Daily Papers

Semantic search for candidate retrieval is an important yet neglected problem in retrieval-based Chatbots, which aims to select a bunch of candidate responses efficiently from a large pool. The existing bottleneck is to ensure the model architecture having two points: 1) rich interactions between a query and a response to produce query-relevant responses; 2) ability of separately projecting the query and the response into latent spaces to apply efficiently in semantic search during online inference. To tackle this problem, we propose a novel approach, called Multitask-based Semantic Search Neural Network (MSSNN) for candidate retrieval, which accomplishes query-response interactions through multi-tasks. The method employs a Seq2Seq modeling task to learn a good query encoder, and then performs a word prediction task to build response embeddings, finally conducts a simple matching model to form the dot-product scorer. Experimental studies have demonstrated the potential of the proposed approach.

We propose a novel text-to-speech (TTS) framework centered around a neural transducer. Our approach divides the whole TTS pipeline into semantic-level sequence-to-sequence (seq2seq) modeling and fine-grained acoustic modeling stages, utilizing discrete semantic tokens obtained from wav2vec2.0 embeddings. For a robust and efficient alignment modeling, we employ a neural transducer named token transducer for the semantic token prediction, benefiting from its hard monotonic alignment constraints. Subsequently, a non-autoregressive (NAR) speech generator efficiently synthesizes waveforms from these semantic tokens. Additionally, a reference speech controls temporal dynamics and acoustic conditions at each stage. This decoupled framework reduces the training complexity of TTS while allowing each stage to focus on semantic and acoustic modeling. Our experimental results on zero-shot adaptive TTS demonstrate that our model surpasses the baseline in terms of speech quality and speaker similarity, both objectively and subjectively. We also delve into the inference speed and prosody control capabilities of our approach, highlighting the potential of neural transducers in TTS frameworks.

Aligning the behavior of Large language models (LLMs) with human intentions and values remains a critical challenge. Reinforcement learning from human feedback (RLHF) aligns LLMs by training a reward model (RM) on human preferences and fine-tuning the LLMs to maximize RM feedback. Despite its effectiveness and popularity, RLHF is prone to biased local optimization. It means RM fails to provide feedback that accurately aligns with human preference, causing LLMs to explore unexpected generalizations, and failing to achieve alignment objectives. To mitigate this issue, we propose a novel sequence-to-sequence (seq2seq) reward modeling method. Its key insight is that learning from language feedback rather than scalar feedback improves RLHF without additional annotations. We replaced the reward modeling target from binary maximum likelihood estimation (MLE) with sequence MLE. This method enables richer and fine-grained language feedback without additional annotations, models, or training stages. Our experiments demonstrated its effectiveness, specifically, reducing the refusal-to-response paradigm in single-turn safety dialogues and the long-response bias in text summarization tasks. We provide further analysis that seq2seq RM improves RLHF performance across 2B and 7B LLMs on 3 NLP tasks, achieving an average win rate of 76.9\%. We further show that seq2seq RM can still improve the performance of RLHF under out-of-distribution prompts.

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.

The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine translation (NMT), have achieved state-of-the-art performance on these tasks by treating source code as a sequence of tokens. We present {scriptsize CODE2SEQ}: an alternative approach that leverages the syntactic structure of programming languages to better encode source code. Our model represents a code snippet as the set of compositional paths in its abstract syntax tree (AST) and uses attention to select the relevant paths while decoding. We demonstrate the effectiveness of our approach for two tasks, two programming languages, and four datasets of up to 16M examples. Our model significantly outperforms previous models that were specifically designed for programming languages, as well as state-of-the-art NMT models. An interactive online demo of our model is available at http://code2seq.org. Our code, data and trained models are available at http://github.com/tech-srl/code2seq.

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.

Recently, diffusion models have emerged as a new paradigm for generative models. Despite the success in domains using continuous signals such as vision and audio, adapting diffusion models to natural language is under-explored due to the discrete nature of texts, especially for conditional generation. We tackle this challenge by proposing DiffuSeq: a diffusion model designed for sequence-to-sequence (Seq2Seq) text generation tasks. Upon extensive evaluation over a wide range of Seq2Seq tasks, we find DiffuSeq achieving comparable or even better performance than six established baselines, including a state-of-the-art model that is based on pre-trained language models. Apart from quality, an intriguing property of DiffuSeq is its high diversity during generation, which is desired in many Seq2Seq tasks. We further include a theoretical analysis revealing the connection between DiffuSeq and autoregressive/non-autoregressive models. Bringing together theoretical analysis and empirical evidence, we demonstrate the great potential of diffusion models in complex conditional language generation tasks. Code is available at https://github.com/Shark-NLP/DiffuSeq

In this work, we demonstrate that multilingual large-scale sequence-to-sequence (seq2seq) models, pre-trained on a mixture of denoising and Causal Language Modeling (CLM) tasks, are more efficient few-shot learners than decoder-only models on various tasks. In particular, we train a 20 billion parameter multilingual seq2seq model called Alexa Teacher Model (AlexaTM 20B) and show that it achieves state-of-the-art (SOTA) performance on 1-shot summarization tasks, outperforming a much larger 540B PaLM decoder model. AlexaTM 20B also achieves SOTA in 1-shot machine translation, especially for low-resource languages, across almost all language pairs supported by the model (Arabic, English, French, German, Hindi, Italian, Japanese, Marathi, Portuguese, Spanish, Tamil, and Telugu) on Flores-101 dataset. We also show in zero-shot setting, AlexaTM 20B outperforms GPT3 (175B) on SuperGLUE and SQuADv2 datasets and provides SOTA performance on multilingual tasks such as XNLI, XCOPA, Paws-X, and XWinograd. Overall, our results present a compelling case for seq2seq models as a powerful alternative to decoder-only models for Large-scale Language Model (LLM) training.

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.

Various Seq2Seq learning models designed for machine translation were applied for abstractive summarization task recently. Despite these models provide high ROUGE scores, they are limited to generate comprehensive summaries with a high level of abstraction due to its degenerated attention distribution. We introduce Diverse Convolutional Seq2Seq Model(DivCNN Seq2Seq) using Determinantal Point Processes methods(Micro DPPs and Macro DPPs) to produce attention distribution considering both quality and diversity. Without breaking the end to end architecture, DivCNN Seq2Seq achieves a higher level of comprehensiveness compared to vanilla models and strong baselines. All the reproducible codes and datasets are available online.

Semantic parsing models with applications in task oriented dialog systems require efficient sequence to sequence (seq2seq) architectures to be run on-device. To this end, we propose a projection based encoder-decoder model referred to as pQRNN-MAtt. Studies based on projection methods were restricted to encoder-only models, and we believe this is the first study extending it to seq2seq architectures. The resulting quantized models are less than 3.5MB in size and are well suited for on-device latency critical applications. We show that on MTOP, a challenging multilingual semantic parsing dataset, the average model performance surpasses LSTM based seq2seq model that uses pre-trained embeddings despite being 85x smaller. Furthermore, the model can be an effective student for distilling large pre-trained models such as T5/BERT.

In text-to-SQL task, seq-to-seq models often lead to sub-optimal performance due to limitations in their architecture. In this paper, we present a simple yet effective approach that adapts transformer-based seq-to-seq model to robust text-to-SQL generation. Instead of inducing constraint to decoder or reformat the task as slot-filling, we propose to train seq-to-seq model with Schema aware Denoising (SeaD), which consists of two denoising objectives that train model to either recover input or predict output from two novel erosion and shuffle noises. These denoising objectives acts as the auxiliary tasks for better modeling the structural data in S2S generation. In addition, we improve and propose a clause-sensitive execution guided (EG) decoding strategy to overcome the limitation of EG decoding for generative model. The experiments show that the proposed method improves the performance of seq-to-seq model in both schema linking and grammar correctness and establishes new state-of-the-art on WikiSQL benchmark. The results indicate that the capacity of vanilla seq-to-seq architecture for text-to-SQL may have been under-estimated.

Sequence-to-sequence (Seq2Seq) models with attention have excelled at tasks which involve generating natural language sentences such as machine translation, image captioning and speech recognition. Performance has further been improved by leveraging unlabeled data, often in the form of a language model. In this work, we present the Cold Fusion method, which leverages a pre-trained language model during training, and show its effectiveness on the speech recognition task. We show that Seq2Seq models with Cold Fusion are able to better utilize language information enjoying i) faster convergence and better generalization, and ii) almost complete transfer to a new domain while using less than 10% of the labeled training data.

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

Splitting and rephrasing a complex sentence into several shorter sentences that convey the same meaning is a challenging problem in NLP. We show that while vanilla seq2seq models can reach high scores on the proposed benchmark (Narayan et al., 2017), they suffer from memorization of the training set which contains more than 89% of the unique simple sentences from the validation and test sets. To aid this, we present a new train-development-test data split and neural models augmented with a copy-mechanism, outperforming the best reported baseline by 8.68 BLEU and fostering further progress on the task.

Extreme multi-label text classification (XMTC) is the task of finding the most relevant subset labels from an extremely large-scale label collection. Recently, some deep learning models have achieved state-of-the-art results in XMTC tasks. These models commonly predict scores for all labels by a fully connected layer as the last layer of the model. However, such models can't predict a relatively complete and variable-length label subset for each document, because they select positive labels relevant to the document by a fixed threshold or take top k labels in descending order of scores. A less popular type of deep learning models called sequence-to-sequence (Seq2Seq) focus on predicting variable-length positive labels in sequence style. However, the labels in XMTC tasks are essentially an unordered set rather than an ordered sequence, the default order of labels restrains Seq2Seq models in training. To address this limitation in Seq2Seq, we propose an autoregressive sequence-to-set model for XMTC tasks named OTSeq2Set. Our model generates predictions in student-forcing scheme and is trained by a loss function based on bipartite matching which enables permutation-invariance. Meanwhile, we use the optimal transport distance as a measurement to force the model to focus on the closest labels in semantic label space. Experiments show that OTSeq2Set outperforms other competitive baselines on 4 benchmark datasets. Especially, on the Wikipedia dataset with 31k labels, it outperforms the state-of-the-art Seq2Seq method by 16.34% in micro-F1 score. The code is available at https://github.com/caojie54/OTSeq2Set.

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.

Recent work has witnessed a paradigm shift from Seq2Seq to Seq2Edit in the field of text editing, with the aim of addressing the slow autoregressive inference problem posed by the former. Despite promising results, Seq2Edit approaches still face several challenges such as inflexibility in generation and difficulty in generalizing to other languages. In this work, we propose a novel non-autoregressive text editing method to circumvent the above issues, by modeling the edit process with latent CTC alignments. We make a crucial extension to CTC by introducing the copy operation into the edit space, thus enabling more efficient management of textual overlap in editing. We conduct extensive experiments on GEC and sentence fusion tasks, showing that our proposed method significantly outperforms existing Seq2Edit models and achieves similar or even better results than Seq2Seq with over 4times speedup. Moreover, it demonstrates good generalizability on German and Russian. In-depth analyses reveal the strengths of our method in terms of the robustness under various scenarios and generating fluent and flexible outputs.

Keyphrase Generation (KPG) is a longstanding task in NLP with widespread applications. The advent of sequence-to-sequence (seq2seq) pre-trained language models (PLMs) has ushered in a transformative era for KPG, yielding promising performance improvements. However, many design decisions remain unexplored and are often made arbitrarily. This paper undertakes a systematic analysis of the influence of model selection and decoding strategies on PLM-based KPG. We begin by elucidating why seq2seq PLMs are apt for KPG, anchored by an attention-driven hypothesis. We then establish that conventional wisdom for selecting seq2seq PLMs lacks depth: (1) merely increasing model size or performing task-specific adaptation is not parameter-efficient; (2) although combining in-domain pre-training with task adaptation benefits KPG, it does partially hinder generalization. Regarding decoding, we demonstrate that while greedy search achieves strong F1 scores, it lags in recall compared with sampling-based methods. Based on these insights, we propose DeSel, a likelihood-based decode-select algorithm for seq2seq PLMs. DeSel improves greedy search by an average of 4.7% semantic F1 across five datasets. Our collective findings pave the way for deeper future investigations into PLM-based KPG.

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.

Translating natural language queries into SQLs in a seq2seq manner has attracted much attention recently. However, compared with abstract-syntactic-tree-based SQL generation, seq2seq semantic parsers face much more challenges, including poor quality on schematical information prediction and poor semantic coherence between natural language queries and SQLs. This paper analyses the above difficulties and proposes a seq2seq-oriented decoding strategy called SR, which includes a new intermediate representation SSQL and a reranking method with score re-estimator to solve the above obstacles respectively. Experimental results demonstrate the effectiveness of our proposed techniques and T5-SR-3b achieves new state-of-the-art results on the Spider dataset.

In this paper, we generalize text infilling (e.g., masked language models) by proposing Sequence Span Rewriting (SSR) as a self-supervised sequence-to-sequence (seq2seq) pre-training objective. SSR provides more fine-grained learning signals for text representations by supervising the model to rewrite imperfect spans to ground truth, and it is more consistent than text infilling with many downstream seq2seq tasks that rewrite a source sentences into a target sentence. Our experiments with T5 models on various seq2seq tasks show that SSR can substantially improve seq2seq pre-training. Moreover, we observe SSR is especially helpful to improve pre-training a small-size seq2seq model with a powerful imperfect span generator, which indicates a new perspective of transferring knowledge from a large model to a smaller model for seq2seq pre-training.

We consider incorporating topic information into the sequence-to-sequence framework to generate informative and interesting responses for chatbots. To this end, we propose a topic aware sequence-to-sequence (TA-Seq2Seq) model. The model utilizes topics to simulate prior knowledge of human that guides them to form informative and interesting responses in conversation, and leverages the topic information in generation by a joint attention mechanism and a biased generation probability. The joint attention mechanism summarizes the hidden vectors of an input message as context vectors by message attention, synthesizes topic vectors by topic attention from the topic words of the message obtained from a pre-trained LDA model, and let these vectors jointly affect the generation of words in decoding. To increase the possibility of topic words appearing in responses, the model modifies the generation probability of topic words by adding an extra probability item to bias the overall distribution. Empirical study on both automatic evaluation metrics and human annotations shows that TA-Seq2Seq can generate more informative and interesting responses, and significantly outperform the-state-of-the-art response generation models.

Diffusion model, a new generative modelling paradigm, has achieved great success in image, audio, and video generation. However, considering the discrete categorical nature of text, it is not trivial to extend continuous diffusion models to natural language, and text diffusion models are less studied. Sequence-to-sequence text generation is one of the essential natural language processing topics. In this work, we apply diffusion models to approach sequence-to-sequence text generation, and explore whether the superiority generation performance of diffusion model can transfer to natural language domain. We propose SeqDiffuSeq, a text diffusion model for sequence-to-sequence generation. SeqDiffuSeq uses an encoder-decoder Transformers architecture to model denoising function. In order to improve generation quality, SeqDiffuSeq combines the self-conditioning technique and a newly proposed adaptive noise schedule technique. The adaptive noise schedule has the difficulty of denoising evenly distributed across time steps, and considers exclusive noise schedules for tokens at different positional order. Experiment results illustrate the good performance on sequence-to-sequence generation in terms of text quality and inference time.

Recently, sequence-to-sequence (seq2seq) models with the Transformer architecture have achieved remarkable performance on various conditional text generation tasks, such as machine translation. However, most of them are trained with teacher forcing with the ground truth label given at each time step, without being exposed to incorrectly generated tokens during training, which hurts its generalization to unseen inputs, that is known as the "exposure bias" problem. In this work, we propose to mitigate the conditional text generation problem by contrasting positive pairs with negative pairs, such that the model is exposed to various valid or incorrect perturbations of the inputs, for improved generalization. However, training the model with naive contrastive learning framework using random non-target sequences as negative examples is suboptimal, since they are easily distinguishable from the correct output, especially so with models pretrained with large text corpora. Also, generating positive examples requires domain-specific augmentation heuristics which may not generalize over diverse domains. To tackle this problem, we propose a principled method to generate positive and negative samples for contrastive learning of seq2seq models. Specifically, we generate negative examples by adding small perturbations to the input sequence to minimize its conditional likelihood, and positive examples by adding large perturbations while enforcing it to have a high conditional likelihood. Such "hard" positive and negative pairs generated using our method guides the model to better distinguish correct outputs from incorrect ones. We empirically show that our proposed method significantly improves the generalization of the seq2seq on three text generation tasks - machine translation, text summarization, and question generation.

This work aims to predict channels in wireless communication systems based on noisy observations, utilizing sequence-to-sequence models with attention (Seq2Seq-attn) and transformer models. Both models are adapted from natural language processing to tackle the complex challenge of channel prediction. Additionally, a new technique called reverse positional encoding is introduced in the transformer model to improve the robustness of the model against varying sequence lengths. Similarly, the encoder outputs of the Seq2Seq-attn model are reversed before applying attention. Simulation results demonstrate that the proposed ordering techniques allow the models to better capture the relationships between the channel snapshots within the sequence, irrespective of the sequence length, as opposed to existing methods.

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.

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.

The goal of text generation is to make machines express in human language. It is one of the most important yet challenging tasks in natural language processing (NLP). Since 2014, various neural encoder-decoder models pioneered by Seq2Seq have been proposed to achieve the goal by learning to map input text to output text. However, the input text alone often provides limited knowledge to generate the desired output, so the performance of text generation is still far from satisfaction in many real-world scenarios. To address this issue, researchers have considered incorporating various forms of knowledge beyond the input text into the generation models. This research direction is known as knowledge-enhanced text generation. In this survey, we present a comprehensive review of the research on knowledge enhanced text generation over the past five years. The main content includes two parts: (i) general methods and architectures for integrating knowledge into text generation; (ii) specific techniques and applications according to different forms of knowledge data. This survey can have broad audiences, researchers and practitioners, in academia and industry.

Long-range dependencies are critical for understanding genomic structure and function, yet most conventional methods struggle with them. Widely adopted transformer-based models, while excelling at short-context tasks, are limited by the attention module's quadratic computational complexity and inability to extrapolate to sequences longer than those seen in training. In this work, we explore State Space Models (SSMs) as a promising alternative by benchmarking two SSM-inspired architectures, Caduceus and Hawk, on long-range genomics modeling tasks under conditions parallel to a 50M parameter transformer baseline. We discover that SSMs match transformer performance and exhibit impressive zero-shot extrapolation across multiple tasks, handling contexts 10 to 100 times longer than those seen during training, indicating more generalizable representations better suited for modeling the long and complex human genome. Moreover, we demonstrate that these models can efficiently process sequences of 1M tokens on a single GPU, allowing for modeling entire genomic regions at once, even in labs with limited compute. Our findings establish SSMs as efficient and scalable for long-context genomic analysis.

One of the recent best attempts at Text-to-SQL is the pre-trained language model. Due to the structural property of the SQL queries, the seq2seq model takes the responsibility of parsing both the schema items (i.e., tables and columns) and the skeleton (i.e., SQL keywords). Such coupled targets increase the difficulty of parsing the correct SQL queries especially when they involve many schema items and logic operators. This paper proposes a ranking-enhanced encoding and skeleton-aware decoding framework to decouple the schema linking and the skeleton parsing. Specifically, for a seq2seq encoder-decode model, its encoder is injected by the most relevant schema items instead of the whole unordered ones, which could alleviate the schema linking effort during SQL parsing, and its decoder first generates the skeleton and then the actual SQL query, which could implicitly constrain the SQL parsing. We evaluate our proposed framework on Spider and its three robustness variants: Spider-DK, Spider-Syn, and Spider-Realistic. The experimental results show that our framework delivers promising performance and robustness. Our code is available at https://github.com/RUCKBReasoning/RESDSQL.

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.

Several recent works have suggested to represent semantic relations with questions and answers, decomposing textual information into separate interrogative natural language statements. In this paper, we consider three QA-based semantic tasks - namely, QA-SRL, QANom and QADiscourse, each targeting a certain type of predication - and propose to regard them as jointly providing a comprehensive representation of textual information. To promote this goal, we investigate how to best utilize the power of sequence-to-sequence (seq2seq) pre-trained language models, within the unique setup of semi-structured outputs, consisting of an unordered set of question-answer pairs. We examine different input and output linearization strategies, and assess the effect of multitask learning and of simple data augmentation techniques in the setting of imbalanced training data. Consequently, we release the first unified QASem parsing tool, practical for downstream applications who can benefit from an explicit, QA-based account of information units in a text.

Recent studies on AMR-to-text generation often formalize the task as a sequence-to-sequence (seq2seq) learning problem by converting an Abstract Meaning Representation (AMR) graph into a word sequence. Graph structures are further modeled into the seq2seq framework in order to utilize the structural information in the AMR graphs. However, previous approaches only consider the relations between directly connected concepts while ignoring the rich structure in AMR graphs. In this paper we eliminate such a strong limitation and propose a novel structure-aware self-attention approach to better modeling the relations between indirectly connected concepts in the state-of-the-art seq2seq model, i.e., the Transformer. In particular, a few different methods are explored to learn structural representations between two concepts. Experimental results on English AMR benchmark datasets show that our approach significantly outperforms the state of the art with 29.66 and 31.82 BLEU scores on LDC2015E86 and LDC2017T10, respectively. To the best of our knowledge, these are the best results achieved so far by supervised models on the benchmarks.

Traditional sequence-to-sequence (seq2seq) models and other variations of the attention-mechanism such as hierarchical attention have been applied to the text summarization problem. Though there is a hierarchy in the way humans use language by forming paragraphs from sentences and sentences from words, hierarchical models have usually not worked that much better than their traditional seq2seq counterparts. This effect is mainly because either the hierarchical attention mechanisms are too sparse using hard attention or noisy using soft attention. In this paper, we propose a method based on extracting the highlights of a document; a key concept that is conveyed in a few sentences. In a typical text summarization dataset consisting of documents that are 800 tokens in length (average), capturing long-term dependencies is very important, e.g., the last sentence can be grouped with the first sentence of a document to form a summary. LSTMs (Long Short-Term Memory) proved useful for machine translation. However, they often fail to capture long-term dependencies while modeling long sequences. To address these issues, we have adapted Neural Semantic Encoders (NSE) to text summarization, a class of memory-augmented neural networks by improving its functionalities and proposed a novel hierarchical NSE that outperforms similar previous models significantly. The quality of summarization was improved by augmenting linguistic factors, namely lemma, and Part-of-Speech (PoS) tags, to each word in the dataset for improved vocabulary coverage and generalization. The hierarchical NSE model on factored dataset outperformed the state-of-the-art by nearly 4 ROUGE points. We further designed and used the first GPU-based self-critical Reinforcement Learning model.

Ordinal regression refers to classifying object instances into ordinal categories. It has been widely studied in many scenarios, such as medical disease grading, movie rating, etc. Known methods focused only on learning inter-class ordinal relationships, but still incur limitations in distinguishing adjacent categories thus far. In this paper, we propose a simple sequence prediction framework for ordinal regression called Ord2Seq, which, for the first time, transforms each ordinal category label into a special label sequence and thus regards an ordinal regression task as a sequence prediction process. In this way, we decompose an ordinal regression task into a series of recursive binary classification steps, so as to subtly distinguish adjacent categories. Comprehensive experiments show the effectiveness of distinguishing adjacent categories for performance improvement and our new approach exceeds state-of-the-art performances in four different scenarios. Codes are available at https://github.com/wjh892521292/Ord2Seq.

Since self-attention layers in Transformers are permutation invariant by design, positional encodings must be explicitly incorporated to enable spatial understanding. However, fixed-size lookup tables used in traditional learnable position embeddings (PEs) limit extrapolation capabilities beyond pre-trained sequence lengths. Expert-designed methods such as ALiBi and RoPE, mitigate this limitation but demand extensive modifications for adapting to new modalities, underscoring fundamental challenges in adaptability and scalability. In this work, we present SeqPE, a unified and fully learnable position encoding framework that represents each n-dimensional position index as a symbolic sequence and employs a lightweight sequential position encoder to learn their embeddings in an end-to-end manner. To regularize SeqPE's embedding space, we introduce two complementary objectives: a contrastive objective that aligns embedding distances with a predefined position-distance function, and a knowledge distillation loss that anchors out-of-distribution position embeddings to in-distribution teacher representations, further enhancing extrapolation performance. Experiments across language modeling, long-context question answering, and 2D image classification demonstrate that SeqPE not only surpasses strong baselines in perplexity, exact match (EM), and accuracy--particularly under context length extrapolation--but also enables seamless generalization to multi-dimensional inputs without requiring manual architectural redesign. We release our code, data, and checkpoints at https://github.com/ghrua/seqpe.

The most fundamental capability of modern AI methods such as Large Language Models (LLMs) is the ability to predict the next token in a long sequence of tokens, known as ``sequence modeling." Although the Transformers model is the current dominant approach to sequence modeling, its quadratic computational cost with respect to sequence length is a significant drawback. State-space models (SSMs) offer a promising alternative due to their linear decoding efficiency and high parallelizability during training. However, existing SSMs often rely on seemingly ad hoc linear recurrence designs. In this work, we explore SSM design through the lens of online learning, conceptualizing SSMs as meta-modules for specific online learning problems. This approach links SSM design to formulating precise online learning objectives, with state transition rules derived from optimizing these objectives. Based on this insight, we introduce a novel deep SSM architecture based on the implicit update for optimizing an online regression objective. Our experimental results show that our models outperform state-of-the-art SSMs, including the Mamba model, on standard sequence modeling benchmarks and language modeling tasks.

Sequential Recommendation (SeqRec) aims to predict the next item by capturing sequential patterns from users' historical interactions, playing a crucial role in many real-world recommender systems. However, existing approaches predominantly adopt a direct forward computation paradigm, where the final hidden state of the sequence encoder serves as the user representation. We argue that this inference paradigm, due to its limited computational depth, struggles to model the complex evolving nature of user preferences and lacks a nuanced understanding of long-tail items, leading to suboptimal performance. To address this issue, we propose ReaRec, the first inference-time computing framework for recommender systems, which enhances user representations through implicit multi-step reasoning. Specifically, ReaRec autoregressively feeds the sequence's last hidden state into the sequential recommender while incorporating special reasoning position embeddings to decouple the original item encoding space from the multi-step reasoning space. Moreover, we introduce two lightweight reasoning-based learning methods, Ensemble Reasoning Learning (ERL) and Progressive Reasoning Learning (PRL), to further effectively exploit ReaRec's reasoning potential. Extensive experiments on five public real-world datasets and different SeqRec architectures demonstrate the generality and effectiveness of our proposed ReaRec. Remarkably, post-hoc analyses reveal that ReaRec significantly elevates the performance ceiling of multiple sequential recommendation backbones by approximately 30\%-50\%. Thus, we believe this work can open a new and promising avenue for future research in inference-time computing for sequential recommendation.

Language model based pre-trained models such as BERT have provided significant gains across different NLP tasks. In this paper, we study different types of transformer based pre-trained models such as auto-regressive models (GPT-2), auto-encoder models (BERT), and seq2seq models (BART) for conditional data augmentation. We show that prepending the class labels to text sequences provides a simple yet effective way to condition the pre-trained models for data augmentation. Additionally, on three classification benchmarks, pre-trained Seq2Seq model outperforms other data augmentation methods in a low-resource setting. Further, we explore how different pre-trained model based data augmentation differs in-terms of data diversity, and how well such methods preserve the class-label information.

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.

Inspired by the great success of Masked Language Modeling (MLM) in the natural language domain, the paradigm of self-supervised pre-training and fine-tuning has also achieved remarkable progress in the field of DNA sequence modeling. However, previous methods often relied on massive pre-training data or large-scale base models with huge parameters, imposing a significant computational burden. To address this, many works attempted to use more compact models to achieve similar outcomes but still fell short by a considerable margin. In this work, we propose a Hybrid Architecture Distillation (HAD) approach, leveraging both distillation and reconstruction tasks for more efficient and effective pre-training. Specifically, we employ the NTv2-500M as the teacher model and devise a grouping masking strategy to align the feature embeddings of visible tokens while concurrently reconstructing the invisible tokens during MLM pre-training. To validate the effectiveness of our proposed method, we conducted comprehensive experiments on the Nucleotide Transformer Benchmark and Genomic Benchmark. Compared to models with similar parameters, our model achieved excellent performance. More surprisingly, it even surpassed the distillation ceiling-teacher model on some sub-tasks, which is more than 500 times larger. Lastly, we utilize t-SNE for more intuitive visualization, which shows that our model can gain a sophisticated understanding of the intrinsic representation pattern in genomic sequences.

The rapid advancements in transformer-based language models have revolutionized natural language processing, yet understanding the internal mechanisms of these models remains a significant challenge. This paper explores the application of sparse autoencoders (SAE) to interpret the internal representations of protein language models, specifically focusing on the ESM-2 8M parameter model. By performing a statistical analysis on each latent component's relevance to distinct protein annotations, we identify potential interpretations linked to various protein characteristics, including transmembrane regions, binding sites, and specialized motifs. We then leverage these insights to guide sequence generation, shortlisting the relevant latent components that can steer the model towards desired targets such as zinc finger domains. This work contributes to the emerging field of mechanistic interpretability in biological sequence models, offering new perspectives on model steering for sequence design.

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.

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

A central challenge in sequence modeling is efficiently handling tasks with extended contexts. While recent state-space models (SSMs) have made significant progress in this area, they often lack input-dependent filtering or require substantial increases in model complexity to handle input variability. We address this gap by introducing S7, a simplified yet powerful SSM that can handle input dependence while incorporating stable reparameterization and specific design choices to dynamically adjust state transitions based on input content, maintaining efficiency and performance. We prove that this reparameterization ensures stability in long-sequence modeling by keeping state transitions well-behaved over time. Additionally, it controls the gradient norm, enabling efficient training and preventing issues like exploding or vanishing gradients. S7 significantly outperforms baselines across various sequence modeling tasks, including neuromorphic event-based datasets, Long Range Arena benchmarks, and various physical and biological time series. Overall, S7 offers a more straightforward approach to sequence modeling without relying on complex, domain-specific inductive biases, achieving significant improvements across key benchmarks.

Incremental Learning (IL) has been a long-standing problem in both vision and Natural Language Processing (NLP) communities. In recent years, as Pre-trained Language Models (PLMs) have achieved remarkable progress in various NLP downstream tasks, utilizing PLMs as backbones has become a common practice in recent research of IL in NLP. Most assume that catastrophic forgetting is the biggest obstacle to achieving superior IL performance and propose various techniques to overcome this issue. However, we find that this assumption is problematic. Specifically, we revisit more than 20 methods on four classification tasks (Text Classification, Intent Classification, Relation Extraction, and Named Entity Recognition) under the two most popular IL settings (Class-Incremental and Task-Incremental) and reveal that most of them severely underestimate the inherent anti-forgetting ability of PLMs. Based on the observation, we propose a frustratingly easy method called SEQ* for IL with PLMs. The results show that SEQ* has competitive or superior performance compared to state-of-the-art (SOTA) IL methods and requires considerably less trainable parameters and training time. These findings urge us to revisit the IL with PLMs and encourage future studies to have a fundamental understanding of the catastrophic forgetting in PLMs. The data, code and scripts are publicly available at https://github.com/zzz47zzz/codebase-for-incremental-learning-with-llm.

Tabular data is a common form of organizing data. Multiple models are available to generate synthetic tabular datasets where observations are independent, but few have the ability to produce relational datasets. Modeling relational data is challenging as it requires modeling both a "parent" table and its relationships across tables. We introduce REaLTabFormer (Realistic Relational and Tabular Transformer), a tabular and relational synthetic data generation model. It first creates a parent table using an autoregressive GPT-2 model, then generates the relational dataset conditioned on the parent table using a sequence-to-sequence (Seq2Seq) model. We implement target masking to prevent data copying and propose the Q_{delta} statistic and statistical bootstrapping to detect overfitting. Experiments using real-world datasets show that REaLTabFormer captures the relational structure better than a baseline model. REaLTabFormer also achieves state-of-the-art results on prediction tasks, "out-of-the-box", for large non-relational datasets without needing fine-tuning.

The transformer model is known to be computationally demanding, and prohibitively costly for long sequences, as the self-attention module uses a quadratic time and space complexity with respect to sequence length. Many researchers have focused on designing new forms of self-attention or introducing new parameters to overcome this limitation, however a large portion of them prohibits the model to inherit weights from large pretrained models. In this work, the transformer's inefficiency has been taken care of from another perspective. We propose Fourier Transformer, a simple yet effective approach by progressively removing redundancies in hidden sequence using the ready-made Fast Fourier Transform (FFT) operator to perform Discrete Cosine Transformation (DCT). Fourier Transformer is able to significantly reduce computational costs while retain the ability to inherit from various large pretrained models. Experiments show that our model achieves state-of-the-art performances among all transformer-based models on the long-range modeling benchmark LRA with significant improvement in both speed and space. For generative seq-to-seq tasks including CNN/DailyMail and ELI5, by inheriting the BART weights our model outperforms the standard BART and other efficient models. Our code is publicly available at \url{https://github.com/LUMIA-Group/FourierTransformer}

Efforts to align Large Language Models (LLMs) are mainly conducted via Reinforcement Learning from Human Feedback (RLHF) methods. However, RLHF encounters major challenges including training reward models, actor-critic engineering, and importantly, it requires access to LLM parameters. Here we introduce Aligner, a new efficient alignment paradigm that bypasses the whole RLHF process by learning the correctional residuals between the aligned and the unaligned answers. Our Aligner offers several key advantages. Firstly, it is an autoregressive seq2seq model that is trained on the query-answer-correction dataset via supervised learning; this offers a parameter-efficient alignment solution with minimal resources. Secondly, the Aligner facilitates weak-to-strong generalization; finetuning large pretrained models by Aligner's supervisory signals demonstrates strong performance boost. Thirdly, Aligner functions as a model-agnostic plug-and-play module, allowing for its direct application on different open-source and API-based models. Remarkably, Aligner-7B improves 11 different LLMs by 21.9% in helpfulness and 23.8% in harmlessness on average (GPT-4 by 17.5% and 26.9%). When finetuning (strong) Llama2-70B with (weak) Aligner-13B's supervision, we can improve Llama2 by 8.2% in helpfulness and 61.6% in harmlessness. See our dataset and code at https://aligner2024.github.io

We propose Speculative Decoding (SpecDec), for the first time ever, to formally study exploiting the idea of speculative execution to accelerate autoregressive (AR) decoding. Speculative Decoding has two innovations: Spec-Drafter -- an independent model specially optimized for efficient and accurate drafting -- and Spec-Verification -- a reliable method for verifying the drafted tokens efficiently in the decoding paradigm. Experimental results on various seq2seq tasks including machine translation and abstractive summarization show our approach can achieve around 5times speedup for the popular Transformer architectures with comparable generation quality to beam search decoding, refreshing the impression that the draft-then-verify paradigm introduces only 1.4timessim2times speedup. In addition to the remarkable speedup, we also demonstrate 3 additional advantages of SpecDec, revealing its practical value for accelerating generative models in real-world applications. Our models and codes are available at https://github.com/hemingkx/SpecDec.

Strong inductive biases enable learning from little data and help generalization outside of the training distribution. Popular neural architectures such as Transformers lack strong structural inductive biases for seq2seq NLP tasks on their own. Consequently, they struggle with systematic generalization beyond the training distribution, e.g. with extrapolating to longer inputs, even when pre-trained on large amounts of text. We show how a structural inductive bias can be efficiently injected into a seq2seq model by pre-training it to simulate structural transformations on synthetic data. Specifically, we inject an inductive bias towards Finite State Transducers (FSTs) into a Transformer by pre-training it to simulate FSTs given their descriptions. Our experiments show that our method imparts the desired inductive bias, resulting in improved systematic generalization and better few-shot learning for FST-like tasks. Our analysis shows that fine-tuned models accurately capture the state dynamics of the unseen underlying FSTs, suggesting that the simulation process is internalized by the fine-tuned model.

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

We present a new approach to modeling sequential data: the deep equilibrium model (DEQ). Motivated by an observation that the hidden layers of many existing deep sequence models converge towards some fixed point, we propose the DEQ approach that directly finds these equilibrium points via root-finding. Such a method is equivalent to running an infinite depth (weight-tied) feedforward network, but has the notable advantage that we can analytically backpropagate through the equilibrium point using implicit differentiation. Using this approach, training and prediction in these networks require only constant memory, regardless of the effective "depth" of the network. We demonstrate how DEQs can be applied to two state-of-the-art deep sequence models: self-attention transformers and trellis networks. On large-scale language modeling tasks, such as the WikiText-103 benchmark, we show that DEQs 1) often improve performance over these state-of-the-art models (for similar parameter counts); 2) have similar computational requirements to existing models; and 3) vastly reduce memory consumption (often the bottleneck for training large sequence models), demonstrating an up-to 88% memory reduction in our experiments. The code is available at https://github.com/locuslab/deq .

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.

Human dialogue contains evolving concepts, and speakers naturally associate multiple concepts to compose a response. However, current dialogue models with the seq2seq framework lack the ability to effectively manage concept transitions and can hardly introduce multiple concepts to responses in a sequential decoding manner. To facilitate a controllable and coherent dialogue, in this work, we devise a concept-guided non-autoregressive model (CG-nAR) for open-domain dialogue generation. The proposed model comprises a multi-concept planning module that learns to identify multiple associated concepts from a concept graph and a customized Insertion Transformer that performs concept-guided non-autoregressive generation to complete a response. The experimental results on two public datasets show that CG-nAR can produce diverse and coherent responses, outperforming state-of-the-art baselines in both automatic and human evaluations with substantially faster inference speed.

In the last years, the Linked Data Cloud has achieved a size of more than 100 billion facts pertaining to a multitude of domains. However, accessing this information has been significantly challenging for lay users. Approaches to problems such as Question Answering on Linked Data and Link Discovery have notably played a role in increasing information access. These approaches are often based on handcrafted and/or statistical models derived from data observation. Recently, Deep Learning architectures based on Neural Networks called seq2seq have shown to achieve state-of-the-art results at translating sequences into sequences. In this direction, we propose Neural SPARQL Machines, end-to-end deep architectures to translate any natural language expression into sentences encoding SPARQL queries. Our preliminary results, restricted on selected DBpedia classes, show that Neural SPARQL Machines are a promising approach for Question Answering on Linked Data, as they can deal with known problems such as vocabulary mismatch and perform graph pattern composition.

We introduce Delayed Streams Modeling (DSM), a flexible formulation for streaming, multimodal sequence-to-sequence learning. Sequence-to-sequence generation is often cast in an offline manner, where the model consumes the complete input sequence before generating the first output timestep. Alternatively, streaming sequence-to-sequence rely on learning a policy for choosing when to advance on the input stream, or write to the output stream. DSM instead models already time-aligned streams with a decoder-only language model. By moving the alignment to a pre-processing step,and introducing appropriate delays between streams, DSM provides streaming inference of arbitrary output sequences, from any input combination, making it applicable to many sequence-to-sequence problems. In particular, given text and audio streams, automatic speech recognition (ASR) corresponds to the text stream being delayed, while the opposite gives a text-to-speech (TTS) model. We perform extensive experiments for these two major sequence-to-sequence tasks, showing that DSM provides state-of-the-art performance and latency while supporting arbitrary long sequences, being even competitive with offline baselines. Code, samples and demos are available at https://github.com/kyutai-labs/delayed-streams-modeling

Inductive transfer learning has taken the entire NLP field by storm, with models such as BERT and BART setting new state of the art on countless NLU tasks. However, most of the available models and research have been conducted for English. In this work, we introduce BARThez, the first large-scale pretrained seq2seq model for French. Being based on BART, BARThez is particularly well-suited for generative tasks. We evaluate BARThez on five discriminative tasks from the FLUE benchmark and two generative tasks from a novel summarization dataset, OrangeSum, that we created for this research. We show BARThez to be very competitive with state-of-the-art BERT-based French language models such as CamemBERT and FlauBERT. We also continue the pretraining of a multilingual BART on BARThez' corpus, and show our resulting model, mBARThez, to significantly boost BARThez' generative performance. Code, data and models are publicly available.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

The transformer architecture has revolutionized bioinformatics and driven progress in the understanding and prediction of the properties of biomolecules. Almost all research on large-scale biosequence transformers has focused on one domain at a time (single-omic), usually nucleotides or peptides. These models have seen incredible success in downstream tasks in each domain and have achieved particularly noteworthy breakthroughs in sequences of peptides and structural modeling. However, these single-omic models are naturally incapable of modeling multi-omic tasks, one of the most biologically critical being nucleotide-peptide interactions. We present our work training the first multi-omic nucleotide-peptide foundation models. We show that these multi-omic models (MOMs) can learn joint representations between various single-omic distributions that are emergently consistent with the Central Dogma of molecular biology, despite only being trained on unlabeled biosequences. We further demonstrate that MOMs can be fine-tuned to achieve state-of-the-art results on peptide-nucleotide interaction tasks, namely predicting the change in Gibbs free energy ({\Delta}G) of the binding interaction between a given oligonucleotide and peptide, as well as the effect on this binding interaction due to mutations in the oligonucleotide sequence ({\Delta}{\Delta}G). Remarkably, we show that multi-omic biosequence transformers emergently learn useful structural information without any prior structural training, allowing us to predict which peptide residues are most involved in the peptide-nucleotide binding interaction. Lastly, we provide evidence that multi-omic biosequence models are non-inferior to foundation models trained on single-omics distributions, suggesting a more generalized or foundational approach to building these models.

Foundation models, now powering most of the exciting applications in deep learning, are almost universally based on the Transformer architecture and its core attention module. Many subquadratic-time architectures such as linear attention, gated convolution and recurrent models, and structured state space models (SSMs) have been developed to address Transformers' computational inefficiency on long sequences, but they have not performed as well as attention on important modalities such as language. We identify that a key weakness of such models is their inability to perform content-based reasoning, and make several improvements. First, simply letting the SSM parameters be functions of the input addresses their weakness with discrete modalities, allowing the model to selectively propagate or forget information along the sequence length dimension depending on the current token. Second, even though this change prevents the use of efficient convolutions, we design a hardware-aware parallel algorithm in recurrent mode. We integrate these selective SSMs into a simplified end-to-end neural network architecture without attention or even MLP blocks (Mamba). Mamba enjoys fast inference (5times higher throughput than Transformers) and linear scaling in sequence length, and its performance improves on real data up to million-length sequences. As a general sequence model backbone, Mamba achieves state-of-the-art performance across several modalities such as language, audio, and genomics. On language modeling, our Mamba-3B model outperforms Transformers of the same size and matches Transformers twice its size, both in pretraining and downstream evaluation.

Large pre-trained language models have been shown to store factual knowledge in their parameters, and achieve state-of-the-art results when fine-tuned on downstream NLP tasks. However, their ability to access and precisely manipulate knowledge is still limited, and hence on knowledge-intensive tasks, their performance lags behind task-specific architectures. Additionally, providing provenance for their decisions and updating their world knowledge remain open research problems. Pre-trained models with a differentiable access mechanism to explicit non-parametric memory can overcome this issue, but have so far been only investigated for extractive downstream tasks. We explore a general-purpose fine-tuning recipe for retrieval-augmented generation (RAG) -- models which combine pre-trained parametric and non-parametric memory for language generation. We introduce RAG models where the parametric memory is a pre-trained seq2seq model and the non-parametric memory is a dense vector index of Wikipedia, accessed with a pre-trained neural retriever. We compare two RAG formulations, one which conditions on the same retrieved passages across the whole generated sequence, the other can use different passages per token. We fine-tune and evaluate our models on a wide range of knowledge-intensive NLP tasks and set the state-of-the-art on three open domain QA tasks, outperforming parametric seq2seq models and task-specific retrieve-and-extract architectures. For language generation tasks, we find that RAG models generate more specific, diverse and factual language than a state-of-the-art parametric-only seq2seq baseline.

We focus on morphological inflection in out-of-vocabulary (OOV) conditions, an under-researched subtask in which state-of-the-art systems usually are less effective. We developed three systems: a retrograde model and two sequence-to-sequence (seq2seq) models based on LSTM and Transformer. For testing in OOV conditions, we automatically extracted a large dataset of nouns in the morphologically rich Czech language, with lemma-disjoint data splits, and we further manually annotated a real-world OOV dataset of neologisms. In the standard OOV conditions, Transformer achieves the best results, with increasing performance in ensemble with LSTM, the retrograde model and SIGMORPHON baselines. On the real-world OOV dataset of neologisms, the retrograde model outperforms all neural models. Finally, our seq2seq models achieve state-of-the-art results in 9 out of 16 languages from SIGMORPHON 2022 shared task data in the OOV evaluation (feature overlap) in the large data condition. We release the Czech OOV Inflection Dataset for rigorous evaluation in OOV conditions. Further, we release the inflection system with the seq2seq models as a ready-to-use Python library.

Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design. However, we lack a sufficient understanding of how very large-scale models and data play a role in effective protein model development. We introduce a suite of protein language models, named ProGen2, that are scaled up to 6.4B parameters and trained on different sequence datasets drawn from over a billion proteins from genomic, metagenomic, and immune repertoire databases. ProGen2 models show state-of-the-art performance in capturing the distribution of observed evolutionary sequences, generating novel viable sequences, and predicting protein fitness without additional finetuning. As large model sizes and raw numbers of protein sequences continue to become more widely accessible, our results suggest that a growing emphasis needs to be placed on the data distribution provided to a protein sequence model. We release the ProGen2 models and code at https://github.com/salesforce/progen.

Conditional language models are predominantly trained with maximum likelihood estimation (MLE), giving probability mass to sparsely observed target sequences. While MLE trained models assign high probability to plausible sequences given the context, the model probabilities often do not accurately rank-order generated sequences by quality. This has been empirically observed in beam search decoding as output quality degrading with large beam sizes, and decoding strategies benefiting from heuristics such as length normalization and repetition-blocking. In this work, we introduce sequence likelihood calibration (SLiC) where the likelihood of model generated sequences are calibrated to better align with reference sequences in the model's latent space. With SLiC, decoding heuristics become unnecessary and decoding candidates' quality significantly improves regardless of the decoding method. Furthermore, SLiC shows no sign of diminishing returns with model scale, and presents alternative ways to improve quality with limited training and inference budgets. With SLiC, we exceed or match SOTA results on a wide range of generation tasks spanning abstractive summarization, question generation, abstractive question answering and data-to-text generation, even with modest-sized models.

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.

Neural sequence-to-sequence models are currently the dominant approach in several natural language processing tasks, but require large parallel corpora. We present a sequence-to-sequence-to-sequence autoencoder (SEQ^3), consisting of two chained encoder-decoder pairs, with words used as a sequence of discrete latent variables. We apply the proposed model to unsupervised abstractive sentence compression, where the first and last sequences are the input and reconstructed sentences, respectively, while the middle sequence is the compressed sentence. Constraining the length of the latent word sequences forces the model to distill important information from the input. A pretrained language model, acting as a prior over the latent sequences, encourages the compressed sentences to be human-readable. Continuous relaxations enable us to sample from categorical distributions, allowing gradient-based optimization, unlike alternatives that rely on reinforcement learning. The proposed model does not require parallel text-summary pairs, achieving promising results in unsupervised sentence compression on benchmark datasets.

Large language models (LLMs) with billions of parameters have demonstrated outstanding performance on various natural language processing tasks. This report presents OpenBA, an open-sourced 15B bilingual asymmetric seq2seq model, to contribute an LLM variant to the Chinese-oriented open-source model community. We enhance OpenBA with effective and efficient techniques as well as adopt a three-stage training strategy to train the model from scratch. Our solution can also achieve very competitive performance with only 380B tokens, which is better than LLaMA-70B on the BELEBELE benchmark, BLOOM-176B on the MMLU benchmark, GLM-130B on the C-Eval (hard) benchmark. This report provides the main details to pre-train an analogous model, including pre-training data processing, Bilingual Flan data collection, the empirical observations that inspire our model architecture design, training objectives of different stages, and other enhancement techniques. We have refactored our code to follow the design principles of the Huggingface Transformers Library, making it more convenient for developers to use, and released checkpoints of different training stages at https://huggingface.co/openBA. More details of our project are available at https://github.com/OpenNLG/openBA.git.

Lip-reading aims to infer the speech content from the lip movement sequence and can be seen as a typical sequence-to-sequence (seq2seq) problem which translates the input image sequence of lip movements to the text sequence of the speech content. However, the traditional learning process of seq2seq models always suffers from two problems: the exposure bias resulted from the strategy of "teacher-forcing", and the inconsistency between the discriminative optimization target (usually the cross-entropy loss) and the final evaluation metric (usually the character/word error rate). In this paper, we propose a novel pseudo-convolutional policy gradient (PCPG) based method to address these two problems. On the one hand, we introduce the evaluation metric (refers to the character error rate in this paper) as a form of reward to optimize the model together with the original discriminative target. On the other hand, inspired by the local perception property of convolutional operation, we perform a pseudo-convolutional operation on the reward and loss dimension, so as to take more context around each time step into account to generate a robust reward and loss for the whole optimization. Finally, we perform a thorough comparison and evaluation on both the word-level and sentence-level benchmarks. The results show a significant improvement over other related methods, and report either a new state-of-the-art performance or a competitive accuracy on all these challenging benchmarks, which clearly proves the advantages of our approach.

As a powerful tool for characterizing cellular subpopulations and cellular heterogeneity, single cell RNA sequencing (scRNA-seq) technology offers advantages of high throughput and multidimensional analysis. However, the process of data acquisition is often constrained by high cost and limited sample availability. To overcome these limitations, we propose a hybrid model based on Diffusion model and White-Box transformer that aims to generate synthetic and biologically plausible scRNA-seq data. Diffusion model progressively introduce noise into the data and then recover the original data through a denoising process, a forward and reverse process that is particularly suitable for generating complex data distributions. White-Box transformer is a deep learning architecture that emphasizes mathematical interpretability. By minimizing the encoding rate of the data and maximizing the sparsity of the representation, it not only reduces the computational burden, but also provides clear insight into underlying structure. Our White-Box Diffusion Transformer combines the generative capabilities of Diffusion model with the mathematical interpretability of White-Box transformer. Through experiments using six different single-cell RNA-Seq datasets, we visualize both generated and real data using t-SNE dimensionality reduction technique, as well as quantify similarity between generated and real data using various metrics to demonstrate comparable performance of White-Box Diffusion Transformer and Diffusion Transformer in generating scRNA-seq data alongside significant improvements in training efficiency and resource utilization. Our code is available at https://github.com/lingximamo/White-Box-Diffusion-Transformer

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

Event sequences, characterized by irregular sampling intervals and a mix of categorical and numerical features, are common data structures in various real-world domains such as healthcare, finance, and user interaction logs. Despite advances in temporal data modeling techniques, there is no standardized benchmarks for evaluating their performance on event sequences. This complicates result comparison across different papers due to varying evaluation protocols, potentially misleading progress in this field. We introduce EBES, a comprehensive benchmarking tool with standardized evaluation scenarios and protocols, focusing on regression and classification problems with sequence-level targets. Our library simplifies benchmarking, dataset addition, and method integration through a unified interface. It includes a novel synthetic dataset and provides preprocessed real-world datasets, including the largest publicly available banking dataset. Our results provide an in-depth analysis of datasets, identifying some as unsuitable for model comparison. We investigate the importance of modeling temporal and sequential components, as well as the robustness and scaling properties of the models. These findings highlight potential directions for future research. Our benchmark aim is to facilitate reproducible research, expediting progress and increasing real-world impacts.

Generative modeling of discrete variables is challenging yet crucial for applications in natural language processing and biological sequence design. We introduce the Shortlisting Model (SLM), a novel simplex-based diffusion model inspired by progressive candidate pruning. SLM operates on simplex centroids, reducing generation complexity and enhancing scalability. Additionally, SLM incorporates a flexible implementation of classifier-free guidance, enhancing unconditional generation performance. Extensive experiments on DNA promoter and enhancer design, protein design, character-level and large-vocabulary language modeling demonstrate the competitive performance and strong potential of SLM. Our code can be found at https://github.com/GenSI-THUAIR/SLM

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.

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.

In this paper we propose a Sequential Representation Quantization AutoEncoder (SeqRQ-AE) to learn from primarily unpaired audio data and produce sequences of representations very close to phoneme sequences of speech utterances. This is achieved by proper temporal segmentation to make the representations phoneme-synchronized, and proper phonetic clustering to have total number of distinct representations close to the number of phonemes. Mapping between the distinct representations and phonemes is learned from a small amount of annotated paired data. Preliminary experiments on LJSpeech demonstrated the learned representations for vowels have relative locations in latent space in good parallel to that shown in the IPA vowel chart defined by linguistics experts. With less than 20 minutes of annotated speech, our method outperformed existing methods on phoneme recognition and is able to synthesize intelligible speech that beats our baseline model.

State Space Models (SSMs) have become the leading alternative to Transformers for sequence modeling. Their primary advantage is efficiency in long-context and long-form generation, enabled by fixed-size memory and linear scaling of computational complexity. We begin this work by showing a simple theoretical result stating that SSMs cannot accurately solve any ``truly long-form'' generation problem (in a sense we formally define), undermining their main competitive advantage. However, we show that this limitation can be mitigated by allowing SSMs interactive access to external tools. In fact, we show that given the right choice of tool access and problem-dependent training data, SSMs can learn to solve any tractable problem and generalize to arbitrary problem length/complexity (i.e., achieve length generalization). Following our theoretical finding, we demonstrate that tool-augmented SSMs achieve remarkable length generalization on a variety of arithmetic, reasoning, and coding tasks. These findings highlight SSMs as a potential efficient alternative to Transformers in interactive tool-based and agentic settings.

Recent advancements in sequence modeling have led to the emergence of Structured State Space Models (SSMs) as an efficient alternative to Recurrent Neural Networks (RNNs) and Transformers, addressing challenges in long-range dependency modeling and computational efficiency. While RNNs suffer from vanishing gradients and sequential inefficiencies, and Transformers face quadratic complexity, SSMs leverage structured recurrence and state-space representations to achieve superior long-sequence processing with linear or near-linear complexity. This survey provides a comprehensive review of SSMs, tracing their evolution from the foundational S4 model to its successors like Mamba, Simplified Structured State Space Sequence Model (S5), and Jamba, highlighting their improvements in computational efficiency, memory optimization, and inference speed. By comparing SSMs with traditional sequence models across domains such as natural language processing (NLP), speech recognition, vision, and time-series forecasting, we demonstrate their advantages in handling long-range dependencies while reducing computational overhead. Despite their potential, challenges remain in areas such as training optimization, hybrid modeling, and interpretability. This survey serves as a structured guide for researchers and practitioners, detailing the advancements, trade-offs, and future directions of SSM-based architectures in AI and deep learning.

Spatial Transcriptomics (ST) technologies provide biologists with rich insights into single-cell biology by preserving spatial context of cells. Building foundational models for ST can significantly enhance the analysis of vast and complex data sources, unlocking new perspectives on the intricacies of biological tissues. However, modeling ST data is inherently challenging due to the need to extract multi-scale information from tissue slices containing vast numbers of cells. This process requires integrating macro-scale tissue morphology, micro-scale cellular microenvironment, and gene-scale gene expression profile. To address this challenge, we propose SToFM, a multi-scale Spatial Transcriptomics Foundation Model. SToFM first performs multi-scale information extraction on each ST slice, to construct a set of ST sub-slices that aggregate macro-, micro- and gene-scale information. Then an SE(2) Transformer is used to obtain high-quality cell representations from the sub-slices. Additionally, we construct SToCorpus-88M, the largest high-resolution spatial transcriptomics corpus for pretraining. SToFM achieves outstanding performance on a variety of downstream tasks, such as tissue region semantic segmentation and cell type annotation, demonstrating its comprehensive understanding of ST data through capturing and integrating multi-scale information.

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

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.

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks such as de novo peptide sequencing and protein modeling by their unidirectional nature, failing to capture crucial global bidirectional token dependencies. Non-Autoregressive (NAR) models offer holistic, bidirectional representations but face challenges with generative coherence and scalability. To transcend this, we propose a hybrid framework enhancing AR generation by dynamically integrating rich contextual information from non-autoregressive mechanisms. Our approach couples a shared input encoder with two decoders: a non-autoregressive one learning latent bidirectional biological features, and an AR decoder synthesizing the biological sequence by leveraging these bidirectional features. A novel cross-decoder attention module enables the AR decoder to iteratively query and integrate these bidirectional features, enriching its predictions. This synergy is cultivated via a tailored training strategy with importance annealing for balanced objectives and cross-decoder gradient blocking for stable, focused learning. Evaluations on a demanding nine-species benchmark of de novo peptide sequencing show that our model substantially surpasses AR and NAR baselines. It uniquely harmonizes AR stability with NAR contextual awareness, delivering robust, superior performance on diverse downstream data. This research advances biological sequence modeling techniques and contributes a novel architectural paradigm for augmenting AR models with enhanced bidirectional understanding for complex sequence generation. Code is available at https://github.com/BEAM-Labs/denovo.

Past work in natural language processing interpretability focused mainly on popular classification tasks while largely overlooking generation settings, partly due to a lack of dedicated tools. In this work, we introduce Inseq, a Python library to democratize access to interpretability analyses of sequence generation models. Inseq enables intuitive and optimized extraction of models' internal information and feature importance scores for popular decoder-only and encoder-decoder Transformers architectures. We showcase its potential by adopting it to highlight gender biases in machine translation models and locate factual knowledge inside GPT-2. Thanks to its extensible interface supporting cutting-edge techniques such as contrastive feature attribution, Inseq can drive future advances in explainable natural language generation, centralizing good practices and enabling fair and reproducible model evaluations.

Linear Recurrence has proven to be a powerful tool for modeling long sequences efficiently. In this work, we show that existing models fail to take full advantage of its potential. Motivated by this finding, we develop GateLoop, a foundational sequence model that generalizes linear recurrent models such as S4, S5, LRU and RetNet, by employing data-controlled state transitions. Utilizing this theoretical advance, GateLoop empirically outperforms existing models for auto-regressive language modeling. Our method comes with a low-cost O(l) recurrent mode and an efficient O(l log_{2} l) parallel mode making use of highly optimized associative scan implementations. Furthermore, we derive an O(l^2) surrogate attention mode, revealing remarkable implications for Transformer and recently proposed architectures. Specifically, we prove that our approach can be interpreted as providing data-controlled relative-positional information to Attention. While many existing models solely rely on data-controlled cumulative sums for context aggregation, our findings suggest that incorporating data-controlled complex cumulative products may be a crucial step towards more powerful sequence models.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our Species-Profile Adaptive Collaborative Experts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners. The code is available at https://github.com/ZhuJiwei111/SPACE.

Large language models (LLMs) and emerging agentic frameworks are beginning to transform single-cell biology by enabling natural-language reasoning, generative annotation, and multimodal data integration. However, progress remains fragmented across data modalities, architectures, and evaluation standards. LLM4Cell presents the first unified survey of 58 foundation and agentic models developed for single-cell research, spanning RNA, ATAC, multi-omic, and spatial modalities. We categorize these methods into five families-foundation, text-bridge, spatial, multimodal, epigenomic, and agentic-and map them to eight key analytical tasks including annotation, trajectory and perturbation modeling, and drug-response prediction. Drawing on over 40 public datasets, we analyze benchmark suitability, data diversity, and ethical or scalability constraints, and evaluate models across 10 domain dimensions covering biological grounding, multi-omics alignment, fairness, privacy, and explainability. By linking datasets, models, and evaluation domains, LLM4Cell provides the first integrated view of language-driven single-cell intelligence and outlines open challenges in interpretability, standardization, and trustworthy model development.

Large pre-trained models have achieved outstanding results in sequence modeling. The Transformer block and its attention mechanism have been the main drivers of the success of these models. Recently, alternative architectures, such as Selective Structured State Space Models (SSMs), have been proposed to address the inefficiencies of Transformers. This paper explores the compression of SSM-based models, particularly Mamba and its hybrids. We study the sensitivity of these models to the removal of selected components at different granularities to reduce the model size and computational overhead, thus improving their efficiency while maintaining accuracy. The proposed solutions, collectively referred to as Mamba-Shedder, achieve a speedup of up to 1.4x during inference, demonstrating that model efficiency can be improved by eliminating several redundancies with minimal impact on the overall model performance. The code is available at https://github.com/IntelLabs/Hardware-Aware-Automated-Machine-Learning.

We analyze automatic speech recognition (ASR) modeling choices under domain mismatch, comparing classic modular and novel sequence-to-sequence (seq2seq) architectures. Across the different ASR architectures, we examine a spectrum of modeling choices, including label units, context length, and topology. To isolate language domain effects from acoustic variation, we synthesize target domain audio using a text-to-speech system trained on LibriSpeech. We incorporate target domain n-gram and neural language models for domain adaptation without retraining the acoustic model. To our knowledge, this is the first controlled comparison of optimized ASR systems across state-of-the-art architectures under domain shift, offering insights into their generalization. The results show that, under domain shift, rather than the decoder architecture choice or the distinction between classic modular and novel seq2seq models, it is specific modeling choices that influence performance.

Large language models (LLMs) have shown impressive ability for open-domain NLP tasks. However, LLMs are sometimes too footloose for natural language understanding (NLU) tasks which always have restricted output and input format. Their performances on NLU tasks are highly related to prompts or demonstrations and are shown to be poor at performing several representative NLU tasks, such as event extraction and entity typing. To this end, we present SeqGPT, a bilingual (i.e., English and Chinese) open-source autoregressive model specially enhanced for open-domain natural language understanding. We express all NLU tasks with two atomic tasks, which define fixed instructions to restrict the input and output format but still ``open'' for arbitrarily varied label sets. The model is first instruction-tuned with extremely fine-grained labeled data synthesized by ChatGPT and then further fine-tuned by 233 different atomic tasks from 152 datasets across various domains. The experimental results show that SeqGPT has decent classification and extraction ability, and is capable of performing language understanding tasks on unseen domains. We also conduct empirical studies on the scaling of data and model size as well as on the transfer across tasks. Our model is accessible at https://github.com/Alibaba-NLP/SeqGPT.

Large language models(LLMs) have shown its outperforming ability on various tasks and question answering. However, LLMs require high computation cost and large memory cost. At the same time, LLMs may cause privacy leakage when training or prediction procedure contains sensitive information. In this paper, we propose SPA(Side Plugin Adaption), a lightweight architecture for fast on-devices inference and privacy retaining on the constraints of strict on-devices computation and memory constraints. Compared with other on-devices seq2seq generation, SPA could make a fast and stable inference on low-resource constraints, allowing it to obtain cost effiency. Our method establish an interaction between a pretrained LLMs on-cloud and additive parameters on-devices, which could provide the knowledge on both pretrained LLMs and private personal feature.Further more, SPA provides a framework to keep feature-base parameters on private guaranteed but low computational devices while leave the parameters containing general information on the high computational devices.

Context-aware STR methods typically use internal autoregressive (AR) language models (LM). Inherent limitations of AR models motivated two-stage methods which employ an external LM. The conditional independence of the external LM on the input image may cause it to erroneously rectify correct predictions, leading to significant inefficiencies. Our method, PARSeq, learns an ensemble of internal AR LMs with shared weights using Permutation Language Modeling. It unifies context-free non-AR and context-aware AR inference, and iterative refinement using bidirectional context. Using synthetic training data, PARSeq achieves state-of-the-art (SOTA) results in STR benchmarks (91.9% accuracy) and more challenging datasets. It establishes new SOTA results (96.0% accuracy) when trained on real data. PARSeq is optimal on accuracy vs parameter count, FLOPS, and latency because of its simple, unified structure and parallel token processing. Due to its extensive use of attention, it is robust on arbitrarily-oriented text which is common in real-world images. Code, pretrained weights, and data are available at: https://github.com/baudm/parseq.

Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector. A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.

Straightening the probability flow of the continuous-time generative models, such as diffusion models or flow-based models, is the key to fast sampling through the numerical solvers, existing methods learn a linear path by directly generating the probability path the joint distribution between the noise and data distribution. One key reason for the slow sampling speed of the ODE-based solvers that simulate these generative models is the global truncation error of the ODE solver, caused by the high curvature of the ODE trajectory, which explodes the truncation error of the numerical solvers in the low-NFE regime. To address this challenge, We propose a novel method called SeqRF, a learning technique that straightens the probability flow to reduce the global truncation error and hence enable acceleration of sampling and improve the synthesis quality. In both theoretical and empirical studies, we first observe the straightening property of our SeqRF. Through empirical evaluations via SeqRF over flow-based generative models, We achieve surpassing results on CIFAR-10, CelebA-64 times 64, and LSUN-Church datasets.

Recently, large language models (LLMs), especially those that are pretrained on code, have demonstrated strong capabilities in generating programs from natural language inputs in a few-shot or even zero-shot manner. Despite promising results, there is a notable lack of a comprehensive evaluation of these models language-to-code generation capabilities. Existing studies often focus on specific tasks, model architectures, or learning paradigms, leading to a fragmented understanding of the overall landscape. In this work, we present L2CEval, a systematic evaluation of the language-to-code generation capabilities of LLMs on 7 tasks across the domain spectrum of semantic parsing, math reasoning and Python programming, analyzing the factors that potentially affect their performance, such as model size, pretraining data, instruction tuning, and different prompting methods. In addition to assessing model performance, we measure confidence calibration for the models and conduct human evaluations of the output programs. This enables us to identify and analyze the typical failure modes across various tasks and models. L2CEval offers a comprehensive understanding of the capabilities and limitations of LLMs in language-to-code generation. We also release the evaluation framework and all model outputs, hoping to lay the groundwork for further future research in this domain.

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.

The output structure of database-like tables, consisting of values structured in horizontal rows and vertical columns identifiable by name, can cover a wide range of NLP tasks. Following this constatation, we propose a framework for text-to-table neural models applicable to problems such as extraction of line items, joint entity and relation extraction, or knowledge base population. The permutation-based decoder of our proposal is a generalized sequential method that comprehends information from all cells in the table. The training maximizes the expected log-likelihood for a table's content across all random permutations of the factorization order. During the content inference, we exploit the model's ability to generate cells in any order by searching over possible orderings to maximize the model's confidence and avoid substantial error accumulation, which other sequential models are prone to. Experiments demonstrate a high practical value of the framework, which establishes state-of-the-art results on several challenging datasets, outperforming previous solutions by up to 15%.

Designing biological sequences is an important challenge that requires satisfying complex constraints and thus is a natural problem to address with deep generative modeling. Diffusion generative models have achieved considerable success in many applications. Score-based generative stochastic differential equations (SDE) model is a continuous-time diffusion model framework that enjoys many benefits, but the originally proposed SDEs are not naturally designed for modeling discrete data. To develop generative SDE models for discrete data such as biological sequences, here we introduce a diffusion process defined in the probability simplex space with stationary distribution being the Dirichlet distribution. This makes diffusion in continuous space natural for modeling discrete data. We refer to this approach as Dirchlet diffusion score model. We demonstrate that this technique can generate samples that satisfy hard constraints using a Sudoku generation task. This generative model can also solve Sudoku, including hard puzzles, without additional training. Finally, we applied this approach to develop the first human promoter DNA sequence design model and showed that designed sequences share similar properties with natural promoter sequences.

State-based sequence models like RWKV-7 offer a compelling alternative to Transformer architectures, achieving linear complexity while demonstrating greater expressive power in short-context scenarios and enabling state tracking beyond the \(TC^0\) complexity class. However, RWKV-7 lacks mechanisms for token-parameter interactions and native scalability, limiting its adaptability and growth without retraining. In this paper, we propose Meta-State, a novel extension to RWKV-7 that replaces attention mechanisms with a fully state-driven approach, integrating token-parameter interactions through a Self-State Encoder (SSE) mechanism. The SSE repurposes a portion of the RWKV-7 Weighted Key-Value (WKV) state as transformation weights to encode token-parameter interactions in a linear, state-driven manner without introducing new trainable matrices or softmax operations, while preserving the autoregressive property of token processing. Meta-State supports progressive model scaling by expanding the WKV state and parameter tokens, reusing existing parameters without retraining. Our approach bridges the gap between state-based modeling, token-parameter interactions, and scalable architectures, offering a flexible framework for efficient and adaptable sequence modeling with linear complexity and constant memory usage.

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.

Event sequences (ESs) arise in many practical domains including finance, retail, social networks, and healthcare. In the context of machine learning, event sequences can be seen as a special type of tabular data with annotated timestamps. Despite the importance of ESs modeling and analysis, little effort was made in adapting large language models (LLMs) to the ESs domain. In this paper, we highlight the common difficulties of ESs processing and propose a novel solution capable of solving multiple downstream tasks with little or no finetuning. In particular, we solve the problem of working with long sequences and improve time and numeric features processing. The resulting method, called ESQA, effectively utilizes the power of LLMs and, according to extensive experiments, achieves state-of-the-art results in the ESs domain.

We present LINGUIST, a method for generating annotated data for Intent Classification and Slot Tagging (IC+ST), via fine-tuning AlexaTM 5B, a 5-billion-parameter multilingual sequence-to-sequence (seq2seq) model, on a flexible instruction prompt. In a 10-shot novel intent setting for the SNIPS dataset, LINGUIST surpasses state-of-the-art approaches (Back-Translation and Example Extrapolation) by a wide margin, showing absolute improvement for the target intents of +1.9 points on IC Recall and +2.5 points on ST F1 Score. In the zero-shot cross-lingual setting of the mATIS++ dataset, LINGUIST out-performs a strong baseline of Machine Translation with Slot Alignment by +4.14 points absolute on ST F1 Score across 6 languages, while matching performance on IC. Finally, we verify our results on an internal large-scale multilingual dataset for conversational agent IC+ST and show significant improvements over a baseline which uses Back-Translation, Paraphrasing and Slot Catalog Resampling. To our knowledge, we are the first to demonstrate instruction fine-tuning of a large-scale seq2seq model to control the outputs of multilingual intent- and slot-labeled data generation.

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.

Recent work has shown the feasibility and benefit of bootstrapping an integrated sequence-to-sequence (Seq2Seq) linguistic frontend from a traditional pipeline-based frontend for text-to-speech (TTS). To overcome the fixed lexical coverage of bootstrapping training data, previous work has proposed to leverage easily accessible transcribed speech audio as an additional training source for acquiring novel pronunciation knowledge for uncovered words, which relies on an auxiliary ASR model as part of a cumbersome implementation flow. In this work, we propose an alternative method to leverage transcribed speech audio as an additional training source, based on multi-task learning (MTL). Experiments show that, compared to a baseline Seq2Seq frontend, the proposed MTL-based method reduces PER from 2.5% to 1.6% for those word types covered exclusively in transcribed speech audio, achieving a similar performance to the previous method but with a much simpler implementation flow.

State-space models (SSMs) offer a promising architecture for sequence modeling, providing an alternative to Transformers by replacing expensive self-attention with linear recurrences. In this paper, we propose a simple yet effective trick to enhance SSMs within given computational budgets by sparsifying them. Our intuition is that tokens in SSMs are highly redundant due to gradual recurrent updates, and dense recurrence operations block the delivery of past information. In particular, we observe that upper layers of SSMs tend to be more redundant as they encode global information, while lower layers encode local information. Motivated by this, we introduce Simba, a hierarchical sparsification method for SSMs based on token pruning. Simba sparsifies upper layers more than lower layers, encouraging the upper layers to behave like highways. To achieve this, we propose a novel token pruning criterion for SSMs, measuring the global impact of tokens on the final output by accumulating local recurrences. We demonstrate that Simba outperforms the baseline model, Mamba, with the same FLOPS in various natural language tasks. Moreover, we illustrate the effect of highways, showing that Simba not only enhances efficiency but also improves the information flow across long sequences. Code is available at https://github.com/woominsong/Simba.

Autoregressive models (ARMs), which predict subsequent tokens one-by-one ``from left to right,'' have achieved significant success across a wide range of sequence generation tasks. However, they struggle to accurately represent sequences that require satisfying sophisticated constraints or whose sequential dependencies are better addressed by out-of-order generation. Masked Diffusion Models (MDMs) address some of these limitations, but the process of unmasking multiple tokens simultaneously in MDMs can introduce incoherences, and MDMs cannot handle arbitrary infilling constraints when the number of tokens to be filled in is not known in advance. In this work, we introduce Insertion Language Models (ILMs), which learn to insert tokens at arbitrary positions in a sequence -- that is, they select jointly both the position and the vocabulary element to be inserted. By inserting tokens one at a time, ILMs can represent strong dependencies between tokens, and their ability to generate sequences in arbitrary order allows them to accurately model sequences where token dependencies do not follow a left-to-right sequential structure. To train ILMs, we propose a tailored network parameterization and use a simple denoising objective. Our empirical evaluation demonstrates that ILMs outperform both ARMs and MDMs on common planning tasks. Furthermore, we show that ILMs outperform MDMs and perform on par with ARMs in an unconditional text generation task while offering greater flexibility than MDMs in arbitrary-length text infilling.

Sequence-to-sequence models are commonly trained via maximum likelihood estimation (MLE). However, standard MLE training considers a word-level objective, predicting the next word given the previous ground-truth partial sentence. This procedure focuses on modeling local syntactic patterns, and may fail to capture long-range semantic structure. We present a novel solution to alleviate these issues. Our approach imposes global sequence-level guidance via new supervision based on optimal transport, enabling the overall characterization and preservation of semantic features. We further show that this method can be understood as a Wasserstein gradient flow trying to match our model to the ground truth sequence distribution. Extensive experiments are conducted to validate the utility of the proposed approach, showing consistent improvements over a wide variety of NLP tasks, including machine translation, abstractive text summarization, and image captioning.

We introduce fairseq S2T, a fairseq extension for speech-to-text (S2T) modeling tasks such as end-to-end speech recognition and speech-to-text translation. It follows fairseq's careful design for scalability and extensibility. We provide end-to-end workflows from data pre-processing, model training to offline (online) inference. We implement state-of-the-art RNN-based, Transformer-based as well as Conformer-based models and open-source detailed training recipes. Fairseq's machine translation models and language models can be seamlessly integrated into S2T workflows for multi-task learning or transfer learning. Fairseq S2T documentation and examples are available at https://github.com/pytorch/fairseq/tree/master/examples/speech_to_text.

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.}

As large language models (LLMs) become more prevalent, there is a growing need for new and improved quantization methods that can meet the computationalast layer demands of these modern architectures while maintaining the accuracy. In this paper, we present TEQ, a trainable equivalent transformation that preserves the FP32 precision of the model output while taking advantage of low-precision quantization, especially 3 and 4 bits weight-only quantization. The training process is lightweight, requiring only 1K steps and fewer than 0.1 percent of the original model's trainable parameters. Furthermore, the transformation does not add any computational overhead during inference. Our results are on-par with the state-of-the-art (SOTA) methods on typical LLMs. Our approach can be combined with other methods to achieve even better performance. The code is available at https://github.com/intel/neural-compressor.

Recently, large language models (LLMs) have shown remarkable capabilities including understanding context, engaging in logical reasoning, and generating responses. However, this is achieved at the expense of stringent computational and memory requirements, hindering their ability to effectively support long input sequences. This survey provides an inclusive review of the recent techniques and methods devised to extend the sequence length in LLMs, thereby enhancing their capacity for long-context understanding. In particular, we review and categorize a wide range of techniques including architectural modifications, such as modified positional encoding and altered attention mechanisms, which are designed to enhance the processing of longer sequences while avoiding a proportional increase in computational requirements. The diverse methodologies investigated in this study can be leveraged across different phases of LLMs, i.e., training, fine-tuning and inference. This enables LLMs to efficiently process extended sequences. The limitations of the current methodologies is discussed in the last section along with the suggestions for future research directions, underscoring the importance of sequence length in the continued advancement of LLMs.

Transformer models have been successful in various sequence processing tasks, but the self-attention mechanism's computational cost limits its practicality for long sequences. Although there are existing attention variants that improve computational efficiency, they have a limited ability to abstract global information effectively based on their hand-crafted mixing strategies. On the other hand, state-space models (SSMs) are tailored for long sequences but cannot capture complicated local information. Therefore, the combination of them as a unified token mixer is a trend in recent long-sequence models. However, the linearized attention degrades performance significantly even when equipped with SSMs. To address the issue, we propose a new method called LongVQ. LongVQ uses the vector quantization (VQ) technique to compress the global abstraction as a length-fixed codebook, enabling the linear-time computation of the attention matrix. This technique effectively maintains dynamic global and local patterns, which helps to complement the lack of long-range dependency issues. Our experiments on the Long Range Arena benchmark, autoregressive language modeling, and image and speech classification demonstrate the effectiveness of LongVQ. Our model achieves significant improvements over other sequence models, including variants of Transformers, Convolutions, and recent State Space Models.

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.

The ability to learn new concepts sequentially is a major weakness for modern neural networks, which hinders their use in non-stationary environments. Their propensity to fit the current data distribution to the detriment of the past acquired knowledge leads to the catastrophic forgetting issue. In this work we tackle the problem of Spoken Language Understanding applied to a continual learning setting. We first define a class-incremental scenario for the SLURP dataset. Then, we propose three knowledge distillation (KD) approaches to mitigate forgetting for a sequence-to-sequence transformer model: the first KD method is applied to the encoder output (audio-KD), and the other two work on the decoder output, either directly on the token-level (tok-KD) or on the sequence-level (seq-KD) distributions. We show that the seq-KD substantially improves all the performance metrics, and its combination with the audio-KD further decreases the average WER and enhances the entity prediction metric.

Transformers have reached remarkable success in sequence modeling. However, these models have efficiency issues as they need to store all the history token-level representations as memory. We present Memformer, an efficient neural network for sequence modeling, that utilizes an external dynamic memory to encode and retrieve past information. Our model achieves linear time complexity and constant memory space complexity when processing long sequences. We also propose a new optimization scheme, memory replay back-propagation (MRBP), which promotes long-range back-propagation through time with a significantly reduced memory requirement. Experimental results show that Memformer has achieved comparable performance compared to the baselines by using 8.1x less memory space and 3.2x faster on inference. Analysis of the attention pattern shows that our external memory slots can encode and retain important information through timesteps.

We present significant extensions to diffusion-based sequence generation models, blurring the line with autoregressive language models. We introduce hyperschedules, which assign distinct noise schedules to individual token positions, generalizing both autoregressive models (e.g., GPT) and conventional diffusion models (e.g., SEDD, MDLM) as special cases. Second, we propose two hybrid token-wise noising processes that interpolate between absorbing and uniform processes, enabling the model to fix past mistakes, and we introduce a novel inference algorithm that leverages this new feature in a simplified context inspired from MDLM. To support efficient training and inference, we design attention masks compatible with KV-caching. Our methods achieve state-of-the-art perplexity and generate diverse, high-quality sequences across standard benchmarks, suggesting a promising path for autoregressive diffusion-based sequence generation.

Model-based reinforcement learning (RL) offers a solution to the data inefficiency that plagues most model-free RL algorithms. However, learning a robust world model often requires complex and deep architectures, which are computationally expensive and challenging to train. Within the world model, sequence models play a critical role in accurate predictions, and various architectures have been explored, each with its own challenges. Currently, recurrent neural network (RNN)-based world models struggle with vanishing gradients and capturing long-term dependencies. Transformers, on the other hand, suffer from the quadratic memory and computational complexity of self-attention mechanisms, scaling as O(n^2), where n is the sequence length. To address these challenges, we propose a state space model (SSM)-based world model, Drama, specifically leveraging Mamba, that achieves O(n) memory and computational complexity while effectively capturing long-term dependencies and enabling efficient training with longer sequences. We also introduce a novel sampling method to mitigate the suboptimality caused by an incorrect world model in the early training stages. Combining these techniques, Drama achieves a normalised score on the Atari100k benchmark that is competitive with other state-of-the-art (SOTA) model-based RL algorithms, using only a 7 million-parameter world model. Drama is accessible and trainable on off-the-shelf hardware, such as a standard laptop. Our code is available at https://github.com/realwenlongwang/Drama.git.

Encoder-decoder models have become an effective approach for sequence learning tasks like machine translation, image captioning and speech recognition, but have yet to show competitive results for handwritten text recognition. To this end, we propose an attention-based sequence-to-sequence model. It combines a convolutional neural network as a generic feature extractor with a recurrent neural network to encode both the visual information, as well as the temporal context between characters in the input image, and uses a separate recurrent neural network to decode the actual character sequence. We make experimental comparisons between various attention mechanisms and positional encodings, in order to find an appropriate alignment between the input and output sequence. The model can be trained end-to-end and the optional integration of a hybrid loss allows the encoder to retain an interpretable and usable output, if desired. We achieve competitive results on the IAM and ICFHR2016 READ data sets compared to the state-of-the-art without the use of a language model, and we significantly improve over any recent sequence-to-sequence approaches.