ICML 2025 Papers

Efficient sampling of unnormalized probability densities such as the Boltzmann distribution of molecular systems is a longstanding challenge. Next to conventional approaches like molecular dynamics or Markov chain Monte Carlo, variational approaches, such as training normalizing flows with the reverse Kullback-Leibler divergence, have been introduced. However, such methods are prone to mode collapse and often do not learn to sample the full configurational space. Here, we present temperature-annealed Boltzmann generators (TA-BG) to address this challenge. First, we demonstrate that training a normalizing flow with the reverse Kullback-Leibler divergence at high temperatures is possible without mode collapse. Furthermore, we introduce a reweighting-based training objective to anneal the distribution to lower target temperatures. We apply this methodology to three molecular systems of increasing complexity and, compared to the baseline, achieve better results in almost all metrics while requiring up to three times fewer target energy evaluations. For the largest system, our approach is the only method that accurately resolves the metastable states of the system.

Solving partial differential equations (PDEs) using neural methods has been a long-standing scientific and engineering research pursuit. Physics-Informed Neural Networks (PINNs) have emerged as a promising alternative to traditional numerical methods for solving PDEs. However, the gap between domain-specific knowledge and deep learning expertise often limits the practical application of PINNs. Previous works typically involve manually conducting extensive PINNs experiments and summarizing heuristic rules for hyperparameter tuning. In this work, we introduce PINNsAgent, a novel surrogation framework that leverages large language models (LLMs) to bridge the gap between domain-specific knowledge and deep learning. PINNsAgent integrates Physics-Guided Knowledge Replay (PGKR) for efficient knowledge transfer from solved PDEs to similar problems, and Memory Tree Reasoning for exploring the search space of optimal PINNs architectures. We evaluate PINNsAgent on 14 benchmark PDEs, demonstrating its effectiveness in automating the surrogation process and significantly improving the accuracy of PINNs-based solutions.

Sparse linear solvers are fundamental to science and engineering, applied in partial differential equations (PDEs), scientific computing, computer vision, and beyond. Indirect solvers possess characteristics that make them undesirable as stable differentiable modules; existing direct solvers, though reliable, are too expensive to be adopted in neural architectures. We substantially accelerate direct sparse solvers or generalized deconvolution by up to 3 orders-of-magnitude faster, violating common assumptions that direct solvers are too slow. We ``condense'' a sparse Laplacian matrix into a dense tensor, a compact data structure that batch-wise stores the Dirichlet-to-Neumann matrices, reducing the sparse solving to recursively merging pairs of dense matrices that are much smaller. The batched small dense systems are sliced and inverted in parallel to take advantage of dense GPU BLAS kernels, highly optimized in the era of deep learning. Our method is efficient, qualified as a strong zero-shot baseline for AI-based PDE solving and a reliable differentiable module integrable into machine learning pipelines.

Imposing input-output constraints in multi-layer perceptrons (MLPs) plays a pivotal role in many real world applications. Monotonicity in particular is a common requirement in applications that need transparent and robust machine learning models. Conventional techniques for imposing monotonicity in MLPs by construction involve the use of non-negative weight constraints and bounded activation functions, which poses well known optimization challenges. In this work, we generalize previous theoretical results, showing that MLPs with non-negative weight constraint and activations that saturate on alternating sides are universal approximators for monotonic functions. Additionally, we show an equivalence between saturation side in the activations and sign of the weight constraint. This connection allows us to prove that MLPs with convex monotone activations and non-positive constrained weights also qualify as universal approximators, in contrast to their non-negative constrained counterparts. This results provide theoretical grounding to the empirical effectiveness observed in previous works, while leading to possible architectural simplification. Moreover, to further alleviate the optimization difficulties, we propose an alternative formulation that allows the network to adjust its activations according to the sign of the weights. This eliminates the requirement for weight reparameterization, easing initialization and improving training stability. Experimental evaluation reinforce the validity of the theoretical results, showing that our novel approach compares favorably to traditional monotonic architectures.

Machine learning interatomic potentials (MLIPs) have become increasingly effective at approximating quantum mechanical calculations at a fraction of the computational cost. However, lower errors on held out test sets do not always translate to improved results on downstream physical property prediction tasks. In this paper, we propose testing MLIPs on their practical ability to conserve energy during molecular dynamic simulations. If passed, improved correlations are found between test errors and their performance on physical property prediction tasks. We identify choices which may lead to models failing this test, and use these observations to improve upon highly-expressive models. The resulting model, eSEN, provides state-of-the-art results on a range of physical property prediction tasks, including materials stability prediction, thermal conductivity prediction, and phonon calculations.

Transition path sampling (TPS), which involves finding probable paths connecting two points on an energy landscape, remains a challenge due to the complexity of real-world atomistic systems. Current machine learning approaches rely on expensive training procedures and under-utilize growing quantities of atomistic data, limiting scalability and generalization. Generative models of atomistic conformational ensembles sample temporally independent states from energy landscapes, but their application to TPS remains mostly unexplored. In this work, we address TPS by interpreting candidate paths as trajectories sampled from stochastic dynamics induced by the learned score function of generative models, namely denoising diffusion and flow matching. Under these dynamics, finding high-likelihood transition paths becomes equivalent to minimizing the Onsager-Machlup (OM) action functional, enabling us to repurpose pre-trained generative models for TPS in a zero-shot fashion. We demonstrate our approach on a Müller-Brown potential and several fast-folding proteins, where we obtain diverse, physically realistic transition pathways, as well as tetrapeptides, where we demonstrate successful TPS on systems not seen by the generative model during training. Our method can be easily incorporated into new generative models, making it practically relevant as models continue to scale and improve.

Tasks that involve complex interactions between objects with unknown dynamics make planning before execution difficult. These tasks require agents to iteratively improve their actions after actively exploring causes and effects in the environment. For these type of tasks, we propose Causal-PIK, a method that leverages Bayesian optimization to reason about causal interactions via a Physics-Informed Kernel to help guide efficient search for the best next action. Experimental results on Virtual Tools and PHYRE physical reasoning benchmarks show that Causal-PIK outperforms state-of-the-art results, requiring fewer actions to reach the goal. We also compare Causal-PIK to human studies, including results from a new user study we conducted on the PHYRE benchmark. We find that Causal-PIK remains competitive on tasks that are very challenging, even for human problem-solvers.

Although social networks have expanded the range of ideas and information accessible to users, they are also criticized for amplifying the polarization of user opinions. Given the inherent complexity of these phenomena, existing approaches to counteract these effects typically rely on handcrafted algorithms and heuristics. We propose an elegant solution: we act on the network weights that model user interactions on social networks (e.g., ranking of users’ shared content in feeds), to optimize a performance metric (e.g., minimize polarization), while users’ opinions follow the classical Friedkin-Johnsen model. Our formulation gives rise to a challenging, large-scale optimization problem with non-convex constraints, for which we develop a gradient-based algorithm. Our scheme is simple, scalable, and versatile, as it can readily integrate different, potentially non-convex, objectives. We demonstrate its merit by: (i) rapidly solving complex social network intervention problems with 4.8 million variables based on the Reddit, LiveJournal, and DBLP datasets; (ii) outperforming competing approaches in terms of both computation time and disagreement reduction.

Cyclic peptides, characterized by geometric constraints absent in linear peptides, offer enhanced biochemical properties, presenting new opportunities to address unmet medical needs. However, designing target-specific cyclic peptides remains underexplored due to limited training data. To bridge the gap, we propose CP-Composer, a novel generative framework that enables zero-shot cyclic peptide generation via composable geometric constraints. Our approach decomposes complex cyclization patterns into unit constraints, which are incorporated into a diffusion model through geometric conditioning on nodes and edges. During training, the model learns from unit constraints and their random combinations in linear peptides, while at inference, novel constraint combinations required for cyclization are imposed as input. Experiments show that our model, despite trained with linear peptides, is capable of generating diverse target-binding cyclic peptides, reaching success rates from 38\% to 84\% on different cyclization strategies.

Multiphysics simulation, which models the interactions between multiple physical processes, and multi-component simulation of complex structures are critical in fields like nuclear and aerospace engineering. Previous studies use numerical solvers or ML-based surrogate models for these simulations. However, multiphysics simulations typically require integrating multiple specialized solvers-each for a specific physical process-into a coupled program, which introduces significant development challenges. Furthermore, existing numerical algorithms struggle with highly complex large-scale structures in multi-component simulations. Here we propose compositional Multiphysics and Multi-component PDE Simulation with Diffusion models (M2PDE) to overcome these challenges. During diffusion-based training, M2PDE learns energy functions modeling the conditional probability of one physical process/component conditioned on other processes/components. In inference, M2PDE generates coupled multiphysics and multi-component solutions by sampling from the joint probability distribution. We evaluate M2PDE on two multiphysics tasks-reaction-diffusion and nuclear thermal coupling--where it achieves more accurate predictions than surrogate models in challenging scenarios. We then apply it to a multi-component prismatic fuel element problem, demonstrating that M2PDE scales from single-component training to a 64-component structure and outperforms existing domain-decomposition and graph-based approaches. The code is available at github.com/AI4Science-WestlakeU/M2PDE.

Quantum Error Mitigation (QEM) has emerged as a pivotal technique for enhancing the reliability of noisy quantum devices in the *Noisy Intermediate-Scale Quantum* (NISQ) era. Recently, machine learning (ML)-based QEM approaches have demonstrated strong generalization capabilities without sampling overheads compared to conventional methods. However, evaluating these techniques is often hindered by a lack of standardized datasets and inconsistent experimental settings across different studies. In this work, we present **QEM-Bench**, a comprehensive benchmark suite of *twenty-two* datasets covering diverse circuit types and noise profiles, which provides a unified platform for comparing and advancing ML-based QEM methods. We further propose a refined ML-based QEM pipeline **QEMFormer**, which leverages a feature encoder that preserves local, global, and topological information, along with a two-branch model that captures short-range and long-range dependencies within the circuit. Empirical evaluations on QEM-Bench illustrate the superior performance of QEMFormer over existing baselines, underscoring the potential of integrated ML-QEM strategies.

Contrast-enhanced MRI enhances pathological visualization but often necessitates Pre-Contrast images for accurate quantitative analysis and comparative assessment. However, Pre-Contrast images are frequently unavailable due to time, cost, or safety constraints, or they may suffer from degradation, making alignment challenging. This limitation hinders clinical diagnostics and the performance of tools requiring combined image types. To address this challenge, we propose a novel staged, physics-grounded learning framework with a hyperintensity prior to synthesize Pre-Contrast images directly from Post-Contrast MRIs. The proposed method can generate high-quality Pre-Contrast images, thus, enabling comprehensive diagnostics while reducing the need for additional imaging sessions, costs, and patient risks. To the best of our knowledge, this is the first Pre-Contrast synthesis model capable of generating images that may be interchangeably used with standard-of-care Pre-Contrast images. Extensive evaluations across multiple datasets, sites, anatomies, and downstream tasks demonstrate the model’s robustness and clinical applicability, positioning it as a valuable tool for contrast-enhanced MRI workflows.

Solving partial differential equations (PDEs) using neural networks has become a central focus in scientific machine learning. Training neural networks for singularly perturbed problems is particularly challenging due to certain parameters in the PDEs that introduce near-singularities in the loss function. In this study, we overcome this challenge by introducing a novel method based on homotopy dynamics to effectively manipulate these parameters. From a theoretical perspective, we analyze the effects of these parameters on training difficulty in these singularly perturbed problems and establish the convergence of the proposed homotopy dynamics method. Experimentally, we demonstrate that our approach significantly accelerates convergence and improves the accuracy of these singularly perturbed problems. These findings present an efficient optimization strategy leveraging homotopy dynamics, offering a robust framework to extend the applicability of neural networks for solving singularly perturbed differential equations.

Although language model (LM) agents have demonstrated increased performance in multiple domains, including coding and web-browsing, their success in cybersecurity has been limited. We present *EnIGMA*, an LM agent for autonomously solving Capture The Flag (CTF) challenges. We introduce new tools and interfaces to improve the agent's ability to find and exploit security vulnerabilities, focusing on interactive terminal programs. These novel *Interactive Agent Tools* enable LM agents, for the first time, to run interactive utilities, such as a debugger and a server connection tool, which are essential for solving these challenges. Empirical analysis on 390 CTF challenges across four benchmarks demonstrate that these new tools and interfaces substantially improve our agent's performance, achieving state-of-the-art results on NYU CTF, Intercode-CTF, and CyBench. Finally, we analyze data leakage, developing new methods to quantify it and identifying a new phenomenon we term *soliloquizing*, where the model self-generates hallucinated observations without interacting with the environment.

Characterizing quantum states is essential for advancing many quantum technologies. Recently, deep neural networks have been applied to learn quantum states by generating compressed implicit representations. Despite their success in predicting properties of the states, these representations remain a black box, lacking insights into strategies for experimental reconstruction. In this work, we aim to open this black box by developing explicit representations through generating surrogate state preparation circuits for property estimation. We design a reinforcement learning agent equipped with a Transformer-based architecture and a local fidelity reward function. Relying solely on measurement data from a few neighboring qubits, our agent accurately recovers properties of target states. We also theoretically analyze the global fidelity the agent can achieve when it learns a good local approximation. Extensive experiments demonstrate the effectiveness of our framework in learning various states of up to 100 qubits, including those generated by shallow Instantaneous Quantum Polynomial circuits, evolved by Ising Hamiltonians, and many-body ground states. Furthermore, the learned circuit representations can be applied to Hamiltonian learning as a downstream task utilizing a simple linear model.

Auto-regressive partial differential equation (PDE) foundation models have shown great potential in handling time-dependent data. However, these models suffer from error accumulation caused by the shortcut problem deeply rooted in auto-regressive prediction. The challenge becomes particularly evident for out-of-distribution data, as the pretraining performance may approach random model initialization for downstream tasks with long-term dynamics. To deal with this problem, we propose physics-informed temporal alignment (PITA), a self-supervised learning framework inspired by inverse problem solving. Specifically, PITA aligns the physical dynamics discovered at different time steps on each given PDE trajectory by integrating physics-informed constraints into the self-supervision signal. The alignment is derived from observation data without relying on known physics priors, indicating strong generalization ability to out-of-distribution data. Extensive experiments show that PITA significantly enhances the accuracy and robustness of existing foundation models on diverse time-dependent PDE data. The code is available at \url{https://github.com/SCAILab-USTC/PITA}.

In this manuscript, we study the learning of deep attention neural networks, defined as the composition of multiple self-attention layers, with tied and low-rank weights. We first establish a mapping of such models to sequence multi-index models, a generalization of the widely studied multi-index model to sequential covariates, for which we establish a number of general results. In the context of Bayes-optimal learning, in the limit of large dimension $D$ and proportionally large number of samples $N$, we derive a sharp asymptotic characterization of the optimal performance as well as the performance of the best-known polynomial-time algorithm for this setting --namely approximate message-passing--, and characterize sharp thresholds on the minimal sample complexity required for better-than-random prediction performance. Our analysis uncovers, in particular, how the different layers are learned sequentially. Finally, we discuss how this sequential learning can also be observed in a realistic setup.

Crystalline materials often exhibit a high level of symmetry. However, most generative models do not account for symmetry, but rather model each atom without any constraints on its position or element. We propose a generative model, Wyckoff Diffusion (WyckoffDiff), which generates symmetry-based descriptions of crystals. This is enabled by considering a crystal structure representation that encodes all symmetry, and we design a novel neural network architecture which enables using this representation inside a discrete generative model framework. In addition to respecting symmetry by construction, the discrete nature of our model enables fast generation. We additionally present a new metric, Fréchet Wrenformer Distance, which captures the symmetry aspects of the materials generated, and we benchmark WyckoffDiff against recently proposed generative models for crystal generation. As a proof-of-concept study, we use WyckoffDiff to find new materials below the convex hull of thermodynamical stability.

The use of machine learning to estimate the energy of a group of atoms, and the forces that drive them to more stable configurations, have revolutionized the fields of computational chemistry and materials discovery. In this domain, rigorous enforcement of symmetry and conservation laws has traditionally been considered essential. For this reason, interatomic forces are usually computed as the derivatives of the potential energy, ensuring energy conservation. Several recent works have questioned this physically constrained approach, suggesting that directly predicting the forces yields a better trade-off between accuracy and computational efficiency -- and that energy conservation can be learned during training. This work investigates the applicability of such non-conservative models in microscopic simulations. We identify and demonstrate several fundamental issues, from ill-defined convergence of geometry optimization to instability in various types of molecular dynamics. Contrary to the case of rotational symmetry, energy conservation is hard to learn, monitor, and correct for. The best approach to exploit the acceleration afforded by direct force prediction might be to use it in tandem with a conservative model, reducing -- rather than eliminating -- the additional cost of backpropagation, but avoiding the pathological behavior associated with non-conservative forces.