NeurIPS 2025 论文列表

Retrieval-augmented generation (RAG) enhances large language models (LLMs) by integrating external knowledge, yet traditional RAG systems struggle with static workflows and limited adaptability for complex, multistep reasoning tasks. Agentic RAG systems, such as DeepResearch, address these issues through dynamic retrieval, iterative context refinement, and adaptive workflows. However, recent methods like Search-R1, which rely on outcome-based reinforcement learning, face challenges such as low exploration efficiency, gradient conflict, and sparse reward signals. To tackle these limitations, we introduce ReasonRAG, a novel method that leverages RAG-ProGUIDE—a high-quality dataset providing fine-grained, process-level rewards for query generation, evidence extraction, and answer generation. By employing process-supervised reinforcement learning, ReasonRAG enhances LLMs’ autonomous capabilities in search, query generation, evidence extraction, and answer synthesis. Experimental results show that ReasonRAG, utilizing RAG-ProGUIDE, outperforms existing approaches like Search-R1 and traditional RAG systems, achieving superior performance on five benchmark datasets with only 5k training instances—significantly fewer than the 90k required by Search-R1. Our code is available at https://github.com/Applied-Machine-Learning-Lab/ReasonRAG.

The task of Knowlegde-Based Visual Question Answering (KB-VQA) requires the model to understand visual features and retrieve external knowledge. Retrieval-Augmented Generation (RAG) have been employed to address this problem through knowledge base querying. However, existing work demonstrate two limitations: insufficient interactivity during knowledge retrieval and ineffective organization of retrieved information for Visual-Language Model (VLM). To address these challenges, we propose a three-stage visual language model with Process, Retrieve and Filter (VLM-PRF) framework. For interactive retrieval, VLM-PRF uses reinforcement learning (RL) to guide the model to strategically process information via tool-driven operations. For knowledge filtering, our method trains the VLM to transform the raw retrieved information into into task-specific knowledge. With a dual reward as supervisory signals, VLM-PRF successfully enable model to optimize retrieval strategies and answer generation capabilities simultaneously. Experiments on two datasets demonstrate the effectiveness of our framework.

Graph Neural Networks learn on graph-structured data by iteratively aggregating local neighborhood information. While this local message passing paradigm imparts a powerful inductive bias and exploits graph sparsity, it also yields three key challenges: (i) oversquashing of long-range information, (ii) oversmoothing of node representations, and (iii) limited expressive power. In this work we inject randomized global embeddings of node features, which we term Sketched Random Features, into standard GNNs, enabling them to efficiently capture long-range dependencies. The embeddings are unique, distance-sensitive, and topology-agnostic---properties which we analytically and empirically show alleviate the aforementioned limitations when injected into GNNs. Experimental results on real-world graph learning tasks confirm that this strategy consistently improves performance over baseline GNNs, offering both a standalone solution and a complementary enhancement to existing techniques such as graph positional encodings.

Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks like 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 9-species benchmark of de novo peptide sequencing task show 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. Our code is available on GitHub: https://github.com/BEAM-Labs/denovo

This paper introduces an approach for training o1-like RAG models that retrieve and reason over relevant information step by step before generating the final answer. Conventional RAG methods usually perform a single retrieval step before the generation process, which limits their effectiveness in addressing complex queries due to imperfect retrieval results. In contrast, our proposed method, CoRAG (Chain-of-Retrieval Augmented Generation), allows the model to dynamically reformulate the query based on the evolving state. To train CoRAG effectively, we utilize rejection sampling to automatically generate intermediate retrieval chains, thereby augmenting existing RAG datasets that only provide the correct final answer. At test time, we propose various decoding strategies to scale the model's test-time compute by controlling the length and number of sampled retrieval chains. Experimental results across multiple benchmarks validate the efficacy of CoRAG, particularly in multi-hop question answering tasks, where we observe more than $10$ points improvement in EM score compared to strong baselines. On the KILT benchmark, CoRAG establishes a new state-of-the-art performance across a diverse range of knowledge-intensive tasks. Furthermore, we offer comprehensive analyses to understand the scaling behavior of CoRAG, laying the groundwork for future research aimed at developing factual and grounded foundation models.

Accurately locating key moments within long videos is crucial for solving long video understanding (LVU) tasks. However, existing benchmarks are either severely limited in terms of video length and task diversity, or they focus solely on the end-to-end LVU performance, making them inappropriate for evaluating whether key moments can be accurately accessed. To address this challenge, we propose MomentSeeker, a novel benchmark for long-video moment retrieval (LVMR), distinguished by the following features. First, it is created based on long and diverse videos, averaging over 1,200 seconds in duration, and collected from various domains, e.g., movie, anomaly, egocentric, and sports. Second, it covers a variety of real-world scenarios in three levels: global-level, event-level, and object-level, covering common tasks like action recognition, object localization, causal reasoning, etc. Third, it incorporates rich forms of queries, including text-only queries, image-conditioned queries, and video-conditioned queries. On top of MomentSeeker, we conduct comprehensive experiments for both generation-based approaches (directly using MLLMs) and retrieval-based approaches (leveraging video retrievers). Our results reveal the significant challenges in long-video moment retrieval in terms of accuracy and efficiency, despite improvements from the latest long-video MLLMs and task-specific fine-tuning. We have publicly released MomentSeeker to facilitate future research in this area.

While an image is worth more than a thousand words, only a few provide crucial information for a given task and thus should be focused on. In light of this, ideal text-to-image (T2I) retrievers should prioritize specific visual attributes relevant to queries. To evaluate current retrievers on handling attribute-focused queries, we build COCO-Facet, a COCO-based benchmark with 9,112 queries about diverse attributes of interest. We find that CLIP-like retrievers, which are widely adopted due to their efficiency and zero-shot ability, have poor and imbalanced performance, possibly because their image embeddings focus on global semantics and subjects while leaving out other details. Notably, we reveal that even recent Multimodal Large Language Model (MLLM)-based, stronger retrievers with a larger output dimension struggle with this limitation. Hence, we hypothesize that retrieving with *general* image embeddings is suboptimal for performing such queries. As a solution, we propose to use *promptable* image embeddings enabled by these multimodal retrievers, which boost performance by highlighting required attributes. Our pipeline for deriving such embeddings generalizes across query types, image pools, and base retriever architectures. To enhance real-world applicability, we offer two acceleration strategies: Pre-processing promptable embeddings and using linear approximations. We show that the former yields a 15\% improvement in Recall@5 when prompts are predefined, while the latter achieves an 8\% improvement when prompts are only available during inference.

Text-3D Scene Retrieval (T3SR) aims to retrieve relevant scenes using linguistic queries. Although traditional T3SR methods have made significant progress in capturing fine-grained associations, they implicitly assume that query descriptions are information-complete. In practical deployments, however, limited by the capabilities of users and models, it is difficult or even impossible to directly obtain a perfect textual query suiting the entire scene and model, thereby leading to performance degradation. To address this issue, we propose a novel Interactive Text-3D Scene Retrieval Method (IDeal), which promotes the enhancement of the alignment between texts and 3D scenes through continuous interaction. To achieve this, we present an Interactive Retrieval Refinement framework (IRR), which employs a questioner to pose contextually relevant questions to an answerer in successive rounds that either promote detailed probing or encourage exploratory divergence within scenes. Upon the iterative responses received from the answerer, IRR adopts a retriever to perform both feature-level and semantic-level information fusion, facilitating scene-level interaction and understanding for more precise re-rankings. To bridge the domain gap between queries and interactive texts, we propose an Interaction Adaptation Tuning strategy (IAT). IAT mitigates the discriminability and diversity risks among augmented text features that approximate the interaction text domain, achieving contrastive domain adaptation for our retriever. Extensive experimental results on three datasets demonstrate the superiority of IDeal.

Protein language models (PLMs) learn probability distributions over natural protein sequences. By learning from hundreds of millions of natural protein sequences, protein understanding and design capabilities emerge. Recent works have shown that scaling these models improves structure prediction, but does not seem to improve mutation understanding and representation quality for protein function prediction. We introduce PoET-2, a multimodal, retrieval-augmented protein foundation model that incorporates in-context learning of family-specific evolutionary constraints with optional structure conditioning to learn generative distributions over protein sequences. PoET-2 uses a hierarchical transformer encoder that is equivariant to sequence context ordering and a dual decoder architecture with both causal and masked language modeling objectives, allowing PoET-2 to operate in both fully generative and bidirectional representation learning modes. PoET-2 achieves state-of-the-art performance on zero-shot variant effect prediction, excelling at scoring variants with multiple mutations and challenging indel mutations. In supervised settings, PoET-2 embeddings outperform previous methods for learning sequence-function relationships, especially with small datasets. This work highlights the benefits of combining retrieval augmentation with multimodal, family-centric modeling for advancing protein foundation models.

The ubiquity of dynamic data in domains such as weather, healthcare, and energy underscores a growing need for effective interpretation and retrieval of time-series data. These data are inherently tied to domain-specific contexts, such as clinical notes or weather narratives, making cross-modal retrieval essential not only for downstream tasks but also for developing robust time-series foundation models by retrieval-augmented generation (RAG). Despite the increasing demand, time-series retrieval remains largely underexplored. Existing methods often lack semantic grounding, struggle to align heterogeneous modalities, and have limited capacity for handling multi-channel signals. To address this gap, we propose TRACE, a generic multimodal retriever that grounds time-series embeddings in aligned textual context. TRACE enables fine-grained channel-level alignment and employs hard negative mining to facilitate semantically meaningful retrieval. It supports flexible cross-modal retrieval modes, including Text-to-Timeseries and Timeseries-to-Text, effectively linking linguistic descriptions with complex temporal patterns. By retrieving semantically relevant pairs, TRACE enriches downstream models with informative context, leading to improved predictive accuracy and interpretability. Beyond a static retrieval engine, TRACE also serves as a powerful standalone encoder, with lightweight task-specific tuning that refines context-aware representations while maintaining strong cross-modal alignment. These representations achieve state-of-the-art performance on downstream forecasting and classification tasks. Extensive experiments across multiple domains highlight its dual utility, as both an effective encoder for downstream applications and a general-purpose retriever to enhance time-series models.

Semantic retrieval is crucial for modern applications yet remains underexplored in current research. Existing datasets are limited to single languages, single images, or singular retrieval conditions, often failing to fully exploit the expressive capacity of visual information as evidenced by maintained performance when images are replaced with captions. However, practical retrieval scenarios frequently involve interleaved multi-condition queries with multiple images. Hence, this paper introduces MERIT, the first multilingual dataset for interleaved multi-condition semantic retrieval, comprising 320,000 queries with 135,000 products in 5 languages, covering 7 distinct product categories. Extensive experiments on MERIT identify existing models's critical limitation: focusing solely on global semantic information while neglecting specific conditional elements in queries. Consequently, we propose Coral, a novel fine-tuning framework that adapts pre-trained MLLMs by integrating embedding reconstruction to preserve fine-grained conditional elements and contrastive learning to extract comprehensive global semantics. Experiments demonstrate that Coral achieves a 45.9% performance improvement over conventional approaches on MERIT, with strong generalization capabilities validated across 8 established retrieval benchmarks. Collectively, our contributions—a novel dataset, identification of critical limitations in existing approaches, and an innovative fine-tuning framework—establish a foundation for future research in interleaved multi-condition semantic retrieval. **Data & Code**: [MERIT-2025.github.io](https://merit-2025.github.io)

Retrieval-augmented generation (RAG) has become a widely adopted paradigm for enabling knowledge-grounded large language models (LLMs). However, standard RAG pipelines often fail to ensure that model reasoning remains consistent with the evidence retrieved, leading to factual inconsistencies or unsupported conclusions. In this work, we reinterpret RAG as \textit{Retrieval-Augmented Reasoning} and identify a central but underexplored problem: \textit{Reasoning Misalignment}—the divergence between an LLM's internal reasoning trajectory and the evidential constraints provided by retrieval. To address this issue, we propose \textsc{AlignRAG}, a novel iterative framework grounded in \textit{Critique-Driven Alignment (CDA)}. We further introduce \textsc{AlignRAG-auto}, an autonomous variant that dynamically terminates refinement, removing the need to pre-specify the number of critique iterations. At the heart of \textsc{AlignRAG} lies a \textit{contrastive critique synthesis} mechanism that generates retrieval-sensitive critiques while mitigating self-bias. This mechanism trains a dedicated retrieval-augmented \textit{Critic Language Model (CLM)} using labeled critiques that distinguish between evidence-aligned and misaligned reasoning. Empirical evaluations show that our approach significantly improves reasoning fidelity. Our 8B-parameter CLM improves performance over the Self-Refine baseline by \textbf{12.1\%} on out-of-domain tasks and outperforms a standard 72B-parameter CLM by \textbf{2.2\%}. Furthermore, \textsc{AlignRAG-auto} achieves this state-of-the-art performance while dynamically determining the optimal number of refinement steps, enhancing efficiency and usability. \textsc{AlignRAG} remains compatible with existing RAG architectures as a \textit{plug-and-play} module and demonstrates strong robustness under both informative and noisy retrieval scenarios. Overall, \textsc{AlignRAG} offers a principled solution for aligning model reasoning with retrieved evidence, substantially improving the factual reliability and robustness of RAG systems. Our source code is provided at \href{https://github.com/upup-wei/RAG-ReasonAlignment}{link}.

We introduce and study the Combinatorial Ski Rental (CSR) problem, which involves multiple items that can be rented or purchased, either individually or in combination. At each time step, a decision-maker must make an irrevocable buy-or-rent decision for items that have not yet been purchased, without knowing the end of the time horizon. We propose a randomized online algorithm, Sorted Optimal Amortized Cost (SOAC), that achieves the optimal competitive ratio. Moreover, SOAC can be extended to address various well-known ski rental variants, including the multi-slope, multi-shop, multi-commodity ski rental and CSR with upgrading problems. Building on the proposed SOAC algorithm, we further develop a learning-augmented algorithm that leverages machine-learned predictions to improve the performance of CSR. This algorithm is capable of recovering or improving upon existing results of learning-augmented algorithms in both the classic ski rental and multi-shop ski rental problems. Experimental results validate our theoretical analysis and demonstrate the advantages of our algorithms over baseline methods for ski rental problems.

Knowledge graph-based retrieval-augmented generation seeks to mitigate hallucinations in Large Language Models (LLMs) caused by insufficient or outdated knowledge. However, existing methods often fail to fully exploit the prior knowledge embedded in knowledge graphs (KGs), particularly their structural information and explicit or implicit constraints. The former can enhance the faithfulness of LLMs' reasoning, while the latter can improve the reliability of response generations. Motivated by these, we propose a trustworthy reasoning framework, termed Deliberation over Priors (\texttt{DP}), which sufficiently utilizes the priors contained in KGs. Specifically, \texttt{DP} adopts a progressive knowledge distillation strategy that integrates structural priors into LLMs through a combination of supervised fine-tuning and Kahneman-Tversky Optimization, thereby improving the faithfulness of relation path generation. Furthermore, our framework employs a reasoning-introspection strategy, which guides LLMs to perform refined reasoning verification based on extracted constraint priors, ensuring the reliability of response generation. Extensive experiments on three benchmark datasets demonstrate that \texttt{DP} achieves new state-of-the-art performance, especially a Hit@1 improvement of 13% on the ComplexWebQuestions dataset, and generates highly trustworthy responses. We also conduct various analyses to verify its flexibility and practicality. Code is available at [https://github.com/reml-group/Deliberation-on-Priors](https://github.com/reml-group/Deliberation-on-Priors).

The rise of GPU-based high-performance computing (HPC) has driven the widespread adoption of parallel programming models such as CUDA. Yet, the inherent complexity of parallel programming creates a demand for the automated sequential-to-parallel approaches. However, data scarcity poses a significant challenge for machine learning-based sequential-to-parallel code translation. Although recent back-translation methods show promise, they still fail to ensure functional equivalence in the translated code. In this paper, we propose \textbf{QiMeng-MuPa}, a novel \textbf{Mu}tual-Supervised Learning framework for Sequential-to-\textbf{Pa}rallel code translation, to address the functional equivalence issue. QiMeng-MuPa consists of two models, a Translator and a Tester. Through an iterative loop consisting of Co-verify and Co-evolve steps, the Translator and the Tester mutually generate data for each other and improve collectively. The Tester generates unit tests to verify and filter functionally equivalent translated code, thereby evolving the Translator, while the Translator generates translated code as augmented input to evolve the Tester. Experimental results demonstrate that QiMeng-MuPa significantly enhances the performance of the base models: when applied to Qwen2.5-Coder, it not only improves Pass@1 by up to 28.91\% and boosts Tester performance by 68.90\%, but also outperforms the previous state-of-the-art method CodeRosetta by 1.56 and 6.92 in BLEU and CodeBLEU scores, while achieving performance comparable to DeepSeek-R1 and GPT-4.1. Our code is available at \url{https://github.com/kcxain/mupa}.

Recent advances in Large Language Models (LLMs) have shown promise in function-level code generation, yet repository-level software engineering tasks remain challenging. Current solutions predominantly rely on proprietary LLM agents, which introduce unpredictability and limit accessibility, raising concerns about data privacy and model customization. This paper investigates whether open-source LLMs can effectively address repository-level tasks without requiring agent-based approaches. We demonstrate this is possible by enabling LLMs to comprehend functions and files within codebases through their semantic information and structural dependencies. To this end, we introduce Code Graph Models (CGMs), which integrate repository code graph structures into the LLM's attention mechanism and map node attributes to the LLM's input space using a specialized adapter. When combined with an agentless graph RAG framework, our approach achieves a 43.00% resolution rate on the SWE-bench Lite benchmark using the open-source Qwen2.5-72B model. This performance ranks first among open weight models, second among methods with open-source systems, and eighth overall, surpassing the previous best open-source model-based method by 12.33%.

Online bipartite matching is a fundamental problem in online optimization, extensively studied both in its integral and fractional forms due to its theoretical significance and practical applications, such as online advertising and resource allocation. Motivated by recent progress in learning-augmented algorithms, we study online bipartite fractional matching when the algorithm is given advice in the form of a suggested matching in each iteration. We develop algorithms for both the vertex-weighted and unweighted variants that provably dominate the naive ``coin flip'' strategy of randomly choosing between the advice-following and advice-free algorithms. Moreover, our algorithm for the vertex-weighted setting extends to the AdWords problem under the small bids assumption, yielding a significant improvement over the seminal work of Mahdian, Nazerzadeh, and Saberi (EC 2007, TALG 2012). Complementing our positive results, we establish a hardness bound on the robustness-consistency tradeoff that is attainable by any algorithm. We empirically validate our algorithms through experiments on synthetic and real-world data.

Scenario-based testing is essential for validating the performance of autonomous driving (AD) systems. However, such testing is limited by the scarcity of long-tailed, safety-critical scenarios in existing datasets collected in the real world. To tackle the data issue, we propose the Adv-BMT framework, which augments real-world scenarios with diverse and realistic adversarial interactions. The core component of Adv-BMT is a bidirectional motion transformer (BMT) model to perform inverse traffic motion predictions, which takes the last frame of the scenario as input and reconstruct the traffic in the inverse of chronological order, till the initial time step. The Adv-BMT framework is a two-stage pipeline: it first conducts adversarial initializations and then inverse motion predictions. Different from previous work, we do not need any collision data for pretraining and are still able to generate realistic and diverse collision interactions. Our experimental results validate the quality of generated collision scenarios by Adv-BMT: training in our augmented dataset would reduce episode collision rates by 20\% compared to previous work. The code will be made available.

Clinical decision making (CDM) is a complex, dynamic process crucial to healthcare delivery, yet it remains a significant challenge for artificial intelligence systems. While Large Language Model (LLM)-based agents have been tested on general medical knowledge using licensing exams and knowledge question-answering tasks, their performance in the CDM in real-world scenarios is limited due to the lack of comprehensive benchmark that mirror actual medical practice. To address this gap, we present MedChain, a dataset of 12,163 clinical cases that covers five key stages of clinical workflow. MedChain distinguishes itself from existing benchmarks with three key features of real-world clinical practice: personalization, interactivity, and sequentiality. Further, to tackle real-world CDM challenges, we also propose MedChain-Agent, an AI system that integrates a feedback mechanism and a MedCase-RAG module to learn from previous cases and adapt its responses. MedChain-Agent demonstrates remarkable adaptability in gathering information dynamically and handling sequential clinical tasks, significantly outperforming existing approaches. The relevant dataset and code will be released upon acceptance of this paper.