NeurIPS 2025 Papers

Effectively retrieving, reasoning and understanding visually rich information remains a challenge for traditional Retrieval-Augmented Generation (RAG) methods. On the one hand, traditional text-based methods cannot handle visual-related information. On the other hand, current vision-based RAG approaches are often limited by fixed pipelines and frequently struggle to reason effectively due to the insufficient activation of the fundamental capabilities of models. As reinforcement learning (RL) has been proven to be beneficial for model reasoning, we introduce VRAG-RL, a novel RL framework tailored for complex reasoning across visually rich information. With this framework, VLMs interact with search engines, autonomously sampling single-turn or multi-turn reasoning trajectories with the help of visual perception tokens and undergoing continual optimization based on these samples. Our approach highlights key limitations of RL in RAG domains: (i) Prior Multi-modal RAG approaches tend to merely incorporate images into the context, leading to insufficient reasoning token allocation and neglecting visual-specific perception; and (ii) When models interact with search engines, their queries often fail to retrieve relevant information due to the inability to articulate requirements, thereby leading to suboptimal performance. To address these challenges, we define an action space tailored for visually rich inputs, with actions including cropping and scaling, allowing the model to gather information from a coarse-to-fine perspective. Furthermore, to bridge the gap between users' original inquiries and the retriever, we employ a simple yet effective reward that integrates query rewriting and retrieval performance with a model-based reward. Our VRAG-RL optimizes VLMs for RAG tasks using specially designed RL strategies, aligning the model with real-world applications. Extensive experiments on diverse and challenging benchmarks show that our VRAG-RL outperforms existing methods by 20\% (Qwen2.5-VL-7B) and 30\% (Qwen2.5-VL-3B), demonstrating the effectiveness of our approach. The code is available at https://github.com/Alibaba-NLP/VRAG.

The rapid extension of context windows in large vision-language models has given rise to long-context vision-language models (LCVLMs), which are capable of handling hundreds of images with interleaved text tokens in a single forward pass. In this work, we introduce MMLongBench, the first benchmark covering a diverse set of long-context vision-language tasks, to evaluate LCVLMs effectively and thoroughly. MMLongBench is composed of 13,331 examples spanning five different categories of downstream tasks, such as Visual RAG and Many-Shot ICL. It also provides broad coverage of image types, including various natural and synthetic images. To assess the robustness of the models to different input lengths, all examples are delivered at five standardized input lengths (8K-128K tokens) via a cross-modal tokenization scheme that combines vision patches and text tokens. Through a thorough benchmarking of 46 closed-source and open-source LCVLMs, we provide a comprehensive analysis of the current models' vision-language long-context ability. Our results show that: i) performance on a single task is a weak proxy for overall long-context capability; ii) both closed-source and open-source models face challenges in long-context vision-language tasks, indicating substantial room for future improvement; iii) models with stronger reasoning ability tend to exhibit better long-context performance. By offering wide task coverage, various image types, and rigorous length control, MMLongBench provides the missing foundation for diagnosing and advancing the next generation of LCVLMs.

Short videos are an effective tool for promoting contents and improving knowledge accessibility. While existing extractive video summarization methods struggle to produce a coherent narrative, existing abstractive methods cannot `quote' from the input videos, i.e., inserting short video clips in their outputs. In this work, we explore novel video editing models for generating shorts that feature a coherent narrative with embedded video insertions extracted from a long input video. We propose a novel retrieval-embedded generation framework that allows a large language model to quote multimodal resources while maintaining a coherent narrative. Our proposed REGen system first generates the output story script with quote placeholders using a finetuned large language model, and then uses a novel retrieval model to replace the quote placeholders by selecting a video clip that best supports the narrative from a pool of candidate quotable video clips. We examine the proposed method on the task of documentary teaser generation, where short interview insertions are commonly used to support the narrative of a documentary. Our objective evaluations show that the proposed method can effectively insert short video clips while maintaining a coherent narrative. In a subjective survey, we show that our proposed method outperforms existing abstractive and extractive approaches in terms of coherence, alignment, and realism in teaser generation.

We explore if it is possible to learn data structures end-to-end with neural networks, with a focus on the problem of nearest-neighbor (NN) search. We introduce a framework for data structure discovery, which adapts to the underlying data distribution and provides fine-grained control over query and space complexity. Crucially, the data structure is learned from scratch, and does not require careful initialization or seeding with candidate data structures. In several settings, we are able to reverse-engineer the learned data structures and query algorithms. For 1D nearest neighbor search, the model discovers optimal distribution (in)dependent algorithms such as binary search and variants of interpolation search. In higher dimensions, the model learns solutions that resemble k-d trees in some regimes, while in others, elements of locality-sensitive hashing emerge. Additionally, the model learns useful representations of high-dimensional data such as images and exploits them to design effective data structures. Beyond NN search, we believe the framework could be a powerful tool for data structure discovery for other problems and adapt our framework to the problem of estimating frequencies over a data stream. To encourage future work in this direction, we conclude with a discussion on some of the opportunities and remaining challenges of learning data structures end-to-end.

Retrieval-Augmented Generation (RAG) enhances Large Language Models by grounding their outputs in external documents. These systems, however, remain vulnerable to attacks on the retrieval corpus, such as prompt injection. RAG-based search systems (e.g., Google’s Search AI Overview) present an interesting setting for studying and protecting against such threats, as defense algorithms can benefit from built-in reliability signals—like document ranking—and represent a non-LLM challenge for the adversary due to decades of work to thwart SEO. Motivated by, but not limited to, this scenario, this work introduces ReliabilityRAG, a framework for adversarial robustness that explicitly leverages reliability information of retrieved documents. Our first contribution adopts a graph-theoretic perspective to identify a ``consistent majority'' among retrieved documents to filter out malicious ones. We introduce a novel algorithm based on finding a Maximum Independent Set (MIS) on a document graph where edges encode contradiction. Our MIS variant explicitly prioritizes higher-reliability documents and provides provable robustness guarantees against bounded adversarial corruption under natural assumptions. Recognizing the computational cost of exact MIS for large retrieval sets, our second contribution is a scalable weighted sample and aggregate framework. It explicitly utilizes reliability information, preserving some robustness guarantees while efficiently handling many documents. We present empirical results showing ReliabilityRAG provides superior robustness against adversarial attacks compared to prior methods, maintains high benign accuracy, and excels in long-form generation tasks where prior robustness-focused methods struggled. Our work is a significant step towards more effective, provably robust defenses against retrieved corpus corruption in RAG.

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.

Large language models (LLMs) integrated with retrieval-augmented generation (RAG) have improved factuality by grounding outputs in external evidence. However, they remain susceptible to unfaithful generation, where outputs contradict retrieved context despite its relevance and accuracy. Existing approaches aiming to improve faithfulness primarily focus on enhancing the utilization of external context, but often overlook the persistent influence of internal parametric knowledge during generation. In this work, we investigate the internal mechanisms behind unfaithful generation and identify a subset of mid-to-deep feed-forward networks (FFNs) that are disproportionately activated in such cases. Building on this insight, we propose Parametric Knowledge Muting through FFN Suppression (ParamMute), a framework that improves contextual faithfulness by suppressing the activation of unfaithfulness-associated FFNs and calibrating the model toward retrieved knowledge. To evaluate our approach, we introduce CoFaithfulQA, a benchmark specifically designed to evaluate faithfulness in scenarios where internal knowledge conflicts with accurate external evidence. Experimental results show that ParamMute significantly enhances faithfulness across both CoFaithfulQA and the established ConFiQA benchmark, achieving substantial reductions in reliance on parametric memory. These findings underscore the importance of mitigating internal knowledge dominance and provide a new direction for improving LLM trustworthiness in RAG. All codes are available at https://github.com/OpenBMB/ParamMute.

Large multimodal models (LMMs) have shown remarkable progress in audiovisual 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, audiovisual retrieval and reasoning encountered in practical applications. To bridge this gap, we introduce a novel task named AVHaystacksQA, 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.

Information seeking demands iterative evidence gathering and reflective reasoning, yet large language models (LLMs) still struggle with it in open-web question answering. Existing prompting and supervised fine-tuning (SFT) methods remain fixed by prompt rules or training corpora, and are usually benchmarked only on well-structured wiki sources, limiting real-world adaptability. We introduce $\textbf{WebPuzzle}$, a 24k-sample training and 275-sample test benchmark that evaluates information seeking on the live internet, across both wiki and open-domain queries. Leveraging 7k WebPuzzle instances, we develop $\textbf{DeepDiver}$, a reinforcement-learning (RL) framework that cultivates $\textbf{Search Intensity Scaling (SIS)}$—an emergent ability to escalate search frequency and depth instead of settling on overconfident, under-evidenced answers. With SIS, Qwen2.5-7B-Instruct and Pangu-7B-Reasoner attain performance on real-web tasks comparable to the 671B-parameter DeepSeek-R1. We detail DeepDiver’s curriculum from cold-start SFT to a well designed RL procedure, and show that its seeking policy generalized from closed-ended queries to open-ended generation such as long-form writing. Our results advance adaptive information seeking in LLMs and provide a rigorous benchmark for future work.

Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but face limitations in binding data, substrate-specific control, and flexibility for de novo enzyme backbone generation. To address this, we introduce **EnzyBind**, a dataset with 11,100 experimentally validated enzyme-substrate pairs specifically curated from PDBbind. Building on this, we propose **EnzyControl**, a method that enables functional and substrate-specific control in enzyme backbone generation. Our approach generates enzyme backbones conditioned on MSA-annotated catalytic sites and their corresponding substrates, which are automatically extracted from curated enzyme-substrate data. At the core of EnzyControl is **EnzyAdapter**, a lightweight, modular component integrated into a pretrained motif-scaffolding model, allowing it to become substrate-aware. A two-stage training paradigm further refines the model's ability to generate accurate and functional enzyme structures. Experiments show that our EnzyControl achieves the best performance across structural and functional metrics on EnzyBind and EnzyBench benchmarks, with particularly notable improvements of 13% in designability and 13% in catalytic efficiency compared to the baseline models. The code is released at https://github.com/Vecteur-libre/EnzyControl.

Designing protein binders targeting specific sites, which requires to generate realistic and functional interaction patterns, is a fundamental challenge in drug discovery. Current structure-based generative models are limited in generating nterfaces with sufficient rationality and interpretability. In this paper, we propose **R**etrieval-**A**ugmented **Di**ffusion for **A**lig**n**ed interfa**ce** (**RADiAnce**), a new framework that leverages known interfaces to guide the design of novel binders. By unifying retrieval and generation in a shared contrastive latent space, our model efficiently identifies relevant interfaces for a given binding site and seamlessly integrates them through a conditional latent diffusion generator, enabling cross-domain interface transfer. Extensive exeriments show that **RADiAnce** significantly outperforms baseline models across multiple metrics, including binding affinity and recovery of geometries and interactions. Additional experimental results validate cross-domain generalization, demonstrating that retrieving interfaces from diverse domains, such as peptides, antibodies, and protein fragments, enhances the generation performance of binders for other domains. Our work establishes a new paradigm for protein binder design that successfully bridges retrieval-based knowledge and generative AI, opening new possibilities for drug discovery.

As major progress in LLM-based long-form text generation enables paradigms such as retrieval-augmented generation (RAG) and inference-time scaling, safely incorporating private information into the generation remains a critical open question. We present InvisibleInk, a highly scalable long-form text generation framework satisfying rigorous differential privacy guarantees with respect to the sensitive reference texts. It interprets sampling from the LLM's next-token-distribution as the exponential mechanism over the LLM logits with two innovations. First, we reduce the privacy cost by isolating and clipping only the sensitive information in the model logits (relative to the public logits). Second, we improve text quality by sampling without any privacy cost from a small superset of the top-$k$ private tokens. Empirical evaluations demonstrate a consistent $8\times$ (or more) reduction in computation cost over state-of-the-art baselines to generate long-form private text of the same utility across privacy levels. InvisibleInk is able to generate, for the first time, high-quality private long-form text at less than $4\text{-}8\times$ times the computation cost of non-private generation, paving the way for its practical use.

The application of AI in psychiatric diagnosis faces significant challenges, including the subjective nature of mental health assessments, symptom overlap across disorders, and privacy constraints limiting data availability. To address these issues, we present MoodAngels, the first specialized multi-agent framework for mood disorder diagnosis. Our approach combines granular-scale analysis of clinical assessments with a structured verification process, enabling more accurate interpretation of complex psychiatric data. Complementing this framework, we introduce MoodSyn, an open-source dataset of 1,173 synthetic psychiatric cases that preserves clinical validity while ensuring patient privacy. Experimental results demonstrate that MoodAngels outperforms conventional methods, with our baseline agent achieving 12.3\% higher accuracy than GPT-4o on real-world cases, and our full multi-agent system delivering further improvements. Together, these contributions provide both an advanced diagnostic tool and a critical research resource for computational psychiatry, bridging important gaps in AI-assisted mental health assessment.

Large Language Models (LLMs) have shown strong abilities in general language tasks, yet adapting them to specific domains remains a challenge. Current method like Domain Adaptive Pretraining (DAPT) requires costly full-parameter training and suffers from catastrophic forgetting. Meanwhile, Retrieval-Augmented Generation (RAG) introduces substantial inference latency due to expensive nearest-neighbor searches and longer context. This paper introduces \textit{Memory Decoder}, a plug-and-play pretrained memory that enables efficient domain adaptation without changing the original model's parameters. Memory Decoder employs a small transformer decoder that learns to imitate the behavior of an external non-parametric retriever. Once trained, Memory Decoder can be seamlessly integrated with any pretrained language model that shares the same tokenizer, requiring no model-specific modifications. Experimental results demonstrate that Memory Decoder enables effective adaptation of various Qwen and Llama models to three distinct specialized domains: biomedicine, finance, and law, reducing perplexity by an average of 6.17 points. Overall, Memory Decoder introduces a novel paradigm centered on a specially pretrained memory component designed for domain-specific adaptation. This memory architecture can be integrated in a plug-and-play manner, consistently enhancing performance across multiple models within the target domain.

Contrastive learning has shown effectiveness in improving sequential recommendation models. However, existing methods still face challenges in generating high-quality contrastive pairs: they either rely on random perturbations that corrupt user preference patterns or depend on sparse collaborative data that generates unreliable contrastive pairs. Furthermore, existing approaches typically require predefined selection rules that impose strong assumptions, limiting the model's ability to autonomously learn optimal contrastive pairs. To address these limitations, we propose a novel approach named Semantic Retrieval Augmented Contrastive Learning (SRA-CL). SRA-CL leverages the semantic understanding and reasoning capabilities of LLMs to generate expressive embeddings that capture both user preferences and item characteristics. These semantic embeddings enable the construction of candidate pools for inter-user and intra-user contrastive learning through semantic-based retrieval. To further enhance the quality of the contrastive samples, we introduce a learnable sample synthesizer that optimizes the contrastive sample generation process during model training. SRA-CL adopts a plug-and-play design, enabling seamless integration with existing sequential recommendation architectures. Extensive experiments on four public datasets demonstrate the effectiveness and model-agnostic nature of our approach. Our code is available at https://github.com/ziqiangcui/SRA-CL

Retrieval-augmented generation (RAG) is widely utilized to incorporate external knowledge into large language models, thereby enhancing factuality and reducing hallucinations in question-answering (QA) tasks. A standard RAG pipeline consists of several components, such as query rewriting, document retrieval, document filtering, and answer generation. However, these components are typically optimized separately through supervised fine-tuning, which can lead to misalignments between the objectives of individual components and the overarching aim of generating accurate answers. Although recent efforts have explored using reinforcement learning (RL) to optimize specific RAG components, these approaches often focus on simple pipelines with only two components or do not adequately address the complex interdependencies and collaborative interactions among the modules. To overcome these limitations, we propose treating the complex RAG pipeline with multiple components as a multi-agent cooperative task, in which each component can be regarded as an RL agent. Specifically, we present MMOA-RAG\footnote{The code of MMOA-RAG is on \url{https://github.com/chenyiqun/MMOA-RAG}.}, \textbf{M}ulti-\textbf{M}odule joint \textbf{O}ptimization \textbf{A}lgorithm for \textbf{RAG}, which employs multi-agent reinforcement learning to harmonize all agents' goals toward a unified reward, such as the F1 score of the final answer. Experiments conducted on various QA benchmarks demonstrate that MMOA-RAG effectively boost the overall performance of the pipeline and outperforms existing baselines. Furthermore, comprehensive ablation studies validate the contributions of individual components and demonstrate MMOA-RAG can be adapted to different RAG pipelines and benchmarks.

3D human motion-text retrieval is essential for accurate motion understanding, targeted at cross-modal alignment learning. Existing methods typically align the global motion-text concepts directly, suffering from sub-optimal generalization due to the uncertainty of correspondence learning between multiple motion concepts coupled in a single motion/text sequence. Therefore, we study the explicit fine-grained concept decomposition for alignment learning and present a novel framework, Structural Generative Augmentation for 3D Human Motion Retrieval (SGAR), to enable generation-augmented retrieval. Specifically, relying on the strong priors of existing large language model (LLM) assets, we effectively decompose human motions structurally into subtler semantic units, \ie, body parts, for fine-grained motion modeling. Based on this, we develop part-mixture learning to better decouple the local motion concept learning, boosting part-level alignment. Moreover, a directional relation alignment strategy exploiting the correspondence between full-body and part motions is incorporated to regularize feature manifold for better consistency. Extensive experiments on three benchmarks, including motion-text retrieval as well as recognition and generation applications, demonstrate the superior performance and promising transferability of our method.

Transformer-based Large Language Models (LLMs) have become increasingly important. However, scaling LLMs to longer contexts incurs slow inference speed and high GPU memory consumption for caching key-value (KV) vectors. This paper presents RetrievalAttention, a training-free approach to both accelerate the decoding phase and reduce GPU memory consumption by pre-building KV vector indexes for fixed contexts and maintaining them in CPU memory for efficient retrieval. Unlike conventional KV cache methods, RetrievalAttention integrate approximate nearest neighbor search (ANNS) indexes into attention computation. We observe that off-the-shelf ANNS techniques often fail due to the out-of-distribution (OOD) nature of query and key vectors in attention mechanisms. RetrievalAttention overcomes this with an attention-aware vector index. Our evaluation shows RetrievalAttention achieves near full attention accuracy while accessing only 1-3\% of the data, significantly reducing inference costs. Remarkably, RetrievalAttention enables LLMs with 8B parameters to handle 128K tokens on a single NVIDIA RTX4090 (24GB), achieving a decoding speed of 0.107 seconds per token.

Competitive programming is widely used to evaluate the coding and reasoning abilities of large language models. However, the growing presence of duplicate or highly similar problems raises concerns not only about competition fairness, but also about the validity of competitive programming as a benchmark for model evaluation. We introduce a retrieval-oriented benchmark suite for competitive programming, covering four retrieval tasks—two code-centric (Text-to-Code, Code-to-Code) and two newly proposed problem-centric tasks (Problem-to-Duplicate, Simplified-to-Full)—built from a combination of automatically crawled problem–solution data and manually curated annotations. Our contribution includes both high-quality training data and temporally separated test sets for reliable evaluation. We develop two task-specialized retrievers based on this dataset: CPRetriever-Code, trained with a novel Group-InfoNCE loss for problem–code alignment, and CPRetriever-Prob, fine-tuned for problem-level similarity. Both models achieve strong results and are open-sourced for local use. Finally, we analyze LiveCodeBench and find that high-similarity problems inflate model pass rates and reduce differentiation, underscoring the need for similarity-aware evaluation in future benchmarks.