architectural modifications to a recurrent model can help push its performance toward Transformer models while retaining its sequential processing capability. Specifically, inspired by the recent success of Legendre Memory Units (LMU) in sequence learning tasks, we propose LMUFormer, which augments the LMU with convolutional patch embedding and convolutional channel mixer. Moreover, we present a spiking version of this architecture, which introduces the benefit of states within the patch embedding and channel mixer modules while simultaneously reducing the computing complexity. We evaluated our architectures on multiple sequence datasets. In comparison to SOTA transformer-based models within the ANN domain on the SCv2 dataset, our LMUFormer demonstrates comparable performance while necessitating a remarkable 53 times reduction in parameters and a substantial 65 times decrement in FLOPs. Additionally, owing to our model's proficiency in real-time data processing, we can achieve a 32.03% reduction in sequence length, all while incurring an inconsequential decline in performance. Our code is publicly available at https://github.com/zeyuliu1037/LMUFormer.git.

The Hyperfitting Phenomenon: Sharpening and Stabilizing LLMs for Open-Ended Text Generation

This paper introduces the counter-intuitive generalization results of overfitting pre-trained large language models (LLMs) on very small datasets. In the setting of open-ended text generation, it is well-documented that LLMs tend to generate repetitive and dull sequences, a phenomenon that is especially apparent when generating using greedy decoding. This issue persists even with state-of-the-art LLMs containing billions of parameters, trained via next-token prediction on large datasets. We find that by further fine-tuning these models to achieve a near-zero training loss on a small set of samples -- a process we refer to as hyperfitting -- the long-sequence generative capabilities are greatly enhanced. Greedy decoding with these Hyperfitted models even outperform Top-P sampling over long-sequences, both in terms of diversity and human preferences. This phenomenon extends to LLMs of various sizes, different domains, and even autoregressive image generation. We further find this phenomena to be distinctly different from that of Grokking and double descent. Surprisingly, our experiments indicate that hyperfitted models rarely fall into repeating sequences they were trained on, and even explicitly blocking these sequences results in high-quality output. All hyperfitted models produce extremely low-entropy predictions, often allocating nearly all probability to a single token.

LASP-2: Rethinking Sequence Parallelism for Linear Attention and Its Hybrid

Linear sequence modeling approaches, such as linear attention, provide advantages like linear-time training and constant-memory inference over sequence lengths. However, existing sequence parallelism (SP) methods are either not optimized for the right-product-first feature of linear attention or use a ring-style communication strategy, which results in lower computation parallelism, limits their scalability for longer sequences in distributed systems. In this paper, we introduce LASP-2, a new SP method to enhance both communication and computation parallelism when training linear attention transformer models with very-long input sequences. Compared to previous work LASP, LASP-2 rethinks the minimal communication requirement for SP on linear attention layers, reorganizes the whole communication-computation workflow of LASP. In this way, only one single AllGather collective communication is needed on intermediate memory states, whose sizes are independent of the sequence length, leading to significant improvements of both communication and computation parallelism, as well as their overlap. Additionally, we extend LASP-2 to LASP-2H by applying similar communication redesign to standard attention modules, offering an efficient SP solution for hybrid models that blend linear and standard attention layers. Our evaluation on a Linear-Llama3 model, a variant of Llama3 with linear attention replacing standard attention, demonstrates the effectiveness of LASP-2 and LASP-2H. Specifically, LASP-2 achieves training speed improvements of 15.2% over LASP and 36.6% over Ring Attention, with a sequence length of 2048K across 64 GPUs. The Code is released as a part of: https://github.com/OpenSparseLLMs/Linear-MoE.

Dataset Decomposition: Faster LLM Training with Variable Sequence Length Curriculum

Large language models (LLMs) are commonly trained on datasets consisting of fixed-length token sequences. These datasets are created by randomly concatenating documents of various lengths and then chunking them into sequences of a predetermined target length. However, this method of concatenation can lead to cross-document attention within a sequence, which is neither a desirable learning signal nor computationally efficient. Additionally, training on long sequences becomes computationally prohibitive due to the quadratic cost of attention. In this study, we introduce dataset decomposition, a novel variable sequence length training technique, to tackle these challenges. We decompose a dataset into a union of buckets, each containing sequences of the same size extracted from a unique document. During training, we use variable sequence length and batch size, sampling simultaneously from all buckets with a curriculum. In contrast to the concat-and-chunk baseline, which incurs a fixed attention cost at every step of training, our proposed method incurs a penalty proportional to the actual document lengths at each step, resulting in significant savings in training time. We train an 8k context-length 1B model at the same cost as a 2k context-length model trained with the baseline approach. Experiments on a web-scale corpus demonstrate that our approach significantly enhances performance on standard language evaluations and long-context benchmarks, reaching target accuracy 3x faster compared to the baseline. Our method not only enables efficient pretraining on long sequences but also scales effectively with dataset size. Lastly, we shed light on a critical yet less studied aspect of training large language models: the distribution and curriculum of sequence lengths, which results in a non-negligible difference in performance.

Sequence-to-Action: Grammatical Error Correction with Action Guided Sequence Generation

The task of Grammatical Error Correction (GEC) has received remarkable attention with wide applications in Natural Language Processing (NLP) in recent years. While one of the key principles of GEC is to keep the correct parts unchanged and avoid over-correction, previous sequence-to-sequence (seq2seq) models generate results from scratch, which are not guaranteed to follow the original sentence structure and may suffer from the over-correction problem. In the meantime, the recently proposed sequence tagging models can overcome the over-correction problem by only generating edit operations, but are conditioned on human designed language-specific tagging labels. In this paper, we combine the pros and alleviate the cons of both models by proposing a novel Sequence-to-Action~(S2A) module. The S2A module jointly takes the source and target sentences as input, and is able to automatically generate a token-level action sequence before predicting each token, where each action is generated from three choices named SKIP, COPY and GENerate. Then the actions are fused with the basic seq2seq framework to provide final predictions. We conduct experiments on the benchmark datasets of both English and Chinese GEC tasks. Our model consistently outperforms the seq2seq baselines, while being able to significantly alleviate the over-correction problem as well as holding better generality and diversity in the generation results compared to the sequence tagging models.

Sparse Modular Activation for Efficient Sequence Modeling

Linear State Space Models (SSMs) have demonstrated strong performance in a variety of sequence modeling tasks due to their efficient encoding of the recurrent structure. However, in more comprehensive tasks like language modeling and machine translation, self-attention-based models still outperform SSMs. Hybrid models employing both SSM and self-attention generally show promising performance, but current approaches apply attention modules statically and uniformly to all elements in the input sequences, leading to sub-optimal quality-efficiency trade-offs. In this work, we introduce Sparse Modular Activation (SMA), a general mechanism enabling neural networks to sparsely and dynamically activate sub-modules for sequence elements in a differentiable manner. Through allowing each element to skip non-activated sub-modules, SMA reduces computation and memory consumption at both training and inference stages of sequence modeling. As a specific instantiation of SMA, we design a novel neural architecture, SeqBoat, which employs SMA to sparsely activate a Gated Attention Unit (GAU) based on the state representations learned from an SSM. By constraining the GAU to only conduct local attention on the activated inputs, SeqBoat can achieve linear inference complexity with theoretically infinite attention span, and provide substantially better quality-efficiency trade-off than the chunking-based models. With experiments on a wide range of tasks, including language modeling, speech classification and long-range arena, SeqBoat brings new state-of-the-art results among hybrid models with linear complexity and reveals the amount of attention needed for each task through the learned sparse activation patterns.

Combining Recurrent, Convolutional, and Continuous-time Models with Linear State-Space Layers

Recurrent neural networks (RNNs), temporal convolutions, and neural differential equations (NDEs) are popular families of deep learning models for time-series data, each with unique strengths and tradeoffs in modeling power and computational efficiency. We introduce a simple sequence model inspired by control systems that generalizes these approaches while addressing their shortcomings. The Linear State-Space Layer (LSSL) maps a sequence u mapsto y by simply simulating a linear continuous-time state-space representation x = Ax + Bu, y = Cx + Du. Theoretically, we show that LSSL models are closely related to the three aforementioned families of models and inherit their strengths. For example, they generalize convolutions to continuous-time, explain common RNN heuristics, and share features of NDEs such as time-scale adaptation. We then incorporate and generalize recent theory on continuous-time memorization to introduce a trainable subset of structured matrices A that endow LSSLs with long-range memory. Empirically, stacking LSSL layers into a simple deep neural network obtains state-of-the-art results across time series benchmarks for long dependencies in sequential image classification, real-world healthcare regression tasks, and speech. On a difficult speech classification task with length-16000 sequences, LSSL outperforms prior approaches by 24 accuracy points, and even outperforms baselines that use hand-crafted features on 100x shorter sequences.

Reprogramming Pretrained Language Models for Antibody Sequence Infilling

Antibodies comprise the most versatile class of binding molecules, with numerous applications in biomedicine. Computational design of antibodies involves generating novel and diverse sequences, while maintaining structural consistency. Unique to antibodies, designing the complementarity-determining region (CDR), which determines the antigen binding affinity and specificity, creates its own unique challenges. Recent deep learning models have shown impressive results, however the limited number of known antibody sequence/structure pairs frequently leads to degraded performance, particularly lacking diversity in the generated sequences. In our work we address this challenge by leveraging Model Reprogramming (MR), which repurposes pretrained models on a source language to adapt to the tasks that are in a different language and have scarce data - where it may be difficult to train a high-performing model from scratch or effectively fine-tune an existing pre-trained model on the specific task. Specifically, we introduce ReprogBert in which a pretrained English language model is repurposed for protein sequence infilling - thus considers cross-language adaptation using less data. Results on antibody design benchmarks show that our model on low-resourced antibody sequence dataset provides highly diverse CDR sequences, up to more than a two-fold increase of diversity over the baselines, without losing structural integrity and naturalness. The generated sequences also demonstrate enhanced antigen binding specificity and virus neutralization ability. Code is available at https://github.com/IBM/ReprogBERT

InfAlign: Inference-aware language model alignment

Language model alignment has become a critical step in training modern generative language models. The goal of alignment is to finetune a reference model such that the win rate of a sample from the aligned model over a sample from the reference model is high, subject to a KL divergence constraint. Today, we are increasingly using inference-time algorithms (e.g., Best-of-N, controlled decoding, tree search) to decode from language models rather than standard sampling. However, the alignment objective does not capture such inference-time decoding procedures. We show that the existing alignment framework is sub-optimal in view of such inference-time methods. We then modify the alignment objective and propose a framework for inference-aware alignment (IAPO). We prove that for any inference-time decoding algorithm, the optimal solution that optimizes the inference-time win rate of the aligned policy against the reference policy is the solution to the typical RLHF problem with a transformation of the reward. This motivates us to provide the KL-regularized calibrate-and-transform RL (CTRL) algorithm to solve this problem, which involves a reward calibration step and a KL-regularized reward maximization step with a transformation of the calibrated reward. We particularize our study to two important inference-time strategies: best-of-N sampling and best-of-N jailbreaking, where N responses are sampled from the model and the one with the highest or lowest reward is selected. We propose specific transformations for these strategies and demonstrate that our framework offers significant improvements over existing state-of-the-art methods for language model alignment. Empirically, we outperform baselines that are designed without taking inference-time decoding into consideration by 8-12% and 4-9% on inference-time win rates over the Anthropic helpfulness and harmlessness dialog benchmark datasets.

Representation, Exploration and Recommendation of Music Playlists

Playlists have become a significant part of our listening experience because of the digital cloud-based services such as Spotify, Pandora, Apple Music. Owing to the meteoric rise in the usage of playlists, recommending playlists is crucial to music services today. Although there has been a lot of work done in playlist prediction, the area of playlist representation hasn't received that level of attention. Over the last few years, sequence-to-sequence models, especially in the field of natural language processing, have shown the effectiveness of learned embeddings in capturing the semantic characteristics of sequences. We can apply similar concepts to music to learn fixed length representations for playlists and use those representations for downstream tasks such as playlist discovery, browsing, and recommendation. In this work, we formulate the problem of learning a fixed-length playlist representation in an unsupervised manner, using Sequence-to-sequence (Seq2seq) models, interpreting playlists as sentences and songs as words. We compare our model with two other encoding architectures for baseline comparison. We evaluate our work using the suite of tasks commonly used for assessing sentence embeddings, along with a few additional tasks pertaining to music, and a recommendation task to study the traits captured by the playlist embeddings and their effectiveness for the purpose of music recommendation.

Machine learning applications to DNA subsequence and restriction site analysis

Based on the BioBricks standard, restriction synthesis is a novel catabolic iterative DNA synthesis method that utilizes endonucleases to synthesize a query sequence from a reference sequence. In this work, the reference sequence is built from shorter subsequences by classifying them as applicable or inapplicable for the synthesis method using three different machine learning methods: Support Vector Machines (SVMs), random forest, and Convolution Neural Networks (CNNs). Before applying these methods to the data, a series of feature selection, curation, and reduction steps are applied to create an accurate and representative feature space. Following these preprocessing steps, three different pipelines are proposed to classify subsequences based on their nucleotide sequence and other relevant features corresponding to the restriction sites of over 200 endonucleases. The sensitivity using SVMs, random forest, and CNNs are 94.9%, 92.7%, 91.4%, respectively. Moreover, each method scores lower in specificity with SVMs, random forest, and CNNs resulting in 77.4%, 85.7%, and 82.4%, respectively. In addition to analyzing these results, the misclassifications in SVMs and CNNs are investigated. Across these two models, different features with a derived nucleotide specificity visually contribute more to classification compared to other features. This observation is an important factor when considering new nucleotide sensitivity features for future studies.

VALL-E R: Robust and Efficient Zero-Shot Text-to-Speech Synthesis via Monotonic Alignment

With the help of discrete neural audio codecs, large language models (LLM) have increasingly been recognized as a promising methodology for zero-shot Text-to-Speech (TTS) synthesis. However, sampling based decoding strategies bring astonishing diversity to generation, but also pose robustness issues such as typos, omissions and repetition. In addition, the high sampling rate of audio also brings huge computational overhead to the inference process of autoregression. To address these issues, we propose VALL-E R, a robust and efficient zero-shot TTS system, building upon the foundation of VALL-E. Specifically, we introduce a phoneme monotonic alignment strategy to strengthen the connection between phonemes and acoustic sequence, ensuring a more precise alignment by constraining the acoustic tokens to match their associated phonemes. Furthermore, we employ a codec-merging approach to downsample the discrete codes in shallow quantization layer, thereby accelerating the decoding speed while preserving the high quality of speech output. Benefiting from these strategies, VALL-E R obtains controllablity over phonemes and demonstrates its strong robustness by approaching the WER of ground truth. In addition, it requires fewer autoregressive steps, with over 60% time reduction during inference. This research has the potential to be applied to meaningful projects, including the creation of speech for those affected by aphasia. Audio samples will be available at: https://aka.ms/valler.

Metasql: A Generate-then-Rank Framework for Natural Language to SQL Translation

The Natural Language Interface to Databases (NLIDB) empowers non-technical users with database access through intuitive natural language (NL) interactions. Advanced approaches, utilizing neural sequence-to-sequence models or large-scale language models, typically employ auto-regressive decoding to generate unique SQL queries sequentially. While these translation models have greatly improved the overall translation accuracy, surpassing 70% on NLIDB benchmarks, the use of auto-regressive decoding to generate single SQL queries may result in sub-optimal outputs, potentially leading to erroneous translations. In this paper, we propose Metasql, a unified generate-then-rank framework that can be flexibly incorporated with existing NLIDBs to consistently improve their translation accuracy. Metasql introduces query metadata to control the generation of better SQL query candidates and uses learning-to-rank algorithms to retrieve globally optimized queries. Specifically, Metasql first breaks down the meaning of the given NL query into a set of possible query metadata, representing the basic concepts of the semantics. These metadata are then used as language constraints to steer the underlying translation model toward generating a set of candidate SQL queries. Finally, Metasql ranks the candidates to identify the best matching one for the given NL query. Extensive experiments are performed to study Metasql on two public NLIDB benchmarks. The results show that the performance of the translation models can be effectively improved using Metasql.