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Applications · Chemistry, Physics, and Earth Sciences

Zhichao Han, Mengyi Chen, Qianxiao Li

Accurately modeling the macroscopic dynamics of high-dimensional microscopic systems is of broad interest across the sciences. Many data-driven approaches learn a low-dimensional latent state through an autoencoder trained for pointwise input reconstruction. These methods typically assume a fixed ordering of microscopic degrees of freedom in the input. However, in many settings such as particle systems the microscopic state is inherently unordered. This motivates an autoencoder framework that learns permutation-invariant latent representations. To this end, we adopt a permutation-invariant encoder and design the decoder to reconstruct the mass distribution centered at the observed points rather than per-sample reconstruction. We then jointly learn the macroscopic dynamics of the observables together with the latent states. We demonstrate the effectiveness and robustness of the proposed method across a range of microscopic settings, including learning the energy in interacting particle systems, predicting mixing dynamics in Lennard–Jones fluids, and modeling the stretching dynamics from videos of a more realistic polymer system.

Applications · Chemistry, Physics, and Earth Sciences

Sirui Lu, Zhijing Jin, Terry Zhang, Pavel Kos, Juan Cirac, Bernhard Schölkopf

Large Language Models (LLMs) are rapidly advancing across diverse domains, yet their application in theoretical physics remains inadequate. While current models show competence in mathematical reasoning and code generation, we identify critical gaps in physical intuition, constraint satisfaction, and reliable reasoning that cannot be addressed through prompting alone. Physics demands approximation judgment, symmetry exploitation, and physical grounding that require AI agents specifically trained on physics reasoning patterns and equipped with physics-aware verification tools. We argue that LLM would require such domain-specialized training and tooling to be useful in real-world for physics research. We envision physics-specialized AI agents that seamlessly handle multimodal data, propose physically consistent hypotheses, and autonomously verify theoretical results. Realizing this vision requires developing physics-specific training datasets, reward signals that capture physical reasoning quality, and verification frameworks encoding fundamental principles. We call for collaborative efforts between physics and AI communities to build the specialized infrastructure necessary for AI-driven scientific discovery.

Applications · Chemistry, Physics, and Earth Sciences

Amir Bazzi, Ramy Nemer, Alves José, Elie Hachem

Learning-based surrogates for partial differential equations have recently matched the accuracy of classical solvers while achieving orders-of-magnitude speedups, predominantly in fluid settings and structured geometries. In contrast, robust surrogates for deformable solids remain underexplored, despite the presence of nonlinear elasticity, plasticity, and transient behavior that challenge standard architectures. We introduce a multigrid graph neural network for solid mechanics that couples an *encoder-processor-decoder* backbone with a physics-informed coarsening strategy. Instead of downsampling via geometric heuristics, our method scores nodes using a residual-based measure of local physical activity and preferentially retains regions of high strain or stress concentration, allocating multiscale capacity where it is most needed. This preserves long-range interactions through hierarchical message passing while improving stability over long rollouts. We evaluate on multiple datasets covering linear, nonlinear, and transient regimes, and observe consistent gains in accuracy and rollout stability compared to standard sampling baselines. Our results highlight the importance of physics-informed coarsening for scalable surrogate modeling in solid mechanics.

Applications · Chemistry, Physics, and Earth Sciences

Maksim Zhdanov, Ana Lucic, Max Welling, Jan-Willem van de Meent

We introduce \textsc{Mosaic}, a probabilistic weather forecasting model that addresses two sources of spectral degradation in ML-based weather prediction: training to predict the ensemble mean deterministically and compressive encoding creating an information bottleneck. \textsc{Mosaic} combines learned functional perturbations for ensemble forecasting with block-sparse attention, a hardware-aligned formulation that shares keys and values across spatially adjacent queries, enabling each block to dynamically attend to the most relevant regions. By capturing arbitrarily long-range dependencies at linear cost, \textsc{Mosaic} processes high-resolution weather data without compression. On IFS HRES data, \textsc{Mosaic} at 1.5° resolution matches or outperforms models trained on 0.25° data, with individual ensemble members exhibiting near-perfect spectral alignment across all resolved frequencies.

Applications · Chemistry, Physics, and Earth Sciences

Michael McCabe, Payel Mukhopadhyay, Tanya Marwah, Bruno Régaldo-Saint Blancard, François Rozet, Cristiana Diaconu, Lucas Meyer, Kaze Wong, Hadi Sotoudeh, Alberto Bietti 等

Foundation models have transformed machine learning for language and vision, but achieving comparable impact in physical simulation remains a challenge. Data heterogeneity and unstable long-term dynamics inhibit learning from sufficiently diverse dynamics, while varying resolutions and dimensionalities challenge efficient training on modern hardware. Through empirical and theoretical analysis, we incorporate new approaches to mitigate these obstacles, including a harmonic-analysis–based stabilization method, load-balanced distributed 2D-3D training strategies, and compute-adaptive tokenization. Using these tools, we develop \Walrus, a transformer-based foundation model developed primarily for fluid-like continuum dynamics. \Walrus\ is pretrained on nineteen diverse scenarios spanning astrophysics, geoscience, rheology, plasma physics, acoustics, and classical fluids. Experiments show that \Walrus\ outperforms prior foundation models on both short- and long-term prediction horizons on downstream tasks and across the breadth of pretraining data, while ablation studies confirm the value of our contributions to forecast stability, training throughput, and transfer performance over conventional approaches.

Applications · Chemistry, Physics, and Earth Sciences

Louis Serrano, Rudy Morel, Jiequn Han, Edouard Oyallon, Shirley Ho

Neural operators have shown promise in learning solution maps of partial differential equations (PDEs), but they often struggle to generalize when test inputs lie outside the training distribution, such as novel initial conditions, unseen PDE coefficients or unseen physics. Prior works address this limitation with large scale multi physics pretraining followed by fine tuning, but this still requires examples from the new dynamics, falling short of true zero shot generalization. In this work, we propose a method to enhance generalization at test-time, i.e, without modifying pretrained weights.Building on DISCO, which provides a dictionary of neural operators trained across different dynamics, we introduce a neural operator splitting strategy that, at test time, searches over compositions of training operators to approximate unseen dynamics. On challenging out-of-distribution tasks including parameter extrapolation and novel combinations of physics phenomena, our approach achieves state-of-the-art zero shot generalization results, while being able to recover the underlying PDE parameters. These results underscore test-time computation as a key avenue for building flexible, compositional, and generalizable neural operators.

Applications · Chemistry, Physics, and Earth Sciences

danyang peng, Yang Chen, Yunlong Zhou, Xiaotong Yuan

Data Assimilation (DA) aims to integrate observations with model forecasts to estimate the state of dynamical systems. Despite the widespread application of diffusion-based assimilation methods, they remain constrained by the high dimensionality of atmospheric states and the reliance on imperfect state-observation mappings. This leaves regions lacking observations spatially unconstrained, leading to severe error accumulation and physical inconsistency.. In this paper, we propose LoPhyDA, a diffusion assimilation algorithm dual-guided by low-rank tensor and physical gradients. By leveraging the low-rank property of meteorological field, we employ tensor completion to exploit spatial continuity and dynamic correlations, reconstructing a globally informative dense field from sparse observations to serve as a global prior. This approach mitigates the information deficit inherent in sparse settings. The framework further incorporates physical constraints into the iterative denoising process, utilizing Partial Differential Equation (PDE) residual gradients to rectify the generative trajectory in real-time. Experimental results demonstrate that LoPhyDA outperforms state-of-the-art generative assimilation models in global weather prediction. It achieves robust and physically consistent assimilation, significantly reducing error accumulation in regions lacking observations.

Applications · Chemistry, Physics, and Earth Sciences

Yunlong Zhou, Chen Zhao, danyang peng, Fanfan Ji, Xiaotong Yuan

Accurate precipitation nowcasting is vital for disaster mitigation, but deep learning methods suffer a key trade-off: regression models produce over-smoothed, spectrally decaying predictions that blur convective details and violate turbulence power laws; diffusion models generate realistic yet unanchored hallucinations lacking physical grounding. We propose Spectral-Decoupled Iterative Refinement (SDIR), a deterministic framework that reformulates nowcasting as progressive frequency-decoupled refinement. SDIR first extracts a stable low-frequency synoptic skeleton, then iteratively refines high-frequency textures under physical constraints, eliminating both blurring and hallucinations. It features a dual-path design: the Synoptic Frequency-Guided Former (SFG-Former) with Scale-Adaptive Transformers for global structure, and the Fourier Residual Refiner (FR-Refiner) with Scale-Conditioned Fourier Neural Operators for fine residuals. A Physically-Consistent Power Spectral Density (PCPSD) loss with dynamic masking enforces turbulence-consistent spectral distribution. Experiments on three benchmarks show SDIR significantly outperforms SOTA in spatial accuracy while achieving spectral fidelity competitive with diffusion-based methods, enabling reliable high-resolution operational nowcasting.

Applications · Chemistry, Physics, and Earth Sciences

Xianwei Zou, Sheikh Md Shakeel Hassan, Arthur Feeney, Aparna Chandramowlishwaran

Reconstructing spatiotemporal fields from partial observations is fundamental to scientific inference, from inferring atmospheric states from satellite data to recovering fluid states from imaging. When observations are incomplete, the inverse problem is fundamentally ill-posed: even when the underlying PDE dynamics are Markovian in the full state, partial observation operators induce a non-Markovian posterior that cannot be resolved from a single timestep. We propose a history-bootstrapped autoregressive flow matching (HB-ARFM) for spatiotemporal inverse reconstruction under partial observability. Observation history bootstraps the initial reconstruction via conditional flow matching, resolving ambiguities. The same conditional transport model is then applied autoregressively, conditioning on both new observations and past predictions to propagate the reconstruction forward in time. We evaluate the method on boiling dynamics reconstruction, recovering full velocity and temperature fields from interface geometry and motion. Across two inverse tasks with varying observation sparsity, HB-ARFM produces physically and temporally valid reconstructions where other models fail.

Applications · Chemistry, Physics, and Earth Sciences

Ziyi Yang, Zitong Tian, Yinjun Jia, Tianyi Zhang, Jiqing Zheng, Hao Wang, Yubu Su, Juncai He, Lei Liu, Yanyan Lan

D-peptide binders targeting L-proteins have promising therapeutic potential. Despite rapid advances in machine learning-based target-conditioned peptide design, generating D-peptide binders remains largely unexplored. In this work, we show that by injecting axial features to E(3)-equivariant (polar) vector features, it is feasible to achieve cross-chirality generalization from homo-chiral (L-L) training data to hetero-chiral (D-L) design tasks. By implementing this method within a latent diffusion model, we achieved D-peptide binder design that not only outperforms existing tools in *in silico* benchmarks, but also demonstrates efficacy in wet-lab validation. To our knowledge, our approach represents the first experimentally validated AI generative model for the *de novo* design of D-peptide binders, offering new perspectives on handling chirality in protein design.

Applications · Chemistry, Physics, and Earth Sciences

Thomas Savary, François Rozet, Gilles Louppe

Bayesian filtering is a well-known problem that aims to estimate plausible states of a dynamical system from observations. Among existing approaches to solve this problem, particles filters are theoretically exact for non-linear dynamics and observations, but suffer from poor scalability in high dimensions. In this work, we show that diffusion-based emulators of dynamical systems can be used to implement, without additional training, an optimal variant of particle filters that has remained largely unexplored due to implementation challenges with classical numerical solvers. Experiments on nonlinear chaotic systems, including atmospheric dynamics, demonstrate that the proposed approach successfully scales particle filtering to high-dimensional settings.

Applications · Chemistry, Physics, and Earth Sciences

Salva Ruhling Cachay, Duncan Watson-Parris, Rose Yu

Global weather forecasting has recently been revolutionized by AI, outperforming traditional physics-based ensembles. However, these state-of-the-art (SOTA) models rely on massive computational resources and increasingly specialized architectures, creating a high barrier to entry. In this work, we demonstrate that such complexity is not a prerequisite for SOTA performance. We introduce U-Cast, a streamlined probabilistic forecaster based on a standard U-Net, trained with Monte Carlo Dropout and the Muon optimizer. By leveraging a novel curriculum—deterministic pre-training followed by probabilistic fine-tuning on the Continuous Ranked Probability Score (CRPS)—our model achieves performance on par with or exceeding GenCast (e.g., up to 15\% CRPS improvement on short-range winds) while reducing training and/or inference compute by an order of magnitude compared to leading baselines. Our $1^\circ$ model trains in less than 15 H200 GPU-days and generates a 60-step forecast in just 12 seconds, suggesting a "Bitter Lesson" for AI weather forecasting: scalable, general-purpose architectures can outperform complex domain-specific designs.

Applications · Chemistry, Physics, and Earth Sciences

Ruiqi Shu, Xiaohui Zhong, Mengyao Fang, Ruijian Gou, Tianrun Gao, Hao Li, Xiaomeng Huang

Global ocean modeling is vital for climate science but struggles to balance computational efficiency with accuracy. Traditional numerical solvers are accurate but computationally expensive, while pure deep learning approaches, though fast, often lack physical consistency and long-term stability. To address this, we introduce HybridOM, a framework integrating a lightweight, differentiable numerical solver as a skeleton to enforce physical laws, with a neural network as the flesh to correct subgrid-scale dynamics. To enable efficient high-resolution modeling, we further introduce a physics-informed regional downscaling mechanism based on flux gating. This design achieves the inference efficiency of AI-based methods while preserving the accuracy and robustness of physical models. Extensive experiments on the GLORYS12V1 and OceanBench dataset validate HybridOM's performance in two distinct regimes: long-term subseasonal-to-seasonal simulation and short-term operational forecasting coupled with the FuXi-2.0 weather model. Results demonstrate that HybridOM achieves state-of-the-art accuracy while maintaining physical consistency, offering a robust solution for next-generation ocean digital twins.

Applications · Chemistry, Physics, and Earth Sciences

Yuxuan Bao, Jan Zajac, Megan Powers, Venkat Raman, J. Nathan Kutz

Bridging the sim2real gap between computationally inexpensive models and complex physical systems remains a central challenge in machine learning applications to engineering problems, particularly in multi-scale settings where reduced-order models typically capture only dominant dynamics. In this work, we present Cheap2Rich, a multi-scale data assimilation framework that reconstructs high-fidelity state spaces from sparse sensor histories by combining a fast low-fidelity prior with learned, interpretable discrepancy corrections. We demonstrate the performance on rotating detonation engines (RDEs), a challenging class of systems that couple detonation-front propagation with injector-driven unsteadiness, mixing, and stiff chemistry across disparate scales. Our approach successfully reconstructs high-fidelity RDE states from sparse measurements while isolating physically meaningful discrepancy dynamics associated with injector-driven effects. The results highlight a general multi-fidelity framework for data assimilation and system identification in complex multi-scale systems, enabling rapid design exploration and real-time monitoring and control while providing interpretable discrepancy dynamics. Anonymous code is available at: anonymous.4open.science/r/Cheap2Rich-4C71.

Applications · Chemistry, Physics, and Earth Sciences

Kiyoung Seong, Sungsoo Ahn, Sehui Han, Changyoung Park

Crystal modeling spans a family of conditional and unconditional generation tasks across different modalities, including crystal structure prediction (CSP) and *de novo* generation (DNG). While recent deep generative models have shown promising performance, they remain largely task-specific, lacking a unified framework that shares crystal representations across different generation tasks. To address this limitation, we propose *Multimodal Crystal Flow (MCFlow)*, a unified multimodal flow model that realizes multiple crystal generation tasks as distinct inference trajectories via independent time variables for atom types and crystal structures. To enable multimodal flow in a standard transformer model, we introduce a composition- and symmetry-aware atom ordering with hierarchical permutation augmentation, injecting strong compositional and crystallographic priors without explicit structural templates. Experiments on the MP-20 and MPTS-52 benchmarks show that MCFlow achieves competitive performance against task-specific baselines across multiple crystal generation tasks. Our code and inference trajectories are available at [https://anonymous.4open.science/r/mcflow-46E4](https://anonymous.4open.science/r/mcflow-46E4).

Applications · Chemistry, Physics, and Earth Sciences

Chenghao Jia, Mengdi Liu, Hong Chang, Shiguang Shan, Xilin Chen

Elucidating molecular structures from spectra is a foundational problem in chemical and materials characterization, yet remains challenging due to spectral ambiguity and the vast molecular space. Although recent diffusion-based generators show strong promise for spectra-conditioned elucidation, existing methods struggle to learn robust spectra-structure relationships from limited paired data when relying solely on global spectral representation. Moreover, the repeated full sampling inference strategy incurs substantial computation overhead. To address these limitations, we propose MAST, a Motif-Augmented diffusion framework with Search Tree, for joint 2D-3D spectroscopic molecular structure elucidation. MAST introduces explicit, interpretable motif priors as intermediate evidences throughout denoising, reducing conditional ambiguity and facilitating spectra-conditioned optimization. We further cast diffusion sampling as reward-guided tree search to prioritize high-reward denoising trajectories, yielding a compact set of spectra-consistent candidates under limited budgets. On the QM9S multi-spectra benchmark, MAST achieves 94.89% exact recovery and improves 3D fidelity, while preserving high chemical validity and stability.

Applications · Chemistry, Physics, and Earth Sciences

Haiyang Yu, Yuchao Lin, Xuan Zhang, Xiaofeng Qian, Shuiwang Ji

We consider the task of predicting Hamiltonian matrices to accelerate electronic structure calculations, which plays an important role in physics, chemistry, and materials science. Motivated by the inherent relationship between the off-diagonal blocks of the Hamiltonian matrix and the SO(2) local frame, we propose a novel and efficient network, called QHNetV2, that achieves global SO(3) equivariance without the costly SO(3) Clebsch–Gordan tensor products. This is achieved by introducing a set of new efficient and powerful SO(2)-equivariant operations and performing all off-diagonal feature updates and message passing within SO(2) local frames, thereby eliminating the need of SO(3) tensor products. Moreover, a continuous SO(2) tensor product is performed within the SO(2) local frame at each node to fuse node features. Extensive experiments on the large QH9 and MD17 datasets demonstrate that our model achieves superior performance across a wide range of molecular structures and trajectories, highlighting its strong generalization capability. The proposed SO(2) operations on SO(2) local frames offer a promising direction for scalable and symmetry-aware learning of electronic structures.

Applications · Chemistry, Physics, and Earth Sciences

Sum Kyun Song, Bong Gyun Shin, JaeYong Lee

Discovering governing differential equations from observational data is a fundamental challenge in scientific machine learning. Existing symbolic regression approaches rely primarily on quantitative metrics; however, real-world differential equation modeling also requires incorporating domain knowledge to ensure physical plausibility. To address this gap, we propose DoLQ, a method for discovering ordinary differential equations with LLM-based qualitative and quantitative evaluation. DoLQ employs a multi-agent architecture: a Sampler Agent proposes dynamic system candidates, a Parameter Optimizer refines equations for accuracy, and a Scientist Agent leverages an LLM to conduct both qualitative and quantitative evaluations and synthesize their results to iteratively guide the search. Experiments on multi-dimensional ordinary differential equation benchmarks demonstrate that DoLQ achieves superior performance compared to existing methods, not only attaining higher success rates but also more accurately recovering the correct symbolic terms of ground truth equations. Our code is available at https://anonymous.4open.science/r/DoLQ/README.md.

Applications · Chemistry, Physics, and Earth Sciences

Xinyu Pang, (Andrew) Zhanke Zhou, Xuan Li, Fangrui Lv, Shanshan Wei, Sen Cui, Bo Han, Changshui Zhang

Symbolic regression (SR) stands as a cornerstone of scientific discovery, deriving mathematical expressions from observing data. Recent advances incorporate large language models (LLMs) into evolutionary optimization, typically relying on iterative refinement driven by scalar feedback (e.g., mean squared error, MSE). However, such coarse feedback lacks directional guidance for strategic lookahead and diagnostic signals to localize structural errors, thereby confining the search to a myopic trial-and-error process. Additionally, treating optimization steps as isolated episodes precludes learning from historical trajectories. Consequently, optimization often degenerates into an inefficient search with substantial computational cost. Motivated by these limitations, we propose Deliberate Evolution, an agentic framework for SR tasks that equips LLM-based candidate proposal with explicit, structured guidance. Our approach steers optimization through adaptive evolutionary operators for directional control, analytical tools for diagnostic feedback, and reflective memory for historical insight. Extensive experiments on LLM-SRBench demonstrate that our approach consistently outperforms prior baselines while using merely 40\% of the sample budget.

Applications · Chemistry, Physics, and Earth Sciences

Ye Liu, Shouyi Liu, Ding Wang, Huiyu Yang, Ruizhe DENG, Qian Li, Yuxiao Hu, Jianghang gu, Yongzheng Liu, Quanshi Zhang 等

High-fidelity vehicle aerodynamics analysis is bottlenecked by costly CFD simulations. Neural surrogates accelerate prediction but lack inverse design capabilities, while existing generative optimization methods suffer from unstable convergence and frequent engineering constraint violations. We present UniDrag, a unified framework bridging multi-field aerodynamic prediction with robust differentiable shape optimization. Given a vehicle geometry, UniDrag predicts surface pressure, volume flow fields, drag coefficient $C_d$, and a streamwise build-up profile localizing drag contributions. Our architecture combines enhanced Physics-Sliced Attention (ePSA), Gated Expert Routing, and Modality-Protected Learning to prevent negative transfer across output modalities. At deployment, the frozen surrogate enables gradient-based optimization via Free-Form Deformation with engineering constraints. We introduce Expectation-over-Transformation to prevent adversarial exploitation of surrogate fragility. We curate a large-scale dataset of 15,000 vehicle geometries spanning four body types with GPU-accelerated LBM simulations. On this benchmark, UniDrag achieves $C_d$ prediction $R^2$ of 0.937 (+7.6\% over baselines) and 13.7\% mean CFD-verified drag reduction with 100\% success rate and only 21.3~mm average displacement (0.46\% vehicle length).