ICML 2025 论文列表

Graph Neural Networks (GNNs) often struggle in preserving high-frequency components of nodal signals when dealing with directed graphs. Such components are crucial for modeling flow dynamics, without which a traditional GNN tends to treat a graph with forward and reverse topologies equal. To make GNNs sensitive to those high-frequency components thereby being capable to capture detailed topological differences, this paper proposes a novel framework that combines 1) explicit difference matrices that model directional gradients and 2) implicit physical constraints that enforce messages passing within GNNs to be consistent with natural laws. Evaluations on two real-world directed graph data, namely, water flux network and urban traffic flow network, demonstrate the effectiveness of our proposal.

Diffusion models are the standard toolkit for generative modelling of 3D atomic systems. However, for different types of atomic systems -- such as molecules and materials -- the generative processes are usually highly specific to the target system despite the underlying physics being the same. We introduce the All-atom Diffusion Transformer (ADiT), a unified latent diffusion framework for jointly generating both periodic materials and non-periodic molecular systems using the same model: (1) An autoencoder maps a unified, all-atom representations of molecules and materials to a shared latent embedding space; and (2) A diffusion model is trained to generate new latent embeddings that the autoencoder can decode to sample new molecules or materials. Experiments on MP20, QM9 and GEOM-DRUGS datasets demonstrate that jointly trained ADiT generates realistic and valid molecules as well as materials, obtaining state-of-the-art results on par with molecule and crystal-specific models. ADiT uses standard Transformers with minimal inductive biases for both the autoencoder and diffusion model, resulting in significant speedups during training and inference compared to equivariant diffusion models. Scaling ADiT up to half a billion parameters predictably improves performance, representing a step towards broadly generalizable foundation models for generative chemistry. Open source code: https://github.com/facebookresearch/all-atom-diffusion-transformer

Recent advances in geometric deep learning and generative modeling have enabled the design of novel proteins with a wide range of desired properties. However, current state-of-the-art approaches are typically restricted to generating proteins with only static target properties, such as motifs and symmetries. In this work, we take a step towards overcoming this limitation by proposing a framework to condition structure generation on flexibility, which is crucial for key functionalities such as catalysis or molecular recognition. We first introduce BackFlip, an equivariant neural network for predicting per-residue flexibility from an input backbone structure. Relying on BackFlip, we propose FliPS, an SE(3)-equivariant conditional flow matching model that solves the inverse problem, that is, generating backbones that display a target flexibility profile. In our experiments, we show that FliPS is able to generate novel and diverse protein backbones with the desired flexibility, verified by Molecular Dynamics (MD) simulations.

We present Mechanistic PDE Networks -- a model for discovery of governing *partial differential equations* from data. Mechanistic PDE Networks represent spatiotemporal data as space-time dependent *linear* partial differential equations in neural network hidden representations. The represented PDEs are then solved and decoded for specific tasks. The learned PDE representations naturally express the spatiotemporal dynamics in data in neural network hidden space, enabling increased modeling power. Solving the PDE representations in a compute and memory-efficient way, however, is a significant challenge. We develop a native, GPU-capable, parallel, sparse and differentiable multigrid solver specialized for linear partial differential equations that acts as a module in Mechanistic PDE Networks. Leveraging the PDE solver we propose a discovery architecture that can discovers nonlinear PDEs in complex settings, while being robust to noise. We validate PDE discovery on a number of PDEs including reaction-diffusion and Navier-Stokes equations.

We present PDE-Controller, a framework that enables large language models (LLMs) to control systems governed by partial differential equations (PDEs). Traditional LLMs have excelled in commonsense reasoning but fall short in rigorous logical reasoning. While recent AI-for-math has made strides in pure mathematics, areas of applied mathematics, particularly PDEs, remain underexplored despite their significant real-world applications. Our approach enables LLMs to transform informal natural language instructions into formal specifications, and then execute reasoning and planning steps to improve the utility of PDE control. We build a holistic solution comprising datasets (both human-written cases and 2 million synthetic samples), math-reasoning models, and novel evaluation metrics, all of which require significant effort. Our PDE-Controller significantly outperforms the latest open-source and GPT models in reasoning, autoformalization, and program synthesis, achieving up to a 62% improvement in utility gain for PDE control. By bridging the gap between language generation and PDE systems, we demonstrate the potential of LLMs in addressing complex scientific and engineering challenges. We promise to release all data, model checkpoints, and code upon acceptance.

Autoregressive surrogate models (or *emulators*) of spatiotemporal systems provide an avenue for fast, approximate predictions, with broad applications across science and engineering. At inference time however, these models are generally unable to provide predictions over long time rollouts due to accumulation of errors leading to diverging trajectories. In essence, emulators operate out of distribution, and controlling the online distribution quickly becomes intractable in large-scale settings. To address this fundamental issue, and focusing on time-stationary systems admitting an invariant measure, we leverage diffusion models to obtain an implicit estimator of the score of this invariant measure. We show that this model of the score function can be used to stabilize autoregressive emulator rollouts by applying on-the-fly denoising during inference, a process we call *thermalization*. Thermalizing an emulator rollout is shown to extend the time horizon of stable predictions by two orders of magnitude in complex systems exhibiting turbulent and chaotic behavior, opening up a novel application of diffusion models in the context of neural emulation.

Most existing 3D Gaussian Splatting (3DGS) compression schemes focus on producing compact 3DGS representation via implicit data embedding. They have long encoding and decoding times and highly customized data format, making it difficult for widespread deployment. This paper presents a new 3DGS compression framework called HybridGS, which takes advantage of both compact generation and standardized point cloud data encoding. HybridGS first generates compact and explicit 3DGS data. A dual-channel sparse representation is introduced to supervise the primitive position and feature bit depth. It then utilizes a canonical point cloud encoder to carry out further data compression and form standard output bitstreams. A simple and effective rate control scheme is proposed to pivot the interpretable data compression scheme. HybridGS does not include any modules aimed at improving 3DGS quality during generation. But experiment results show that it still provides comparable reconstruction performance against state-of-the-art methods, with evidently faster encoding and decoding speed. The code is publicly available at https://github.com/Qi-Yangsjtu/HybridGS .

Neural PDE surrogates can improve the cost-accuracy tradeoff of classical solvers, but often generalize poorly to new initial conditions and accumulate errors over time. Physical and symmetry constraints have shown promise in closing this performance gap, but existing techniques for imposing these inductive biases are incompatible with the staggered grids commonly used in computational fluid dynamics. Here we introduce novel input and output layers that respect physical laws and symmetries on the staggered grids, and for the first time systematically investigate how these constraints, individually and in combination, affect the accuracy of PDE surrogates. We focus on two challenging problems: shallow water equations with closed boundaries and decaying incompressible turbulence. Compared to strong baselines, symmetries and physical constraints consistently improve performance across tasks, architectures, autoregressive prediction steps, accuracy measures, and network sizes. Symmetries are more effective than physical constraints, but surrogates with both performed best, even compared to baselines with data augmentation or pushforward training, while themselves benefiting from the pushforward trick. Doubly-constrained surrogates also generalize better to initial conditions and durations beyond the range of the training data, and more accurately predict real-world ocean currents.

We address the problem of predicting the next states of a dynamical system governed by *unknown* temporal partial differential equations (PDEs) using only a short trajectory. While standard transformers provide a natural black-box solution to this task, the presence of a well-structured evolution operator in the data suggests a more tailored and efficient approach. Specifically, when the PDE is fully known, classical numerical solvers can evolve the state accurately with only a few parameters. Building on this observation, we introduce DISCO, a model that uses a large hypernetwork to process a short trajectory and generate the parameters of a much smaller operator network, which then predicts the next states through time integration. Our framework decouples dynamics estimation -- i.e., DISCovering an evolution Operator from a short trajectory -- from state prediction -- i.e., evolving this operator. Experiments show that pretraining our model on diverse physics datasets achieves state-of-the-art performance while requiring significantly fewer epochs. Moreover, it generalizes well to unseen initial conditions and remains competitive when fine-tuned on downstream tasks.

Hierarchical clustering is a widely used method for unsupervised learning with numerous applications. However, in the application of modern algorithms, the datasets studied are usually large and dynamic. If the hierarchical clustering is sensitive to small perturbations of the dataset, the usability of the algorithm will be greatly reduced. In this paper, we focus on the hierarchical $k$ -median clustering problem, which bridges hierarchical and centroid-based clustering while offering theoretical appeal, practical utility, and improved interpretability. We analyze the average sensitivity of algorithms for this problem by measuring the expected change in the output when a random data point is deleted. We propose an efficient algorithm for hierarchical $k$-median clustering and theoretically prove its low average sensitivity and high clustering quality. Additionally, we show that single linkage clustering and a deterministic variant of the CLNSS algorithm exhibit high average sensitivity, making them less stable. Finally, we validate the robustness and effectiveness of our algorithm through experiments.

Most successful applications of deep learning involve similar training and test conditions. However, tasks such as biological sequence design involve searching for sequences that improve desirable properties beyond previously known values, which requires novel hypotheses that \emph{extrapolate} beyond training data. In these settings, extrapolation may be achieved by using random search methods such as Markov chain Monte Carlo (MCMC), which, given an initial state, sample local transformations to approximate a target density that rewards states with the desired properties. However, even with a well-designed proposal, MCMC may struggle to explore large structured state spaces efficiently. Rather than relying on stochastic search, it would be desirable to have a model that greedily optimizes the properties of interest, successfully extrapolating in as few steps as possible. We propose to learn such a model from the Markov chains resulting from MCMC search. Specifically, our approach uses selected states from Markov chains as a source of training data for an autoregressive model, which is then able to efficiently generate novel sequences that extrapolate along the sequence-level properties of interest. The proposed approach is validated on three problems: protein sequence design, text sentiment control, and text anonymization. We find that the autoregressive model can extrapolate as well or better than MCMC, but with the additional benefits of scalability and significantly higher sample efficiency.

Physics-informed neural networks (PINNs) aim to constrain the outputs and gradients of deep learning models to satisfy specified governing physics equations, which have demonstrated significant potential for solving partial differential equations (PDEs). Although existing PINN methods have achieved pleasing performance, they always treat both easy and hard sample points indiscriminately, especially ones in the physical boundaries. This easily causes the PINN model to fall into undesirable local minima and unstable learning, thereby resulting in an Unbalanced Prediction Problem (UPP). To deal with this daunting problem, we propose a novel framework named Cognitive Physical Informed Neural Network (CoPINN) that imitates the human cognitive learning manner from easy to hard. Specifically, we first employ separable subnetworks to encode independent one-dimensional coordinates and apply an aggregation scheme to generate multi-dimensional predicted physical variables. Then, during the training phase, we dynamically evaluate the difficulty of each sample according to the gradient of the PDE residuals. Finally, we propose a cognitive training scheduler to progressively optimize the entire sampling regions from easy to hard, thereby embracing robustness and generalization against predicting physical boundary regions. Extensive experiments demonstrate that our CoPINN achieves state-of-the-art performance, particularly significantly reducing prediction errors in stubborn regions.

Many generative applications, such as synthesis-based 3D molecular design, involve constructing compositional objects with continuous features. Here, we introduce Compositional Generative Flows (CGFlow), a novel framework that extends flow matching to generate objects in compositional steps while modeling continuous states. Our key insight is that modeling compositional state transitions can be formulated as a straightforward extension of the flow matching interpolation process. We further build upon the theoretical foundations of generative flow networks (GFlowNets), enabling reward-guided sampling of compositional structures. We apply CGFlow to synthesizable drug design by jointly designing the molecule's synthetic pathway with its 3D binding pose. Our approach achieves state-of-the-art binding affinity and synthesizability on all 15 targets from the LIT-PCBA benchmark, and 4.2x improvement in sampling efficiency compared to 2D synthesis-based baseline. To our best knowledge, our method is also the first to achieve state of-art-performance in both Vina Dock (-9.42) and AiZynth success rate (36.1\%) on the CrossDocked2020 benchmark.

Neural operators generalize neural networks to learn mappings between function spaces from data. They are commonly used to learn solution operators of parametric partial differential equations (PDEs) or propagators of time-dependent PDEs. However, to make them useful in high-stakes simulation scenarios, their inherent predictive error must be quantified reliably. We introduce LUNO, a novel framework for approximate Bayesian uncertainty quantification in trained neural operators. Our approach leverages model linearization to push (Gaussian) weight-space uncertainty forward to the neural operator's predictions. We show that this can be interpreted as a probabilistic version of the concept of currying from functional programming, yielding a function-valued (Gaussian) random process belief. Our framework provides a practical yet theoretically sound way to apply existing Bayesian deep learning methods such as the linearized Laplace approximation to neural operators. Just as the underlying neural operator, our approach is resolution-agnostic by design. The method adds minimal prediction overhead, can be applied post-hoc without retraining the network, and scales to large models and datasets. We evaluate these aspects in a case study on Fourier neural operators.

The cellular Potts model (CPM) is a powerful computational method for simulating collective spatiotemporal dynamics of biological cells. To drive the dynamics, CPMs rely on physics-inspired Hamiltonians. However, as first principles remain elusive in biology, these Hamiltonians only approximate the full complexity of real multicellular systems. To address this limitation, we propose NeuralCPM, a more expressive cellular Potts model that can be trained directly on observational data. At the core of NeuralCPM lies the Neural Hamiltonian, a neural network architecture that respects universal symmetries in collective cellular dynamics. Moreover, this approach enables seamless integration of domain knowledge by combining known biological mechanisms and the expressive Neural Hamiltonian into a hybrid model. Our evaluation with synthetic and real-world multicellular systems demonstrates that NeuralCPM is able to model cellular dynamics that cannot be accounted for by traditional analytical Hamiltonians.

Current generative models for drug discovery primarily use molecular docking as an oracle to guide the generation of active compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show real-world experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. To address this challenge, we propose Multi-Fidelity Latent space Active Learning (MF-LAL), a generative modeling framework that integrates a set of oracles with varying cost-accuracy tradeoffs. Using active learning, we train a surrogate model for each oracle and use these surrogates to guide generation of compounds with high predicted activity. Unlike previous approaches that separately learn the surrogate model and generative model, MF-LAL combines the generative and multi-fidelity surrogate models into a single framework, allowing for more accurate activity prediction and higher quality samples. Our experiments on two disease-relevant proteins show that MF-LAL produces compounds with significantly better binding free energy scores than other single and multi-fidelity approaches (~50% improvement in mean binding free energy score). The code is available at https://github.com/Rose-STL-Lab/MF-LAL.

Large language model (LLM) agents are increasingly capable of autonomously conducting cyberattacks, posing significant threats to existing applications. This growing risk highlights the urgent need for a real-world benchmark to evaluate the ability of LLM agents to exploit web application vulnerabilities. However, existing benchmarks fall short as they are limited to abstracted Capture-the-Flag competitions or lack comprehensive coverage. Building a benchmark for real-world vulnerabilities involves both specialized exper- tise to reproduce exploits and a systematic approach to evaluating unpredictable attacks. To address this challenge, we introduce CVE-Bench, a real-world cybersecurity benchmark based on critical-severity Common Vulnerabilities and Exposures. In CVE-Bench, we design a sandbox framework that enables LLM agents to exploit vulnerable web applications in scenarios that mimic real-world conditions, while also providing effective evaluation of their exploits. Our experiments show that the state-of-the-art agent framework can exploit up to 13% of the vulnerabilities.

We introduce PDE-Transformer, an improved transformer-based architecture for surrogate modeling of physics simulations on regular grids. We combine recent architectural improvements of diffusion transformers with adjustments specific for large-scale simulations to yield a more scalable and versatile general-purpose transformer architecture, which can be used as the backbone for building large-scale foundation models in physical sciences. We demonstrate that our proposed architecture outperforms state-of-the-art transformer architectures for computer vision on a large dataset of 16 different types of PDEs. We propose to embed different physical channels individually as spatio-temporal tokens, which interact via channel-wise self-attention. This helps to maintain a consistent information density of tokens when learning multiple types of PDEs simultaneously. We demonstrate that our pre-trained models achieve improved performance on several challenging downstream tasks compared to training from scratch and also beat other foundation model architectures for physics simulations. Our source code is available at https://github.com/tum-pbs/pde-transformer.