Daily Papers

Reinforcement learning with verifiable rewards (RLVR) has become a central paradigm for improving reasoning and code generation in large language models, and GRPO-style training is widely adopted for its simplicity and effectiveness. However, an important design choice remains underexplored: how token-level policy gradient terms are aggregated within each sampled group. Standard GRPO uses sequence aggregation, while recent work has advocated token aggregation as a better alternative. We show that these two rules induce different optimization biases: token aggregation introduces sign-length coupling, while sequence aggregation implicitly downweights longer responses through sequence-level equal weighting. To address this tension, we propose Balanced Aggregation (BA), a simple drop-in replacement that computes token-level means separately within the positive and negative subsets and then combines them with sequence-count-based weights. Experiments with Qwen2.5-Math-7B and Qwen3-1.7B on DAPO-17k and Polaris, evaluated on six reasoning and coding benchmarks, show that BA consistently improves training stability and final performance over standard token and sequence aggregation. Our analysis further shows that the relative effectiveness of token and sequence aggregation is largely governed by response-length variation and the positive-negative length gap, highlighting aggregation as a critical design dimension in GRPO-style RLVR.

We introduce GigaEmbeddings, a novel framework for training high-performance Russian-focused text embeddings through hierarchical instruction tuning of the decoder-only LLM designed specifically for Russian language (GigaChat-3B). Our three-stage pipeline, comprising large-scale contrastive pre-training in web-scale corpora, fine-tuning with hard negatives, and multitask generalization across retrieval, classification, and clustering tasks, addresses key limitations of existing methods by unifying diverse objectives and leveraging synthetic data generation. Architectural innovations include bidirectional attention for contextual modeling, latent attention pooling for robust sequence aggregation, and strategic pruning of 25% of transformer layers to enhance efficiency without compromising performance. Evaluated on the ruMTEB benchmark spanning 23 multilingual tasks, GigaEmbeddings achieves state-of-the-art results (69.1 avg. score), outperforming strong baselines with a larger number of parameters.

We introduce SessionRec, a novel next-session prediction paradigm (NSPP) for generative sequential recommendation, addressing the fundamental misalignment between conventional next-item prediction paradigm (NIPP) and real-world recommendation scenarios. Unlike NIPP's item-level autoregressive generation that contradicts actual session-based user interactions, our framework introduces a session-aware representation learning through hierarchical sequence aggregation (intra/inter-session), reducing attention computation complexity while enabling implicit modeling of massive negative interactions, and a session-based prediction objective that better captures users' diverse interests through multi-item recommendation in next sessions. Moreover, we found that incorporating a rank loss for items within the session under the next session prediction paradigm can significantly improve the ranking effectiveness of generative sequence recommendation models. We also verified that SessionRec exhibits clear power-law scaling laws similar to those observed in LLMs. Extensive experiments conducted on public datasets and online A/B test in Meituan App demonstrate the effectiveness of SessionRec. The proposed paradigm establishes new foundations for developing industrial-scale generative recommendation systems through its model-agnostic architecture and computational efficiency.

Pretrained transformer models, such as BERT and T5, have shown to be highly effective at ad-hoc passage and document ranking. Due to inherent sequence length limits of these models, they need to be run over a document's passages, rather than processing the entire document sequence at once. Although several approaches for aggregating passage-level signals have been proposed, there has yet to be an extensive comparison of these techniques. In this work, we explore strategies for aggregating relevance signals from a document's passages into a final ranking score. We find that passage representation aggregation techniques can significantly improve over techniques proposed in prior work, such as taking the maximum passage score. We call this new approach PARADE. In particular, PARADE can significantly improve results on collections with broad information needs where relevance signals can be spread throughout the document (such as TREC Robust04 and GOV2). Meanwhile, less complex aggregation techniques may work better on collections with an information need that can often be pinpointed to a single passage (such as TREC DL and TREC Genomics). We also conduct efficiency analyses, and highlight several strategies for improving transformer-based aggregation.

Online inclusive financial services encounter significant financial risks due to their expansive user base and low default costs. By real-world practice, we reveal that utilizing longer-term user payment behaviors can enhance models' ability to forecast financial risks. However, learning long behavior sequences is non-trivial for deep sequential models. Additionally, the diverse fields of payment behaviors carry rich information, requiring thorough exploitation. These factors collectively complicate the task of long-term user behavior modeling. To tackle these challenges, we propose a Long-term Payment Behavior Sequence Folding method, referred to as LBSF. In LBSF, payment behavior sequences are folded based on merchants, using the merchant field as an intrinsic grouping criterion, which enables informative parallelism without reliance on external knowledge. Meanwhile, we maximize the utility of payment details through a multi-field behavior encoding mechanism. Subsequently, behavior aggregation at the merchant level followed by relational learning across merchants facilitates comprehensive user financial representation. We evaluate LBSF on the financial risk assessment task using a large-scale real-world dataset. The results demonstrate that folding long behavior sequences based on internal behavioral cues effectively models long-term patterns and changes, thereby generating more accurate user financial profiles for practical applications.

Visual Place Recognition (VPR) is the task of matching current visual imagery from a camera to images stored in a reference map of the environment. While initial VPR systems used simple direct image methods or hand-crafted visual features, recent work has focused on learning more powerful visual features and further improving performance through either some form of sequential matcher / filter or a hierarchical matching process. In both cases the performance of the initial single-image based system is still far from perfect, putting significant pressure on the sequence matching or (in the case of hierarchical systems) pose refinement stages. In this paper we present a novel hybrid system that creates a high performance initial match hypothesis generator using short learnt sequential descriptors, which enable selective control sequential score aggregation using single image learnt descriptors. Sequential descriptors are generated using a temporal convolutional network dubbed SeqNet, encoding short image sequences using 1-D convolutions, which are then matched against the corresponding temporal descriptors from the reference dataset to provide an ordered list of place match hypotheses. We then perform selective sequential score aggregation using shortlisted single image learnt descriptors from a separate pipeline to produce an overall place match hypothesis. Comprehensive experiments on challenging benchmark datasets demonstrate the proposed method outperforming recent state-of-the-art methods using the same amount of sequential information. Source code and supplementary material can be found at https://github.com/oravus/seqNet.

Vision-language models achieve strong performance across a wide range of multimodal understanding and reasoning tasks, yet their multi-step reasoning remains unstable. Repeated sampling over the same input often produces divergent reasoning trajectories and inconsistent final predictions. To address this, we introduce two complementary approaches inspired by test-time scaling: (1) CASHEW, an inference-time framework that stabilizes reasoning by iteratively aggregating multiple candidate trajectories into higher-quality reasoning traces, with explicit visual verification filtering hallucinated steps and grounding reasoning in visual evidence, and (2) CASHEW-RL, a learned variant that internalizes this aggregation behavior within a single model. CASHEW-RL is trained using Group Sequence Policy Optimization (GSPO) with a composite reward that encourages correct answers grounded in minimal yet sufficient visual evidence, while adaptively allocating reasoning effort based on task difficulty. This training objective enables robust self-aggregation at inference. Extensive experiments on 13 image understanding, video understanding, and video reasoning benchmarks show significant performance improvements, including gains of up to +23.6 percentage points on ScienceQA and +8.1 percentage points on EgoSchema.

Blind Omnidirectional Image Quality Assessment (BOIQA) aims to objectively assess the human perceptual quality of omnidirectional images (ODIs) without relying on pristine-quality image information. It is becoming more significant with the increasing advancement of virtual reality (VR) technology. However, the quality assessment of ODIs is severely hampered by the fact that the existing BOIQA pipeline lacks the modeling of the observer's browsing process. To tackle this issue, we propose a novel multi-sequence network for BOIQA called Assessor360, which is derived from the realistic multi-assessor ODI quality assessment procedure. Specifically, we propose a generalized Recursive Probability Sampling (RPS) method for the BOIQA task, combining content and details information to generate multiple pseudo-viewport sequences from a given starting point. Additionally, we design a Multi-scale Feature Aggregation (MFA) module with a Distortion-aware Block (DAB) to fuse distorted and semantic features of each viewport. We also devise Temporal Modeling Module (TMM) to learn the viewport transition in the temporal domain. Extensive experimental results demonstrate that Assessor360 outperforms state-of-the-art methods on multiple OIQA datasets. The code and models are available at https://github.com/TianheWu/Assessor360.

The exponential growth of Large Multimodal Models (LMMs) has driven advancements in cross-modal reasoning but at significant computational costs. In this work, we focus on visual language models. We highlight the redundancy and inefficiency in current vision encoders, and seek to construct an adaptive compression method for multimodal data. In this work, we characterize a panoply of visual token selection and merging approaches through both benchmarking and qualitative analysis. In particular, we demonstrate that simple cluster-level token aggregation outperforms prior state-of-the-art works in token selection and merging, including merging at the vision encoder level and attention-based approaches. We underline the redundancy in current vision encoders, and shed light on several puzzling trends regarding principles of visual token selection through cross-modal attention visualizations. This work is a first effort towards more effective encoding and processing of high-dimensional data, and paves the way for more scalable and sustainable multimodal systems.

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

Gait recognition aims to identify individual-specific walking patterns by observing the different periodic movements of each body part. However, most existing methods treat each part equally and fail to account for the data redundancy caused by the different step frequencies and sampling rates of gait sequences. In this study, we propose a multi-granularity motion representation network (GaitMM) for gait sequence learning. In GaitMM, we design a combined full-body and fine-grained sequence learning module (FFSL) to explore part-independent spatio-temporal representations. Moreover, we utilize a frame-wise compression strategy, referred to as multi-scale motion aggregation (MSMA), to capture discriminative information in the gait sequence. Experiments on two public datasets, CASIA-B and OUMVLP, show that our approach reaches state-of-the-art performances.

Multimodal learning has seen great success mining data features from multiple modalities with remarkable model performance improvement. Meanwhile, federated learning (FL) addresses the data sharing problem, enabling privacy-preserved collaborative training to provide sufficient precious data. Great potential, therefore, arises with the confluence of them, known as multimodal federated learning. However, limitation lies in the predominant approaches as they often assume that each local dataset records samples from all modalities. In this paper, we aim to bridge this gap by proposing an Unimodal Training - Multimodal Prediction (UTMP) framework under the context of multimodal federated learning. We design HA-Fedformer, a novel transformer-based model that empowers unimodal training with only a unimodal dataset at the client and multimodal testing by aggregating multiple clients' knowledge for better accuracy. The key advantages are twofold. Firstly, to alleviate the impact of data non-IID, we develop an uncertainty-aware aggregation method for the local encoders with layer-wise Markov Chain Monte Carlo sampling. Secondly, to overcome the challenge of unaligned language sequence, we implement a cross-modal decoder aggregation to capture the hidden signal correlation between decoders trained by data from different modalities. Our experiments on popular sentiment analysis benchmarks, CMU-MOSI and CMU-MOSEI, demonstrate that HA-Fedformer significantly outperforms state-of-the-art multimodal models under the UTMP federated learning frameworks, with 15%-20% improvement on most attributes.

The past year has witnessed the significant advancement of video-based large language models. However, the challenge of developing a unified model for both short and long video understanding remains unresolved. Most existing video LLMs cannot handle hour-long videos, while methods custom for long videos tend to be ineffective for shorter videos and images. In this paper, we identify the key issue as the redundant content in videos. To address this, we propose a novel pooling strategy that simultaneously achieves token compression and instruction-aware visual feature aggregation. Our model is termed Prompt-guided Pooling LLaVA, or PPLLaVA for short. Specifically, PPLLaVA consists of three core components: the CLIP-based visual-prompt alignment that extracts visual information relevant to the user's instructions, the prompt-guided pooling that compresses the visual sequence to arbitrary scales using convolution-style pooling, and the clip context extension designed for lengthy prompt common in visual dialogue. Moreover, our codebase also integrates the most advanced video Direct Preference Optimization (DPO) and visual interleave training. Extensive experiments have validated the performance of our model. With superior throughput and only 1024 visual context, PPLLaVA achieves better results on image benchmarks as a video LLM, while achieving state-of-the-art performance across various video benchmarks, excelling in tasks ranging from caption generation to multiple-choice questions, and handling video lengths from seconds to hours. Codes have been available at https://github.com/farewellthree/PPLLaVA.

Despite seemingly performant web agents on the task-completion benchmarks, most existing methods evaluate the agents based on a presupposition: the web navigation task consists of linear sequence of actions with an end state that marks task completion. In contrast, our work focuses on web navigation for information aggregation, wherein the agent must explore different websites to gather information for a complex query. We consider web information aggregation from two different perspectives: (i) Direct API-driven Access relies on a text-only view of the Web, leveraging external tools such as Google Search API to navigate the web and a scraper to extract website contents. (ii) Interactive Visual Access uses screenshots of the webpages and requires interaction with the browser to navigate and access information. Motivated by these diverse information access settings, we introduce Infogent, a novel modular framework for web information aggregation involving three distinct components: Navigator, Extractor and Aggregator. Experiments on different information access settings demonstrate Infogent beats an existing SOTA multi-agent search framework by 7% under Direct API-Driven Access on FRAMES, and improves over an existing information-seeking web agent by 4.3% under Interactive Visual Access on AssistantBench.

The [CLS] token in BERT is commonly used as a fixed-length representation for classification tasks, yet prior work has shown that both other tokens and intermediate layers encode valuable contextual information. In this work, we propose MaxPoolBERT, a lightweight extension to BERT that refines the [CLS] representation by aggregating information across layers and tokens. Specifically, we explore three modifications: (i) max-pooling the [CLS] token across multiple layers, (ii) enabling the [CLS] token to attend over the entire final layer using an additional multi-head attention (MHA) layer, and (iii) combining max-pooling across the full sequence with MHA. Our approach enhances BERT's classification accuracy (especially on low-resource tasks) without requiring pre-training or significantly increasing model size. Experiments on the GLUE benchmark show that MaxPoolBERT consistently achieves a better performance on the standard BERT-base model.

Recent advances in language models (LMs) have led to significant improvements in quality on complex NLP tasks, but at the expense of increased inference costs. Cascading offers a simple strategy to achieve more favorable cost-quality tradeoffs: here, a small model is invoked for most "easy" instances, while a few "hard" instances are deferred to the large model. While the principles underpinning cascading are well-studied for classification tasks - with deferral based on predicted class uncertainty favored theoretically and practically - a similar understanding is lacking for generative LM tasks. In this work, we initiate a systematic study of deferral rules for LM cascades. We begin by examining the natural extension of predicted class uncertainty to generative LM tasks, namely, the predicted sequence uncertainty. We show that this measure suffers from the length bias problem, either over- or under-emphasizing outputs based on their lengths. This is because LMs produce a sequence of uncertainty values, one for each output token; and moreover, the number of output tokens is variable across examples. To mitigate this issue, we propose to exploit the richer token-level uncertainty information implicit in generative LMs. We argue that naive predicted sequence uncertainty corresponds to a simple aggregation of these uncertainties. By contrast, we show that incorporating token-level uncertainty through learned post-hoc deferral rules can significantly outperform such simple aggregation strategies, via experiments on a range of natural language benchmarks with FLAN-T5 models. We further show that incorporating embeddings from the smaller model and intermediate layers of the larger model can give an additional boost in the overall cost-quality tradeoff.

Efficiently quantifying renal structures can provide distinct spatial context and facilitate biomarker discovery for kidney morphology. However, the development and evaluation of the transformer model to segment the renal cortex, medulla, and collecting system remains challenging due to data inefficiency. Inspired by the hierarchical structures in vision transformer, we propose a novel method using a 3D block aggregation transformer for segmenting kidney components on contrast-enhanced CT scans. We construct the first cohort of renal substructures segmentation dataset with 116 subjects under institutional review board (IRB) approval. Our method yields the state-of-the-art performance (Dice of 0.8467) against the baseline approach of 0.8308 with the data-efficient design. The Pearson R achieves 0.9891 between the proposed method and manual standards and indicates the strong correlation and reproducibility for volumetric analysis. We extend the proposed method to the public KiTS dataset, the method leads to improved accuracy compared to transformer-based approaches. We show that the 3D block aggregation transformer can achieve local communication between sequence representations without modifying self-attention, and it can serve as an accurate and efficient quantification tool for characterizing renal structures.

3D meshes are widely used in computer vision and graphics for their efficiency in animation and minimal memory use, playing a crucial role in movies, games, AR, and VR. However, creating temporally consistent and realistic textures for mesh sequences remains labor-intensive for professional artists. On the other hand, while video diffusion models excel at text-driven video generation, they often lack 3D geometry awareness and struggle with achieving multi-view consistent texturing for 3D meshes. In this work, we present Tex4D, a zero-shot approach that integrates inherent 3D geometry knowledge from mesh sequences with the expressiveness of video diffusion models to produce multi-view and temporally consistent 4D textures. Given an untextured mesh sequence and a text prompt as inputs, our method enhances multi-view consistency by synchronizing the diffusion process across different views through latent aggregation in the UV space. To ensure temporal consistency, we leverage prior knowledge from a conditional video generation model for texture synthesis. However, straightforwardly combining the video diffusion model and the UV texture aggregation leads to blurry results. We analyze the underlying causes and propose a simple yet effective modification to the DDIM sampling process to address this issue. Additionally, we introduce a reference latent texture to strengthen the correlation between frames during the denoising process. To the best of our knowledge, Tex4D is the first method specifically designed for 4D scene texturing. Extensive experiments demonstrate its superiority in producing multi-view and multi-frame consistent videos based on untextured mesh sequences.

Hybrid data combining both tabular and textual content (e.g., financial reports) are quite pervasive in the real world. However, Question Answering (QA) over such hybrid data is largely neglected in existing research. In this work, we extract samples from real financial reports to build a new large-scale QA dataset containing both Tabular And Textual data, named TAT-QA, where numerical reasoning is usually required to infer the answer, such as addition, subtraction, multiplication, division, counting, comparison/sorting, and the compositions. We further propose a novel QA model termed TAGOP, which is capable of reasoning over both tables and text. It adopts sequence tagging to extract relevant cells from the table along with relevant spans from the text to infer their semantics, and then applies symbolic reasoning over them with a set of aggregation operators to arrive at the final answer. TAGOPachieves 58.0% inF1, which is an 11.1% absolute increase over the previous best baseline model, according to our experiments on TAT-QA. But this result still lags far behind performance of expert human, i.e.90.8% in F1. It is demonstrated that our TAT-QA is very challenging and can serve as a benchmark for training and testing powerful QA models that address hybrid form data.

Modern mobile burst photography pipelines capture and merge a short sequence of frames to recover an enhanced image, but often disregard the 3D nature of the scene they capture, treating pixel motion between images as a 2D aggregation problem. We show that in a ''long-burst'', forty-two 12-megapixel RAW frames captured in a two-second sequence, there is enough parallax information from natural hand tremor alone to recover high-quality scene depth. To this end, we devise a test-time optimization approach that fits a neural RGB-D representation to long-burst data and simultaneously estimates scene depth and camera motion. Our plane plus depth model is trained end-to-end, and performs coarse-to-fine refinement by controlling which multi-resolution volume features the network has access to at what time during training. We validate the method experimentally, and demonstrate geometrically accurate depth reconstructions with no additional hardware or separate data pre-processing and pose-estimation steps.

LiDAR representation learning aims to extract rich structural and semantic information from large-scale, readily available datasets, reducing reliance on costly human annotations. However, existing LiDAR representation strategies often overlook the inherent spatiotemporal cues in LiDAR sequences, limiting their effectiveness. In this work, we propose LiMA, a novel long-term image-to-LiDAR Memory Aggregation framework that explicitly captures longer range temporal correlations to enhance LiDAR representation learning. LiMA comprises three key components: 1) a Cross-View Aggregation module that aligns and fuses overlapping regions across neighboring camera views, constructing a more unified and redundancy-free memory bank; 2) a Long-Term Feature Propagation mechanism that efficiently aligns and integrates multi-frame image features, reinforcing temporal coherence during LiDAR representation learning; and 3) a Cross-Sequence Memory Alignment strategy that enforces consistency across driving sequences, improving generalization to unseen environments. LiMA maintains high pretraining efficiency and incurs no additional computational overhead during downstream tasks. Extensive experiments on mainstream LiDAR-based perception benchmarks demonstrate that LiMA significantly improves both LiDAR semantic segmentation and 3D object detection. We hope this work inspires more effective pretraining paradigms for autonomous driving. The code has be made publicly accessible for future research.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Visual Place Recognition (VPR) has been traditionally formulated as a single-image retrieval task. Using multiple views offers clear advantages, yet this setting remains relatively underexplored and existing methods often struggle to generalize across diverse environments. In this work we introduce UniPR-3D, the first VPR architecture that effectively integrates information from multiple views. UniPR-3D builds on a VGGT backbone capable of encoding multi-view 3D representations, which we adapt by designing feature aggregators and fine-tune for the place recognition task. To construct our descriptor, we jointly leverage the 3D tokens and intermediate 2D tokens produced by VGGT. Based on their distinct characteristics, we design dedicated aggregation modules for 2D and 3D features, allowing our descriptor to capture fine-grained texture cues while also reasoning across viewpoints. To further enhance generalization, we incorporate both single- and multi-frame aggregation schemes, along with a variable-length sequence retrieval strategy. Our experiments show that UniPR-3D sets a new state of the art, outperforming both single- and multi-view baselines and highlighting the effectiveness of geometry-grounded tokens for VPR. Our code and models will be made publicly available on Github https://github.com/dtc111111/UniPR-3D.

In this paper, we propose SPECTRUM, a temporal-frequency synergistic model that unlocks the untapped potential of multi-domain representation learning for online handwriting verification (OHV). SPECTRUM comprises three core components: (1) a multi-scale interactor that finely combines temporal and frequency features through dual-modal sequence interaction and multi-scale aggregation, (2) a self-gated fusion module that dynamically integrates global temporal and frequency features via self-driven balancing. These two components work synergistically to achieve micro-to-macro spectral-temporal integration. (3) A multi-domain distance-based verifier then utilizes both temporal and frequency representations to improve discrimination between genuine and forged handwriting, surpassing conventional temporal-only approaches. Extensive experiments demonstrate SPECTRUM's superior performance over existing OHV methods, underscoring the effectiveness of temporal-frequency multi-domain learning. Furthermore, we reveal that incorporating multiple handwritten biometrics fundamentally enhances the discriminative power of handwriting representations and facilitates verification. These findings not only validate the efficacy of multi-domain learning in OHV but also pave the way for future research in multi-domain approaches across both feature and biometric domains. Code is publicly available at https://github.com/NiceRingNode/SPECTRUM.

In data-to-text (D2T) generation, training on in-domain data leads to overfitting to the data representation and repeating training data noise. We examine how to avoid finetuning pretrained language models (PLMs) on D2T generation datasets while still taking advantage of surface realization capabilities of PLMs. Inspired by pipeline approaches, we propose to generate text by transforming single-item descriptions with a sequence of modules trained on general-domain text-based operations: ordering, aggregation, and paragraph compression. We train PLMs for performing these operations on a synthetic corpus WikiFluent which we build from English Wikipedia. Our experiments on two major triple-to-text datasets -- WebNLG and E2E -- show that our approach enables D2T generation from RDF triples in zero-shot settings.

This paper presents TS2Vec, a universal framework for learning representations of time series in an arbitrary semantic level. Unlike existing methods, TS2Vec performs contrastive learning in a hierarchical way over augmented context views, which enables a robust contextual representation for each timestamp. Furthermore, to obtain the representation of an arbitrary sub-sequence in the time series, we can apply a simple aggregation over the representations of corresponding timestamps. We conduct extensive experiments on time series classification tasks to evaluate the quality of time series representations. As a result, TS2Vec achieves significant improvement over existing SOTAs of unsupervised time series representation on 125 UCR datasets and 29 UEA datasets. The learned timestamp-level representations also achieve superior results in time series forecasting and anomaly detection tasks. A linear regression trained on top of the learned representations outperforms previous SOTAs of time series forecasting. Furthermore, we present a simple way to apply the learned representations for unsupervised anomaly detection, which establishes SOTA results in the literature. The source code is publicly available at https://github.com/yuezhihan/ts2vec.

Innovations like protein diffusion have enabled significant progress in de novo protein design, which is a vital topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Thus far, only several simple encoders, such as IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we proffer the Vector Field Network (VFN), which enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential universal encoder. In protein diffusion (frame modeling), VFN exhibits an impressive performance advantage over IPA, excelling in terms of both designability (67.04% vs. 53.58%) and diversity (66.54% vs. 51.98%). In inverse folding (frame and atom modeling), VFN outperforms the previous SoTA model, PiFold (54.7% vs. 51.66%), on sequence recovery rate. We also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA (62.67% vs. 55.65%), LM-Design, by a substantial margin.

The long-context capability of recent large transformer models can be surmised to rely on techniques such as attention/model parallelism, as well as hardware-level optimizations. While these strategies allow input lengths to scale to millions of tokens, they do not fundamentally mitigate the quadratic computational and memory complexity of the core attention mechanism. In this paper, we address the challenge of long-context processing on a single device using generic implementations by reducing the quadratic memory footprint and inference cost. Existing approaches to extend the context length for generic single device implementations -- such as token merging and modified attentions -- are often modality specific and attain a suboptimal tradeoff between accuracy and efficiency. To overcome these limitations, we propose MAELRE (Modality Agnostic Efficient Long Range Encoder), a unified and efficient transformer architecture designed for long-range encoding across diverse modalities. MAELRE integrates token merging with attention approximation, progressively merging tokens at different stages of internal computational blocks. It employs a lightweight attention approximation when the number of tokens is large, and switches to standard dot-product attention as the sequence becomes shorter through successive aggregation. We demonstrate that MAELRE achieves superior accuracy while reducing computational cost compared to existing long-context models on classification tasks spanning multiple modalities, including text, time series, audio, and vision.

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

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.

Visualizing multiple time series presents fundamental tradeoffs between scalability and visual clarity. Time series capture the behavior of many large-scale real-world processes, from stock market trends to urban activities. Users often gain insights by visualizing them as line charts, juxtaposing or superposing multiple time series to compare them and identify trends and patterns. However, existing representations struggle with scalability: when covering long time spans, leading to visual clutter from too many small multiples or overlapping lines. We propose TiVy, a new algorithm that summarizes time series using sequential patterns. It transforms the series into a set of symbolic sequences based on subsequence visual similarity using Dynamic Time Warping (DTW), then constructs a disjoint grouping of similar subsequences based on the frequent sequential patterns. The grouping result, a visual summary of time series, provides uncluttered superposition with fewer small multiples. Unlike common clustering techniques, TiVy extracts similar subsequences (of varying lengths) aligned in time. We also present an interactive time series visualization that renders large-scale time series in real-time. Our experimental evaluation shows that our algorithm (1) extracts clear and accurate patterns when visualizing time series data, (2) achieves a significant speed-up (1000X) compared to a straightforward DTW clustering. We also demonstrate the efficiency of our approach to explore hidden structures in massive time series data in two usage scenarios.

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.

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

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.

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.

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.

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 explore the relations between the zeta distribution and algorithmic information theory via a new model of the transfer learning problem. The program distribution is approximated by a zeta distribution with parameter near 1. We model the training sequence as a stochastic process. We analyze the upper temporal bound for learning a training sequence and its entropy rates, assuming an oracle for the transfer learning problem. We argue from empirical evidence that power-law models are suitable for natural processes. Four sequence models are proposed. Random typing model is like no-free lunch where transfer learning does not work. Zeta process independently samples programs from the zeta distribution. A model of common sub-programs inspired by genetics uses a database of sub-programs. An evolutionary zeta process samples mutations from Zeta distribution. The analysis of stochastic processes inspired by evolution suggest that AI may be feasible in nature, countering no-free lunch sort of arguments.

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.

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

Discrete event sequences are ubiquitous, such as an ordered event series of process interactions in Information and Communication Technology systems. Recent years have witnessed increasing efforts in detecting anomalies with discrete-event sequences. However, it still remains an extremely difficult task due to several intrinsic challenges including data imbalance issues, the discrete property of the events, and sequential nature of the data. To address these challenges, in this paper, we propose OC4Seq, a multi-scale one-class recurrent neural network for detecting anomalies in discrete event sequences. Specifically, OC4Seq integrates the anomaly detection objective with recurrent neural networks (RNNs) to embed the discrete event sequences into latent spaces, where anomalies can be easily detected. In addition, given that an anomalous sequence could be caused by either individual events, subsequences of events, or the whole sequence, we design a multi-scale RNN framework to capture different levels of sequential patterns simultaneously. Experimental results on three benchmark datasets show that OC4Seq consistently outperforms various representative baselines by a large margin. Moreover, through both quantitative and qualitative analysis, the importance of capturing multi-scale sequential patterns for event anomaly detection is verified.

Transformers have been established as the de-facto backbones for most recent advances in sequence modeling, mainly due to their growing memory capacity that scales with the context length. While plausible for retrieval tasks, it causes quadratic complexity and so has motivated recent studies to explore viable subquadratic recurrent alternatives. Despite showing promising preliminary results in diverse domains, such recurrent architectures underperform Transformers in recall-intensive tasks, often attributed to their fixed-size memory. In this paper, we introduce Memory Caching (MC), a simple yet effective technique that enhances recurrent models by caching checkpoints of their memory states (a.k.a. hidden states). Memory Caching allows the effective memory capacity of RNNs to grow with sequence length, offering a flexible trade-off that interpolates between the fixed memory (i.e., O(L) complexity) of RNNs and the growing memory (i.e., O(L^2) complexity) of Transformers. We propose four variants of MC, including gated aggregation and sparse selective mechanisms, and discuss their implications on both linear and deep memory modules. Our experimental results on language modeling, and long-context understanding tasks show that MC enhances the performance of recurrent models, supporting its effectiveness. The results of in-context recall tasks indicate that while Transformers achieve the best accuracy, our MC variants show competitive performance, close the gap with Transformers, and performs better than state-of-the-art recurrent models.

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

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.

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.

Efficiently capturing the long-range patterns in sequential data sources salient to a given task -- such as classification and generative modeling -- poses a fundamental challenge. Popular approaches in the space tradeoff between the memory burden of brute-force enumeration and comparison, as in transformers, the computational burden of complicated sequential dependencies, as in recurrent neural networks, or the parameter burden of convolutional networks with many or large filters. We instead take inspiration from wavelet-based multiresolution analysis to define a new building block for sequence modeling, which we call a MultiresLayer. The key component of our model is the multiresolution convolution, capturing multiscale trends in the input sequence. Our MultiresConv can be implemented with shared filters across a dilated causal convolution tree. Thus it garners the computational advantages of convolutional networks and the principled theoretical motivation of wavelet decompositions. Our MultiresLayer is straightforward to implement, requires significantly fewer parameters, and maintains at most a O(Nlog N) memory footprint for a length N sequence. Yet, by stacking such layers, our model yields state-of-the-art performance on a number of sequence classification and autoregressive density estimation tasks using CIFAR-10, ListOps, and PTB-XL datasets.

Time series play a fundamental role in many domains, capturing a plethora of information about the underlying data-generating processes. When a process generates multiple synchronized signals we are faced with multidimensional time series. In this context a fundamental problem is that of motif mining, where we seek patterns repeating twice with minor variations, spanning some of the dimensions. State of the art exact solutions for this problem run in time quadratic in the length of the input time series. We provide a scalable method to find the top-k motifs in multidimensional time series with probabilistic guarantees on the quality of the results. Our algorithm runs in time subquadratic in the length of the input, and returns the exact solution with probability at least 1-δ, where δ is a user-defined parameter. The algorithm is designed to be adaptive to the input distribution, self-tuning its parameters while respecting user-defined limits on the memory to use. Our theoretical analysis is complemented by an extensive experimental evaluation, showing that our algorithm is orders of magnitude faster than the state of the art.

Diffusion language models have emerged as a promising approach for text generation. One would naturally expect this method to be an efficient replacement for autoregressive models since multiple tokens can be sampled in parallel during each diffusion step. However, its efficiency-accuracy trade-off is not yet well understood. In this paper, we present a rigorous theoretical analysis of a widely used type of diffusion language model, the Masked Diffusion Model (MDM), and find that its effectiveness heavily depends on the target evaluation metric. Under mild conditions, we prove that when using perplexity as the metric, MDMs can achieve near-optimal perplexity in sampling steps regardless of sequence length, demonstrating that efficiency can be achieved without sacrificing performance. However, when using the sequence error rate--which is important for understanding the "correctness" of a sequence, such as a reasoning chain--we show that the required sampling steps must scale linearly with sequence length to obtain "correct" sequences, thereby eliminating MDM's efficiency advantage over autoregressive models. Our analysis establishes the first theoretical foundation for understanding the benefits and limitations of MDMs. All theoretical findings are supported by empirical studies.

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.

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.

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.

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

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.

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

This analysis explores the temporal sequencing of objects in a movie trailer. Temporal sequencing of objects in a movie trailer (e.g., a long shot of an object vs intermittent short shots) can convey information about the type of movie, plot of the movie, role of the main characters, and the filmmakers cinematographic choices. When combined with historical customer data, sequencing analysis can be used to improve predictions of customer behavior. E.g., a customer buys tickets to a new movie and maybe the customer has seen movies in the past that contained similar sequences. To explore object sequencing in movie trailers, we propose a video convolutional network to capture actions and scenes that are predictive of customers' preferences. The model learns the specific nature of sequences for different types of objects (e.g., cars vs faces), and the role of sequences in predicting customer future behavior. We show how such a temporal-aware model outperforms simple feature pooling methods proposed in our previous works and, importantly, demonstrate the additional model explain-ability allowed by such a model.

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.

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

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

We present TableSeq, an image-only, end-to-end framework for joint table structure recognition, content recognition, and cell localization. The model formulates these tasks as a single sequence-generation problem: one decoder produces an interleaved stream of HTML tags, cell text, and discretized coordinate tokens, thereby aligning logical structure, textual content, and cell geometry within a unified autoregressive sequence. This design avoids external OCR, auxiliary decoders, and complex multi-stage post-processing. TableSeq combines a lightweight high-resolution FCN-H16 encoder with a minimal structure-prior head and a single-layer transformer encoder, yielding a compact architecture that remains effective on challenging layouts. Across standard benchmarks, TableSeq achieves competitive or state-of-the-art results while preserving architectural simplicity. It reaches 95.23 TEDS / 96.83 S-TEDS on PubTabNet, 97.45 TEDS / 98.69 S-TEDS on FinTabNet, and 99.79 / 99.54 / 99.66 precision / recall / F1 on SciTSR under the CAR protocol, while remaining competitive on PubTables-1M under GriTS. Beyond TSR/TCR, the same sequence interface generalizes to index-based table querying without task-specific heads, achieving the best IRDR score and competitive ICDR/ICR performance. We also study multi-token prediction for faster blockwise decoding and show that it reduces inference latency with only limited accuracy degradation. Overall, TableSeq provides a practical and reproducible single-stream baseline for unified table recognition, and the source code will be made publicly available at https://github.com/hamdilaziz/TableSeq.

This project aims to investigate a novel sequence generation method inspired by the AlphaGo paradigm, adapting it for use with large language models (LLMs). The proposed approach involves creating search trees of different possible completions and evaluating these completions based on model confidence. By considering various paths in the search tree and scoring them according to the model's confidence in each completion, we can generate diverse and high-quality sequences. This research explores the implementation of this paradigm by using confidence as a proxy for response quality akin to beam search vijayakumar2016diverse. The primary goal of this paper is to outline the paradigm and demonstrate its potential, rather than focusing on achieving perfect results. The paper will outline the reasons why we believe this paradigm has the potential to improve LLMs in the following manners: 1) increase output quality, 2) decrease errors, 3) eliminate or reduce the compound error problems, 4) generate diverse and creative completions, 5) allow for iterative problem-solving, and 6) self-training. We expect this approach to yield a set of diverse and coherent sequences, offering insights into balancing exploration and exploitation in sequence generation. Potential applications include creative text generation tasks, such as storytelling and content creation, as well as other natural language processing domains, like machine translation and automated summarization. The goal is that the model will be far more effective as it will be able to consider many possible variations allowing it to find the ideal completion. This research aims to contribute to the understanding of effective search strategies in sequence generation and their impact on generating high-quality, varied textual outputs.

Autoregressive models (ARMs) have become the workhorse for sequence generation tasks, since many problems can be modeled as next-token prediction. While there appears to be a natural ordering for text (i.e., left-to-right), for many data types, such as graphs, the canonical ordering is less obvious. To address this problem, we introduce a variant of ARM that generates high-dimensional data using a probabilistic ordering that is sequentially inferred from data. This model incorporates a trainable probability distribution, referred to as an order-policy, that dynamically decides the autoregressive order in a state-dependent manner. To train the model, we introduce a variational lower bound on the exact log-likelihood, which we optimize with stochastic gradient estimation. We demonstrate experimentally that our method can learn meaningful autoregressive orderings in image and graph generation. On the challenging domain of molecular graph generation, we achieve state-of-the-art results on the QM9 and ZINC250k benchmarks, evaluated using the Fr\'{e}chet ChemNet Distance (FCD).

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

The encoder-decoder framework has achieved promising process for many sequence generation tasks, such as neural machine translation and text summarization. Such a framework usually generates a sequence token by token from left to right, hence (1) this autoregressive decoding procedure is time-consuming when the output sentence becomes longer, and (2) it lacks the guidance of future context which is crucial to avoid under translation. To alleviate these issues, we propose a synchronous bidirectional sequence generation (SBSG) model which predicts its outputs from both sides to the middle simultaneously. In the SBSG model, we enable the left-to-right (L2R) and right-to-left (R2L) generation to help and interact with each other by leveraging interactive bidirectional attention network. Experiments on neural machine translation (En-De, Ch-En, and En-Ro) and text summarization tasks show that the proposed model significantly speeds up decoding while improving the generation quality compared to the autoregressive Transformer.

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.

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

In reasoning about sequential events it is natural to pose probabilistic queries such as "when will event A occur next" or "what is the probability of A occurring before B", with applications in areas such as user modeling, medicine, and finance. However, with machine learning shifting towards neural autoregressive models such as RNNs and transformers, probabilistic querying has been largely restricted to simple cases such as next-event prediction. This is in part due to the fact that future querying involves marginalization over large path spaces, which is not straightforward to do efficiently in such models. In this paper we introduce a general typology for predictive queries in neural autoregressive sequence models and show that such queries can be systematically represented by sets of elementary building blocks. We leverage this typology to develop new query estimation methods based on beam search, importance sampling, and hybrids. Across four large-scale sequence datasets from different application domains, as well as for the GPT-2 language model, we demonstrate the ability to make query answering tractable for arbitrary queries in exponentially-large predictive path-spaces, and find clear differences in cost-accuracy tradeoffs between search and sampling methods.

Sequence models lie at the heart of modern deep learning. However, rapid advancements have produced a diversity of seemingly unrelated architectures, such as Transformers and recurrent alternatives. In this paper, we introduce a unifying framework to understand and derive these sequence models, inspired by the empirical importance of associative recall, the capability to retrieve contextually relevant tokens. We formalize associative recall as a two-step process, memorization and retrieval, casting memorization as a regression problem. Layers that combine these two steps perform associative recall via ``test-time regression'' over its input tokens. Prominent layers, including linear attention, state-space models, fast-weight programmers, online learners, and softmax attention, arise as special cases defined by three design choices: the regression weights, the regressor function class, and the test-time optimization algorithm. Our approach clarifies how linear attention fails to capture inter-token correlations and offers a mathematical justification for the empirical effectiveness of query-key normalization in softmax attention. Further, it illuminates unexplored regions within the design space, which we use to derive novel higher-order generalizations of softmax attention. Beyond unification, our work bridges sequence modeling with classic regression methods, a field with extensive literature, paving the way for developing more powerful and theoretically principled architectures.

This paper proposes a fundamentally new paradigm for image generation through set-based tokenization and distribution modeling. Unlike conventional methods that serialize images into fixed-position latent codes with a uniform compression ratio, we introduce an unordered token set representation to dynamically allocate coding capacity based on regional semantic complexity. This TokenSet enhances global context aggregation and improves robustness against local perturbations. To address the critical challenge of modeling discrete sets, we devise a dual transformation mechanism that bijectively converts sets into fixed-length integer sequences with summation constraints. Further, we propose Fixed-Sum Discrete Diffusion--the first framework to simultaneously handle discrete values, fixed sequence length, and summation invariance--enabling effective set distribution modeling. Experiments demonstrate our method's superiority in semantic-aware representation and generation quality. Our innovations, spanning novel representation and modeling strategies, advance visual generation beyond traditional sequential token paradigms. Our code and models are publicly available at https://github.com/Gengzigang/TokenSet.

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

Sequential recommender systems rank relevant items by modeling a user's interaction history and computing the inner product between the resulting user representation and stored item embeddings. To avoid the significant memory overhead of storing large item sets, the generative recommendation paradigm instead models each item as a series of discrete semantic codes. Here, the next item is predicted by an autoregressive model that generates the code sequence corresponding to the predicted item. However, despite promising ranking capabilities on small datasets, these methods have yet to surpass traditional sequential recommenders on large item sets, limiting their adoption in the very scenarios they were designed to address. To resolve this, we propose MSCGRec, a Multimodal Semantic and Collaborative Generative Recommender. MSCGRec incorporates multiple semantic modalities and introduces a novel self-supervised quantization learning approach for images based on the DINO framework. Additionally, MSCGRec fuses collaborative and semantic signals by extracting collaborative features from sequential recommenders and treating them as a separate modality. Finally, we propose constrained sequence learning that restricts the large output space during training to the set of permissible tokens. We empirically demonstrate on three large real-world datasets that MSCGRec outperforms both sequential and generative recommendation baselines and provide an extensive ablation study to validate the impact of each component.

Sequential dependencies present a fundamental bottleneck in deploying large-scale autoregressive models, particularly for real-time applications. While traditional optimization approaches like pruning and quantization often compromise model quality, recent advances in generation-refinement frameworks demonstrate that this trade-off can be significantly mitigated. This survey presents a comprehensive taxonomy of generation-refinement frameworks, analyzing methods across autoregressive sequence tasks. We categorize methods based on their generation strategies (from simple n-gram prediction to sophisticated draft models) and refinement mechanisms (including single-pass verification and iterative approaches). Through systematic analysis of both algorithmic innovations and system-level implementations, we examine deployment strategies across computing environments and explore applications spanning text, images, and speech generation. This systematic examination of both theoretical frameworks and practical implementations provides a foundation for future research in efficient autoregressive decoding.

Recent advancements in large language models and their multi-modal extensions have demonstrated the effectiveness of unifying generation and understanding through autoregressive next-token prediction. However, despite the critical role of 3D structural generation and understanding ({3D GU}) in AI for science, these tasks have largely evolved independently, with autoregressive methods remaining underexplored. To bridge this gap, we introduce Uni-3DAR, a unified framework that seamlessly integrates {3D GU} tasks via autoregressive prediction. At its core, Uni-3DAR employs a novel hierarchical tokenization that compresses 3D space using an octree, leveraging the inherent sparsity of 3D structures. It then applies an additional tokenization for fine-grained structural details, capturing key attributes such as atom types and precise spatial coordinates in microscopic 3D structures. We further propose two optimizations to enhance efficiency and effectiveness. The first is a two-level subtree compression strategy, which reduces the octree token sequence by up to 8x. The second is a masked next-token prediction mechanism tailored for dynamically varying token positions, significantly boosting model performance. By combining these strategies, Uni-3DAR successfully unifies diverse {3D GU} tasks within a single autoregressive framework. Extensive experiments across multiple microscopic {3D GU} tasks, including molecules, proteins, polymers, and crystals, validate its effectiveness and versatility. Notably, Uni-3DAR surpasses previous state-of-the-art diffusion models by a substantial margin, achieving up to 256\% relative improvement while delivering inference speeds up to 21.8x faster. The code is publicly available at https://github.com/dptech-corp/Uni-3DAR.

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

Visual place recognition (VPR) is typically regarded as a specific image retrieval task, whose core lies in representing images as global descriptors. Over the past decade, dominant VPR methods (e.g., NetVLAD) have followed a paradigm that first extracts the patch features/tokens of the input image using a backbone, and then aggregates these patch features into a global descriptor via an aggregator. This backbone-plus-aggregator paradigm has achieved overwhelming dominance in the CNN era and remains widely used in transformer-based models. In this paper, however, we argue that a dedicated aggregator is not necessary in the transformer era, that is, we can obtain robust global descriptors only with the backbone. Specifically, we introduce some learnable aggregation tokens, which are prepended to the patch tokens before a particular transformer block. All these tokens will be jointly processed and interact globally via the intrinsic self-attention mechanism, implicitly aggregating useful information within the patch tokens to the aggregation tokens. Finally, we only take these aggregation tokens from the last output tokens and concatenate them as the global representation. Although implicit aggregation can provide robust global descriptors in an extremely simple manner, where and how to insert additional tokens, as well as the initialization of tokens, remains an open issue worthy of further exploration. To this end, we also propose the optimal token insertion strategy and token initialization method derived from empirical studies. Experimental results show that our method outperforms state-of-the-art methods on several VPR datasets with higher efficiency and ranks 1st on the MSLS challenge leaderboard. The code is available at https://github.com/lu-feng/image.

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 success of large language models (LLMs) for time series has been demonstrated in previous work. Utilizing a symbolic time series representation, one can efficiently bridge the gap between LLMs and time series. However, the remaining challenge is to exploit the semantic information hidden in time series by using symbols or existing tokens of LLMs, while aligning the embedding space of LLMs according to the hidden information of time series. The symbolic time series approximation (STSA) method called adaptive Brownian bridge-based symbolic aggregation (ABBA) shows outstanding efficacy in preserving salient time series features by modeling time series patterns in terms of amplitude and period while using existing tokens of LLMs. In this paper, we introduce a method, called LLM-ABBA, that integrates ABBA into large language models for various downstream time series tasks. By symbolizing time series, LLM-ABBA compares favorably to the recent state-of-the-art (SOTA) in UCR and three medical time series classification tasks. Meanwhile, a fixed-polygonal chain trick in ABBA is introduced to avoid obvious drifting during forecasting tasks by significantly mitigating the effects of cumulative error arising from misused symbols during the transition from symbols to numerical values. In time series regression tasks, LLM-ABBA achieves the new SOTA on Time Series Extrinsic Regression (TSER) benchmarks. LLM-ABBA also shows competitive forecasting capability compared to recent SOTA time series forecasting results. We believe this framework can also seamlessly extend to other time series tasks. Our simulation code is publicly available at: https://github.com/inEXASCALE/llm-abba

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.

Long sequences are critical for applications like RAG, long document summarization, multi-modality, etc., and modern LLMs, like Llama 4 Scout, support max sequence length of up to 10 million tokens. However, outside of enterprise labs, long sequence training is challenging for the AI community with limited system support in the open-source space. Out-of-box, even on a modern NVIDIA H100 80GB GPU cluster, training Llama 8B model with sequence over 32K runs out of memory on a basic Hugging Face (HF) model due to two reasons: i) LLM training workloads are not optimized to fully leverage a single GPU memory, ii) existing solutions for leveraging multiple GPU memory are not easily available to HF models, making long sequence training inaccessible. We address this with Arctic Long Sequence Training (ALST). It offers a combination of attention-agnostic single GPU and multi-GPU memory optimizations, that enables it to support out-of-box training of multi-million sequence length for a wide variety of HF models. ALST supports training Meta's Llama 8B model with 500K sequence length on a single H100 GPU, 3.7M on a single 8xH100 GPU node, and over 15M on a 4 node cluster, an increase of over 400x compared to the 32K baseline for the latter. ALST is fully compatible with HF models and open-sourced via Deepspeed https://www.deepspeed.ai/tutorials/ulysses-alst-sequence-pallellism/ and Arctic Training https://github.com/snowflakedb/ArcticTraining/blob/main/projects/sequence-parallelism/README.md.

Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments (reads) of the individual microbes can be obtained, which through assembly graphs can be combined into long contiguous DNA sequences (contigs). Given the complexity of microbial communities, single contig microbial genomes are rarely obtained. Instead, contigs are eventually clustered into bins, with each bin ideally making up a full genome. This process is referred to as metagenomic binning. Current state-of-the-art techniques for metagenomic binning rely only on the local features for the individual contigs. These techniques therefore fail to exploit the similarities between contigs as encoded by the assembly graph, in which the contigs are organized. In this paper, we propose to use Graph Neural Networks (GNNs) to leverage the assembly graph when learning contig representations for metagenomic binning. Our method, VaeG-Bin, combines variational autoencoders for learning latent representations of the individual contigs, with GNNs for refining these representations by taking into account the neighborhood structure of the contigs in the assembly graph. We explore several types of GNNs and demonstrate that VaeG-Bin recovers more high-quality genomes than other state-of-the-art binners on both simulated and real-world datasets.

Effective attention modules have played a crucial role in the success of Transformer-based large language models (LLMs), but the quadratic time and memory complexities of these attention modules also pose a challenge when processing long sequences. One potential solution for the long sequence problem is to utilize distributed clusters to parallelize the computation of attention modules across multiple devices (e.g., GPUs). However, adopting a distributed approach inevitably introduces extra memory overheads to store local attention results and incurs additional communication costs to aggregate local results into global ones. In this paper, we propose a distributed attention framework named ``BurstAttention'' to optimize memory access and communication operations at both the global cluster and local device levels. In our experiments, we compare BurstAttention with other competitive distributed attention solutions for long sequence processing. The experimental results under different length settings demonstrate that BurstAttention offers significant advantages for processing long sequences compared with these competitive baselines, reducing 40% communication overheads and achieving 2 X speedup during training 32K sequence length on 8 X A100.

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.

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

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

Accurate sequence-to-sequence (seq2seq) alignment is critical for applications like medical speech analysis and language learning tools relying on automatic speech recognition (ASR). State-of-the-art end-to-end (E2E) ASR systems, such as the Connectionist Temporal Classification (CTC) and transducer-based models, suffer from peaky behavior and alignment inaccuracies. In this paper, we propose a novel differentiable alignment framework based on one-dimensional optimal transport, enabling the model to learn a single alignment and perform ASR in an E2E manner. We introduce a pseudo-metric, called Sequence Optimal Transport Distance (SOTD), over the sequence space and discuss its theoretical properties. Based on the SOTD, we propose Optimal Temporal Transport Classification (OTTC) loss for ASR and contrast its behavior with CTC. Experimental results on the TIMIT, AMI, and LibriSpeech datasets show that our method considerably improves alignment performance compared to CTC and the more recently proposed Consistency-Regularized CTC, though with a trade-off in ASR performance. We believe this work opens new avenues for seq2seq alignment research, providing a solid foundation for further exploration and development within the community. Our code is publicly available at: https://github.com/idiap/OTTC

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

Deep learning has contributed remarkably to the advancement of time series analysis. Still, deep models can encounter performance bottlenecks in real-world small-sample scenarios, which can be concealed due to the performance saturation with small models on current benchmarks. Meanwhile, large models have demonstrated great powers in these scenarios through large-scale pre-training. Continuous progresses have been achieved as the emergence of large language models, exhibiting unprecedented ability in few-shot generalization, scalability, and task generality, which is however absent in time series models. To change the current practices of training small models on specific datasets from scratch, this paper aims at an early development of large time series models (LTSM). During pre-training, we curate large-scale datasets with up to 1 billion time points, unify heterogeneous time series into single-series sequence (S3) format, and develop the GPT-style architecture toward LTSMs. To meet diverse application needs, we convert forecasting, imputation, and anomaly detection of time series into a unified generative task. The outcome of this study is a Time Series Transformer (Timer), that is pre-trained by autoregressive next token prediction on large multi-domain datasets, and is fine-tuned to downstream scenarios with promising abilities as an LTSM.

Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of Natural Language Processing is to understand sequences of words, a major objective in biology is to understand biological sequences. Genomic Language Models (gLMs), which are LLMs trained on DNA sequences, have the potential to significantly advance our understanding of genomes and how DNA elements at various scales interact to give rise to complex functions. To showcase this potential, we highlight key applications of gLMs, including functional constraint prediction, sequence design, and transfer learning. Despite notable recent progress, however, developing effective and efficient gLMs presents numerous challenges, especially for species with large, complex genomes. Here, we discuss major considerations for developing and evaluating gLMs.

This paper studies the error metric selection for long-term memory learning in sequence modelling. We examine the bias towards short-term memory in commonly used errors, including mean absolute/squared error. Our findings show that all temporally positive-weighted errors are biased towards short-term memory in learning linear functionals. To reduce this bias and improve long-term memory learning, we propose the use of a temporally rescaled error. In addition to reducing the bias towards short-term memory, this approach can also alleviate the vanishing gradient issue. We conduct numerical experiments on different long-memory tasks and sequence models to validate our claims. Numerical results confirm the importance of appropriate temporally rescaled error for effective long-term memory learning. To the best of our knowledge, this is the first work that quantitatively analyzes different errors' memory bias towards short-term memory in sequence modelling.

This paper presents Okapi, a new dataset for Natural Language to executable web Application Programming Interfaces (NL2API). This dataset is in English and contains 22,508 questions and 9,019 unique API calls, covering three domains. We define new compositional generalization tasks for NL2API which explore the models' ability to extrapolate from simple API calls in the training set to new and more complex API calls in the inference phase. Also, the models are required to generate API calls that execute correctly as opposed to the existing approaches which evaluate queries with placeholder values. Our dataset is different than most of the existing compositional semantic parsing datasets because it is a non-synthetic dataset studying the compositional generalization in a low-resource setting. Okapi is a step towards creating realistic datasets and benchmarks for studying compositional generalization alongside the existing datasets and tasks. We report the generalization capabilities of sequence-to-sequence baseline models trained on a variety of the SCAN and Okapi datasets tasks. The best model achieves 15\% exact match accuracy when generalizing from simple API calls to more complex API calls. This highlights some challenges for future research. Okapi dataset and tasks are publicly available at https://aka.ms/nl2api/data.

Sequence and channel mixers, the core mechanism in sequence models, have become the de facto standard in time series analysis (TSA). However, recent studies have questioned the necessity of complex sequence mixers, such as attention mechanisms, demonstrating that simpler architectures can achieve comparable or even superior performance. This suggests that the benefits attributed to complex sequencemixers might instead emerge from other architectural or optimization factors. Based on this observation, we pose a central question: Are common sequence mixers necessary for time-series analysis? Therefore, we propose JustDense, an empirical study that systematically replaces sequence mixers in various well-established TSA models with dense layers. Grounded in the MatrixMixer framework, JustDense treats any sequence mixer as a mixing matrix and replaces it with a dense layer. This substitution isolates the mixing operation, enabling a clear theoretical foundation for understanding its role. Therefore, we conducted extensive experiments on 29 benchmarks covering five representative TSA tasks using seven state-of-the-art TSA models to address our research question. The results show that replacing sequence mixers with dense layers yields comparable or even superior performance. In the cases where dedicated sequence mixers still offer benefits, JustDense challenges the assumption that "deeper and more complex architectures are inherently better" in TSA.

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

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

Sequence parallelism (SP), which divides the sequence dimension of input tensors across multiple computational devices, is becoming key to unlocking the long-context capabilities of generative AI models. This paper investigates the state-of-the-art SP approaches, i.e. DeepSpeed-Ulysses and Ring-Attention, and proposes a unified SP approach, which is more robust to transformer model architectures and network hardware topology. This paper compares the communication and memory cost of SP and existing parallelism, including data/tensor/zero/expert/pipeline parallelism, and discusses the best practices for designing hybrid 4D parallelism involving SP. We achieved 86% MFU on two 8xA800 nodes using SP for sequence length 208K for the LLAMA3-8B model. Our code is publicly available on https://github.com/feifeibear/long-context-attention.

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

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

Effective training of today's large language models (LLMs) depends on large batches and long sequences for throughput and accuracy. To handle variable-length sequences on hardware accelerators, it is common practice to introduce padding tokens, so that all sequences in a batch have the same length. We show in this paper that the variation in sequence lengths in common NLP datasets is such that up to 50% of all tokens can be padding. In less common, but not extreme, cases (e.g. GLUE-cola with sequence length 128), the ratio is up to 89%. Existing methods to address the resulting inefficiency are complicated by the need to avoid cross-contamination in self-attention, by a reduction in accuracy when sequence ordering information is lost, or by customized kernel implementations only valid for specific accelerators. This paper introduces a new formalization of sequence packing in the context of the well-studied bin packing problem, and presents new algorithms based on this formulation which, for example, confer a 2x speedup for phase 2 pre-training in BERT. We show how existing models can be adapted to ensure mathematical equivalence between the original and packed models, meaning that packed models can be trained with existing pre-training and fine-tuning practices.

Byte-Pair Encoding (BPE) is a popular algorithm used for tokenizing data in NLP, despite being devised initially as a compression method. BPE appears to be a greedy algorithm at face value, but the underlying optimization problem that BPE seeks to solve has not yet been laid down. We formalize BPE as a combinatorial optimization problem. Via submodular functions, we prove that the iterative greedy version is a 1{{sigma(mu^star)}}(1-e^{-{sigma(mu^star)}})-approximation of an optimal merge sequence, where {sigma(mu^star)} is the total backward curvature with respect to the optimal merge sequence mu^star. Empirically the lower bound of the approximation is approx 0.37. We provide a faster implementation of BPE which improves the runtime complexity from Oleft(N Mright) to Oleft(N log Mright), where N is the sequence length and M is the merge count. Finally, we optimize the brute-force algorithm for optimal BPE using memoization.

Diffusion language models (DLMs) have strong theoretical efficiency but are limited by fixed-length decoding and incompatibility with key-value (KV) caches. Block diffusion mitigates these issues, yet still enforces a fixed block size and requires expensive training. We introduce Next Sequence Prediction (NSP), which unifies next-token and next-block prediction, enabling the model to adaptively determine the generation length at each step. When the length is fixed to 1, NSP reduces to standard next-token prediction. Building on NSP, we propose Sequential Diffusion Language Model (SDLM), which can retrofit pre-trained autoregressive language models (ALMs) at minimal cost. Specifically, SDLM performs diffusion inference within fixed-size mask blocks, but dynamically decodes consecutive subsequences based on model confidence, thereby preserving KV-cache compatibility and improving robustness to varying uncertainty and semantics across the sequence. Experiments show that SDLM matches or surpasses strong autoregressive baselines using only 3.5M training samples, while achieving 2.1 higher throughput than Qwen-2.5. Notably, the SDLM-32B model delivers even more pronounced efficiency gains, demonstrating the strong scalability potential of our modeling paradigm. Project page and codes: https://github.com/OpenGVLab/SDLM

Sequence Parallel (SP) serves as a prevalent strategy to handle long sequences that exceed the memory limit of a single GPU. However, existing SP methods do not take advantage of linear attention features, resulting in sub-optimal parallelism efficiency and usability for linear attention-based language models. In this paper, we introduce Linear Attention Sequence Parallel (LASP), an efficient SP method tailored to linear attention-based language models. Specifically, we design an efficient point-to-point communication mechanism to leverage the right-product kernel trick of linear attention, which sharply decreases the communication overhead of SP. We also enhance the practical efficiency of LASP by performing kernel fusion and intermediate state caching, making the implementation of LASP hardware-friendly on GPU clusters. Furthermore, we meticulously ensure the compatibility of sequence-level LASP with all types of batch-level data parallel methods, which is vital for distributed training on large clusters with long sequences and large batches. We conduct extensive experiments on two linear attention-based models with varying sequence lengths and GPU cluster sizes. LASP scales sequence length up to 4096K using 128 A100 80G GPUs on 1B models, which is 8 times longer than existing SP methods while being significantly faster. The code is available at https://github.com/OpenNLPLab/LASP.

Training large language models (LLMs) with increasingly long and varying sequence lengths introduces severe load imbalance challenges in large-scale data-parallel training. Recent frameworks attempt to mitigate these issues through data reorganization or hybrid parallel strategies. However, they often overlook how computational and communication costs scale with sequence length, resulting in suboptimal performance. We identify three critical challenges: (1) varying computation-to-communication ratios across sequences of different lengths in distributed attention, (2) mismatch between static NIC-GPU affinity and dynamic parallel workloads, and (3) distinct optimal partitioning strategies required for quadratic attention versus linear components. To address these challenges, we present Zeppelin, a novel training system that integrates three key techniques: (1) a hierarchical sequence partitioning method for the attention module that reduces communication overhead and balances computation, supported by an efficient attention engine that applies divergent parallel strategies; (2) a routing layer that orchestrates inter-node transfers to fully utilize NIC bandwidth; and (3) a remapping layer that transforms sequence layouts between attention and linear modules, ensuring high computational efficiency across both. Comprehensive evaluations across diverse configurations show that Zeppelin delivers an average 2.80x speedup over state-of-the-art methods.

Deep learning methods for Visual Place Recognition (VPR) have advanced significantly, largely driven by large-scale datasets. However, most existing approaches are trained on a single dataset, which can introduce dataset-specific inductive biases and limit model generalization. While multi-dataset joint training offers a promising solution for developing universal VPR models, divergences among training datasets can saturate limited information capacity in feature aggregation layers, leading to suboptimal performance. To address these challenges, we propose Query-based Adaptive Aggregation (QAA), a novel feature aggregation technique that leverages learned queries as reference codebooks to effectively enhance information capacity without significant computational or parameter complexity. We show that computing the Cross-query Similarity (CS) between query-level image features and reference codebooks provides a simple yet effective way to generate robust descriptors. Our results demonstrate that QAA outperforms state-of-the-art models, achieving balanced generalization across diverse datasets while maintaining peak performance comparable to dataset-specific models. Ablation studies further explore QAA's mechanisms and scalability. Visualizations reveal that the learned queries exhibit diverse attention patterns across datasets. Code will be publicly released.

One of the most striking findings in modern research on large language models (LLMs) is that scaling up compute during training leads to better results. However, less attention has been given to the benefits of scaling compute during inference. This survey focuses on these inference-time approaches. We explore three areas under a unified mathematical formalism: token-level generation algorithms, meta-generation algorithms, and efficient generation. Token-level generation algorithms, often called decoding algorithms, operate by sampling a single token at a time or constructing a token-level search space and then selecting an output. These methods typically assume access to a language model's logits, next-token distributions, or probability scores. Meta-generation algorithms work on partial or full sequences, incorporating domain knowledge, enabling backtracking, and integrating external information. Efficient generation methods aim to reduce token costs and improve the speed of generation. Our survey unifies perspectives from three research communities: traditional natural language processing, modern LLMs, and machine learning systems.

Efficiently modeling sequences with infinite context length has been a long-standing problem. Past works suffer from either the quadratic computation complexity or the limited extrapolation ability on length generalization. In this work, we present Samba, a simple hybrid architecture that layer-wise combines Mamba, a selective State Space Model (SSM), with Sliding Window Attention (SWA). Samba selectively compresses a given sequence into recurrent hidden states while still maintaining the ability to precisely recall memories with the attention mechanism. We scale Samba up to 3.8B parameters with 3.2T training tokens and show that Samba substantially outperforms the state-of-the-art models based on pure attention or SSMs on a wide range of benchmarks. When trained on 4K length sequences, Samba can be efficiently extrapolated to 256K context length with perfect memory recall and show improved token predictions up to 1M context length. As a linear-time sequence model, Samba enjoys a 3.73x higher throughput compared to Transformers with grouped-query attention when processing user prompts of 128K length, and 3.64x speedup when generating 64K tokens with unlimited streaming. A sample implementation of Samba is publicly available in https://github.com/microsoft/Samba.

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

Sequence modeling has produced diverse architectures -- from classical recurrent neural networks to modern Transformers and state space models (SSMs) -- yet a unified theoretical understanding of expressivity and trainability trade-offs remains limited. We introduce a unified framework that represents a broad class of sequence maps via an input-dependent effective interaction operator W_{ij}(X), making explicit two recurring construction patterns: (i) the Unified Factorized Framework (Explicit) (attention-style mixing), in which W_{ij}(X) varies through scalar coefficients applied to shared value maps, and (ii) Structured Dynamics (Implicit) (state-space recurrences), in which W_{ij} is induced by a latent dynamical system. Using this framework, we derive three theoretical results. First, we establish the Interaction Rank Gap: models in the Unified Factorized Framework, such as single-head attention, are constrained to a low-dimensional operator span and cannot represent certain structured dynamical maps. Second, we prove an Equivalence (Head-Count) Theorem showing that, within our multi-head factorized class, representing a linear SSM whose lag operators span a k-dimensional subspace on length-n sequences requires and is achievable with H=k heads. Third, we prove a Gradient Highway Result, showing that attention layers admit inputs with distance-independent gradient paths, whereas stable linear dynamics exhibit distance-dependent gradient attenuation. Together, these results formalize a fundamental trade-off between algebraic expressivity (interaction/operator span) and long-range gradient propagation, providing theoretical grounding for modern sequence architecture design.

In-context learning (ICL) -- the capacity of a model to infer and apply abstract patterns from examples provided within its input -- has been extensively studied in large language models trained for next-token prediction on human text. In fact, prior work often attributes this emergent behavior to distinctive statistical properties in human language. This raises a fundamental question: can ICL arise organically in other sequence domains purely through large-scale predictive training? To explore this, we turn to genomic sequences, an alternative symbolic domain rich in statistical structure. Specifically, we study the Evo2 genomic model, trained predominantly on next-nucleotide (A/T/C/G) prediction, at a scale comparable to mid-sized LLMs. We develop a controlled experimental framework comprising symbolic reasoning tasks instantiated in both linguistic and genomic forms, enabling direct comparison of ICL across genomic and linguistic models. Our results show that genomic models, like their linguistic counterparts, exhibit log-linear gains in pattern induction as the number of in-context demonstrations increases. To the best of our knowledge, this is the first evidence of organically emergent ICL in genomic sequences, supporting the hypothesis that ICL arises as a consequence of large-scale predictive modeling over rich data. These findings extend emergent meta-learning beyond language, pointing toward a unified, modality-agnostic view of in-context learning.

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.

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from discontinuities in the training target and further pathologies. To overcome this, we develop Dirichlet flow matching on the simplex based on mixtures of Dirichlet distributions as probability paths. In this framework, we derive a connection between the mixtures' scores and the flow's vector field that allows for classifier and classifier-free guidance. Further, we provide distilled Dirichlet flow matching, which enables one-step sequence generation with minimal performance hits, resulting in O(L) speedups compared to autoregressive models. On complex DNA sequence generation tasks, we demonstrate superior performance compared to all baselines in distributional metrics and in achieving desired design targets for generated sequences. Finally, we show that our classifier-free guidance approach improves unconditional generation and is effective for generating DNA that satisfies design targets. Code is available at https://github.com/HannesStark/dirichlet-flow-matching.

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

Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in distinguishing sequences from varied species like chimpanzees, dogs, and humans, becoming a staple in contemporary genomic research. However, these approaches often demand extensive computational resources, posing a challenge in terms of scalability and efficiency. Addressing this issue, our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis. This innovative approach utilizes a variety of compression algorithms, such as Gzip, Brotli, and LZMA, to efficiently process and classify genomic sequences. Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods. Our comprehensive evaluation demonstrates the proposed method's effectiveness in accurately classifying DNA sequences from multiple species. We present a detailed analysis of the performance of each algorithm used, highlighting the strengths and limitations of our approach in various genomic contexts. Furthermore, we discuss the broader implications of our findings for bioinformatics, particularly in genomic data processing and analysis. The results of our study pave the way for more efficient and scalable DNA sequence classification methods, offering significant potential for advancements in genomic research and applications.

Multi-behavior sequential recommendation (MBSR) aims to incorporate behavior types of interactions for better recommendations. Existing approaches focus on the next-item prediction objective, neglecting the value of integrating the target behavior type into the learning objective. In this paper, we propose MBGen, a novel Multi-Behavior sequential Generative recommendation framework. We formulate the MBSR task into a consecutive two-step process: (1) given item sequences, MBGen first predicts the next behavior type to frame the user intention, (2) given item sequences and a target behavior type, MBGen then predicts the next items. To model such a two-step process, we tokenize both behaviors and items into tokens and construct one single token sequence with both behaviors and items placed interleaved. Furthermore, MBGen learns to autoregressively generate the next behavior and item tokens in a unified generative recommendation paradigm, naturally enabling a multi-task capability. Additionally, we exploit the heterogeneous nature of token sequences in the generative recommendation and propose a position-routed sparse architecture to efficiently and effectively scale up models. Extensive experiments on public datasets demonstrate that MBGen significantly outperforms existing MBSR models across multiple tasks.

Sequence-to-sequence language models can be used to produce abstractive summaries which are coherent, relevant, and concise. Still, model sizes can make deployment in latency-sensitive or web-scale implementations difficult. This paper studies the relationship between model size, structured pruning, inference efficiency, and summarization accuracy on widely used summarization datasets. We show that model accuracy is tied to the encoder size while inference efficiency is connected to the decoder. Using asymmetric pruning can lead to nearly 3x improvement in inference latency with ~1 point loss in Rouge-2. Moreover, we find both the average degradation and the role of asymmetry to be consistent across model sizes and variations in datasets.

Elastic distances like dynamic time warping (DTW) are central to time series machine learning because they compare sequences under local temporal misalignment. Soft-DTW is an adaptation of DTW that can be used as a gradient-based loss by replacing the hard minimum in its dynamic-programming recursion with a smooth relaxation. However, this approach does not directly extend to elastic distances whose transition costs depend on the local alignment context. Move-Split-Merge (MSM) is one such distance: it uses context-aware split and merge penalties and has often outperformed DTW in supervised and unsupervised time series machine learning tasks such as classification and clustering. We introduce Soft-MSM, a smooth relaxation of MSM and an elastic alignment loss with context-aware transition costs. Central to the formulation is a smooth gated surrogate for MSM's piecewise split/merge cost, which enables gradients through both the dynamic-programming recursion and the local transition structure. We derive the forward recursion, backward recursion, soft alignment matrix, closed-form gradient, limiting behaviour, and divergence-corrected formulation. Experiments on 112 UCR datasets show that Soft-MSM gives lower MSM barycentre loss than existing MSM barycentre methods, and yields significantly better clustering and nearest-centroid classification performance than Soft-DTW-based alternatives. An implementation is available in the open-source aeon toolkit.

We study the problem of optimizing biological sequences, e.g., proteins, DNA, and RNA, to maximize a black-box score function that is only evaluated in an offline dataset. We propose a novel solution, bootstrapped training of score-conditioned generator (BootGen) algorithm. Our algorithm repeats a two-stage process. In the first stage, our algorithm trains the biological sequence generator with rank-based weights to enhance the accuracy of sequence generation based on high scores. The subsequent stage involves bootstrapping, which augments the training dataset with self-generated data labeled by a proxy score function. Our key idea is to align the score-based generation with a proxy score function, which distills the knowledge of the proxy score function to the generator. After training, we aggregate samples from multiple bootstrapped generators and proxies to produce a diverse design. Extensive experiments show that our method outperforms competitive baselines on biological sequential design tasks. We provide reproducible source code: https://github.com/kaist-silab/bootgen{https://github.com/kaist-silab/bootgen}.

As text generation has become a core capability of modern Large Language Models (LLMs), it underpins a wide range of downstream applications. However, most existing LLMs rely on autoregressive (AR) generation, producing one token at a time based on previously generated context-resulting in limited generation speed due to the inherently sequential nature of the process. To address this challenge, an increasing number of researchers have begun exploring parallel text generation-a broad class of techniques aimed at breaking the token-by-token generation bottleneck and improving inference efficiency. Despite growing interest, there remains a lack of comprehensive analysis on what specific techniques constitute parallel text generation and how they improve inference performance. To bridge this gap, we present a systematic survey of parallel text generation methods. We categorize existing approaches into AR-based and Non-AR-based paradigms, and provide a detailed examination of the core techniques within each category. Following this taxonomy, we assess their theoretical trade-offs in terms of speed, quality, and efficiency, and examine their potential for combination and comparison with alternative acceleration strategies. Finally, based on our findings, we highlight recent advancements, identify open challenges, and outline promising directions for future research in parallel text generation. We have also created a GitHub repository for indexing relevant papers and open resources available at https://github.com/zhanglingzhe0820/Awesome-Parallel-Text-Generation.

Generating ultra-long sequences with large language models (LLMs) has become increasingly crucial but remains a highly time-intensive task, particularly for sequences up to 100K tokens. While traditional speculative decoding methods exist, simply extending their generation limits fails to accelerate the process and can be detrimental. Through an in-depth analysis, we identify three major challenges hindering efficient generation: frequent model reloading, dynamic key-value (KV) management and repetitive generation. To address these issues, we introduce TOKENSWIFT, a novel framework designed to substantially accelerate the generation process of ultra-long sequences while maintaining the target model's inherent quality. Experimental results demonstrate that TOKENSWIFT achieves over 3 times speedup across models of varying scales (1.5B, 7B, 8B, 14B) and architectures (MHA, GQA). This acceleration translates to hours of time savings for ultra-long sequence generation, establishing TOKENSWIFT as a scalable and effective solution at unprecedented lengths. Code can be found at https://github.com/bigai-nlco/TokenSwift.

In recent years, self-attention has become the dominant paradigm for sequence modeling in a variety of domains. However, in domains with very long sequence lengths the O(T^2) memory and O(T^2 H) compute costs can make using transformers infeasible. Motivated by problems in malware detection, where sequence lengths of T geq 100,000 are a roadblock to deep learning, we re-cast self-attention using the neuro-symbolic approach of Holographic Reduced Representations (HRR). In doing so we perform the same high-level strategy of the standard self-attention: a set of queries matching against a set of keys, and returning a weighted response of the values for each key. Implemented as a ``Hrrformer'' we obtain several benefits including O(T H log H) time complexity, O(T H) space complexity, and convergence in 10times fewer epochs. Nevertheless, the Hrrformer achieves near state-of-the-art accuracy on LRA benchmarks and we are able to learn with just a single layer. Combined, these benefits make our Hrrformer the first viable Transformer for such long malware classification sequences and up to 280times faster to train on the Long Range Arena benchmark. Code is available at https://github.com/NeuromorphicComputationResearchProgram/Hrrformer

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

Recently, recurrent models such as state space models and linear attention have become popular due to their linear complexity in the sequence length. Thanks to their recurrent nature, in principle they can process arbitrarily long sequences, but their performance sometimes drops considerably beyond their training context lengths-i.e. they fail to length generalize. In this work, we provide comprehensive empirical and theoretical analysis to support the unexplored states hypothesis, which posits that models fail to length generalize when during training they are only exposed to a limited subset of the distribution of all attainable states (i.e. states that would be attained if the recurrence was applied to long sequences). Furthermore, we investigate simple training interventions that aim to increase the coverage of the states that the model is trained on, e.g. by initializing the state with Gaussian noise or with the final state of a different input sequence. With only 500 post-training steps (sim 0.1% of the pre-training budget), these interventions enable length generalization for sequences that are orders of magnitude longer than the training context (e.g. 2klongrightarrow 128k) and show improved performance in long context tasks, thus presenting a simple and efficient way to enable robust length generalization in general recurrent models.