OpenRaiser/Intern-Atlas huggingface dataset:
Less is More: Unlocking Specialization of Time Series Foundation Models via Structured Pruning
Venue: Conference NeurIPS 2025
Year: 2025

Scaling laws motivate the development of Time Series Foundation Models (TSFMs) that pre-train vast parameters and achieve remarkable zero-shot forecasting performance. Surprisingly, even after fine-tuning, TSFMs cannot consistently outperform smaller, specialized models trained on full-shot downstream data. A key question is how to realize effective adaptation of TSFMs for a target forecasting task. Through empirical studies on various TSFMs, the pre-trained models often exhibit inherent sparsity and redundancy in computation, suggesting that TSFMs have learned to activate task-relevant network substructures to accommodate diverse forecasting tasks. To preserve this valuable prior knowledge, we propose a structured pruning method to regularize the subsequent fine-tuning process by focusing it on a more relevant and compact parameter space. Extensive experiments on seven TSFMs and six benchmarks demonstrate that fine-tuning a smaller, pruned TSFM significantly improves forecasting performance compared to fine-tuning original models. This prune-then-finetune paradigm often enables TSFMs to achieve state-of-the-art performance and surpass strong specialized baselines. Source code is made publicly available at https://github.com/SJTU-DMTai/Prune-then-Finetune.
OmniTalker: One-shot Real-time Text-Driven Talking Audio-Video Generation With Multimodal Style Mimicking
Venue: Conference NeurIPS 2025
Year: 2025

Although significant progress has been made in audio-driven talking head generation, text-driven methods remain underexplored. In this work, we present OmniTalker, a unified framework that jointly generates synchronized talking audio-video content from input text while emulating the speaking and facial movement styles of the target identity, including speech characteristics, head motion, and facial dynamics. Our framework adopts a dual-branch diffusion transformer (DiT) architecture, with one branch dedicated to audio generation and the other to video synthesis. At the shallow layers, cross-modal fusion modules are introduced to integrate information between the two modalities. In deeper layers, each modality is processed independently, with the generated audio decoded by a vocoder and the video rendered using a GAN-based high-quality visual renderer. Leveraging the in-context learning capability of DiT through a masked-infilling strategy, our model can simultaneously capture both audio and visual styles without requiring explicit style extraction modules. Thanks to the efficiency of the DiT backbone and the optimized visual renderer, OmniTalker achieves real-time inference at 25 FPS. To the best of our knowledge, OmniTalker is the first one-shot framework capable of jointly modeling speech and facial styles in real time. Extensive experiments demonstrate its superiority over existing methods in terms of generation quality, particularly in preserving style consistency and ensuring precise audio-video synchronization, all while maintaining efficient inference.
Born a Transformer -- Always a Transformer? On the Effect of Pretraining on Architectural Abilities
Venue: Conference NeurIPS 2025
Year: 2025

Transformers have theoretical limitations in modeling certain sequence-to-sequence tasks, yet it remains largely unclear if these limitations play a role in large-scale pretrained LLMs, or whether LLMs might effectively overcome these constraints in practice due to the scale of both the models themselves and their pretraining data. We explore how these architectural constraints manifest after pretraining, by studying a family of $\textit{retrieval}$ and $\textit{copying}$ tasks inspired by Liu et al. [2024a]. We use a recently proposed framework for studying length generalization [Huang et al., 2025] to provide guarantees for each of our settings. Empirically, we observe an $\textit{induction-versus-anti-induction}$ asymmetry, where pretrained models are better at retrieving tokens to the right (induction) rather than the left (anti-induction) of a query token. This asymmetry disappears upon targeted fine-tuning if length-generalization is guaranteed by theory. Mechanistic analysis reveals that this asymmetry is connected to the differences in the strength of induction versus anti-induction circuits within pretrained transformers. We validate our findings through practical experiments on real-world tasks demonstrating reliability risks. Our results highlight that pretraining selectively enhances certain transformer capabilities, but does not overcome fundamental length-generalization limits.
Solver-Free Decision-Focused Learning for Linear Optimization Problems
Venue: Conference NeurIPS 2025
Year: 2025

Mathematical optimization is a fundamental tool for decision-making in a wide range of applications. However, in many real-world scenarios, the parameters of the optimization problem are not known a priori and must be predicted from contextual features. This gives rise to predict-then-optimize problems, where a machine learning model predicts problem parameters that are then used to make decisions via optimization. A growing body of work on decision-focused learning (DFL) addresses this setting by training models specifically to produce predictions that maximize downstream decision quality, rather than accuracy. While effective, DFL is computationally expensive, because it requires solving the optimization problem with the predicted parameters at each loss evaluation. In this work, we address this computational bottleneck for linear optimization problems, a common class of problems in both DFL literature and real-world applications. We propose a solver-free training method that exploits the geometric structure of linear optimization to enable efficient training with minimal degradation in solution quality. Our method is based on the insight that a solution is optimal if and only if it achieves an objective value that is at least as good as that of its adjacent vertices on the feasible polytope. Building on this, our method compares the estimated quality of the ground-truth optimal solution with that of its precomputed adjacent vertices, and uses this as loss function. Experiments demonstrate that our method significantly reduces computational cost while maintaining high decision quality.
Cooperative Retrieval-Augmented Generation for Question Answering: Mutual Information Exchange and Ranking by Contrasting Layers
Venue: Conference NeurIPS 2025
Year: 2025

Since large language models (LLMs) have a tendency to generate factually inaccurate output, retrieval-augmented generation (RAG) has gained significant attention as a key means to mitigate this downside of harnessing only LLMs. However, existing RAG methods for simple and multi-hop question answering (QA) are still prone to incorrect retrievals and hallucinations. To address these limitations, we propose CoopRAG, a novel RAG framework for the question answering task in which a retriever and an LLM work cooperatively with each other by exchanging informative knowledge, and the earlier and later layers of the retriever model work cooperatively with each other to accurately rank the retrieved documents relevant to a given query. In this framework, we (i) unroll a question into sub-questions and a reasoning chain in which uncertain positions are masked, (ii) retrieve the documents relevant to the question augmented with the sub-questions and the reasoning chain, (iii) rerank the documents by contrasting layers of the retriever, and (iv) reconstruct the reasoning chain by filling the masked positions via the LLM. Our experiments demonstrate that CoopRAG consistently outperforms state-of-the-art QA methods on three multi-hop QA datasets as well as a simple QA dataset in terms of both the retrieval and QA performances. Our code is available.
Noise Injection Reveals Hidden Capabilities of Sandbagging Language Models
Venue: Conference NeurIPS 2025
Year: 2025

Capability evaluations play a crucial role in assessing and regulating frontier AI systems. The effectiveness of these evaluations faces a significant challenge: strategic underperformance, or ``sandbagging'', where models deliberately underperform during evaluation. Sandbagging can manifest either through explicit developer intervention or through unintended model behavior, presenting a fundamental obstacle to accurate capability assessment. We introduce a novel sandbagging detection method based on injecting noise of varying magnitudes into model weights. While non-sandbagging models show predictable performance degradation with increasing noise, we demonstrate that sandbagging models exhibit anomalous performance improvements, likely due to disruption of underperformance mechanisms while core capabilities remain partially intact. Through experiments across various model architectures, sizes, and sandbagging techniques, we establish this distinctive response pattern as a reliable, model-agnostic signal for detecting sandbagging behavior. Importantly, we find noise-injection is capable of eliciting the full performance of Mistral Large 120B in a setting where the model underperforms without being instructed to do so. Our findings provide a practical tool for AI evaluation and oversight, addressing a challenge in ensuring accurate capability assessment of frontier AI systems.
Overcoming Long Context Limitations of State Space Models via Context Dependent Sparse Attention
Venue: Conference NeurIPS 2025
Year: 2025

Efficient long-context modeling remains a critical challenge for natural language processing (NLP), as the time complexity of the predominant Transformer architecture scales quadratically with the sequence length. While state-space models (SSMs) offer alternative sub-quadratic solutions, they struggle to capture long-range dependencies effectively. In this work, we focus on analyzing and improving the long-context modeling capabilities of SSMs. We show that the widely used synthetic task, associative recall, which requires a model to recall a value associated with a single key without context, insufficiently represents the complexities of real-world long-context modeling. To address this limitation, we extend the associative recall to a novel synthetic task, \emph{joint recall}, which requires a model to recall the value associated with a key given in a specified context. Theoretically, we prove that SSMs do not have the expressiveness to solve multi-query joint recall in sub-quadratic time complexity. To resolve this issue, we propose a solution based on integrating SSMs with Context-Dependent Sparse Attention (CDSA), which has the expressiveness to solve multi-query joint recall with sub-quadratic computation. To bridge the gap between theoretical analysis and real-world applications, we propose locality-sensitive Hashing Attention with sparse Key Selection (HAX), which instantiates the theoretical solution and is further tailored to natural language domains. Extensive experiments on both synthetic and real-world long-context benchmarks show that HAX consistently outperforms SSM baselines and SSMs integrated with context-independent sparse attention (CISA).
Contextual Tokenization for Graph Inverted Indices
Venue: Conference NeurIPS 2025
Year: 2025

Retrieving graphs from a large corpus, that contain a subgraph isomorphic to a given query graph, is a core operation in many real-world applications. While recent multi-vector graph representations and scores based on set alignment and containment can provide accurate subgraph isomorphism tests, their use in retrieval remains limited by their need to score corpus graphs exhaustively. We introduce CORGII (Contextual Representation of Graphs for Inverted Indexing), a graph indexing framework in which, starting with a contextual dense graph representation, a differentiable discretization module computes sparse binary codes over a learned latent vocabulary. This text document-like representation allows us to leverage classic, highly optimized inverted indices, while supporting soft (vector) set containment scores. Pushing this paradigm further, we replace the classical, fixed impact weight of a `token' on a graph (such as TFIDF or BM25) with a data-driven, trainable impact weight. Finally, we explore token expansion to support multi-probing the index for smoother accuracy-efficiency tradeoffs. To our knowledge, CORGII is the first indexer of dense graph representations using discrete tokens mapping to efficient inverted lists. Extensive experiments show that CORGII provides better trade-offs between accuracy and efficiency, compared to several baselines.
Neural Collapse in Cumulative Link Models for Ordinal Regression: An Analysis with Unconstrained Feature Model
Venue: Conference NeurIPS 2025
Year: 2025

A phenomenon known as ''Neural Collapse (NC)'' in deep classification tasks, in which the penultimate-layer features and the final classifiers exhibit an extremely simple geometric structure, has recently attracted considerable attention, with the expectation that it can deepen our understanding of how deep neural networks behave. The Unconstrained Feature Model (UFM) has been proposed to explain NC theoretically, and there emerges a growing body of work that extends NC to tasks other than classification and leverages it for practical applications. In this study, we investigate whether a similar phenomenon arises in deep Ordinal Regression (OR) tasks, via combining the cumulative link model for OR and UFM. We show that a phenomenon we call Ordinal Neural Collapse (ONC) indeed emerges and is characterized by the following three properties: (ONC1) all optimal features in the same class collapse to their within-class mean when regularization is applied; (ONC2) these class means align with the classifier, meaning that they collapse onto a one-dimensional subspace; (ONC3) the optimal latent variables (corresponding to logits or preactivations in classification tasks) are aligned according to the class order, and in particular, in the zero-regularization limit, a highly local and simple geometric relationship emerges between the latent variables and the threshold values. We prove these properties analytically within the UFM framework with fixed threshold values and corroborate them empirically across a variety of datasets. We also discuss how these insights can be leveraged in OR, highlighting the use of fixed thresholds.
Reinforcement Learning with Action Chunking
Venue: Conference NeurIPS 2025
Year: 2025

We present Q-chunking, a simple yet effective recipe for improving reinforcement learning (RL) algorithms for long-horizon, sparse-reward tasks. Our recipe is designed for the offline-to-online RL setting, where the goal is to leverage an offline prior dataset to maximize the sample-efficiency of online learning. Effective exploration and sample-efficient learning remain central challenges in this setting, as it is not obvious how the offline data should be utilized to acquire a good exploratory policy. Our key insight is that action chunking, a technique popularized in imitation learning where sequences of future actions are predicted rather than a single action at each timestep, can be applied to temporal difference (TD)-based RL methods to mitigate the exploration challenge. Q-chunking adopts action chunking by directly running RL in a 'chunked' action space, enabling the agent to (1) leverage temporally consistent behaviors from offline data for more effective online exploration and (2) use unbiased $n$-step backups for more stable and efficient TD learning. Our experimental results demonstrate that Q-chunking exhibits strong offline performance and online sample efficiency, outperforming prior best offline-to-online methods on a range of long-horizon, sparse-reward manipulation tasks.
Protein Design with Dynamic Protein Vocabulary
Venue: Conference NeurIPS 2025
Year: 2025

Protein design is a fundamental challenge in biotechnology, aiming to design novel sequences with specific functions within the vast space of possible proteins. Recent advances in deep generative models have enabled function-based protein design from textual descriptions, yet struggle with structural plausibility. Inspired by classical protein design methods that leverage natural protein structures, we explore whether incorporating fragments from natural proteins can enhance foldability in generative models. Our empirical results show that even random incorporation of fragments improves foldability. Building on this insight, we introduce ProDVa, a novel protein design approach that integrates a text encoder for functional descriptions, a protein language model for designing proteins, and a fragment encoder to dynamically retrieve protein fragments based on textual functional descriptions. Experimental results demonstrate that our approach effectively designs protein sequences that are both functionally aligned and structurally plausible. Compared to state-of-the-art models, ProDVa achieves comparable function alignment using less than 0.04% of the training data, while designing significantly more well-folded proteins, with the proportion of proteins having pLDDT above 70 increasing by 7.38% and those with PAE below 10 increasing by 9.6%.
MAGNET: A Multi-agent Framework for Finding Audio-Visual Needles by Reasoning over Multi-Video Haystacks
Venue: Conference NeurIPS 2025
Year: 2025

Large multimodal models (LMMs) have shown remarkable progress in audio-visual understanding, yet they struggle with real-world scenarios that require complex reasoning across extensive video collections. Existing benchmarks for video question answering remain limited in scope, typically involving one clip per query, which falls short of representing the challenges of large-scale, audio-visual retrieval and reasoning encountered in practical applications. To bridge this gap, we introduce a novel task named AV-HaystacksQA, where the goal is to identify salient segments across different videos in response to a query and link them together to generate the most informative answer. To this end, we present AVHaystacks, an audio-visual benchmark comprising 3100 annotated QA pairs designed to assess the capabilities of LMMs in multi-video retrieval and temporal grounding task. Additionally, we propose a model-agnostic, multi-agent framework MAGNET to address this challenge, achieving up to 89% and 65% relative improvements over baseline methods on BLEU@4 and GPT evaluation scores in QA task on our proposed AVHaystacks. To enable robust evaluation of multi-video retrieval and temporal grounding for optimal response generation, we introduce two new metrics, STEM, which captures alignment errors between a ground truth and a predicted step sequence and MTGS, to facilitate balanced and interpretable evaluation of segment-level grounding performance. Project: https://schowdhury671.github.io/magnet_project/
Soft Thinking: Unlocking the Reasoning Potential of LLMs in Continuous Concept Space
Venue: Conference NeurIPS 2025
Year: 2025

Human cognition typically involves thinking through abstract, fluid concepts rather than strictly using discrete linguistic tokens. Current reasoning models, however, are constrained to reasoning within the boundaries of human language, processing discrete token embeddings that represent fixed points in the semantic space. This discrete constraint restricts the expressive power and upper potential of such reasoning models, often causing incomplete exploration of reasoning paths, as standard Chain-of-Thought (CoT) methods rely on sampling one token per step. In this work, we introduce Soft Thinking, a training-free method that emulates human-like "soft" reasoning by generating soft, abstract concept tokens in a continuous concept space. These concept tokens are created by the probability-weighted mixture of token embeddings, which form the continuous concept space, enabling smooth transitions and richer representations that transcend traditional discrete boundaries. In essence, each generated concept token encapsulates multiple meanings from related discrete tokens, implicitly exploring various reasoning paths to converge effectively toward the correct answer. Empirical evaluations on diverse mathematical and coding benchmarks consistently demonstrate the effectiveness and efficiency of Soft Thinking, improving pass@1 accuracy by up to 2.48 points while simultaneously reducing token usage by up to 22.4% compared to standard CoT. Qualitative analysis further reveals that Soft Thinking outputs remain highly interpretable and readable, highlighting the potential of Soft Thinking to break the inherent bottleneck of discrete language-based reasoning. Code is available at https://github.com/eric-ai-lab/Soft-Thinking.
ReSearch: Learning to Reason with Search for LLMs via Reinforcement Learning
Venue: Conference NeurIPS 2025
Year: 2025

Large Language Models (LLMs) have shown remarkable capabilities in reasoning, exemplified by the success of OpenAI-o1 and DeepSeek-R1. However, integrating reasoning with external search processes remains challenging, especially for complex multi-hop questions requiring multiple retrieval steps. We propose ReSearch, a novel framework that trains LLMs to Reason with Search via reinforcement learning without using any supervised data on reasoning steps. Our approach treats search operations as integral components of the reasoning chain, where when and how to perform searches is guided by text-based thinking, and search results subsequently influence further reasoning. We train ReSearch on Qwen2.5-7B(-Instruct) and Qwen2.5-32B(-Instruct) models and conduct extensive experiments. Despite being trained on only one dataset, our models demonstrate strong generalizability across various benchmarks. Analysis reveals that ReSearch naturally elicits advanced reasoning capabilities such as reflection and self-correction during the reinforcement learning process.
Reasoning Models Hallucinate More: Factuality-Aware Reinforcement Learning for Large Reasoning Models
Venue: Conference NeurIPS 2025
Year: 2025

Large language models (LLMs) have significantly advanced in reasoning tasks through reinforcement learning (RL) optimization, achieving impressive capabilities across various challenging benchmarks. However, our empirical analysis reveals a critical drawback: reasoning-oriented RL fine-tuning significantly increases the prevalence of hallucinations. We theoretically analyze the RL training dynamics, identifying high-variance gradient, entropy-induced randomness, and susceptibility to spurious local optima as key factors leading to hallucinations. To address this drawback, we propose Factuality-aware Step-wise Policy Optimization (FSPO), an innovative RL fine-tuning algorithm incorporating explicit factuality verification at each reasoning step. FSPO leverages automated verification against given evidence to dynamically adjust token-level advantage values, incentivizing factual correctness throughout the reasoning process. Experiments across mathematical reasoning and hallucination benchmarks using Qwen2.5 and Llama models demonstrate that FSPO effectively reduces hallucinations while enhancing reasoning accuracy, substantially improving both reliability and performance.