NeurIPS 2025 论文列表

Designing functional proteins is a critical yet challenging problem due to the intricate interplay between backbone structures, sequences, and side-chains. Current approaches often decompose protein design into separate tasks, which can lead to accumulated errors, while recent efforts increasingly focus on all-atom protein design. However, we observe that existing all-atom generation approaches suffering from an information shortcut issue, where models inadvertently infer sequences from side-chain information, compromising their ability to accurately learn sequence distributions. To address this, we introduce a novel rationalized information flow strategy to eliminate the information shortcut. Furthermore, motivated by the advantages of Bayesian flows over differential equation–based methods, we propose the first Bayesian flow formulation for protein backbone orientations by recasting orientation modeling as an equivalent hyperspherical generation problem with antipodal symmetry. To validate, our method delivers consistently exceptional performance in both peptide and antibody design tasks.

We study the multi-objective linear contextual bandit problem, where multiple possible conflicting objectives must be optimized simultaneously. We propose $\texttt{MOL-TS}$, the first Thompson Sampling algorithm with Pareto regret guarantees for this problem. Unlike standard approaches that compute an empirical Pareto front each round, $\texttt{MOL-TS}$ samples parameters across objectives and efficiently selects an arm from a novel effective Pareto front, which accounts for repeated selections over time. Our analysis shows that $\texttt{MOL-TS}$ achieves a worst-case Pareto regret bound of $\widetilde{O}(d^{3/2}\sqrt{T})$, where $d$ is the dimension of the feature vectors, $T$ is the total number of rounds, matching the best known order for randomized linear bandit algorithms for single objective. Empirical results confirm the benefits of our proposed approach, demonstrating improved regret minimization and strong multi-objective performance.

The paper proposes a novel machine learning-based approach to the pathfinding problem on extremely large graphs. This method leverages diffusion distance estimation via a neural network and uses beam search for pathfinding. We demonstrate its efficiency by finding solutions for 4x4x4 and 5x5x5 Rubik's cubes with unprecedentedly short solution lengths, outperforming all available solvers and introducing the first machine learning solver beyond the 3x3x3 case. In particular, it surpasses every single case of the combined best results in the Kaggle Santa 2023 challenge, which involved over 1,000 teams. For the 3x3x3 Rubik's cube, our approach achieves an optimality rate exceeding 98%, matching the performance of task-specific solvers and significantly outperforming prior solutions such as DeepCubeA (60.3%) and EfficientCube (69.6%). Our solution in its current implementation is approximately 25.6 times faster in solving 3x3x3 Rubik's cubes while requiring up to 8.5 times less model training time than the most efficient state-of-the-art competitor. Finally, it is demonstrated that even a single agent trained using a relatively small number of examples can robustly solve a broad range of puzzles represented by Cayley graphs of size up to $10^{145}$, confirming the generality of the proposed method.

Retrosynthetic planning is a fundamental task in chemical discovery. Due to the vast combinatorial search space, identifying viable synthetic routes remains a significant challenge--even for expert chemists. Recent advances in Large Language Models (LLMs), particularly equipped with reinforcement learning, have demonstrated strong human-like reasoning and planning abilities, especially in mathematics and code problem solving. This raises a natural question: Can the reasoning capabilities of LLMs be harnessed to develop an AI chemist capable of learning effective policies for multi-step retrosynthesis? In this study, we introduce Retro-R1, a novel LLM-based retrosynthesis agent trained via reinforcement learning to design molecular synthesis pathways. Unlike prior approaches, which typically rely on single-turn, question-answering formats, Retro-R1 interacts dynamically with plug-in single-step retrosynthesis tools and learns from environmental feedback. Experimental results show that Retro-R1 achieves a 55.79\% pass@1 success rate, surpassing the previous state of the art by 8.95\%. Notably, Retro-R1 demonstrates strong generalization to out-of-domain test cases, where existing methods tend to fail despite their high in-domain performance. Our work marks a significant step toward equipping LLMs with advanced, chemist-like reasoning abilities, highlighting the promise of reinforcement learning for enabling data-efficient, generalizable, and sophisticated scientific problem-solving in LLM-based agents.

Options markets represent one of the most sophisticated segments of the financial ecosystem, with prices that directly reflect market uncertainty. In this paper, we introduce the first reinforcement learning (RL) framework specifically designed for volatility trading through options, focusing on profit from the difference between implied volatility and realized volatility. Our multi-agent architecture consists of an Option Position Agent (OP-Agent) responsible for volatility timing by controlling long/short volatility positions, and a Hedger Routing Agent (HR-Agent) that manages risk and maximizes path-dependent profits by selecting optimal hedging strategies with different risk preferences. Evaluating our approach using cryptocurrency options data from 2021-2024, we demonstrate superior performance on BTC and ETH, significantly outperforming traditional strategies and machine learning baselines across all profit and risk-adjusted metrics while exhibiting sophisticated trading behavior. The code framework and sample data of this paper have been released on https://github.com/Edwicn/OPHR-MasteringVolatilityTradingwithMultiAgentDeepReinforcementLearning

The performance of an algorithm often critically depends on its hyperparameter configuration. Dynamic algorithm configuration (DAC) is a recent trend in automated machine learning, which can dynamically adjust the algorithm’s configuration during the execution process and relieve users from tedious trial-and-error tuning tasks. Recently, multi-agent reinforcement learning (MARL) approaches have improved the configuration of multiple heterogeneous hyperparameters, making various parameter configurations for complex algorithms possible. However, many complex algorithms have inherent inter-dependencies among multiple parameters (e.g., determining the operator type first and then the operator's parameter), which are, however, not considered in previous approaches, thus leading to sub-optimal results. In this paper, we propose the sequential multi-agent DAC (Seq-MADAC) framework to address this issue by considering the inherent inter-dependencies of multiple parameters. Specifically, we propose a sequential advantage decomposition network, which can leverage action-order information through sequential advantage decomposition. Experiments from synthetic functions to the configuration of multi-objective optimization algorithms demonstrate Seq-MADAC's superior performance over state-of-the-art MARL methods and show strong generalization across problem classes. Seq-MADAC establishes a new paradigm for the widespread dependency-aware automated algorithm configuration. Our code is available at https://github.com/lamda-bbo/seq-madac.

Plasticity and stability denote the ability to assimilate new tasks while preserving previously acquired knowledge, representing two important concepts in continual learning. Recent research addresses stability by leveraging pre-trained models to provide informative representations, yet the efficacy of these methods is highly reliant on the choice of the pre-trained backbone, which may not yield optimal plasticity. This paper addresses this limitation by introducing a streamlined and potent framework that orchestrates multiple different pre-trained backbones to derive semantically rich multi-source representations. We propose an innovative Multi-Scale Interaction and Dynamic Fusion (MSIDF) technique to process and selectively capture the most relevant parts of multi-source features through a series of learnable attention modules, thereby helping to learn better decision boundaries to boost performance. Furthermore, we introduce a novel Multi-Level Representation Optimization (MLRO) strategy to adaptively refine the representation networks, offering adaptive representations that enhance plasticity. To mitigate over-regularization issues, we propose a novel Adaptive Regularization Optimization (ARO) method to manage and optimize a switch vector that selectively governs the updating process of each representation layer, which promotes the new task learning. The proposed MLRO and ARO approaches are collectively optimized within a unified optimization framework to achieve an optimal trade-off between plasticity and stability. Our extensive experimental evaluations reveal that the proposed framework attains state-of-the-art performance. The source code of our algorithm is available at https://github.com/CL-Coder236/LMSRR.

Multi-compartment Hodgkin-Huxley models are biophysical models of how electrical signals propagate throughout a neuron, and they form the basis of our knowledge of neural computation at the cellular level. However, these models have many free parameters that must be estimated for each cell, and existing fitting methods rely on intracellular voltage measurements that are highly challenging to obtain in-vivo. Recent advances in neural recording technology with high-density probes and arrays enable dense sampling of extracellular voltage from many sites surrounding a neuron, allowing indirect measurement of many compartments of a cell simultaneously. Here, we propose a method for inferring the underlying membrane voltage, biophysical parameters, and the neuron's position relative to the probe, using extracellular measurements alone. We use an Extended Kalman Filter to infer membrane voltage and channel states using efficient, differentiable simulators. Then, we learn the model parameters by maximizing the marginal likelihood using gradient-based methods. We demonstrate the performance of this approach using simulated data and real neuron morphologies.

Communication is one of the effective means to improve the learning of cooperative policy in multi-agent systems. However, in most real-world scenarios, lossy communication is a prevalent issue. Existing multi-agent reinforcement learning with communication, due to their limited scalability and robustness, struggles to apply to complex and dynamic real-world environments. To address these challenges, we propose a generalized communication-constrained model to uniformly characterize communication conditions across different scenarios. Based on this, we utilize it as a learning prior to distinguish between lossy and lossless messages for specific scenarios. Additionally, we decouple the impact of lossy and lossless messages on distributed decision-making, drawing on a dual mutual information estimatior, and introduce a communication-constrained multi-agent reinforcement learning framework, quantifying the impact of communication messages into the global reward. Finally, we validate the effectiveness of our approach across several communication-constrained benchmarks.

Autonomous exploration in complex multi-agent reinforcement learning (MARL) with sparse rewards critically depends on providing agents with effective intrinsic motivation. While artificial curiosity offers a powerful self-supervised signal, it often confuses environmental stochasticity with meaningful novelty. Moreover, existing curiosity mechanisms exhibit a uniform novelty bias, treating all unexpected observations equally. However, peer behavior novelty, which encode latent task dynamics, are often overlooked, resulting in suboptimal exploration in decentralized, communication-free MARL settings. To this end, inspired by how human children adaptively calibrate their own exploratory behaviors via observing peers, we propose a novel approach to enhance multi-agent exploration. We introduce CERMIC, a principled framework that empowers agents to robustly filter noisy surprise signals and guide exploration by dynamically calibrating their intrinsic curiosity with inferred multi-agent context. Additionally, CERMIC generates theoretically-grounded intrinsic rewards, encouraging agents to explore state transitions with high information gain. We evaluate CERMIC on benchmark suites including VMAS, Meltingpot, and SMACv2. Empirical results demonstrate that exploration with CERMIC significantly outperforms SoTA algorithms in sparse-reward environments.

Designing effective agentic systems requires the seamless composition and integration of agents, tools, and models within dynamic and uncertain environments. Most existing methods rely on static, semantic retrieval approaches for tool or agent discovery. However, effective reuse and composition of existing components remain challenging due to incomplete capability descriptions and the limitations of retrieval methods. Component selection suffers because the decisions are not based on capability, cost, and real-time utility. To address these challenges, we introduce a structured, automated framework for agentic system composition that is inspired by the knapsack problem. Our framework enables a composer agent to systematically identify, select, and assemble an optimal set of agentic components by jointly considering performance, budget constraints, and compatibility. By dynamically testing candidate components and modeling their utility in real-time, our approach streamlines the assembly of agentic systems and facilitates scalable reuse of resources. Empirical evaluation with Claude 3.5 Sonnet across five benchmarking datasets shows that our online-knapsack-based composer consistently lies on the Pareto frontier, achieving higher success rates at significantly lower component costs compared to our baselines. In the single-agent setup, the online knapsack composer shows a success rate improvement of up to 31.6\% in comparison to the retrieval baselines. In multi-agent systems, the online knapsack composer increases success rate from 37\% to 87\% when agents are selected from an agent inventory of 100+ agents. The substantial performance gap confirms the robust adaptability of our method across diverse domains and budget constraints.

Large language models (LLMs) have achieved notable progress. Despite their success, next-token prediction (NTP), the dominant method for LLM training and inference, is constrained in both contextual coverage and inference efficiency due to its inherently sequential process. To overcome these challenges, we propose leap multi-token prediction~(L-MTP), an innovative token prediction method that extends the capabilities of multi-token prediction (MTP) by introducing a leap-based mechanism. Unlike conventional MTP, which generates multiple tokens at adjacent positions, L-MTP strategically skips over intermediate tokens, predicting non-sequential ones in a single forward pass. This structured leap not only enhances the model's ability to capture long-range dependencies but also enables a decoding strategy specially optimized for non-sequential leap token generation, effectively accelerating inference. We theoretically demonstrate the benefit of L-MTP in improving inference efficiency. Experiments across diverse benchmarks validate its merit in boosting both LLM performance and inference speed. The source code is available at https://github.com/Xiaohao-Liu/L-MTP.

Multi-view multi-label learning typically suffers from dual data incompleteness due to limitations in feature storage and annotation costs. The interplay of hetero geneous features, numerous labels, and missing information significantly degrades model performance. To tackle the complex yet highly practical challenges, we propose a Theory-Driven Label-Specific Representation (TDLSR) framework. Through constructing the view-specific sample topology and prototype association graph, we develop the proximity-aware imputation mechanism, while deriving class representatives that capture the label correlation semantics. To obtain semantically distinct view representations, we introduce principles of information shift, inter action and orthogonality, which promotes the disentanglement of representation information, and mitigates message distortion and redundancy. Besides, label semantic-guided feature learning is employed to identify the discriminative shared and specific representations and refine the label preference across views. Moreover, we theoretically investigate the characteristics of representation learning and the generalization performance. Finally, extensive experiments on public datasets and real-world applications validate the effectiveness of TDLSR.

The Restricted Boltzmann Machine (RBM) is one of the simplest generative neural networks capable of learning input distributions. Despite its simplicity, the analysis of its performance in learning from the training data is only well understood in cases that essentially reduce to singular value decomposition of the data. Here, we consider the limit of a large dimension of the input space and a constant number of hidden units. In this limit, we simplify the standard RBM training objective into a form that is equivalent to the multi-index model with non-separable regularization. This opens a path to analyze training of the RBM using methods that are established for multi-index models, such as Approximate Message Passing (AMP) and its state evolution, and the analysis of Gradient Descent (GD) via the dynamical mean-field theory. We then give rigorous asymptotics of the training dynamics of RBMs on data generated by the spiked covariance model as a prototype of a structure suitable for unsupervised learning. We show in particular that RBMs reach the optimal computational weak recovery threshold, aligning with the Baik-Ben Arous-Péché (BBP) transition, in the spiked covariance model.