NeurIPS 2025 Papers

Large language models (LLMs) have achieved significant performance progress in various natural language processing applications. However, LLMs still struggle to meet the strict requirements for accuracy and reliability in the medical field and face many challenges in clinical applications. Existing clinical diagnostic evaluation benchmarks for evaluating medical agents powered by LLMs have severe limitations. To address these limitations, we introduce ClinicalLab, a comprehensive clinical diagnosis agent alignment suite. ClinicalLab includes ClinicalBench, an end-to-end multi-departmental clinical diagnostic evaluation benchmark for evaluating medical agents and LLMs. ClinicalBench is based on real cases that cover 24 departments and 150 diseases. We ensure that ClinicalBench does not have data leakage. ClinicalLab also includes four novel metrics (ClinicalMetrics) for evaluating the effectiveness of LLMs in clinical diagnostic tasks. We evaluate 17 general and medical-domain LLMs and find that their performance varies significantly across different departments. Based on these findings, in ClinicalLab, we propose ClinicalAgent, an end-to-end clinical agent that aligns with real-world clinical diagnostic practices. We systematically investigate the performance and applicable scenarios of variants of ClinicalAgent on ClinicalBench. Our findings demonstrate the importance of aligning with modern medical practices in designing medical agents.

Repeated multi-unit auctions, where a seller allocates multiple identical items over many rounds, are common mechanisms in electricity markets and treasury auctions. We compare the two predominant formats: uniform-price and discriminatory auctions, focusing on the perspective of a single bidder learning to bid against stochastic adversaries. We characterize the learning difficulty in each format, showing that the regret scales similarly for both auction formats under both full-information and bandit feedback, as $\tilde{\Theta} ( \sqrt{T} )$ and $\tilde{\Theta} ( T^{2/3} )$, respectively. However, analysis beyond worst-case regret reveals structural differences: uniform-price auctions may admit faster learning rates, with regret scaling as $\tilde{\Theta} ( \sqrt{T} )$ in settings where discriminatory auctions remain at $\tilde{\Theta} ( T^{2/3} )$. Finally, we provide a specific analysis for auctions in which the other participants are symmetric and have unit-demand, and show that in these instances a similar regret rate separation appears.

Multi-label complementary label learning (MLCLL) is a weakly supervised paradigm that addresses multi-label learning (MLL) tasks using complementary labels (i.e., irrelevant labels) instead of relevant labels. Existing methods typically adopt an unbiased risk estimator (URE) under the assumption that complementary labels follow a uniform distribution. However, this assumption fails in real-world scenarios due to instance-specific annotation biases, making URE-based methods ineffective under such conditions. Furthermore, existing methods underutilize label correlations inherent in MLL. To address these limitations, we propose ComRank, a ranking loss framework for MLCLL, which encourages complementary labels to be ranked lower than non-complementary ones, thereby modeling pairwise label relationships. Theoretically, our surrogate loss ensures Bayes consistency under both uniform and biased cases. Experiments demonstrate the effectiveness of our method in MLCLL tasks. The code is available at https://github.com/JellyJamZhu/ComRank.

We study a stochastic principal-agent model. A principal and an agent interact in a stochastic environment, each privy to observations about the state not available to the other. The principal has the power of commitment, both to elicit information from the agent and to signal her own information. The players communicate with each other and then select actions independently. Both players are {\em far-sighted}, aiming to maximize their total payoffs over the entire time horizon. We consider both the computation and learning of the principal's optimal policy. The key challenge lies in enabling {\em history-dependent} policies, which are essential for achieving optimality in this model but difficult to cope with because of the exponential growth of possible histories as the size of the model increases; explicit representation of history-dependent policies is infeasible as a result. To address this challenge, we develop algorithmic techniques based on the concept of {\em inducible value set}. The techniques yield an efficient algorithm that computes an $\epsilon$-approximate optimal policy in time polynomial in $1/\epsilon$. We also present an efficient learning algorithm for an episodic reinforcement learning setting with unknown transition probabilities. The algorithm achieves sublinear regret $\widetilde{\mathcal{O}}(T^{2/3})$ for both players over $T$ episodes.

Natural language has long enabled human cooperation, but its lossy, ambiguous, and indirect nature limits the potential of collective intelligence. While machines are not subject to these constraints, most LLM-based multi-agent systems still rely solely on natural language, exchanging tokens or their embeddings. To go beyond language, we introduce a new paradigm, *thought communication*, which enables agents to interact directly mind-to-mind, akin to telepathy. To uncover these latent thoughts in a principled way, we formalize the process as a general latent variable model, where agent states are generated by an unknown function of underlying thoughts. We prove that, in a nonparametric setting without auxiliary information, both shared and private latent thoughts between any pair of agents can be identified. Moreover, the global structure of thought sharing, including which agents share which thoughts and how these relationships are structured, can also be recovered with theoretical guarantees. Guided by the established theory, we develop a framework that extracts latent thoughts from all agents prior to communication and assigns each agent the relevant thoughts, along with their sharing patterns. This paradigm naturally extends beyond LLMs to all modalities, as most observational data arise from hidden generative processes. Experiments on both synthetic and real-world benchmarks validate the theory and demonstrate the collaborative advantages of thought communication. We hope this work illuminates the potential of leveraging the hidden world, as many challenges remain unsolvable through surface-level observation alone, regardless of compute or data scale.

The rapid advancement of Large Language Models (LLMs) has catalyzed the development of multi-agent systems, where multiple LLM-based agents collaborate to solve complex tasks. However, existing systems predominantly rely on centralized coordination, which introduces scalability bottlenecks, limits adaptability, and creates single points of failure. Additionally, concerns over privacy and proprietary knowledge sharing hinder cross-organizational collaboration, leading to siloed expertise. To address these challenges, we propose AgentNet, a decentralized, Retrieval-Augmented Generation (RAG)-based framework that enables LLM-based agents to autonomously evolve their capabilities and collaborate efficiently in a Directed Acyclic Graph (DAG)-structured network. Unlike traditional multi-agent systems that depend on static role assignments or centralized control, AgentNet allows agents to specialize dynamically, adjust their connectivity, and route tasks without relying on predefined workflows. AgentNet’s core design is built upon several key innovations: (1) Fully Decentralized Paradigm: Removing the central orchestrator, allowing agents to coordinate and specialize autonomously, fostering fault tolerance and emergent collective intelligence. (2) Dynamically Evolving Graph Topology: Real-time adaptation of agent connections based on task demands, ensuring scalability and resilience. (3) Adaptive Learning for Expertise Refinement: A retrieval-based memory system that enables agents to continuously update and refine their specialized skills. By eliminating centralized control, AgentNet enhances fault tolerance, promotes scalable specialization, and enables privacy-preserving collaboration across organizations. Through decentralized coordination and minimal data exchange, agents can leverage diverse knowledge sources while safeguarding sensitive information. Experimental results demonstrate that AgentNet outperforms traditional centralized multi-agent systems, significantly improving efficiency, adaptability, and scalability in dynamic environments, making it a promising foundation for next-generation autonomous, privacy-respecting multi-agent ecosystems.

Effective conversational agents must personalize their interactions to adapt to user preferences, personalities, and attributes across diverse domains like education and healthcare. Current methods like Reinforcement Learning from Human Feedback (RLHF), often prioritize helpfulness and safety but fall short in fostering truly empathetic, adaptive, and personalized dialogues. Existing personalization approaches typically rely on extensive user history, limiting their effectiveness for new or context-limited users. To address these limitations, we propose leveraging a user model to incorporate a curiosity-based intrinsic reward into multi-turn RLHF. This novel reward mechanism encourages the agent to actively infer user traits by optimizing conversations to improve its user model's accuracy. Consequently, the agent delivers more personalized interactions by learning more about the user. We demonstrate our method's effectiveness in two distinct domains: significantly improving personalization performance in a conversational recommendation task, and personalizing conversations for different learning styles in an educational setting with improved generalization capabilities compared to traditional multi-turn RLHF, all while maintaining conversation quality. Our method offers a promising solution for creating more personalized, adaptive, and engaging conversational agents.

Advances in single-cell sequencing have enabled high-resolution profiling of diverse molecular modalities, while integrating unpaired multi-omics single-cell data remains challenging. Existing approaches either rely on pair information or prior correspondences, or require computing a global pairwise coupling matrix, limiting their scalability and flexibility. In this paper, we introduce a scalable and flexible generative framework called single-cell Multi-omics Regularized Disentangled Representations (scMRDR) for unpaired multi-omics integration. Specifically, we disentangle each cell’s latent representations into modality-shared and modality-specific components using a well-designed $\beta$-VAE architecture, which are augmented with isometric regularization to preserve intra-omics biological heterogeneity, adversarial objective to encourage cross-modal alignment, and masked reconstruction loss strategy to address the issue of missing features across modalities. Our method achieves excellent performance on benchmark datasets in terms of batch correction, modality alignment, and biological signal preservation. Crucially, it scales effectively to large-level datasets and supports integration of more than two omics, offering a powerful and flexible solution for large-scale multi-omics data integration and downstream biological discovery.

Large Language Models exhibit logical inconsistency across multi-turn inference processes, undermining correctness in complex inferential tasks. Challenges arise from ensuring that outputs align with both factual correctness and human intent. Approaches like single-agent reflection and multi-agent debate frequently prioritize consistency, but at the expense of accuracy. To address this problem, we propose a novel game-theoretic consensus mechanism that enables LLMs to self-check their outputs during the decoding stage of output generation. Our method models the decoding process as a multistage Bayesian Decoding Game, where strategic interactions dynamically converge to a consensus on the most reliable outputs without human feedback or additional training. Remarkably, our game design allows smaller models to outperform much larger models through game mechanisms (e.g., 78.1 LLaMA13B vs. 76.6 PaLM540B). As a model-agnostic method, our approach consistently improves even the latest models, enhancing DeepSeek-7B's performance on MMLU by 12.4%. Our framework effectively balances correctness and consistency, demonstrating that properly designed game-theoretic mechanisms can significantly enhance the self-verification capabilities of language models across various tasks and model architectures.

In cooperative Multi-Agent Reinforcement Learning (MARL), it is a common practice to tune hyperparameters in ideal simulated environments to maximize cooperative performance. However, policies tuned for cooperation often fail to maintain robustness and resilience under real-world uncertainties. Building trustworthy MARL systems requires a deep understanding of \emph{robustness}, which ensures stability under uncertainties, and \emph{resilience}, the ability to recover from disruptions—a concept extensively studied in control systems but largely overlooked in MARL. In this paper, we present a large-scale empirical study comprising over 82,620 experiments to evaluate cooperation, robustness, and resilience in MARL across 4 real-world environments, 13 uncertainty types, and 15 hyperparameters. Our key findings are: (1) Under mild uncertainty, optimizing cooperation improves robustness and resilience, but this link weakens as perturbations intensify. Robustness and resilience also varies by algorithm and uncertainty type. (2) Robustness and resilience do not generalize across uncertainty modalities or agent scopes: policies robust to action noise for all agents may fail under observation noise on a single agent. (3) Hyperparameter tuning is critical for trustworthy MARL: surprisingly, standard practices like parameter sharing, GAE, and PopArt can hurt robustness, while early stopping, high critic learning rates, and Leaky ReLU consistently help. By optimizing hyperparameters only, we observe substantial improvement in cooperation, robustness and resilience across all MARL backbones, with the phenomenon also generalizing to robust MARL methods across these backbones.

We consider a common case of the combinatorial semi-bandit problem, the $m$-set semi-bandit, where the learner exactly selects $m$ arms from the total $d$ arms. In the adversarial setting, the best regret bound, known to be $\mathcal{O}(\sqrt{nmd})$ for time horizon $n$, is achieved by the well-known Follow-the-Regularized-Leader (FTRL) policy. However, this requires to explicitly compute the arm-selection probabilities via optimizing problems at each time step and sample according to them. This problem can be avoided by the Follow-the-Perturbed-Leader (FTPL) policy, which simply pulls the $m$ arms that rank among the $m$ smallest (estimated) loss with random perturbation. In this paper, we show that FTPL with a Fr\'echet perturbation also enjoys the near optimal regret bound $\mathcal{O}(\sqrt{nm}(\sqrt{d\log(d)}+m^{5/6}))$ in the adversarial setting and approaches best-of-both-world regret bounds, i.e., achieves a logarithmic regret for the stochastic setting. Moreover, our lower bounds show that the extra factors are unavoidable with our approach; any improvement would require a fundamentally different and more challenging method.

Contrastive self-supervised learning has emerged as a powerful paradigm for extracting meaningful representations without labels. While effective at capturing broad categorical distinctions, current methods often struggle to preserve the fine-grained and hierarchical relationships inherent in real-world data. From the perspective of semantic alignment, conventional contrastive learning aligns representations to semantic structure at a global level, treating the entire embedding space uniformly and frequently overlooking rich local structural information. In this paper, we propose \emph{Adaptive Multi-scale Affinity alignment (AMA-alignment)}, a framework that introduces localized contrastive objectives and a dynamic multi-scale optimization strategy to adaptively identify and refine poorly aligned regions within the embedding space. Although our model is inherently more complex due to its \emph{multi-scale} and \emph{adaptive} design, we provide the theoretical guarantees indicating that its convergence rate remains comparable to that of standard smooth non-convex optimization. We conduct a set of experiments on diverse benchmarks to show that AMA-alignment can effectively preserve hierarchical structure; moreover, AMA-alignment also outperforms existing contrastive methods on a range of downstream tasks.

Multi-modal contrastive learning as a self-supervised representation learning technique has achieved great success in foundation model training, such as CLIP~\citep{radford2021learning}. In this paper, we study the theoretical properties of the learned representations from multi-modal contrastive learning beyond linear representations and specific data distributions. Our analysis reveals that, enabled by temperature optimization, multi-modal contrastive learning not only maximizes mutual information between modalities but also adapts to intrinsic dimensions of data, which can be much lower than user-specified dimensions for representation vectors. Experiments on both synthetic and real-world datasets demonstrate the ability of contrastive learning to learn low-dimensional and informative representations, bridging theoretical insights and practical performance.

Language bias in Visual Question Answering (VQA) arises when models exploit spurious statistical correlations between question templates and answers, particularly in out-of-distribution scenarios, thereby neglecting essential visual cues and compromising genuine multimodal reasoning. Despite numerous efforts to enhance the robustness of VQA models, a principled understanding of how such bias originates and influences model behavior remains underdeveloped. In this paper, we address this gap through a comprehensive empirical and theoretical analysis, revealing that modality-specific gradient imbalances, which originate from the inherent heterogeneity of multimodal data, lead to skewed feature fusion and biased classifier weights. To alleviate these issues, we propose a novel Multi-Margin Collaborative Debiasing (MMCD) framework that adaptively integrates frequency-, confidence-, and difficulty-aware angular margins with a dynamic difficulty-aware contrastive learning mechanism, to dynamically reshape decision boundaries. Extensive experiments across multiple challenging VQA benchmarks confirm the consistent superiority of our proposed MMCD over state-of-the-art baselines in combating language bias.

This paper firstly addresses the challenge of few-shot universal cross-domain retrieval (FS-UCDR), enabling machines trained with limited data to generalize to novel retrieval scenarios, with queries from entirely unknown domains and categories. To achieve this, we first formally define the FS-UCDR task and propose the Multi-Modal Interactive Agent Layer (MAIL), which enhances the cross-modal interaction in vision-language models (VLMs) by aligning the parameter updates of target layer pairs across modalities. Specifically, MAIL freezes the selected target layer pair and introduces a trainable agent layer pair to approximate localized parameter updates. A bridge function is then introduced to couple the agent layer pair, enabling gradient communication across modalities to facilitate update alignment. The proposed MAIL offers four key advantages: 1) its cross-modal interaction mechanism improves knowledge acquisition from limited data, making it highly effective in low-data scenarios; 2) during inference, MAIL integrates seamlessly into the VLM via reparameterization, preserving inference complexity; 3) extensive experiments validate the superiority of MAIL, which achieves substantial performance gains over data-efficient UCDR methods while requiring significantly fewer training samples; 4) beyond UCDR, MAIL also performs competitively on few-shot classification tasks, underscoring its strong generalization ability. Code.

Multi-class tissue-type classification of colorectal cancer (CRC) histopathologic images is a significant step in the development of downstream machine learning models for diagnosis and treatment planning. However, publicly available CRC datasets used to build tissue classifiers often suffer from insufficient morphologic diversity, class imbalance, and low-quality image tiles, limiting downstream model performance and generalizability. To address this research gap, we introduce STARC-9 (STAnford coloRectal Cancer), a large-scale dataset for multi-class tissue classification. STARC-9 comprises 630,000 histopathologic image tiles uniformly sampled across nine clinically relevant tissue classes (each represented by 70,000 tiles), systematically extracted from hematoxylin & eosin-stained whole-slide images (WSI) from 200 CRC patients at the Stanford University School of Medicine. To construct STARC-9, we propose a novel framework, DeepCluster++, consisting of two primary steps to ensure diversity within each tissue class, followed by pathologist verification. First, an encoder from an autoencoder trained specifically on histopathologic images is used to extract feature vectors from all tiles within a given input WSI. Next, K-means clustering groups morphologically similar tiles, followed by an equal-frequency binning method to sample diverse patterns within each tissue class. Finally, the selected tiles are verified by expert gastrointestinal pathologists to ensure classification accuracy. This semi-automated approach significantly reduces the manual effort required for dataset curation while producing high-quality training examples. To validate the utility of STARC-9, we benchmarked baseline convolutional neural networks, transformers, and pathology-specific foundation models on downstream multi-class CRC tissue classification and segmentation tasks when trained on STARC-9 versus publicly available datasets, demonstrating superior generalizability of models trained on STARC-9. Although we demonstrate the utility of DeepCluster++ on CRC as a pilot use-case, it is a flexible framework that can be used for constructing high-quality datasets from large WSI repositories across a wide range of cancer and non-cancer applications.

Human social interactions depend on the ability to infer others' unspoken intentions, emotions, and beliefs—a cognitive skill grounded in the psychological concept of Theory of Mind (ToM). While large language models (LLMs) excel in semantic understanding tasks, they struggle with the ambiguity and contextual nuance inherent in human communication. To bridge this gap, we introduce **MetaMind**, a multi-agent framework inspired by psychological theories of metacognition, designed to emulate human-like social reasoning. MetaMind decomposes social understanding into three collaborative stages: (1) a *Theory-of-Mind Agent* generates hypotheses about user mental states (e.g., intent, emotion), (2) a *Moral Agent* refines these hypotheses using cultural norms and ethical constraints, and (3) a *Response Agent* generates contextually appropriate responses while validating alignment with inferred intent. Our framework achieves state-of-the-art performance across three challenging benchmarks, with 35.7% improvement in real-world social scenarios and 6.2% gain in ToM reasoning. Notably, it enables LLMs to match human-level performance on key ToM tasks for the first time. Ablation studies confirm the necessity of all components, which showcase the framework’s ability to balance contextual plausibility, social appropriateness, and user adaptation. This work advances AI systems toward human-like social intelligence, with applications in empathetic dialogue and culturally sensitive interactions. Code is available at https://github.com/XMZhangAI/MetaMind.

LLM-agent systems often decompose high-level objectives into subtask dependency graphs, assuming that each subtask’s output is reliable and conditionally independent of others given its parent responses. However, this assumption frequently breaks during execution, as ground-truth responses are inaccessible, leading to inter-agent misalignment—failures caused by inconsistencies and coordination breakdowns among agents. To address this, we propose SeqCV, a dynamic framework for reliable execution under violated conditional independence. SeqCV executes subtasks sequentially, each conditioned on all prior verified responses, and performs consistency checks immediately after agents generate short token sequences. At each checkpoint, a token sequence is accepted only if it represents shared knowledge consistently supported across diverse LLM models; otherwise, it is discarded, triggering recursive subtask decomposition for finer-grained reasoning. Despite its sequential nature, SeqCV avoids repeated corrections on the same misalignment and achieves higher effective throughput than parallel pipelines. Across multiple reasoning and coordination tasks, SeqCV improves accuracy by up to 30\% over existing LLM-agent systems. Code is available at https://github.com/tmllab/2025_NeurIPS_SeqCV.

Multi-agent inverse reinforcement learning (MAIRL) aims to recover agent reward functions from expert demonstrations. We characterize the feasible reward set in Markov games, identifying all reward functions that rationalize a given equilibrium. However, equilibrium-based observations are often ambiguous: a single Nash equilibrium can correspond to many reward structures, potentially changing the game's nature in multi-agent systems. We address this by introducing entropy-regularized Markov games, which yield a unique equilibrium while preserving strategic incentives. For this setting, we provide a sample complexity analysis detailing how errors affect learned policy performance. Our work establishes theoretical foundations and practical insights for MAIRL.