ICML 2025 论文列表

The design of target-specific molecules such as small molecules, peptides, and antibodies is vital for biological research and drug discovery. Existing generative methods are restricted to single-domain molecules, failing to address versatile therapeutic needs or utilize cross-domain transferability to enhance model performance. In this paper, we introduce **Uni**fied generative **Mo**deling of 3D **Mo**lecules (UniMoMo), the first framework capable of designing binders of multiple molecular domains using a single model. In particular, UniMoMo unifies the representations of different molecules as graphs of blocks, where each block corresponds to either a standard amino acid or a molecular fragment. Based on these unified representations, UniMoMo utilizes a geometric latent diffusion model for 3D molecular generation, featuring an iterative full-atom autoencoder to compress blocks into latent space points, followed by an E(3)-equivariant diffusion process. Extensive benchmarks across peptides, antibodies, and small molecules demonstrate the superiority of our unified framework over existing domain-specific models, highlighting the benefits of multi-domain training.

Function learning forms the foundation of numerous scientific and engineering tasks. While modern machine learning (ML) methods model complex functions effectively, their escalating complexity and computational demands pose challenges to efficient deployment. In contrast, natural dynamical systems exhibit remarkable computational efficiency in representing and solving complex functions. However, existing dynamical system approaches are limited by low expressivity and inefficient training. To this end, we propose EADS, an Expressive and self-Adaptive Dynamical System capable of accurately learning a wide spectrum of functions with extraordinary efficiency. Specifically, (1) drawing inspiration from biological dynamical systems, we integrate hierarchical architectures and heterogeneous dynamics into EADS, significantly enhancing its capacity to represent complex functions. (2) We propose an efficient on-device training method that leverages intrinsic electrical signals to update parameters, making EADS self-adaptive at negligible cost. Experimental results across diverse domains demonstrate that EADS achieves higher accuracy than existing works, while offering orders-of-magnitude speedups and energy efficiency over traditional neural network solutions on GPUs for both inference and training, showcasing its broader impact in overcoming computational bottlenecks across various fields.

Test-Time Training has emerged as a promising solution to address distribution shifts in 3D point cloud classification. However, existing methods often rely on computationally expensive backpropagation during adaptation, limiting their applicability in real-world, time-sensitive scenarios. In this paper, we introduce SMART-PC, a skeleton-based framework that enhances resilience to corruptions by leveraging the geometric structure of 3D point clouds. During pre-training, our method predicts skeletal representations, enabling the model to extract robust and meaningful geometric features that are less sensitive to corruptions, thereby improving adaptability to test-time distribution shifts. Unlike prior approaches, SMART-PC achieves real-time adaptation by eliminating backpropagation and updating only BatchNorm statistics, resulting in a lightweight and efficient framework capable of achieving high frame-per-second rates while maintaining superior classification performance. Extensive experiments on benchmark datasets, including ModelNet40-C, ShapeNet-C, and ScanObjectNN-C, demonstrate that SMART-PC achieves state-of-the-art results, outperforming existing methods such as MATE in terms of both accuracy and computational efficiency. The implementation is available at: \url{https://github.com/AliBahri94/SMART-PC}.

Brain network analysis plays a critical role in brain disease prediction and diagnosis. Graph mining tools have made remarkable progress. Graph neural networks (GNNs) and Transformers, which rely on the message-passing scheme, recently dominated this field due to their powerful expressive ability on graph data. Unfortunately, by considering brain network construction using pairwise Pearson’s coefficients between any pairs of ROIs, model analysis and experimental verification reveal that *the message-passing under both GNNs and Transformers can NOT be fully explored and exploited*. Surprisingly, this paper observes the significant performance and efficiency enhancements of the Hadamard product compared to the matrix product, which is the matrix form of message passing, in processing the brain network. Inspired by this finding, a novel Brain Quadratic Network (BQN) is proposed by incorporating quadratic networks, which possess better universal approximation properties. Moreover, theoretical analysis demonstrates that BQN implicitly performs community detection along with representation learning. Extensive evaluations verify the superiority of the proposed BQN compared to the message-passing-based brain network modeling. Source code is available at [https://github.com/LYWJUN/BQN-demo](https://github.com/LYWJUN/BQN-demo).

The sustainable performance improvements of integrated circuits (ICs) drive the continuous advancement of nearly all transformative technologies. Since its invention, IC performance enhancements have been dominated by scaling the semiconductor technology. Yet, as Moore's law tapers off, a crucial question arises: ***How can we sustain IC performance in the post-Moore era?*** Creating new circuit topologies has emerged as a promising pathway to address this fundamental need. This work proposes AnalogGenie-Lite, a decoder-only transformer that discovers novel analog IC topologies with significantly enhanced scalability and precision via lightweight graph modeling. AnalogGenie-Lite makes several unique contributions, including concise device-pin representations (i.e., advancing the best prior art from $O\left(n^2\right)$ to $O\left(n\right)$), frequent sub-graph mining, and optimal sequence modeling. Compared to state-of-the-art circuit topology discovery methods, it achieves $5.15\times$ to $71.11\times$ gains in scalability and 23.5\% to 33.6\% improvements in validity. Case studies on other domains' graphs are also provided to show the broader applicability of the proposed graph modeling approach. Source code: https://github.com/xz-group/AnalogGenie-Lite.

Graph generative models are essential across diverse scientific domains by capturing complex distributions over relational data. Among them, graph diffusion models achieve superior performance but face inefficient sampling and limited flexibility due to the tight coupling between training and sampling stages. We introduce DeFoG, a novel graph generative framework that disentangles sampling from training, enabling a broader design space for more effective and efficient model optimization. DeFoG employs a discrete flow-matching formulation that respects the inherent symmetries of graphs. We theoretically ground this disentangled formulation by explicitly relating the training loss to the sampling algorithm and showing that DeFoG faithfully replicates the ground truth graph distribution. Building on these foundations, we thoroughly investigate DeFoG's design space and propose novel sampling methods that significantly enhance performance and reduce the required number of refinement steps. Extensive experiments demonstrate state-of-the-art performance across synthetic, molecular, and digital pathology datasets, covering both unconditional and conditional generation settings. It also outperforms most diffusion-based models with just 5–10\% of their sampling steps.

Generalized Category Discovery (GCD) aims to identify both known and novel categories in unlabeled data by leveraging knowledge from old classes. However, existing methods are limited to non-graph data; lack theoretical foundations to answer *When and how known classes can help GCD*. We introduce the Graph GCD task; provide the first rigorous theoretical analysis of *parametric GCD*. By quantifying the relationship between old and new classes in the embedding space using the Wasserstein distance W, we derive the first provable GCD loss bound based on W. This analysis highlights two necessary conditions for effective GCD. However, we uncover, through a Pairwise Markov Random Field perspective, that popular graph contrastive learning (GCL) methods inherently violate these conditions. To address this limitation, we propose SWIRL, a novel GCL method for GCD. Experimental results validate our (theoretical) findings and demonstrate SWIRL's effectiveness.

Despite rapid progress in neural combinatorial optimization (NCO) for solving CO problems (COPs), as the problem scale grows, several bottlenecks persist: 1) solvers in the Global Prediction (GP) paradigm struggle in long-range decisions where the overly smooth intermediate heatmaps impede effective decoding, and 2) solvers in the Local Construction (LC) paradigm are time-consuming and incapable of tackling large instances due to the onerous auto-regressive process. Observing these challenges, we propose a new paradigm named Adaptive Expansion AE with its instantiation COExpander, positioned to leverage both advantages of GP and LC. COExpander utilizes informative heatmaps generated by a global predictor, which is learned under the guidance of locally determined partial solutions, to in turn direct the expansion of determined decision variables with adaptive step-sizes. To ensure transparent evaluation, we further take the lead to canonicalize 29 benchmarks spanning 6 popular COPs (MIS, MCl, MVC, MCut, TSP, ATSP) and various scales (50-10K nodes), upon which experiments demonstrate concrete SOTA performance of COExpander over these tasks. Source code and our standardized datasets will be made public.

Drug discovery is a complex process that involves multiple stages and tasks. However, existing molecular generative models can only tackle some of these tasks. We present *Generalist Molecular generative model* (GenMol), a versatile framework that uses only a *single* discrete diffusion model to handle diverse drug discovery scenarios. GenMol generates Sequential Attachment-based Fragment Embedding (SAFE) sequences through non-autoregressive bidirectional parallel decoding, thereby allowing the utilization of a molecular context that does not rely on the specific token ordering while having better sampling efficiency. GenMol uses fragments as basic building blocks for molecules and introduces *fragment remasking*, a strategy that optimizes molecules by regenerating masked fragments, enabling effective exploration of chemical space. We further propose *molecular context guidance* (MCG), a guidance method tailored for masked discrete diffusion of GenMol. GenMol significantly outperforms the previous GPT-based model in *de novo* generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design.

Advancing planning and reasoning capabilities of Large Language Models (LLMs) is one of the key prerequisites towards unlocking their potential for performing reliably in complex and impactful domains. In this paper, we aim to demonstrate this across board games (Chess, Fischer Random / Chess960, Connect Four, and Hex), and we show that search-based planning can yield significant improvements in LLM game-playing strength. We introduce, compare and contrast two major approaches: In *external search*, the model guides Monte Carlo Tree Search (MCTS) rollouts and evaluations without calls to an external game engine, and in *internal search*, the model is trained to generate in-context a linearized tree of search and a resulting final choice. Both build on a language model pre-trained on relevant domain knowledge, reliably capturing the transition and value functions in the respective environments, with minimal hallucinations. We evaluate our LLM search implementations against game-specific state-of-the-art engines, showcasing substantial improvements in strength over the base model, and reaching Grandmaster-level performance in chess while operating closer to the human search budget. Our proposed approach, combining search with domain knowledge, is not specific to board games, hinting at more general future applications.

Recurrent neural networks (RNNs) are powerful models used widely in both machine learning and neuroscience to learn tasks with temporal dependencies and to model neural dynamics. However, despite significant advancements in the theory of RNNs, there is still limited understanding of their learning process and the impact of the temporal structure of data. Here, we bridge this gap by analyzing the learning dynamics of linear RNNs (LRNNs) analytically, enabled by a novel framework that accounts for task dynamics. Our mathematical result reveals four key properties of LRNNs: (1) Learning of data singular values is ordered by both scale and temporal precedence, such that singular values that are larger and occur later are learned faster. (2) Task dynamics impact solution stability and extrapolation ability. (3) The loss function contains an effective regularization term that incentivizes small weights and mediates a tradeoff between recurrent and feedforward computation. (4) Recurrence encourages feature learning, as shown through a novel derivation of the neural tangent kernel for finite-width LRNNs. As a final proof-of-concept, we apply our theoretical framework to explain the behavior of LRNNs performing sensory integration tasks. Our work provides a first analytical treatment of the relationship between the temporal dependencies in tasks and learning dynamics in LRNNs, building a foundation for understanding how complex dynamic behavior emerges in cognitive models.

Long-Context Transformer Models (LCTMs) are vital for real-world applications but suffer high computational costs due to attention's quadratic complexity. Block-sparse attention mitigates this by focusing computation on critical regions, yet existing methods struggle with balancing accuracy and efficiency due to costly block importance measurements. In this paper, we introduce XAttention, a plug-and-play framework that dramatically accelerates long-context inference in Transformers models using sparse attention. XAttention's key innovation is the insight that the sum of antidiagonal values (i.e., from the lower-left to upper-right) in the attention matrix provides a powerful proxy for block importance. This allows for precise identification and pruning of non-essential blocks, resulting in high sparsity and dramatically accelerated inference. Across comprehensive evaluations on demanding long-context benchmarks—including RULER and LongBench for language, VideoMME for video understanding, and VBench for video generation—XAttention achieves accuracy comparable to full attention while delivering substantial computational gains. We demonstrate up to 13.5x acceleration in attention computation. These results underscore XAttention's ability to unlock the practical potential of block sparse attention, paving the way for scalable and efficient deployment of LCTMs in real-world applications.

Parameter-sharing (PS) techniques have been widely adopted in cooperative Multi-Agent Reinforcement Learning (MARL). In PS, all the agents share a policy network with identical parameters, which enjoys good sample efficiency. However, PS could lead to homogeneous policies that limit MARL performance. We tackle this problem from the angle of gradient conflict among agents. We find that the existence of futile neurons whose update is canceled out by gradient conflicts among agents leads to poor learning efficiency and diversity. To address this deficiency, we propose GradPS, a gradient-based PS method. It dynamically creates multiple clones for each futile neuron. For each clone, a group of agents with low gradient-conflict shares the neuron's parameters. Our method can enjoy good sample efficiency by sharing the gradients among agents of the same clone neuron. Moreover, it can encourage diverse behaviors through independently updating an exclusive clone neuron. Through extensive experiments, we show that GradPS can learn diverse policies with promising performance. The source code for GradPS is available in \url{https://github.com/xmu-rl-3dv/GradPS}.

Deep reinforcement learning (DRL) has been widely used for dynamic algorithm configuration, particularly in evolutionary computation, which benefits from the adaptive update of parameters during the algorithmic execution. However, applying DRL to algorithm configuration for multi-objective combinatorial optimization (MOCO) problems remains relatively unexplored. This paper presents a novel graph neural network (GNN) based DRL to configure multi-objective evolutionary algorithms. We model the dynamic algorithm configuration as a Markov decision process, representing the convergence of solutions in the objective space by a graph, with their embeddings learned by a GNN to enhance the state representation. Experiments on diverse MOCO challenges indicate that our method outperforms traditional and DRL-based algorithm configuration methods in terms of efficacy and adaptability. It also exhibits advantageous generalizability across objective types and problem sizes, and applicability to different evolutionary computation methods.

We analyze the convergence rates of two popular variants of coordinate descent (CD): random CD (RCD), in which the coordinates are sampled uniformly at random, and random-permutation CD (RPCD), in which random permutations are used to select the update indices. Despite abundant empirical evidence that RPCD outperforms RCD in various tasks, the theoretical gap between the two algorithms’ performance has remained elusive. Even for the benign case of positive-definite quadratic functions with permutation-invariant Hessians, previous efforts have failed to demonstrate a provable performance gap between RCD and RPCD. To this end, we present novel results showing that, for a class of quadratics with permutation-invariant structures, the contraction rate upper bound for RPCD is always strictly smaller than the contraction rate lower bound for RCD for every individual problem instance. Furthermore, we conjecture that this function class contains the worst-case examples of RPCD among all positive-definite quadratics. Combined with our RCD lower bound, this conjecture extends our results to the general class of positive-definite quadratic functions.

Building helpful and harmless large language models (LLMs) requires effective model alignment approach based on human instructions and feedback, which necessitates high-quality human-labeled data. Constructing such datasets is often expensive and hard to scale, and may face potential limitations on diversity and generalization. To address these challenges, we introduce Mixture of Agents Alignment (MoAA), that leverages the collective strengths of various language models to provide high-quality data for model alignment. By employing MoAA, we enhance both supervised fine-tuning and preference optimization, leading to improved performance compared to using a single model alone to generate alignment data (e.g. using GPT-4o alone). Evaluation results show that our approach can improve win rate of LLaMA-3.1-8B-Instruct from 19.5 to 48.3 on Arena-Hard and from 22.33 to 57.23 on AlpacaEval2, highlighting a promising direction for model alignment through this new scalable and diverse synthetic data recipe. Furthermore, we demonstrate that MoAA enables a self-improvement pipeline, where models fine-tuned on MoA-generated data surpass their own initial capabilities, providing evidence that our approach can push the frontier of open-source LLMs without reliance on stronger external supervision. Data and code will be released.

Navigating in an unfamiliar environment during deployment poses a critical challenge for a vision-language navigation (VLN) agent. Yet, test-time adaptation (TTA) remains relatively underexplored in robotic navigation, leading us to the fundamental question: what are the key properties of TTA for online VLN? In our view, effective adaptation requires three qualities: 1) flexibility in handling different navigation outcomes, 2) interactivity with external environment, and 3) maintaining a harmony between plasticity and stability. To address this, we introduce FeedTTA, a novel TTA framework for online VLN utilizing feedback-based reinforcement learning. Specifically, FeedTTA learns by maximizing binary episodic feedback, a practical setup in which the agent receives a binary scalar after each episode that indicates the success or failure of the navigation. Additionally, we propose a gradient regularization technique that leverages the binary structure of FeedTTA to achieve a balance between plasticity and stability during adaptation. Our extensive experiments on challenging VLN benchmarks demonstrate the superior adaptability of FeedTTA, even outperforming the state-of-the-art offline training methods in REVERIE benchmark with a single stream of learning.

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost—driven by high-order tensor product (TP) operations—restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce **SPH**Net, an efficient and scalable equivariant network, that incorporates adaptive **SP**arsity into **H**amiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70\%. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact.

Fine-tuning pre-trained diffusion models under limited budgets has gained great success. In particular, the recent advances that directly fine-tune the quantized weights using Low-rank Adaptation (LoRA) further reduces training costs. Despite these progress, we point out that existing adaptation recipes are not inference-efficient. Specifically, additional post-training quantization (PTQ) on tuned weights is needed during deployment, which results in noticeable performance drop when the bit-width is low. Based on this observation, we introduce IntLoRA, which adapts quantized diffusion models with integer-type low-rank parameters, to include inference efficiency during tuning. Specifically, IntLoRA enables pre-trained weights to remain quantized during training, facilitating fine-tuning on consumer-level GPUs. During inference, IntLoRA weights can be seamlessly merged into pre-trained weights to directly obtain quantized downstream weights without PTQ. Extensive experiments show our IntLoRA achieves significant speedup on both training and inference without losing performance.