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Applications · Chemistry, Physics, and Earth Sciences

Yuan Gao, Hao Wu, Ruiqi Shu, huanshuo dong, Fan Xu, Rui Chen, Yibo Yan, Qingsong Wen, Xuming Hu, Kun Wang 等

Accurate weather forecasts are important for disaster prevention, agricultural planning, etc. Traditional numerical weather prediction (NWP) methods offer physically interpretable high-accuracy predictions but are computationally expensive and fail to fully leverage rapidly growing historical data. In recent years, deep learning models have made significant progress in weather forecasting, but challenges remain, such as balancing global and regional high-resolution forecasts, excessive smoothing in extreme event predictions, and insufficient dynamic system modeling. To address these issues, this paper proposes a global-regional nested weather forecasting framework (OneForecast) based on graph neural networks. By combining a dynamic system perspective with multi-grid theory, we construct a multi-scale graph structure and densify the target region to capture local high-frequency features. We introduce an adaptive messaging mechanism, using dynamic gating units to deeply integrate node and edge features for more accurate extreme event forecasting. For high-resolution regional forecasts, we propose a neural nested grid method to mitigate boundary information loss. Experimental results show that OneForecast performs excellently across global to regional scales and short-term to long-term forecasts, especially in extreme event predictions. Codes link: \url{https://github.com/YuanGao-YG/OneForecast}.

Applications · Chemistry, Physics, and Earth Sciences

Cheng Huang, Pan Mu, Cong Bai, Peter Watson

Deep learning methods have made significant progress in regular rainfall forecasting, yet the more hazardous tropical cyclone (TC) rainfall has not received the same attention. While regular rainfall models can offer valuable insights for designing TC rainfall forecasting models, most existing methods suffer from cumulative errors and lack physical consistency. Additionally, these methods overlook the importance of meteorological factors in TC rainfall and their integration with the numerical weather prediction (NWP) model. To address these issues, we propose Tropical Cyclone Precipitation Diffusion (TCP-Diffusion), a multi-modal model for forecasting of TC precipitation given an existing TC in any location globally. It forecasts rainfall around the TC center for the next 12 hours at 3 hourly resolution based on past rainfall observations and multi-modal environmental variables. Adjacent residual prediction (ARP) changes the training target from the absolute rainfall value to the rainfall trend and gives our model the capability of rainfall change awareness, reducing cumulative errors and ensuring physical consistency. Considering the influence of TC-related meteorological factors and the useful information from NWP model forecasts, we propose a multi-model framework with specialized encoders to extract richer information from environmental variables and results provided by NWP models. The results of extensive experiments show that our method outperforms other DL methods and the NWP method from the European Centre for Medium-Range Weather Forecasts (ECMWF).

Applications · Chemistry, Physics, and Earth Sciences

Chaitanya Joshi, Xiang Fu, Yi-Lun Liao, Vahe Gharakhanyan, Benjamin Kurt Miller, Anuroop Sriram, Zachary Ulissi

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

Social Aspects · Security

Shuai Yuan, Hongwei Li, Rui Zhang, Hangcheng Cao, Wenbo Jiang, Tao Ni, Wenshu Fan, Qingchuan Zhao, Guowen Xu

Deep learning models employed in face recognition (FR) systems have been shown to be vulnerable to physical adversarial attacks through various modalities, including patches, projections, and infrared radiation. However, existing adversarial examples targeting FR systems often suffer from issues such as conspicuousness, limited effectiveness, and insufficient robustness. To address these challenges, we propose a novel approach for adversarial face generation, UVHat, which utilizes ultraviolet (UV) emitters mounted on a hat to enable invisible and potent attacks in black-box settings. Specifically, UVHat simulates UV light sources via video interpolation and models the positions of these light sources on a curved surface, specifically the human head in our study. To optimize attack performance, UVHat integrates a reinforcement learning-based optimization strategy, which explores a vast parameter search space, encompassing factors such as shooting distance, power, and wavelength. Extensive experimental evaluations validate that UVHat substantially improves the attack success rate in black-box settings, enabling adversarial attacks from multiple angles with enhanced robustness.

Deep Learning · Other Representation Learning

Siyuan Duan, Wenyuan Wu, Peng Hu, Zhenwen Ren, Dezhong Peng, Yuan Sun

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.

Applications · Chemistry, Physics, and Earth Sciences

Tony Shen, Seonghwan Seo, Ross Irwin, Kieran Didi, Simon Olsson, Woo Youn Kim, Martin Ester

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.

General Machine Learning · Evaluation

Shimin Zhang, Ziyuan Ye, Yinsong Yan, Zeyang Song, Yujie Wu, Jibin Wu

Determining the similarity between dynamical systems remains a long-standing challenge in both machine learning and neuroscience. Recent works based on Koopman operator theory have proven effective in analyzing dynamical similarity by examining discrepancies in the Koopman spectrum. Nevertheless, existing similarity metrics can be severely constrained when systems exhibit complex nonlinear behaviors across multiple temporal scales. In this work, we propose **KoopSTD**, a dynamical similarity measurement framework that precisely characterizes the underlying dynamics by approximating the Koopman spectrum with explicit timescale decoupling and spectral residual control. We show that KoopSTD maintains invariance under several common representation-space transformations, which ensures robust measurements across different coordinate systems. Our extensive experiments on physical and neural systems validate the effectiveness, scalability, and robustness of KoopSTD compared to existing similarity metrics. We also apply KoopSTD to explore two open-ended research questions in neuroscience and large language models, highlighting its potential to facilitate future scientific and engineering discoveries. Code is available at [link](https://github.com/ZhangShimin1/KoopSTD).

Applications · Chemistry, Physics, and Earth Sciences

Liming Shen, Liang Deng, Chongke Bi, Yu Wang, Xinhai Chen, Yueqing Wang, Jie Liu

Implicit neural representation (INR) has now been thrust into the limelight with its flexibility in high-fidelity flow field reconstruction tasks. However, the lack of standard benchmarking datasets and the grid independence assumption for INR-based methods hinder progress and adoption in real-world simulation scenarios. Moreover, naive adoptions of existing INR frameworks suffer from limited accuracy in capturing fine-scale structures and spatiotemporal dynamics. Tacking these issues, we first introduce HFR-Beach, a 5.4 TB public large-scale CFD dataset with 33,600 unsteady 2D and 3D vector fields for reconstructing high-fidelity flow fields. We further present PEINR, a physics-enhanced INR framework, to enrich the flow fields by concurrently enhancing numerical-precision and grid-resolution. Specifically, PEINR is mainly composed of physical encoding and transformer-based spatiotemporal fuser (TransSTF). Physical encoding decouples temporal and spatial components, employing Gaussian coordinate encoding and localized encoding techniques to capture the nonlinear characteristics of spatiotemporal dynamics and the stencil discretization of spatial dimensions, respectively. TransSTF fuses both spatial and temporal information via transformer for capturing long-range temporal dependencies. Qualitative and quantitative experiments and demonstrate that PEINR outperforms state-of-the-art INR-based methods in reconstruction quality.

General Machine Learning · Scalable Algorithms

Maricela Best Mckay, Avleen Kaur, Chen Greif, Brian Wetton

Natural gradient methods for PINNs have achieved state-of-the-art performance with errors several orders of magnitude smaller than those achieved by standard optimizers such as ADAM or L-BFGS. However, computing natural gradients for PINNs is prohibitively computationally costly and memory-intensive for all but small neural network architectures. We develop a randomized algorithm for natural gradient descent for PINNs that uses sketching to approximate the natural gradient descent direction. We prove that the change of coordinate Gram matrix used in a natural gradient descent update has rapidly-decaying eigenvalues for a one-layer, one-dimensional neural network and empirically demonstrate that this structure holds for four different example problems. Under this structure, our sketching algorithm is guaranteed to provide a near-optimal low-rank approximation of the Gramian. Our algorithm dramatically speeds up computation time and reduces memory overhead. Additionally, in our experiments, the sketched natural gradient outperforms the original natural gradient in terms of accuracy, often achieving an error that is an order of magnitude smaller. Training time for a network with around 5,000 parameters is reduced from several hours to under two minutes. Training can be practically scaled to large network sizes; we optimize a PINN for a network with over a million parameters within a few minutes, a task for which the full Gram matrix does not fit in memory.

Applications · Chemistry, Physics, and Earth Sciences

Peiyan Hu, Xiaowei Qian, Wenhao Deng, Rui Wang, Haodong Feng, Ruiqi Feng, Tao Zhang, Long Wei, Yue Wang, Zhi-Ming Ma 等

The application of deep learning for partial differential equation (PDE)-constrained control is gaining increasing attention. However, existing methods rarely consider safety requirements crucial in real-world applications. To address this limitation, we propose Safe Diffusion Models for PDE Control (SafeDiffCon), which introduce the uncertainty quantile as model uncertainty quantification to achieve optimal control under safety constraints through both post-training and inference phases. Firstly, our approach post-trains a pre-trained diffusion model to generate control sequences that better satisfy safety constraints while achieving improved control objectives via a reweighted diffusion loss, which incorporates the uncertainty quantile estimated using conformal prediction. Secondly, during inference, the diffusion model dynamically adjusts both its generation process and parameters through iterative guidance and fine-tuning, conditioned on control targets while simultaneously integrating the estimated uncertainty quantile. We evaluate SafeDiffCon on three control tasks: 1D Burgers' equation, 2D incompressible fluid, and controlled nuclear fusion problem. Results demonstrate that SafeDiffCon is the only method that satisfies all safety constraints, whereas other classical and deep learning baselines fail. Furthermore, while adhering to safety constraints, SafeDiffCon achieves the best control performance. The code can be found at https://github.com/AI4Science-WestlakeU/safediffcon.

Applications · Chemistry, Physics, and Earth Sciences

Tao Zhang, Zhenhai Liu, Feipeng Qi, Yongjun Jiao, Tailin Wu

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.

Applications · Computer Vision

Pierrick Leroy, Antonio Mastropietro, Marco Nurisso, Francesco Vaccarino

Face Recognition (FR) tasks have made significant progress with the advent of Deep Neural Networks, particularly through margin-based triplet losses that embed facial images into high-dimensional feature spaces. During training, these contrastive losses focus exclusively on identity information as labels. However, we observe a multiscale geometric structure emerging in the embedding space, influenced by interpretable facial (e.g., hair color) and image attributes (e.g., contrast).We propose a geometric approach to describe the dependence or invariance of FR models to these attributes and introduce a physics-inspired alignment metric. We evaluate the proposed metric on controlled, simplified models and widely used FR models fine-tuned with synthetic data for targeted attribute augmentation. Our findings reveal that the models exhibit varying degrees of invariance across different attributes, providing insight into their strengths and weaknesses and enabling deeper interpretability.Code available here: https://github.com/mantonios107/attrs-fr-embs.

Deep Learning

Shiba Biswal, Karthik Elamvazhuthi, Rishi Sonthalia

This paper investigates the use of transformers to approximate the mean-field dynamics of interacting particle systems exhibiting collective behavior. Such systems are fundamental in modeling phenomena across physics, biology, and engineering, including opinion formation, biological networks, and swarm robotics. The key characteristic of these systems is that the particles are indistinguishable, leading to permutation-equivariant dynamics. First, we empirically demonstrate that transformers are well-suited for approximating a variety of mean field models, including the Cucker-Smale model for flocking and milling, and the mean-field system for training two-layer neural networks. We validate our numerical experiments via mathematical theory. Specifically, we prove that if a finite-dimensional transformer effectively approximates the finite-dimensional vector field governing the particle system, then the $L_\infty$ distance between the \textit{expected transformer} and the infinite-dimensional mean-field vector field can be bounded by a function of the number of particles observed during training. Leveraging this result, we establish theoretical bounds on the distance between the true mean-field dynamics and those obtained using the transformer.

Applications · Chemistry, Physics, and Earth Sciences

Philipp Höllmer, Thomas Egg, Maya Martirossyan, Eric Fuemmeler, Zeren Shui, Amit Gupta, Pawan Prakash, Adrian Roitberg, Mingjie Liu, George Karypis 等

The discovery of new materials is essential for enabling technological advancements. Computational approaches for predicting novel materials must effectively learn the manifold of stable crystal structures within an infinite design space. We introduce Open Materials Generation (OMatG), a unifying framework for the generative design and discovery of inorganic crystalline materials. OMatG employs stochastic interpolants (SI) to bridge an arbitrary base distribution to the target distribution of inorganic crystals via a broad class of tunable stochastic processes, encompassing both diffusion models and flow matching as special cases. In this work, we adapt the SI framework by integrating an equivariant graph representation of crystal structures and extending it to account for periodic boundary conditions in unit cell representations. Additionally, we couple the SI flow over spatial coordinates and lattice vectors with discrete flow matching for atomic species. We benchmark OMatG's performance on two tasks: Crystal Structure Prediction (CSP) for specified compositions, and de novo generation (DNG) aimed at discovering stable, novel, and unique structures. In our ground-up implementation of OMatG, we refine and extend both CSP and DNG metrics compared to previous works. OMatG establishes a new state of the art in generative modeling for materials discovery, outperforming purely flow-based and diffusion-based implementations. These results underscore the importance of designing flexible deep learning frameworks to accelerate progress in materials science. The OMatG code is available at https://github.com/FERMat-ML/OMatG.

Deep Learning · Graph Neural Networks

Zongzhao Li, Jiacheng Cen, Bing Su, Tingyang Xu, Yu Rong, Deli Zhao, Wenbing Huang

Accurately predicting 3D structures and dynamics of physical systems is crucial in scientific applications. Existing approaches that rely on geometric Graph Neural Networks (GNNs) effectively enforce $\mathrm{E}(3)$-equivariance, but they often fail in leveraging extensive broader information. While direct application of Large Language Models (LLMs) can incorporate external knowledge, they lack the capability for spatial reasoning with guaranteed equivariance. In this paper, we propose EquiLLM, a novel framework for representing 3D physical systems that seamlessly integrates $\mathrm{E}(3)$-equivariance with LLM capabilities. Specifically, EquiLLM comprises four key components: geometry-aware prompting, an equivariant encoder, an LLM, and an equivariant adapter. Essentially, the LLM guided by the instructive prompt serves as a sophisticated invariant feature processor, while 3D directional information is exclusively handled by the equivariant encoder and adapter modules. Experimental results demonstrate that EquiLLM delivers significant improvements over previous methods across molecular dynamics simulation, human motion simulation, and antibody design, highlighting its promising generalizability.

Applications · Chemistry, Physics, and Earth Sciences

Prateek Gupta, Andrea Ferrari, Nabil Iqbal

The notion of duality -- that a given physical system can have two different mathematical descriptions -- is a key idea in modern theoretical physics. Establishing a duality in lattice statistical mechanics models requires the construction of a dual Hamiltonian and a map from the original to the dual observables. By using neural networks to parameterize these maps and introducing a loss function that penalises the difference between correlation functions in original and dual models, we formulate the process of duality discovery as an optimization problem. We numerically solve this problem and show that our framework can rediscover the celebrated Kramers-Wannier duality for the 2d Ising model, numerically reconstructing the known mapping of temperatures. We further investigate the 2d Ising model deformed by a plaquette coupling and find families of ``approximate duals''. We discuss future directions and prospects for discovering new dualities within this framework.

Deep Learning · Sequential Models, Time series

Weiwei Ye, Zhuopeng Xu, Ning Gui

Due to the dynamics of underlying physics and external influences, the uncertainty of time series often varies over time. However, existing Denoising Diffusion Probabilistic Models (DDPMs) often fail to capture this non-stationary nature, constrained by their constant variance assumption from the additive noise model (ANM). In this paper, we innovatively utilize the Location-Scale Noise Model (LSNM) to relax the fixed uncertainty assumption of ANM. A diffusion-based probabilistic forecasting framework, termed Non-stationary Diffusion (NsDiff), is designed based on LSNM that is capable of modeling the changing pattern of uncertainty. Specifically, NsDiff combines a denoising diffusion-based conditional generative model with a pre-trained conditional mean and variance estimator, enabling adaptive endpoint distribution modeling. Furthermore, we propose an uncertainty-aware noise schedule, which dynamically adjusts the noise levels to accurately reflect the data uncertainty at each step and integrates the time-varying variances into the diffusion process. Extensive experiments conducted on nine real-world and synthetic datasets demonstrate the superior performance of NsDiff compared to existing approaches. Code is available at https://github.com/wwy155/NsDiff.

Reinforcement Learning · Deep RL

Brett Barkley, David Fridovich-Keil

Dyna-style off-policy model-based reinforcement learning (DMBRL) algorithms are a family of techniques for generating synthetic state transition data and thereby enhancing the sample efficiency of off-policy RL algorithms. This paper identifies and investigates a surprising performance gap observed when applying DMBRL algorithms across different benchmark environments with proprioceptive observations. We show that, while DMBRL algorithms perform well in control tasks in OpenAI Gym, their performance can drop significantly in DeepMind Control Suite (DMC), even though these settings offer similar tasks and identical physics backends. Modern techniques designed to address several key issues that arise in these settings do not provide a consistent improvement across all environments, and overall our results show that adding synthetic rollouts to the training process --- the backbone of Dyna-style algorithms --- significantly degrades performance across most DMC environments. Our findings contribute to a deeper understanding of several fundamental challenges in model-based RL and show that, like many optimization fields, there is no free lunch when evaluating performance across diverse benchmarks in RL.

Theory · Learning Theory

Xianliang Xu, Ye Li, Zhongyi Huang

In this paper, we derive refined generalization bounds for the Deep Ritz Method (DRM) and Physics-Informed Neural Networks (PINNs). For the DRM, we focus on two prototype elliptic partial differential equations (PDEs): Poisson equation and static Schrödinger equation on the $d$-dimensional unit hypercube with the Neumann boundary condition. Furthermore, sharper generalization bounds are derived based on the localization techniques under the assumptions that the exact solutions of the PDEs lie in the Barron spaces or the general Sobolev spaces. For the PINNs, we investigate the general linear second order elliptic PDEs with Dirichlet boundary condition using the local Rademacher complexity in the multi-task learning setting. Finally, we discuss the generalization error in the setting of over-parameterization when solutions of PDEs belong to Barron space.

Deep Learning · Graph Neural Networks

Sungwon Kim, Namkyeong Lee, Yunyoung Doh, Seungmin Shin, Guimok Cho, Seung-Won Jeon, Sangkook Kim, Chanyoung Park

Mesh-based 3D static analysis methods have recently emerged as efficient alternatives to traditional computational numerical solvers, significantly reducing computational costs and runtime for various physics-based analyses. However, these methods primarily focus on surface topology and geometry, often overlooking the inherent thickness of real-world 3D objects, which exhibits high correlations and similar behavior between opposing surfaces. This limitation arises from the disconnected nature of these surfaces and the absence of internal edge connections within the mesh. In this work, we propose a novel framework, the Thickness-aware E(3)-Equivariant 3D Mesh Neural Network (T-EMNN), that effectively integrates the thickness of 3D objects while maintaining the computational efficiency of surface meshes. Additionally, we introduce data-driven coordinates that encode spatial information while preserving E(3)-equivariance or invariance properties, ensuring consistent and robust analysis. Evaluations on a real-world industrial dataset demonstrate the superior performance of T-EMNN in accurately predicting node-level 3D deformations, effectively capturing thickness effects while maintaining computational efficiency.