Daily Papers

We study the problem of extrapolative controlled generation, i.e., generating sequences with attribute values beyond the range seen in training. This task is of significant importance in automated design, especially drug discovery, where the goal is to design novel proteins that are better (e.g., more stable) than existing sequences. Thus, by definition, the target sequences and their attribute values are out of the training distribution, posing challenges to existing methods that aim to directly generate the target sequence. Instead, in this work, we propose Iterative Controlled Extrapolation (ICE) which iteratively makes local edits to a sequence to enable extrapolation. We train the model on synthetically generated sequence pairs that demonstrate small improvement in the attribute value. Results on one natural language task (sentiment analysis) and two protein engineering tasks (ACE2 stability and AAV fitness) show that ICE considerably outperforms state-of-the-art approaches despite its simplicity. Our code and models are available at: https://github.com/vishakhpk/iter-extrapolation.

Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTACs and molecular glues, have thus gained attention as pharmacological alternatives, but still require small molecule docking at binding pockets for targeted protein degradation (TPD). The computational design of protein-based binders presents unique opportunities to access undruggable targets, but have often relied on stable 3D structures or predictions for effective binder generation. Recently, we have leveraged the expressive latent spaces of protein language models (pLMs) for the prioritization of peptide binders from sequence alone, which we have then fused to E3 ubiquitin ligase domains, creating a CRISPR-analogous TPD system for target proteins. However, our methods rely on training discriminator models for ranking heuristically or unconditionally-derived guide peptides for their target binding capability. In this work, we introduce PepMLM, a purely target sequence-conditioned de novo generator of linear peptide binders. By employing a novel masking strategy that uniquely positions cognate peptide sequences at the terminus of target protein sequences, PepMLM tasks the state-of-the-art ESM-2 pLM to fully reconstruct the binder region, achieving low perplexities matching or improving upon previously-validated peptide-protein sequence pairs. After successful in silico benchmarking with AlphaFold-Multimer, we experimentally verify PepMLM's efficacy via fusion of model-derived peptides to E3 ubiquitin ligase domains, demonstrating endogenous degradation of target substrates in cellular models. In total, PepMLM enables the generative design of candidate binders to any target protein, without the requirement of target structure, empowering downstream programmable proteome editing applications.

Improving the alignment of language models with human preferences remains an active research challenge. Previous approaches have primarily utilized Reinforcement Learning from Human Feedback (RLHF) via online RL methods such as Proximal Policy Optimization (PPO). Recently, offline methods such as Sequence Likelihood Calibration (SLiC) and Direct Preference Optimization (DPO) have emerged as attractive alternatives, offering improvements in stability and scalability while maintaining competitive performance. SLiC refines its loss function using sequence pairs sampled from a supervised fine-tuned (SFT) policy, while DPO directly optimizes language models based on preference data, foregoing the need for a separate reward model. However, the maximum likelihood estimator (MLE) of the target optimal policy requires labeled preference pairs sampled from that policy. DPO's lack of a reward model constrains its ability to sample preference pairs from the optimal policy, and SLiC is restricted to sampling preference pairs only from the SFT policy. To address these limitations, we introduce a novel approach called Statistical Rejection Sampling Optimization (RSO) that aims to source preference data from the target optimal policy using rejection sampling, enabling a more accurate estimation of the optimal policy. We also propose a unified framework that enhances the loss functions used in both SLiC and DPO from a preference modeling standpoint. Through extensive experiments across three diverse tasks, we demonstrate that RSO consistently outperforms both SLiC and DPO on evaluations from both Large Language Model (LLM) and human raters.

Existing Video Object Segmentation (VOS) relies on explicit user instructions, such as categories, masks, or short phrases, restricting their ability to perform complex video segmentation requiring reasoning with world knowledge. In this paper, we introduce a new task, Reasoning Video Object Segmentation (ReasonVOS). This task aims to generate a sequence of segmentation masks in response to implicit text queries that require complex reasoning abilities based on world knowledge and video contexts, which is crucial for structured environment understanding and object-centric interactions, pivotal in the development of embodied AI. To tackle ReasonVOS, we introduce VISA (Video-based large language Instructed Segmentation Assistant), to leverage the world knowledge reasoning capabilities of multi-modal LLMs while possessing the ability to segment and track objects in videos with a mask decoder. Moreover, we establish a comprehensive benchmark consisting of 35,074 instruction-mask sequence pairs from 1,042 diverse videos, which incorporates complex world knowledge reasoning into segmentation tasks for instruction-tuning and evaluation purposes of ReasonVOS models. Experiments conducted on 8 datasets demonstrate the effectiveness of VISA in tackling complex reasoning segmentation and vanilla referring segmentation in both video and image domains. The code and dataset are available at https://github.com/cilinyan/VISA.

Creating CAD digital twins from the physical world is crucial for manufacturing, design, and simulation. However, current methods typically rely on costly 3D scanning with labor-intensive post-processing. To provide a user-friendly design process, we explore the problem of reverse engineering from unconstrained real-world CAD images that can be easily captured by users of all experiences. However, the scarcity of real-world CAD data poses challenges in directly training such models. To tackle these challenges, we propose CADCrafter, an image-to-parametric CAD model generation framework that trains solely on synthetic textureless CAD data while testing on real-world images. To bridge the significant representation disparity between images and parametric CAD models, we introduce a geometry encoder to accurately capture diverse geometric features. Moreover, the texture-invariant properties of the geometric features can also facilitate the generalization to real-world scenarios. Since compiling CAD parameter sequences into explicit CAD models is a non-differentiable process, the network training inherently lacks explicit geometric supervision. To impose geometric validity constraints, we employ direct preference optimization (DPO) to fine-tune our model with the automatic code checker feedback on CAD sequence quality. Furthermore, we collected a real-world dataset, comprised of multi-view images and corresponding CAD command sequence pairs, to evaluate our method. Experimental results demonstrate that our approach can robustly handle real unconstrained CAD images, and even generalize to unseen general objects.

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

Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent developments in steering protein generative models (e.g diffusion models, language models) offer a promising approach. However, by and large, past studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured by low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages compared to alternatives such as reinforcement learning with protein language models.

We present a scientific reasoning foundation model that aligns natural language with heterogeneous scientific representations. The model is pretrained on a 206B-token corpus spanning scientific text, pure sequences, and sequence-text pairs, then aligned via SFT on 40M instructions, annealed cold-start bootstrapping to elicit long-form chain-of-thought, and reinforcement learning with task-specific reward shaping, which instills deliberate scientific reasoning. It supports four capability families, covering up to 103 tasks across workflows: (i) faithful translation between text and scientific formats, (ii) text/knowledge extraction, (iii) property prediction, (iv) property classification, (v) unconditional and conditional sequence generation and design. Compared with specialist systems, our approach broadens instruction coverage, improves cross-domain generalization, and enhances fidelity. We detail data curation and training and show that cross-discipline learning strengthens transfer and downstream reliability. The model, instruct tuning datasets and the evaluation code are open-sourced at https://huggingface.co/SciReason and https://github.com/open-sciencelab/SciReason.

Monte Carlo Tree Search (MCTS) has recently emerged as a powerful technique for enhancing the reasoning capabilities of LLMs. Techniques such as SFT or DPO have enabled LLMs to distill high-quality behaviors from MCTS, improving their reasoning performance. However, existing distillation methods underutilize the rich trajectory information generated by MCTS, limiting the potential for improvements in LLM reasoning. In this paper, we propose AlphaLLM-CPL, a novel pairwise training framework that enables LLMs to self-improve through MCTS behavior distillation. AlphaLLM-CPL efficiently leverages MCTS trajectories via two key innovations: (1) AlphaLLM-CPL constructs stepwise trajectory pairs from child nodes sharing the same parent in the search tree, providing step-level information for more effective MCTS behavior distillation. (2) AlphaLLM-CPL introduces curriculum preference learning, dynamically adjusting the training sequence of trajectory pairs in each offline training epoch to prioritize critical learning steps and mitigate overfitting. Experimental results on mathematical reasoning tasks demonstrate that AlphaLLM-CPL significantly outperforms previous MCTS behavior distillation methods, substantially boosting the reasoning capabilities of LLMs.

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.

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.

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which is crucial for biology research. To address this gap, we introduce PRING, the first comprehensive benchmark that evaluates protein-protein interaction prediction from a graph-level perspective. PRING curates a high-quality, multi-species PPI network dataset comprising 21,484 proteins and 186,818 interactions, with well-designed strategies to address both data redundancy and leakage. Building on this golden-standard dataset, we establish two complementary evaluation paradigms: (1) topology-oriented tasks, which assess intra and cross-species PPI network construction, and (2) function-oriented tasks, including protein complex pathway prediction, GO module analysis, and essential protein justification. These evaluations not only reflect the model's capability to understand the network topology but also facilitate protein function annotation, biological module detection, and even disease mechanism analysis. Extensive experiments on four representative model categories, consisting of sequence similarity-based, naive sequence-based, protein language model-based, and structure-based approaches, demonstrate that current PPI models have potential limitations in recovering both structural and functional properties of PPI networks, highlighting the gap in supporting real-world biological applications. We believe PRING provides a reliable platform to guide the development of more effective PPI prediction models for the community. The dataset and source code of PRING are available at https://github.com/SophieSarceau/PRING.

Large Language Models (LLMs) have exhibited impressive capabilities in various tasks, yet their vast parameter sizes restrict their applicability in resource-constrained settings. Knowledge distillation (KD) offers a viable solution by transferring expertise from large teacher models to compact student models. However, traditional KD techniques face specific challenges when applied to LLMs, including restricted access to LLM outputs, significant teacher-student capacity gaps, and the inherited mis-calibration issue. In this work, we present PLaD, a novel preference-based LLM distillation framework. PLaD exploits the teacher-student capacity discrepancy to generate pseudo-preference pairs where teacher outputs are preferred over student outputs. Then, PLaD leverages a ranking loss to re-calibrate student's estimation of sequence likelihood, which steers the student's focus towards understanding the relative quality of outputs instead of simply imitating the teacher. PLaD bypasses the need for access to teacher LLM's internal states, tackles the student's expressivity limitations, and mitigates the student mis-calibration issue. Through extensive experiments on two sequence generation tasks and with various LLMs, we demonstrate the effectiveness of our proposed PLaD framework.

Large Language Models (LLMs), despite their impressive performance on a wide range of tasks, require significant GPU memory and consume substantial computational resources. In addition to model weights, the memory occupied by KV cache increases linearly with sequence length, becoming a main bottleneck for inference. In this paper, we introduce a novel approach for optimizing the KV cache which significantly reduces its memory footprint. Through a comprehensive investigation, we find that on LLaMA2 series models, (i) the similarity between adjacent tokens' query vectors is remarkably high, and (ii) current query's attention calculation can rely solely on the attention information of a small portion of the preceding queries. Based on these observations, we propose CORM, a KV cache eviction policy that dynamically retains important key-value pairs for inference without finetuning the model. We validate that CORM reduces the inference memory usage of KV cache by up to 70% without noticeable performance degradation across six tasks in LongBench.

In recent years, substantial advancements in pre-trained language models have paved the way for the development of numerous non-English language versions, with a particular focus on encoder-only and decoder-only architectures. While Spanish language models encompassing BERT, RoBERTa, and GPT have exhibited prowess in natural language understanding and generation, there remains a scarcity of encoder-decoder models designed for sequence-to-sequence tasks involving input-output pairs. This paper breaks new ground by introducing the implementation and evaluation of renowned encoder-decoder architectures, exclusively pre-trained on Spanish corpora. Specifically, we present Spanish versions of BART, T5, and BERT2BERT-style models and subject them to a comprehensive assessment across a diverse range of sequence-to-sequence tasks, spanning summarization, rephrasing, and generative question answering. Our findings underscore the competitive performance of all models, with BART and T5 emerging as top performers across all evaluated tasks. As an additional contribution, we have made all models publicly available to the research community, fostering future exploration and development in Spanish language processing.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Classification is one of the most widespread tasks in AI applications, serving often as the first step in filtering, sorting, and categorizing data. Since modern AI systems must handle large volumes of input data and early pipeline stages can propagate errors downstream, achieving high efficiency and accuracy is critical. Moreover, classification requirements can change dynamically based on user needs, necessitating models with strong zero-shot capabilities. While generative LLMs have become mainstream for zero-shot classification due to their versatility, they suffer from inconsistent instruction following and computational inefficiency. Cross-encoders, commonly used as rerankers in RAG pipelines, face a different bottleneck: they must process text-label pairs sequentially, significantly reducing efficiency with large label sets. Embedding-based approaches offer good efficiency but struggle with complex scenarios involving logical and semantic constraints. We propose GLiClass, a novel method that adapts the GLiNER architecture for sequence classification tasks. Our approach achieves strong accuracy and efficiency comparable to embedding-based methods, while maintaining the flexibility needed for zero-shot and few-shot learning scenarios. Additionally, we adapted proximal policy optimization (PPO) for multi-label text classification, enabling training classifiers in data-sparse conditions or from human feedback.

Current LLM benchmarks focus on evaluating models' memory of facts and semantic relations, primarily assessing semantic aspects of long-term memory. However, in humans, long-term memory also includes episodic memory, which links memories to their contexts, such as the time and place they occurred. The ability to contextualize memories is crucial for many cognitive tasks and everyday functions. This form of memory has not been evaluated in LLMs with existing benchmarks. To address the gap in evaluating memory in LLMs, we introduce Sequence Order Recall Tasks (SORT), which we adapt from tasks used to study episodic memory in cognitive psychology. SORT requires LLMs to recall the correct order of text segments, and provides a general framework that is both easily extendable and does not require any additional annotations. We present an initial evaluation dataset, Book-SORT, comprising 36k pairs of segments extracted from 9 books recently added to the public domain. Based on a human experiment with 155 participants, we show that humans can recall sequence order based on long-term memory of a book. We find that models can perform the task with high accuracy when relevant text is given in-context during the SORT evaluation. However, when presented with the book text only during training, LLMs' performance on SORT falls short. By allowing to evaluate more aspects of memory, we believe that SORT will aid in the emerging development of memory-augmented models.

Following a navigation instruction such as 'Walk down the stairs and stop at the brown sofa' requires embodied AI agents to ground scene elements referenced via language (e.g. 'stairs') to visual content in the environment (pixels corresponding to 'stairs'). We ask the following question -- can we leverage abundant 'disembodied' web-scraped vision-and-language corpora (e.g. Conceptual Captions) to learn visual groundings (what do 'stairs' look like?) that improve performance on a relatively data-starved embodied perception task (Vision-and-Language Navigation)? Specifically, we develop VLN-BERT, a visiolinguistic transformer-based model for scoring the compatibility between an instruction ('...stop at the brown sofa') and a sequence of panoramic RGB images captured by the agent. We demonstrate that pretraining VLN-BERT on image-text pairs from the web before fine-tuning on embodied path-instruction data significantly improves performance on VLN -- outperforming the prior state-of-the-art in the fully-observed setting by 4 absolute percentage points on success rate. Ablations of our pretraining curriculum show each stage to be impactful -- with their combination resulting in further positive synergistic effects.

Recent advances in Behavior Cloning (BC) have led to strong performance in robotic manipulation, driven by expressive models, sequence modeling of actions, and large-scale demonstration data. However, BC faces significant challenges when applied to heterogeneous datasets, such as visual shift with different camera poses or object appearances, where performance degrades despite the benefits of learning at scale. This stems from BC's tendency to overfit individual demonstrations rather than capture shared structure, limiting generalization. To address this, we introduce Contrastive Learning via Action Sequence Supervision (CLASS), a method for learning behavioral representations from demonstrations using supervised contrastive learning. CLASS leverages weak supervision from similar action sequences identified via Dynamic Time Warping (DTW) and optimizes a soft InfoNCE loss with similarity-weighted positive pairs. We evaluate CLASS on 5 simulation benchmarks and 3 real-world tasks to achieve competitive results using retrieval-based control with representations only. Most notably, for downstream policy learning under significant visual shifts, Diffusion Policy with CLASS pre-training achieves an average success rate of 75%, while all other baseline methods fail to perform competitively. Project webpage: https://class-robot.github.io.

Real world deployments of word alignment are almost certain to cover both high and low resource languages. However, the state-of-the-art for this task recommends a different model class depending on the availability of gold alignment training data for a particular language pair. We propose BinaryAlign, a novel word alignment technique based on binary sequence labeling that outperforms existing approaches in both scenarios, offering a unifying approach to the task. Additionally, we vary the specific choice of multilingual foundation model, perform stratified error analysis over alignment error type, and explore the performance of BinaryAlign on non-English language pairs. We make our source code publicly available.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

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 curvature of space-time (Einstein, 1921), we introduce Curved Contrastive Learning (CCL), a novel representation learning technique for learning the relative turn distance between utterance pairs in multi-turn dialogues. The resulting bi-encoder models can guide transformers as a response ranking model towards a goal in a zero-shot fashion by projecting the goal utterance and the corresponding reply candidates into a latent space. Here the cosine similarity indicates the distance/reachability of a candidate utterance toward the corresponding goal. Furthermore, we explore how these forward-entailing language representations can be utilized for assessing the likelihood of sequences by the entailment strength i.e. through the cosine similarity of its individual members (encoded separately) as an emergent property in the curved space. These non-local properties allow us to imagine the likelihood of future patterns in dialogues, specifically by ordering/identifying future goal utterances that are multiple turns away, given a dialogue context. As part of our analysis, we investigate characteristics that make conversations (un)plannable and find strong evidence of planning capability over multiple turns (in 61.56% over 3 turns) in conversations from the DailyDialog (Li et al., 2017) dataset. Finally, we show how we achieve higher efficiency in sequence modeling tasks compared to previous work thanks to our relativistic approach, where only the last utterance needs to be encoded and computed during inference.

In this work, we pursue a unified paradigm for multimodal pretraining to break the scaffolds of complex task/modality-specific customization. We propose OFA, a Task-Agnostic and Modality-Agnostic framework that supports Task Comprehensiveness. OFA unifies a diverse set of cross-modal and unimodal tasks, including image generation, visual grounding, image captioning, image classification, language modeling, etc., in a simple sequence-to-sequence learning framework. OFA follows the instruction-based learning in both pretraining and finetuning stages, requiring no extra task-specific layers for downstream tasks. In comparison with the recent state-of-the-art vision & language models that rely on extremely large cross-modal datasets, OFA is pretrained on only 20M publicly available image-text pairs. Despite its simplicity and relatively small-scale training data, OFA achieves new SOTAs in a series of cross-modal tasks while attaining highly competitive performances on uni-modal tasks. Our further analysis indicates that OFA can also effectively transfer to unseen tasks and unseen domains. Our code and models are publicly available at https://github.com/OFA-Sys/OFA.

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

The success of self-supervised contrastive learning hinges on identifying positive data pairs, such that when they are pushed together in embedding space, the space encodes useful information for subsequent downstream tasks. Constructing positive pairs is non-trivial as the pairing must be similar enough to reflect a shared semantic meaning, but different enough to capture within-class variation. Classical approaches in vision use augmentations to exploit well-established invariances to construct positive pairs, but invariances in the time-series domain are much less obvious. In our work, we propose a novel method of using a learned measure for identifying positive pairs. Our Retrieval-Based Reconstruction (REBAR) measure measures the similarity between two sequences as the reconstruction error that results from reconstructing one sequence with retrieved information from the other. Then, if the two sequences have high REBAR similarity, we label them as a positive pair. Through validation experiments, we show that the REBAR error is a predictor of mutual class membership. Once integrated into a contrastive learning framework, our REBAR method learns an embedding that achieves state-of-the-art performance on downstream tasks across various modalities.

Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence alignments, such as MSA Transformer and the EvoFormer module of AlphaFold. We formulate the problem of pairing interacting partners among the paralogs of two protein families in a differentiable way. We introduce a method called DiffPALM that solves it by exploiting the ability of MSA Transformer to fill in masked amino acids in multiple sequence alignments using the surrounding context. MSA Transformer encodes coevolution between functionally or structurally coupled amino acids. We show that it captures inter-chain coevolution, while it was trained on single-chain data, which means that it can be used out-of-distribution. Relying on MSA Transformer without fine-tuning, DiffPALM outperforms existing coevolution-based pairing methods on difficult benchmarks of shallow multiple sequence alignments extracted from ubiquitous prokaryotic protein datasets. It also outperforms an alternative method based on a state-of-the-art protein language model trained on single sequences. Paired alignments of interacting protein sequences are a crucial ingredient of supervised deep learning methods to predict the three-dimensional structure of protein complexes. DiffPALM substantially improves the structure prediction of some eukaryotic protein complexes by AlphaFold-Multimer, without significantly deteriorating any of those we tested. It also achieves competitive performance with using orthology-based pairing.

In this note (work in progress towards a full-length paper) we show that a family of sequence models based on recurrent linear layers~(including S4, S5, and the LRU) interleaved with position-wise multi-layer perceptrons~(MLPs) can approximate arbitrarily well any sufficiently regular non-linear sequence-to-sequence map. The main idea behind our result is to see recurrent layers as compression algorithms that can faithfully store information about the input sequence into an inner state, before it is processed by the highly expressive MLP.

Recent large-scale neural autoregressive sequence models have shown impressive performances on a variety of natural language generation tasks. However, their generated sequences often exhibit degenerate properties such as non-termination, undesirable repetition, and premature termination, when generated with decoding algorithms such as greedy search, beam search, top-k sampling, and nucleus sampling. In this paper, we focus on the problem of non-terminating sequences resulting from an incomplete decoding algorithm. We first define an incomplete probable decoding algorithm which includes greedy search, top-k sampling, and nucleus sampling, beyond the incomplete decoding algorithm originally put forward by Welleck et al. (2020). We then propose a non-monotonic self-terminating language model, which significantly relaxes the constraint of monotonically increasing termination probability in the originally proposed self-terminating language model by Welleck et al. (2020), to address the issue of non-terminating sequences when using incomplete probable decoding algorithms. We prove that our proposed model prevents non-terminating sequences when using not only incomplete probable decoding algorithms but also beam search. We empirically validate our model on sequence completion tasks with various architectures.

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.

Neural sequence-to-sequence models provide a competitive approach to the task of mapping a question in natural language to an SQL query, also referred to as text-to-SQL generation. The Byte-Pair Encoding algorithm (BPE) has previously been used to improve machine translation (MT) between natural languages. In this work, we adapt BPE for text-to-SQL generation. As the datasets for this task are rather small compared to MT, we present a novel stopping criterion that prevents overfitting the BPE encoding to the training set. Additionally, we present AST BPE, which is a version of BPE that uses the Abstract Syntax Tree (AST) of the SQL statement to guide BPE merges and therefore produce BPE encodings that generalize better. We improved the accuracy of a strong attentive seq2seq baseline on five out of six English text-to-SQL tasks while reducing training time by more than 50% on four of them due to the shortened targets. Finally, on two of these tasks we exceeded previously reported accuracies.

Many machine learning tasks can be expressed as the transformation---or transduction---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few. One of the key challenges in sequence transduction is learning to represent both the input and output sequences in a way that is invariant to sequential distortions such as shrinking, stretching and translating. Recurrent neural networks (RNNs) are a powerful sequence learning architecture that has proven capable of learning such representations. However RNNs traditionally require a pre-defined alignment between the input and output sequences to perform transduction. This is a severe limitation since finding the alignment is the most difficult aspect of many sequence transduction problems. Indeed, even determining the length of the output sequence is often challenging. This paper introduces an end-to-end, probabilistic sequence transduction system, based entirely on RNNs, that is in principle able to transform any input sequence into any finite, discrete output sequence. Experimental results for phoneme recognition are provided on the TIMIT speech corpus.

Autoregressive models, such as the GPT family, use a fixed order, usually left-to-right, to generate sequences. However, this is not a necessity. In this paper, we challenge this assumption and show that by simply adding a positional encoding for the output, this order can be modulated on-the-fly per-sample which offers key advantageous properties. It allows for the sampling of and conditioning on arbitrary subsets of tokens, and it also allows sampling in one shot multiple tokens dynamically according to a rejection strategy, leading to a sub-linear number of model evaluations. We evaluate our method across various domains, including language modeling, path-solving, and aircraft vertical rate prediction, decreasing the number of steps required for generation by an order of magnitude.

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.

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.

Synthesizing SQL queries from natural language is a long-standing open problem and has been attracting considerable interest recently. Toward solving the problem, the de facto approach is to employ a sequence-to-sequence-style model. Such an approach will necessarily require the SQL queries to be serialized. Since the same SQL query may have multiple equivalent serializations, training a sequence-to-sequence-style model is sensitive to the choice from one of them. This phenomenon is documented as the "order-matters" problem. Existing state-of-the-art approaches rely on reinforcement learning to reward the decoder when it generates any of the equivalent serializations. However, we observe that the improvement from reinforcement learning is limited. In this paper, we propose a novel approach, i.e., SQLNet, to fundamentally solve this problem by avoiding the sequence-to-sequence structure when the order does not matter. In particular, we employ a sketch-based approach where the sketch contains a dependency graph so that one prediction can be done by taking into consideration only the previous predictions that it depends on. In addition, we propose a sequence-to-set model as well as the column attention mechanism to synthesize the query based on the sketch. By combining all these novel techniques, we show that SQLNet can outperform the prior art by 9% to 13% on the WikiSQL task.

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

Recently, dense passage retrieval has become a mainstream approach to finding relevant information in various natural language processing tasks. A number of studies have been devoted to improving the widely adopted dual-encoder architecture. However, most of the previous studies only consider query-centric similarity relation when learning the dual-encoder retriever. In order to capture more comprehensive similarity relations, we propose a novel approach that leverages both query-centric and PAssage-centric sImilarity Relations (called PAIR) for dense passage retrieval. To implement our approach, we make three major technical contributions by introducing formal formulations of the two kinds of similarity relations, generating high-quality pseudo labeled data via knowledge distillation, and designing an effective two-stage training procedure that incorporates passage-centric similarity relation constraint. Extensive experiments show that our approach significantly outperforms previous state-of-the-art models on both MSMARCO and Natural Questions datasets.

Visual storytelling aims to generate compelling narratives from image sequences. Existing models often focus on enhancing the representation of the image sequence, e.g., with external knowledge sources or advanced graph structures. Despite recent progress, the stories are often repetitive, illogical, and lacking in detail. To mitigate these issues, we present a novel framework which integrates visual representations with pretrained language models and planning. Our model translates the image sequence into a visual prefix, a sequence of continuous embeddings which language models can interpret. It also leverages a sequence of question-answer pairs as a blueprint plan for selecting salient visual concepts and determining how they should be assembled into a narrative. Automatic and human evaluation on the VIST benchmark (Huang et al., 2016) demonstrates that blueprint-based models generate stories that are more coherent, interesting, and natural compared to competitive baselines and state-of-the-art systems.

Recent advancements in Large Language Models (LLMs) have spurred interest in numerous applications requiring robust long-range capabilities, essential for processing extensive input contexts and continuously generating extended outputs. As sequence lengths increase, the number of Key-Value (KV) pairs in LLMs escalates, creating a significant efficiency bottleneck. In this paper, we propose a new KV cache optimization paradigm called LaCache, a training-free method for efficient and accurate generative inference of LLMs. LaCache enables LLMs to simultaneously address both of the critical challenges in long-range modeling: robust long-range capabilities and continuous generation without running out-of-memory (OOM). Specifically, LaCache integrates two key innovations: (1) a ladder-shaped KV cache pattern that stores KV pairs not only sequentially (left-to-right within each layer) but also across layers (from shallow to deep), providing an extended span for capturing long-range dependencies under a fixed storage budget, thereby boosting long-range capabilities; and (2) an iterative compaction mechanism that progressively compresses older caches, freeing up space for new tokens within a fixed cache size. This token distance-based dynamic compression enables more effective continuous generation under constrained cache budgets. Experiments across various tasks, benchmarks, and LLM models consistently validate LaCache's effectiveness in enhancing LLMs' long-range capabilities. Our code is available at https://github.com/GATECH-EIC/LaCache.

While long-context inference is crucial for advancing large language model (LLM) applications, its prefill speed remains a significant bottleneck. Current approaches, including sequence parallelism strategies and compute reduction through approximate attention mechanisms, still fall short of delivering optimal inference efficiency. This hinders scaling the inputs to longer sequences and processing long-context queries in a timely manner. To address this, we introduce APB, an efficient long-context inference framework that leverages multi-host approximate attention to enhance prefill speed by reducing compute and enhancing parallelism simultaneously. APB introduces a communication mechanism for essential key-value pairs within a sequence parallelism framework, enabling a faster inference speed while maintaining task performance. We implement APB by incorporating a tailored FlashAttn kernel alongside optimized distribution strategies, supporting diverse models and parallelism configurations. APB achieves speedups of up to 9.2x, 4.2x, and 1.6x compared with FlashAttn, RingAttn, and StarAttn, respectively, without any observable task performance degradation. We provide the implementation and experiment code of APB in https://github.com/thunlp/APB.

The evolution of Large Language Models (LLMs) has catalyzed a paradigm shift from superficial instruction following to rigorous long-horizon reasoning. While Group Relative Policy Optimization (GRPO) has emerged as a pivotal mechanism for eliciting such post-training reasoning capabilities due to its exceptional performance, it remains plagued by significant training instability and poor sample efficiency. We theoretically identify the root cause of these issues as the lack of distinctiveness within on-policy rollouts: for routine queries, highly homogeneous samples induce destructive gradient conflicts; whereas for hard queries, the scarcity of valid positive samples results in ineffective optimization. To bridge this gap, we propose Distinctiveness-aware Group Relative Policy Optimization (DaGRPO). DaGRPO incorporates two core mechanisms: (1) Sequence-level Gradient Rectification, which utilizes fine-grained scoring to dynamically mask sample pairs with low distinctiveness, thereby eradicating gradient conflicts at the source; and (2) Off-policy Data Augmentation, which introduces high-quality anchors to recover training signals for challenging tasks. Extensive experiments across 9 mathematical reasoning and out-of-distribution (OOD) generalization benchmarks demonstrate that DaGRPO significantly surpasses existing SFT, GRPO, and hybrid baselines, achieving new state-of-the-art performance (e.g., a +4.7% average accuracy gain on math benchmarks). Furthermore, in-depth analysis confirms that DaGRPO effectively mitigates gradient explosion and accelerates the emergence of long-chain reasoning capabilities.

Novel view synthesis from a single input image is a challenging task, where the goal is to generate a new view of a scene from a desired camera pose that may be separated by a large motion. The highly uncertain nature of this synthesis task due to unobserved elements within the scene (i.e. occlusion) and outside the field-of-view makes the use of generative models appealing to capture the variety of possible outputs. In this paper, we propose a novel generative model capable of producing a sequence of photorealistic images consistent with a specified camera trajectory, and a single starting image. Our approach is centred on an autoregressive conditional diffusion-based model capable of interpolating visible scene elements, and extrapolating unobserved regions in a view, in a geometrically consistent manner. Conditioning is limited to an image capturing a single camera view and the (relative) pose of the new camera view. To measure the consistency over a sequence of generated views, we introduce a new metric, the thresholded symmetric epipolar distance (TSED), to measure the number of consistent frame pairs in a sequence. While previous methods have been shown to produce high quality images and consistent semantics across pairs of views, we show empirically with our metric that they are often inconsistent with the desired camera poses. In contrast, we demonstrate that our method produces both photorealistic and view-consistent imagery.

When language models are trained on textual data, they acquire both knowledge about the structure of language as well as knowledge of facts about the world. At inference time, their knowledge of facts can be leveraged to solve interesting problems and perform useful knowledge work for users. It is well known that language models can verbatim memorize long sequences from their training data. However, it is much less well understood how language models memorize facts seen during training. In this work, we propose a new dataset to specifically empower researchers to study the dual processes of fact memorization and verbatim sequence memorization. The dataset consists of synthetically-generated, webtext-like documents about fictional events, as well as question-answer pairs about the events. We conduct training experiments showing how synthetic data about fictional events can be effective in teasing apart different forms of memorization. We also document the challenges in effectively building realistic, fictional synthetic data.

This paper studies Chinese Spelling Correction (CSC), which aims to detect and correct the potential spelling errors in a given sentence. Current state-of-the-art methods regard CSC as a sequence tagging task and fine-tune BERT-based models on sentence pairs. However, we note a critical flaw in the process of tagging one character to another, that the correction is excessively conditioned on the error. This is opposite from human mindset, where individuals rephrase the complete sentence based on its semantics, rather than solely on the error patterns memorized before. Such a counter-intuitive learning process results in the bottleneck of generalizability and transferability of machine spelling correction. To address this, we propose Rephrasing Language Model (ReLM), where the model is trained to rephrase the entire sentence by infilling additional slots, instead of character-to-character tagging. This novel training paradigm achieves the new state-of-the-art results across fine-tuned and zero-shot CSC benchmarks, outperforming previous counterparts by a large margin. Our method also learns transferable language representation when CSC is jointly trained with other tasks.

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.

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.

The reproduction of state-of-the-art multimodal LLM pre-training faces barriers at every stage of the pipeline, including high-quality data filtering, multimodal data mixture strategies, sequence packing techniques, and training frameworks. We introduce Open-Qwen2VL, a fully open-source 2B-parameter Multimodal Large Language Model pre-trained efficiently on 29M image-text pairs using only 442 A100-40G GPU hours. Our approach employs low-to-high dynamic image resolution and multimodal sequence packing to significantly enhance pre-training efficiency. The training dataset was carefully curated using both MLLM-based filtering techniques (e.g., MLM-Filter) and conventional CLIP-based filtering methods, substantially improving data quality and training efficiency. The Open-Qwen2VL pre-training is conducted on academic level 8xA100-40G GPUs at UCSB on 5B packed multimodal tokens, which is 0.36\% of 1.4T multimodal pre-training tokens of Qwen2-VL. The final instruction-tuned Open-Qwen2VL outperforms partially-open state-of-the-art MLLM Qwen2-VL-2B on various multimodal benchmarks of MMBench, SEEDBench, MMstar, and MathVista, indicating the remarkable training efficiency of Open-Qwen2VL. We open-source all aspects of our work, including compute-efficient and data-efficient training details, data filtering methods, sequence packing scripts, pre-training data in WebDataset format, FSDP-based training codebase, and both base and instruction-tuned model checkpoints. We redefine "fully open" for multimodal LLMs as the complete release of: 1) the training codebase, 2) detailed data filtering techniques, and 3) all pre-training and supervised fine-tuning data used to develop the model.

3D medical image generation is essential for data augmentation and patient privacy, calling for reliable and efficient models suited for clinical practice. However, current methods suffer from limited anatomical fidelity, restricted axial length, and substantial computational cost, placing them beyond reach for regions with limited resources and infrastructure. We introduce TRACE, a framework that generates 3D medical images with spatiotemporal alignment using a 2D multimodal-conditioned diffusion approach. TRACE models sequential 2D slices as video frame pairs, combining segmentation priors and radiology reports for anatomical alignment, incorporating optical flow to sustain temporal coherence. During inference, an overlapping-frame strategy links frame pairs into a flexible length sequence, reconstructed into a spatiotemporally and anatomically aligned 3D volume. Experimental results demonstrate that TRACE effectively balances computational efficiency with preserving anatomical fidelity and spatiotemporal consistency. Code is available at: https://github.com/VinyehShaw/TRACE.

Due to the diversity of assessment requirements in various application scenarios for the IQA task, existing IQA methods struggle to directly adapt to these varied requirements after training. Thus, when facing new requirements, a typical approach is fine-tuning these models on datasets specifically created for those requirements. However, it is time-consuming to establish IQA datasets. In this work, we propose a Prompt-based IQA (PromptIQA) that can directly adapt to new requirements without fine-tuning after training. On one hand, it utilizes a short sequence of Image-Score Pairs (ISP) as prompts for targeted predictions, which significantly reduces the dependency on the data requirements. On the other hand, PromptIQA is trained on a mixed dataset with two proposed data augmentation strategies to learn diverse requirements, thus enabling it to effectively adapt to new requirements. Experiments indicate that the PromptIQA outperforms SOTA methods with higher performance and better generalization. The code will be available.

Question-Options Generation (QOG) is a task that involves generating a set of question-options pairs given context. This task has various applications, including fine-tuning large models, information retrieval, and automated multiple-choice question generation for education. In this paper, we develop QOG models using three different methods based on fine-tuning sequence-to-sequence language models (LMs). Experiments demonstrate that the end-to-end QOG model is computationally efficient and stable during both training and inference, outperforming other methods. Furthermore, our analysis indicates that our QOG models are competitive on the QOG task compared to the large language model Llama 3-8B.

Modern day conversational agents are trained to emulate the manner in which humans communicate. To emotionally bond with the user, these virtual agents need to be aware of the affective state of the user. Transformers are the recent state of the art in sequence-to-sequence learning that involves training an encoder-decoder model with word embeddings from utterance-response pairs. We propose an emotion-aware transformer encoder for capturing the emotional quotient in the user utterance in order to generate human-like empathetic responses. The contributions of our paper are as follows: 1) An emotion detector module trained on the input utterances determines the affective state of the user in the initial phase 2) A novel transformer encoder is proposed that adds and normalizes the word embedding with emotion embedding thereby integrating the semantic and affective aspects of the input utterance 3) The encoder and decoder stacks belong to the Transformer-XL architecture which is the recent state of the art in language modeling. Experimentation on the benchmark Facebook AI empathetic dialogue dataset confirms the efficacy of our model from the higher BLEU-4 scores achieved for the generated responses as compared to existing methods. Emotionally intelligent virtual agents are now a reality and inclusion of affect as a modality in all human-machine interfaces is foreseen in the immediate future.

Machine learning plays an increasing role in intelligent tutoring systems as both the amount of data available and specialization among students grow. Nowadays, these systems are frequently deployed on mobile applications. Users on such mobile education platforms are dynamic, frequently being added, accessing the application with varying levels of focus, and changing while using the service. The education material itself, on the other hand, is often static and is an exhaustible resource whose use in tasks such as problem recommendation must be optimized. The ability to update user models with respect to educational material in real-time is thus essential; however, existing approaches require time-consuming re-training of user features whenever new data is added. In this paper, we introduce a neural pedagogical agent for real-time user modeling in the task of predicting user response correctness, a central task for mobile education applications. Our model, inspired by work in natural language processing on sequence modeling and machine translation, updates user features in real-time via bidirectional recurrent neural networks with an attention mechanism over embedded question-response pairs. We experiment on the mobile education application SantaTOEIC, which has 559k users, 66M response data points as well as a set of 10k study problems each expert-annotated with topic tags and gathered since 2016. Our model outperforms existing approaches over several metrics in predicting user response correctness, notably out-performing other methods on new users without large question-response histories. Additionally, our attention mechanism and annotated tag set allow us to create an interpretable education platform, with a smart review system that addresses the aforementioned issue of varied user attention and problem exhaustion.

Convolution models with long filters have demonstrated state-of-the-art reasoning abilities in many long-sequence tasks but lag behind the most optimized Transformers in wall-clock time. A major bottleneck is the Fast Fourier Transform (FFT)--which allows long convolutions to run in O(N logN) time in sequence length N but has poor hardware utilization. In this paper, we study how to optimize the FFT convolution. We find two key bottlenecks: the FFT does not effectively use specialized matrix multiply units, and it incurs expensive I/O between layers of the memory hierarchy. In response, we propose FlashFFTConv. FlashFFTConv uses a matrix decomposition that computes the FFT using matrix multiply units and enables kernel fusion for long sequences, reducing I/O. We also present two sparse convolution algorithms--1) partial convolutions and 2) frequency-sparse convolutions--which can be implemented simply by skipping blocks in the matrix decomposition, enabling further opportunities for memory and compute savings. FlashFFTConv speeds up exact FFT convolutions by up to 7.93times over PyTorch and achieves up to 4.4times speedup end-to-end. Given the same compute budget, FlashFFTConv allows Hyena-GPT-s to achieve 2.3 points better perplexity on the PILE and M2-BERT-base to achieve 3.3 points higher GLUE score--matching models with twice the parameter count. FlashFFTConv also achieves 96.1% accuracy on Path-512, a high-resolution vision task where no model had previously achieved better than 50%. Furthermore, partial convolutions enable longer-sequence models--yielding the first DNA model that can process the longest human genes (2.3M base pairs)--and frequency-sparse convolutions speed up pretrained models while maintaining or improving model quality.

Despite recent advances in Large Video Language Models (LVLMs), they still struggle with fine-grained temporal understanding, hallucinate, and often make simple mistakes on even simple video question-answering tasks, all of which pose significant challenges to their safe and reliable deployment in real-world applications. To address these limitations, we propose a self-alignment framework that enables LVLMs to learn from their own errors. Our proposed framework first obtains a training set of preferred and non-preferred response pairs, where non-preferred responses are generated by incorporating common error patterns that often occur due to inadequate spatio-temporal understanding, spurious correlations between co-occurring concepts, and over-reliance on linguistic cues while neglecting the vision modality, among others. To facilitate self-alignment of LVLMs with the constructed preferred and non-preferred response pairs, we introduce Refined Regularized Preference Optimization (RRPO), a novel preference optimization method that utilizes sub-sequence-level refined rewards and token-wise KL regularization to address the limitations of Direct Preference Optimization (DPO). We demonstrate that RRPO achieves more precise alignment and more stable training compared to DPO. Our experiments and analysis validate the effectiveness of our approach across diverse video tasks, including video hallucination, short- and long-video understanding, and fine-grained temporal reasoning.

This paper introduces GeoChain, a large-scale benchmark for evaluating step-by-step geographic reasoning in multimodal large language models (MLLMs). Leveraging 1.46 million Mapillary street-level images, GeoChain pairs each image with a 21-step chain-of-thought (CoT) question sequence (over 30 million Q&A pairs). These sequences guide models from coarse attributes to fine-grained localization across four reasoning categories - visual, spatial, cultural, and precise geolocation - annotated by difficulty. Images are also enriched with semantic segmentation (150 classes) and a visual locatability score. Our benchmarking of contemporary MLLMs (GPT-4.1 variants, Claude 3.7, Gemini 2.5 variants) on a diverse 2,088-image subset reveals consistent challenges: models frequently exhibit weaknesses in visual grounding, display erratic reasoning, and struggle to achieve accurate localization, especially as the reasoning complexity escalates. GeoChain offers a robust diagnostic methodology, critical for fostering significant advancements in complex geographic reasoning within MLLMs.

This paper presents a unified Vision-Language Pre-training (VLP) model. The model is unified in that (1) it can be fine-tuned for either vision-language generation (e.g., image captioning) or understanding (e.g., visual question answering) tasks, and (2) it uses a shared multi-layer transformer network for both encoding and decoding, which differs from many existing methods where the encoder and decoder are implemented using separate models. The unified VLP model is pre-trained on a large amount of image-text pairs using the unsupervised learning objectives of two tasks: bidirectional and sequence-to-sequence (seq2seq) masked vision-language prediction. The two tasks differ solely in what context the prediction conditions on. This is controlled by utilizing specific self-attention masks for the shared transformer network. To the best of our knowledge, VLP is the first reported model that achieves state-of-the-art results on both vision-language generation and understanding tasks, as disparate as image captioning and visual question answering, across three challenging benchmark datasets: COCO Captions, Flickr30k Captions, and VQA 2.0. The code and the pre-trained models are available at https://github.com/LuoweiZhou/VLP.

Large language models (LMs) are able to in-context learn -- perform a new task via inference alone by conditioning on a few input-label pairs (demonstrations) and making predictions for new inputs. However, there has been little understanding of how the model learns and which aspects of the demonstrations contribute to end task performance. In this paper, we show that ground truth demonstrations are in fact not required -- randomly replacing labels in the demonstrations barely hurts performance on a range of classification and multi-choce tasks, consistently over 12 different models including GPT-3. Instead, we find that other aspects of the demonstrations are the key drivers of end task performance, including the fact that they provide a few examples of (1) the label space, (2) the distribution of the input text, and (3) the overall format of the sequence. Together, our analysis provides a new way of understanding how and why in-context learning works, while opening up new questions about how much can be learned from large language models through inference alone.

In this paper, we aim to do code completion based on implementing a Neural Network from Li et. al.. Our contribution is that we use an encoding that is in-between character and word encoding called Byte Pair Encoding (BPE). We use this on the source code files treating them as natural text without first going through the abstract syntax tree (AST). We have implemented two models: an attention-enhanced LSTM and a pointer network, where the pointer network was originally introduced to solve out of vocabulary problems. We are interested to see if BPE can replace the need for the pointer network for code completion.

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

Large Language Models (LLMs) have been widely adopted in commercial code completion engines, significantly enhancing coding efficiency and productivity. However, LLMs may generate code with quality issues that violate coding standards and best practices, such as poor code style and maintainability, even when the code is functionally correct. This necessitates additional effort from developers to improve the code, potentially negating the efficiency gains provided by LLMs. To address this problem, we propose a novel comparative prefix-tuning method for controllable high-quality code generation. Our method introduces a single, property-specific prefix that is prepended to the activations of the LLM, serving as a lightweight alternative to fine-tuning. Unlike existing methods that require training multiple prefixes, our approach trains only one prefix and leverages pairs of high-quality and low-quality code samples, introducing a sequence-level ranking loss to guide the model's training. This comparative approach enables the model to better understand the differences between high-quality and low-quality code, focusing on aspects that impact code quality. Additionally, we design a data construction pipeline to collect and annotate pairs of high-quality and low-quality code, facilitating effective training. Extensive experiments on the Code Llama 7B model demonstrate that our method improves code quality by over 100% in certain task categories, while maintaining functional correctness. We also conduct ablation studies and generalization experiments, confirming the effectiveness of our method's components and its strong generalization capability.

In-context learning is one of the surprising and useful features of large language models. How it works is an active area of research. Recently, stylized meta-learning-like setups have been devised that train these models on a sequence of input-output pairs (x, f(x)) from a function class using the language modeling loss and observe generalization to unseen functions from the same class. One of the main discoveries in this line of research has been that for several problems such as linear regression, trained transformers learn algorithms for learning functions in context. However, the inductive biases of these models resulting in this behavior are not clearly understood. A model with unlimited training data and compute is a Bayesian predictor: it learns the pretraining distribution. It has been shown that high-capacity transformers mimic the Bayesian predictor for linear regression. In this paper, we show empirical evidence of transformers exhibiting the behavior of this ideal learner across different linear and non-linear function classes. We also extend the previous setups to work in the multitask setting and verify that transformers can do in-context learning in this setup as well and the Bayesian perspective sheds light on this setting also. Finally, via the example of learning Fourier series, we study the inductive bias for in-context learning. We find that in-context learning may or may not have simplicity bias depending on the pretraining data distribution.

Transformer-based models are widely used in natural language processing (NLP). Central to the transformer model is the self-attention mechanism, which captures the interactions of token pairs in the input sequences and depends quadratically on the sequence length. Training such models on longer sequences is expensive. In this paper, we show that a Bernoulli sampling attention mechanism based on Locality Sensitive Hashing (LSH), decreases the quadratic complexity of such models to linear. We bypass the quadratic cost by considering self-attention as a sum of individual tokens associated with Bernoulli random variables that can, in principle, be sampled at once by a single hash (although in practice, this number may be a small constant). This leads to an efficient sampling scheme to estimate self-attention which relies on specific modifications of LSH (to enable deployment on GPU architectures). We evaluate our algorithm on the GLUE benchmark with standard 512 sequence length where we see favorable performance relative to a standard pretrained Transformer. On the Long Range Arena (LRA) benchmark, for evaluating performance on long sequences, our method achieves results consistent with softmax self-attention but with sizable speed-ups and memory savings and often outperforms other efficient self-attention methods. Our code is available at https://github.com/mlpen/YOSO

Large-scale sequence-to-sequence models have shown to be adept at both multiple-choice and open-domain commonsense reasoning tasks. However, the current systems do not provide the ability to control the various attributes of the reasoning chain. To enable better controllability, we propose to study the commonsense reasoning as a template filling task (TemplateCSR) -- where the language models fills reasoning templates with the given constraints as control factors. As an approach to TemplateCSR, we (i) propose a dataset of commonsense reasoning template-expansion pairs and (ii) introduce POTTER, a pretrained sequence-to-sequence model using prompts to perform commonsense reasoning across concepts. Our experiments show that our approach outperforms baselines both in generation metrics and factuality metrics. We also present a detailed error analysis on our approach's ability to reliably perform commonsense reasoning.

Sequence-to-sequence models have recently gained the state of the art performance in summarization. However, not too many large-scale high-quality datasets are available and almost all the available ones are mainly news articles with specific writing style. Moreover, abstractive human-style systems involving description of the content at a deeper level require data with higher levels of abstraction. In this paper, we present WikiHow, a dataset of more than 230,000 article and summary pairs extracted and constructed from an online knowledge base written by different human authors. The articles span a wide range of topics and therefore represent high diversity styles. We evaluate the performance of the existing methods on WikiHow to present its challenges and set some baselines to further improve it.

Generating educational questions of fairytales or storybooks is vital for improving children's literacy ability. However, it is challenging to generate questions that capture the interesting aspects of a fairytale story with educational meaningfulness. In this paper, we propose a novel question generation method that first learns the question type distribution of an input story paragraph, and then summarizes salient events which can be used to generate high-cognitive-demand questions. To train the event-centric summarizer, we finetune a pre-trained transformer-based sequence-to-sequence model using silver samples composed by educational question-answer pairs. On a newly proposed educational question answering dataset FairytaleQA, we show good performance of our method on both automatic and human evaluation metrics. Our work indicates the necessity of decomposing question type distribution learning and event-centric summary generation for educational question generation.

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.

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.

The performance of large language models (LLMs) and large multimodal models (LMMs) depends heavily on the quality and scale of their pre-training datasets. Recent research shows that large multimodal models trained on natural documents where images and text are interleaved outperform those trained only on image-text pairs across a wide range of benchmarks, leveraging advanced pre- trained models to enforce semantic alignment, image-sequence consistency, and textual coherence. For Arabic, however, the lack of high-quality multimodal datasets that preserve document structure has limited progress. In this paper, we present our pipeline Wasm for processing the Common Crawl dataset to create a new Arabic multimodal dataset that uniquely provides markdown output. Unlike existing Arabic corpora that focus solely on text extraction, our approach preserves the structural integrity of web content while maintaining flexibility for both text-only and multimodal pre-training scenarios. We provide a comprehensive comparative analysis of our data processing pipeline against those used for major existing datasets, highlighting the convergences in filtering strategies and justifying our specific design choices. To support future research, we publicly release a representative dataset dump along with the multimodal processing pipeline for Arabic.

While large language models excel on high-resource multilingual tasks, low- and extremely low-resource Indic languages remain severely under-evaluated. We present IndicParam, a human-curated benchmark of over 13,000 multiple-choice questions covering 11 such languages (Nepali, Gujarati, Marathi, Odia as low-resource; Dogri, Maithili, Rajasthani, Sanskrit, Bodo, Santali, Konkani as extremely low-resource) plus Sanskrit-English code-mixed set. We evaluated 19 LLMs, both proprietary and open-weights, which reveals that even the top-performing GPT-5 reaches only 45.0% average accuracy, followed by DeepSeek-3.2 (43.1) and Claude-4.5 (42.7). We additionally label each question as knowledge-oriented or purely linguistic to discriminate factual recall from grammatical proficiency. Further, we assess the ability of LLMs to handle diverse question formats-such as list-based matching, assertion-reason pairs, and sequence ordering-alongside conventional multiple-choice questions. IndicParam provides insights into limitations of cross-lingual transfer and establishes a challenging benchmark for Indic languages. The dataset is available at https://huggingface.co/datasets/bharatgenai/IndicParam. Scripts to run benchmark are present at https://github.com/ayushbits/IndicParam.

Large language models have been widely evaluated on tasks such as comprehension, summarization, code generation, etc. However, their performance on graduate-level, culturally grounded questions in the Indian context remains largely unexplored. Existing Indian benchmarks emphasise basic fact-orientated queries that offer limited assessment of a deeper disciplinary understanding tailored to the Indian setting. In this paper, we present ParamBench, consisting of more than 17K questions in the Hindi language, comprising questionnaires from 21 diverse subjects. These questions are primarily derived from a nationwide graduate-level entrance examination covering topics such as history, music, instruments, yoga, literature, philosophy, law, etc.~ specifically for the Indian context. Additionally, we assess the ability of LLMs to handle diverse question formats - such as list-based matching, assertion-reason pairs, and sequence ordering - alongside conventional multiple-choice questions. We evaluated the performance of more than 16 open source LLMs on this benchmark, observing that Gemma3-27B attains the highest overall accuracy of 56.4\%. Furthermore, subject-wise analysis indicates that even for the best-performing LLMs, performance remains weak on topics such as music, classical instruments, and law, underscoring persistent challenges in culturally grounded reasoning. The dataset and source code is present at https://github.com/ayushbits/ParamBench.

Autoregressive Transformers adopted in Large Language Models (LLMs) are hard to scale to long sequences. Despite several works trying to reduce their computational cost, most of LLMs still adopt attention layers between all pairs of tokens in the sequence, thus incurring a quadratic cost. In this study, we present a novel approach that dynamically prunes contextual information while preserving the model's expressiveness, resulting in reduced memory and computational requirements during inference. Our method employs a learnable mechanism that determines which uninformative tokens can be dropped from the context at any point across the generation process. By doing so, our approach not only addresses performance concerns but also enhances interpretability, providing valuable insight into the model's decision-making process. Our technique can be applied to existing pre-trained models through a straightforward fine-tuning process, and the pruning strength can be specified by a sparsity parameter. Notably, our empirical findings demonstrate that we can effectively prune up to 80\% of the context without significant performance degradation on downstream tasks, offering a valuable tool for mitigating inference costs. Our reference implementation achieves up to 2times increase in inference throughput and even greater memory savings.

Video-language pre-trained models have shown remarkable success in guiding video question-answering (VideoQA) tasks. However, due to the length of video sequences, training large-scale video-based models incurs considerably higher costs than training image-based ones. This motivates us to leverage the knowledge from image-based pretraining, despite the obvious gaps between image and video domains. To bridge these gaps, in this paper, we propose Tem-Adapter, which enables the learning of temporal dynamics and complex semantics by a visual Temporal Aligner and a textual Semantic Aligner. Unlike conventional pretrained knowledge adaptation methods that only concentrate on the downstream task objective, the Temporal Aligner introduces an extra language-guided autoregressive task aimed at facilitating the learning of temporal dependencies, with the objective of predicting future states based on historical clues and language guidance that describes event progression. Besides, to reduce the semantic gap and adapt the textual representation for better event description, we introduce a Semantic Aligner that first designs a template to fuse question and answer pairs as event descriptions and then learns a Transformer decoder with the whole video sequence as guidance for refinement. We evaluate Tem-Adapter and different pre-train transferring methods on two VideoQA benchmarks, and the significant performance improvement demonstrates the effectiveness of our method.

One technique to improve the retrieval effectiveness of a search engine is to expand documents with terms that are related or representative of the documents' content.From the perspective of a question answering system, this might comprise questions the document can potentially answer. Following this observation, we propose a simple method that predicts which queries will be issued for a given document and then expands it with those predictions with a vanilla sequence-to-sequence model, trained using datasets consisting of pairs of query and relevant documents. By combining our method with a highly-effective re-ranking component, we achieve the state of the art in two retrieval tasks. In a latency-critical regime, retrieval results alone (without re-ranking) approach the effectiveness of more computationally expensive neural re-rankers but are much faster.

We introduce a full-stack framework that scales up reasoning in vision-language models (VLMs) to long videos, leveraging reinforcement learning. We address the unique challenges of long video reasoning by integrating three critical components: (1) a large-scale dataset, LongVideo-Reason, comprising 52K long video QA pairs with high-quality reasoning annotations across diverse domains such as sports, games, and vlogs; (2) a two-stage training pipeline that extends VLMs with chain-of-thought supervised fine-tuning (CoT-SFT) and reinforcement learning (RL); and (3) a training infrastructure for long video RL, named Multi-modal Reinforcement Sequence Parallelism (MR-SP), which incorporates sequence parallelism and a vLLM-based engine tailored for long video, using cached video embeddings for efficient rollout and prefilling. In experiments, LongVILA-R1-7B achieves strong performance on long video QA benchmarks such as VideoMME. It also outperforms Video-R1-7B and even matches Gemini-1.5-Pro across temporal reasoning, goal and purpose reasoning, spatial reasoning, and plot reasoning on our LongVideo-Reason-eval benchmark. Notably, our MR-SP system achieves up to 2.1x speedup on long video RL training. LongVILA-R1 demonstrates consistent performance gains as the number of input video frames scales. LongVILA-R1 marks a firm step towards long video reasoning in VLMs. In addition, we release our training system for public availability that supports RL training on various modalities (video, text, and audio), various models (VILA and Qwen series), and even image and video generation models. On a single A100 node (8 GPUs), it supports RL training on hour-long videos (e.g., 3,600 frames / around 256k tokens).

Vision Language Models (VLMs) perform well on standard video tasks but struggle with physics-driven reasoning involving motion dynamics and spatial interactions. This limitation reduces their ability to interpret real or AI-generated content (AIGC) videos and to generate physically consistent content. We present an approach that addresses this gap by translating physical-world context cues into interpretable representations aligned with VLMs' perception, comprehension, and reasoning. We introduce MASS-Bench, a comprehensive benchmark consisting of 4,350 real-world and AIGC videos and 8,361 free-form video question-answering pairs focused on physics-related comprehension tasks, with detailed annotations including visual detections, sub-segment grounding, and full-sequence 3D motion tracking of entities. We further present MASS, a model-agnostic method that injects spatial-temporal signals into the VLM language space via depth-based 3D encoding and visual grounding, coupled with a motion tracker for object dynamics. To strengthen cross-modal alignment and reasoning, we apply reinforcement fine-tuning. Experiments and ablations show that our refined VLMs outperform comparable and larger baselines, as well as prior state-of-the-art models, by 8.7% and 6.0%, achieving performance comparable to close-source SoTA VLMs such as Gemini-2.5-Flash on physics reasoning and comprehension. These results validate the effectiveness of our approach.

The outstanding performance of Large Multimodal Models (LMMs) has made them widely applied in vision-related tasks. However, various corruptions in the real world mean that images will not be as ideal as in simulations, presenting significant challenges for the practical application of LMMs. To address this issue, we introduce R-Bench, a benchmark focused on the **Real-world Robustness of LMMs**. Specifically, we: (a) model the complete link from user capture to LMMs reception, comprising 33 corruption dimensions, including 7 steps according to the corruption sequence, and 7 groups based on low-level attributes; (b) collect reference/distorted image dataset before/after corruption, including 2,970 question-answer pairs with human labeling; (c) propose comprehensive evaluation for absolute/relative robustness and benchmark 20 mainstream LMMs. Results show that while LMMs can correctly handle the original reference images, their performance is not stable when faced with distorted images, and there is a significant gap in robustness compared to the human visual system. We hope that R-Bench will inspire improving the robustness of LMMs, **extending them from experimental simulations to the real-world application**. Check https://q-future.github.io/R-Bench for details.

We present DFormer, a novel RGB-D pretraining framework to learn transferable representations for RGB-D segmentation tasks. DFormer has two new key innovations: 1) Unlike previous works that encode RGB-D information with RGB pretrained backbone, we pretrain the backbone using image-depth pairs from ImageNet-1K, and hence the DFormer is endowed with the capacity to encode RGB-D representations; 2) DFormer comprises a sequence of RGB-D blocks, which are tailored for encoding both RGB and depth information through a novel building block design. DFormer avoids the mismatched encoding of the 3D geometry relationships in depth maps by RGB pretrained backbones, which widely lies in existing methods but has not been resolved. We finetune the pretrained DFormer on two popular RGB-D tasks, i.e., RGB-D semantic segmentation and RGB-D salient object detection, with a lightweight decoder head. Experimental results show that our DFormer achieves new state-of-the-art performance on these two tasks with less than half of the computational cost of the current best methods on two RGB-D semantic segmentation datasets and five RGB-D salient object detection datasets. Our code is available at: https://github.com/VCIP-RGBD/DFormer.

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

Do state-of-the-art natural language understanding models care about word order - one of the most important characteristics of a sequence? Not always! We found 75% to 90% of the correct predictions of BERT-based classifiers, trained on many GLUE tasks, remain constant after input words are randomly shuffled. Despite BERT embeddings are famously contextual, the contribution of each individual word to downstream tasks is almost unchanged even after the word's context is shuffled. BERT-based models are able to exploit superficial cues (e.g. the sentiment of keywords in sentiment analysis; or the word-wise similarity between sequence-pair inputs in natural language inference) to make correct decisions when tokens are arranged in random orders. Encouraging classifiers to capture word order information improves the performance on most GLUE tasks, SQuAD 2.0 and out-of-samples. Our work suggests that many GLUE tasks are not challenging machines to understand the meaning of a sentence.

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.

We prove an inverse approximation theorem for the approximation of nonlinear sequence-to-sequence relationships using recurrent neural networks (RNNs). This is a so-called Bernstein-type result in approximation theory, which deduces properties of a target function under the assumption that it can be effectively approximated by a hypothesis space. In particular, we show that nonlinear sequence relationships that can be stably approximated by nonlinear RNNs must have an exponential decaying memory structure - a notion that can be made precise. This extends the previously identified curse of memory in linear RNNs into the general nonlinear setting, and quantifies the essential limitations of the RNN architecture for learning sequential relationships with long-term memory. Based on the analysis, we propose a principled reparameterization method to overcome the limitations. Our theoretical results are confirmed by numerical experiments. The code has been released in https://github.com/radarFudan/Curse-of-memory

In this paper, we propose a novel neural network model called RNN Encoder-Decoder that consists of two recurrent neural networks (RNN). One RNN encodes a sequence of symbols into a fixed-length vector representation, and the other decodes the representation into another sequence of symbols. The encoder and decoder of the proposed model are jointly trained to maximize the conditional probability of a target sequence given a source sequence. The performance of a statistical machine translation system is empirically found to improve by using the conditional probabilities of phrase pairs computed by the RNN Encoder-Decoder as an additional feature in the existing log-linear model. Qualitatively, we show that the proposed model learns a semantically and syntactically meaningful representation of linguistic phrases.

Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must be trained on a large multiple sequence alignment (MSA) from the specific family of interest, making them unable to benefit from transfer learning across families. To address this, we propose Protein Evolutionary Transformer (PoET), an autoregressive generative model of whole protein families that learns to generate sets of related proteins as sequences-of-sequences across tens of millions of natural protein sequence clusters. PoET can be used as a retrieval-augmented language model to generate and score arbitrary modifications conditioned on any protein family of interest, and can extrapolate from short context lengths to generalize well even for small families. This is enabled by a unique Transformer layer; we model tokens sequentially within sequences while attending between sequences order invariantly, allowing PoET to scale to context lengths beyond those used during training. In extensive experiments on deep mutational scanning datasets, we show that PoET outperforms existing protein language models and evolutionary sequence models for variant function prediction across proteins of all MSA depths. We also demonstrate PoET's ability to controllably generate new protein sequences.

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.

Existing cross-encoder models can be categorized as pointwise, pairwise, or listwise. Pairwise and listwise models allow passage interactions, which typically makes them more effective than pointwise models but less efficient and less robust to input passage order permutations. To enable efficient permutation-invariant passage interactions during re-ranking, we propose a new cross-encoder architecture with inter-passage attention: the Set-Encoder. In experiments on TREC Deep Learning and TIREx, the Set-Encoder is as effective as state-of-the-art listwise models while being more efficient and invariant to input passage order permutations. Compared to pointwise models, the Set-Encoder is particularly more effective when considering inter-passage information, such as novelty, and retains its advantageous properties compared to other listwise models. Our code is publicly available at https://github.com/webis-de/ECIR-25.

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.

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.

Sequence models such as transformers require inputs to be represented as one-dimensional sequences. In vision, this typically involves flattening images using a fixed row-major (raster-scan) order. While full self-attention is permutation-equivariant, modern long-sequence transformers increasingly rely on architectural approximations that break this invariance and introduce sensitivity to patch ordering. We show that patch order significantly affects model performance in such settings, with simple alternatives like column-major or Hilbert curves yielding notable accuracy shifts. Motivated by this, we propose REOrder, a two-stage framework for discovering task-optimal patch orderings. First, we derive an information-theoretic prior by evaluating the compressibility of various patch sequences. Then, we learn a policy over permutations by optimizing a Plackett-Luce policy using REINFORCE. This approach enables efficient learning in a combinatorial permutation space. REOrder improves top-1 accuracy over row-major ordering on ImageNet-1K by up to 3.01% and Functional Map of the World by 13.35%.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

Efficient computation or approximation of Levenshtein distance, a widely-used metric for evaluating sequence similarity, has attracted significant attention with the emergence of DNA storage and other biological applications. Sequence embedding, which maps Levenshtein distance to a conventional distance between embedding vectors, has emerged as a promising solution. In this paper, a novel neural network-based sequence embedding technique using Poisson regression is proposed. We first provide a theoretical analysis of the impact of embedding dimension on model performance and present a criterion for selecting an appropriate embedding dimension. Under this embedding dimension, the Poisson regression is introduced by assuming the Levenshtein distance between sequences of fixed length following a Poisson distribution, which naturally aligns with the definition of Levenshtein distance. Moreover, from the perspective of the distribution of embedding distances, Poisson regression approximates the negative log likelihood of the chi-squared distribution and offers advancements in removing the skewness. Through comprehensive experiments on real DNA storage data, we demonstrate the superior performance of the proposed method compared to state-of-the-art approaches.

The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein structure prediction, AF2's accuracy is significantly influenced by the depth of multiple sequence alignment (MSA), which requires extensive exploration of a large protein database for similar sequences. However, not all protein sequences possess abundant homologous families, and consequently, AF2's performance can degrade on such queries, at times failing to produce meaningful results. To address this, we introduce a novel generative language model, MSA-Augmenter, which leverages protein-specific attention mechanisms and large-scale MSAs to generate useful, novel protein sequences not currently found in databases. These sequences supplement shallow MSAs, enhancing the accuracy of structural property predictions. Our experiments on CASP14 demonstrate that MSA-Augmenter can generate de novo sequences that retain co-evolutionary information from inferior MSAs, thereby improving protein structure prediction quality on top of strong AF2.

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

For most deep learning practitioners, sequence modeling is synonymous with recurrent networks. Yet recent results indicate that convolutional architectures can outperform recurrent networks on tasks such as audio synthesis and machine translation. Given a new sequence modeling task or dataset, which architecture should one use? We conduct a systematic evaluation of generic convolutional and recurrent architectures for sequence modeling. The models are evaluated across a broad range of standard tasks that are commonly used to benchmark recurrent networks. Our results indicate that a simple convolutional architecture outperforms canonical recurrent networks such as LSTMs across a diverse range of tasks and datasets, while demonstrating longer effective memory. We conclude that the common association between sequence modeling and recurrent networks should be reconsidered, and convolutional networks should be regarded as a natural starting point for sequence modeling tasks. To assist related work, we have made code available at http://github.com/locuslab/TCN .

Transformers have impressive generalization capabilities on tasks with a fixed context length. However, they fail to generalize to sequences of arbitrary length, even for seemingly simple tasks such as duplicating a string. Moreover, simply training on longer sequences is inefficient due to the quadratic computation complexity of the global attention mechanism. In this work, we demonstrate that this failure mode is linked to positional encodings being out-of-distribution for longer sequences (even for relative encodings) and introduce a novel family of positional encodings that can overcome this problem. Concretely, our randomized positional encoding scheme simulates the positions of longer sequences and randomly selects an ordered subset to fit the sequence's length. Our large-scale empirical evaluation of 6000 models across 15 algorithmic reasoning tasks shows that our method allows Transformers to generalize to sequences of unseen length (increasing test accuracy by 12.0% on average).

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.

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.

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

In recent years, Transformers have become the de-facto architecture for sequence modeling on text and a variety of multi-dimensional data, such as images and video. However, the use of self-attention layers in a Transformer incurs prohibitive compute and memory complexity that scales quadratically w.r.t. the sequence length. A recent architecture, Mamba, based on state space models has been shown to achieve comparable performance for modeling text sequences, while scaling linearly with the sequence length. In this work, we present Mamba-ND, a generalized design extending the Mamba architecture to arbitrary multi-dimensional data. Our design alternatively unravels the input data across different dimensions following row-major orderings. We provide a systematic comparison of Mamba-ND with several other alternatives, based on prior multi-dimensional extensions such as Bi-directional LSTMs and S4ND. Empirically, we show that Mamba-ND demonstrates performance competitive with the state-of-the-art on a variety of multi-dimensional benchmarks, including ImageNet-1K classification, HMDB-51 action recognition, and ERA5 weather forecasting.

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.

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 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

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.}

We report a peculiar observation that LLMs can assign hidden meanings to sequences that seem visually incomprehensible to humans: for example, a nonsensical phrase consisting of Byzantine musical symbols is recognized by gpt-4o as "say abracadabra". Moreover, some models can communicate using these sequences. Some of these meanings are hypothesized to partly originate in the massive spurious correlations due to BPE tokenization. We systematically evaluate the presence of such abilities in a wide range of models: Claude-3.5 Haiku, Claude-3.5 Sonnet (New and Old), Claude-3.7 Sonnet, gpt-4o mini, gpt-4o, o1-mini, Llama-3.3 70B, DeepSeek-R1-Distill-Lllama 70B, Qwen2.5 1.5B, Qwen2.5 32B, Phi-3.5 mini, GigaChat-Max, Vikhr-Llama-3.2 1B. We argue that this observation might have far-reaching consequences for both safety and security of the modern and future LLMs and systems that employ them. As an illustration, we show that applying this method in combination with simple templates is sufficient to jailbreak previous generation models, with ASR = 0.4 on gpt-4o mini. Our code and data artifacts are available at https://github.com/L3G5/llm-hidden-meanings

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.

Sequential recommendation aims to model user preferences based on historical behavior sequences, which is crucial for various online platforms. Data sparsity remains a significant challenge in this area as most users have limited interactions and many items receive little attention. To mitigate this issue, contrastive learning has been widely adopted. By constructing positive sample pairs from the data itself and maximizing their agreement in the embedding space,it can leverage available data more effectively. Constructing reasonable positive sample pairs is crucial for the success of contrastive learning. However, current approaches struggle to generate reliable positive pairs as they either rely on representations learned from inherently sparse collaborative signals or use random perturbations which introduce significant uncertainty. To address these limitations, we propose a novel approach named Semantic Retrieval Augmented Contrastive Learning (SRA-CL), which leverages semantic information to improve the reliability of contrastive samples. SRA-CL comprises two main components: (1) Cross-Sequence Contrastive Learning via User Semantic Retrieval, which utilizes large language models (LLMs) to understand diverse user preferences and retrieve semantically similar users to form reliable positive samples through a learnable sample synthesis method; and (2) Intra-Sequence Contrastive Learning via Item Semantic Retrieval, which employs LLMs to comprehend items and retrieve similar items to perform semantic-based item substitution, thereby creating semantically consistent augmented views for contrastive learning. SRA-CL is plug-and-play and can be integrated into standard sequential recommendation models. Extensive experiments on four public datasets demonstrate the effectiveness and generalizability of the proposed approach.

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.

Integer sequences are of central importance to the modeling of concepts admitting complete finitary descriptions. We introduce a novel view on the learning of such concepts and lay down a set of benchmarking tasks aimed at conceptual understanding by machine learning models. These tasks indirectly assess model ability to abstract, and challenge them to reason both interpolatively and extrapolatively from the knowledge gained by observing representative examples. To further aid research in knowledge representation and reasoning, we present FACT, the Finitary Abstraction Comprehension Toolkit. The toolkit surrounds a large dataset of integer sequences comprising both organic and synthetic entries, a library for data pre-processing and generation, a set of model performance evaluation tools, and a collection of baseline model implementations, enabling the making of the future advancements with ease.

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.

Automatic math word problem solving has attracted growing attention in recent years. The evaluation datasets used by previous works have serious limitations in terms of scale and diversity. In this paper, we release a new large-scale and template-rich math word problem dataset named Ape210K. It consists of 210K Chinese elementary school-level math problems, which is 9 times the size of the largest public dataset Math23K. Each problem contains both the gold answer and the equations needed to derive the answer. Ape210K is also of greater diversity with 56K templates, which is 25 times more than Math23K. Our analysis shows that solving Ape210K requires not only natural language understanding but also commonsense knowledge. We expect Ape210K to be a benchmark for math word problem solving systems. Experiments indicate that state-of-the-art models on the Math23K dataset perform poorly on Ape210K. We propose a copy-augmented and feature-enriched sequence to sequence (seq2seq) model, which outperforms existing models by 3.2% on the Math23K dataset and serves as a strong baseline of the Ape210K dataset. The gap is still significant between human and our baseline model, calling for further research efforts. We make Ape210K dataset publicly available at https://github.com/yuantiku/ape210k

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.

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

In order to make the foundation model more efficient and effective, our idea is combining sequence transformation and state transformation. First, we prove the availability of rotary position embedding in the state space duality algorithm, which reduces the perplexity of the hybrid quadratic causal self-attention and state space duality by more than 4%, to ensure that the combining sequence transformation unifies position encoding. Second, we propose dynamic mask attention, which maintains 100% accuracy in the more challenging multi-query associative recall task, improving by more than 150% compared to quadratic causal self-attention and state space duality, to ensure that the combining sequence transformation selectively filters relevant information. Third, we design cross domain mixture of experts, which makes the computational speed of expert retrieval with more than 1024 experts 8 to 10 times faster than the mixture of experts, to ensure that the combining state transformation quickly retrieval mixture. Finally, we summarize these matrix algorithms that can form the foundation model: Wonderful Matrices, which can be a competitor to popular model architectures.

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.

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

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.

Scaling multi-dimensional transformers to long sequences is indispensable across various domains. However, the challenges of large memory requirements and slow speeds of such sequences necessitate sequence parallelism. All existing approaches fall under the category of embedded sequence parallelism, which are limited to shard along a single sequence dimension, thereby introducing significant communication overhead. However, the nature of multi-dimensional transformers involves independent calculations across multiple sequence dimensions. To this end, we propose Dynamic Sequence Parallelism (DSP) as a novel abstraction of sequence parallelism. DSP dynamically switches the parallel dimension among all sequences according to the computation stage with efficient resharding strategy. DSP offers significant reductions in communication costs, adaptability across modules, and ease of implementation with minimal constraints. Experimental evaluations demonstrate DSP's superiority over state-of-the-art embedded sequence parallelism methods by remarkable throughput improvements ranging from 32.2% to 10x, with less than 25% communication volume.

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

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.