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Applications · Chemistry, Physics, and Earth Sciences

Christopher Subich, Syed Husain, Leo Separovic, Jing Yang

Recent advancements in data-driven weather forecasting models have delivered deterministic models that outperform the leading operational forecast systems based on traditional, physics-based models. However, these data-driven models are typically trained with a mean squared error loss function, which causes smoothing of fine scales through a ``double penalty'' effect. We develop a simple, parameter-free modification to this loss function that avoids this problem by separating the loss attributable to decorrelation from the loss attributable to spectral amplitude errors. Fine-tuning the GraphCast model with this new loss function results in sharp deterministic weather forecasts, an increase of the model's effective resolution from 1,250km to 160km, improvements to ensemble spread, and improvements to predictions of tropical cyclone strength and surface wind extremes.

Applications · Chemistry, Physics, and Earth Sciences

Yusheng Zhao, Chi Zhang, Yuxuan Du

Characterizing the ground state properties of quantum systems is fundamental to capturing their behavior but computationally challenging. Recent advances in AI have introduced novel approaches, with diverse machine learning (ML) and deep learning (DL) models proposed for this purpose. However, the necessity and specific role of DL models in these tasks remain unclear, as prior studies often employ varied or impractical quantum resources to construct datasets, resulting in unfair comparisons. To address this, we systematically benchmark DL models against traditional ML approaches across three families of Hamiltonian, scaling up to $127$ qubits in three crucial ground-state learning tasks while enforcing equivalent quantum resource usage. Our results reveal that ML models often achieve performance comparable to or even exceeding that of DL approaches across all tasks. Furthermore, a randomization test demonstrates that measurement input features have minimal impact on DL models' prediction performance. These findings challenge the necessity of current DL models in many quantum system learning scenarios and provide valuable insights into their effective utilization.

Applications · Chemistry, Physics, and Earth Sciences

Wangzhi Zhan, Chen Jianpeng, Dongqi Fu, Dawei Zhou

Metamaterials are artificial materials that are designed to meet unseen properties in nature, such as ultra-stiffness and negative materials indices. In mechanical metamaterial design, three key modalities are typically involved, i.e., 3D topology, density condition, and mechanical property. Real-world complex application scenarios place the demanding requirements on machine learning models to consider all three modalities together. However, a comprehensive literature review indicates that most existing works only consider two modalities, e.g., predicting mechanical properties given the 3D topology or generating 3D topology given the required properties. Therefore, there is still a significant gap for the state-of-the-art machine learning models capturing the whole. Hence, we propose a unified model named UniMate, which consists of a modality alignment module and a synergetic diffusion generation module. Experiments indicate that UniMate outperforms the other baseline models in topology generation task, property prediction task, and condition confirmation task by up to 80.2%, 5.1%, and 50.2%, respectively. We open-source our proposed UniMate model and corresponding results at https://github.com/wzhan24/UniMate.

Applications · Computer Vision

Xingxing Yang, Jie Chen, Zaifeng Yang

This paper presents a novel approach to hyperspectral image (HSI) reconstruction from RGB images, addressing fundamental limitations in existing learning-based methods from a physical perspective. We discuss and aim to address the ``colorimetric dilemma": failure to consistently reproduce ground-truth RGB from predicted HSI, thereby compromising physical integrity and reliability in practical applications. To tackle this issue, we propose PhySpec, a physically consistent framework for robust HSI reconstruction. Our approach fundamentally exploits the intrinsic physical relationship between HSIs and corresponding RGBs by employing orthogonal subspace decomposition, which enables explicit estimation of camera spectral sensitivity (CSS). This ensures that our reconstructed spectra align with well-established physical principles, enhancing their reliability and fidelity. Moreover, to efficiently use internal information from test samples, we propose a self-supervised meta-auxiliary learning (MAXL) strategy that rapidly adapts the trained parameters to unseen samples using only a few gradient descent steps at test time, while simultaneously constraining the generated HSIs to accurately recover ground-truth RGB values. Thus, MAXL reinforces the physical integrity of the reconstruction process. Extensive qualitative and quantitative evaluations validate the efficacy of our proposed framework, showing superior performance compared to SOTA methods.

Applications · Chemistry, Physics, and Earth Sciences

Chenhui Xu, Dancheng Liu, Yuting Hu, Jiajie Li, Ruiyang Qin, Qingxiao Zheng, Jinjun Xiong

Physics-Informed Neural Networks (PINNs) are a kind of deep-learning-based numerical solvers for partial differential equations (PDEs). Existing PINNs often suffer from failure modes of being unable to propagate patterns of initial conditions. We discover that these failure modes are caused by the simplicity bias of neural networks and the mismatch between PDE's continuity and PINN's discrete sampling. We reveal that the State Space Model (SSM) can be a continuous-discrete articulation allowing initial condition propagation, and that simplicity bias can be eliminated by aligning a sequence of moderate granularity. Accordingly, we propose PINNMamba, a novel framework that introduces sub-sequence modeling with SSM. Experimental results show that PINNMamba can reduce errors by up to 86.3\% compared with state-of-the-art architecture. Our code is available at Supplementary Material.

Applications · Chemistry, Physics, and Earth Sciences

Cailong Hua, Sivaraman Rajaganapathy, Rebecca Slick, Joseph Vavra, Joseph Muretta, James Ervasti, Murti Salapaka

Deciphering protein folding and unfolding pathways under tension is essential for deepening our understanding of fundamental biological mechanisms. Such insights hold the promise of developing treatments for a range of debilitating and fatal conditions, including muscular disorders like Duchenne Muscular Dystrophy and neurodegenerative diseases such as Parkinson's disease. Single molecule force spectroscopy (SMFS) is a powerful technique for investigating forces involved in protein domains folding and unfolding. However, SMFS trials often involve multiple protein molecules, necessitating filtering to isolate measurements from single-molecule trials. Currently, manual visual inspection is the primary method for classifying single-molecule data; a process that is both time-consuming and requires significant expertise. Here, we both apply state-of-the-art machine learning models and present a novel deep learning model tailored to SMFS data. The proposed model employs a dual-branch fusion strategy; one branch integrates the physics of protein molecules, and the other operates independently of physical constraints. This model automates the isolation of single-molecule measurements, significantly enhancing data processing efficiency. To train and validate our approach, we developed a physics-based Monte Carlo engine to simulate force spectroscopy datasets, including trials involving single molecules, multiple molecules, and no molecules. Our model achieves state-of-the-art performance, outperforming five baseline methods on both simulated and experimental datasets. It attains nearly 100\% accuracy across all simulated datasets and an average accuracy of $79.6 \pm 5.2$\% on experimental datasets, using only $\sim$30 training samples, surpassing baseline methods by 11.4\%. Notably, even without expert annotations on experimental data, the model achieves an average accuracy of $72.0 \pm 5.9$\% when pre-trained on corresponding simulated datasets. With our deep learning approach, the time required to extract meaningful statistics from single-molecule SMFS trials is reduced from a day to under an hour. This work results in SMFS experimental datasets from four important protein molecules crucial to many biological pathways. To support further research, we have made our datasets publicly available and provided a Python-based toolbox (https://github.com/SalapakaLab-SIMBioSys/SMFS-Identification).

Applications · Robotics

Manan Tayal, Aditya Singh, Shishir Nadubettu Yadukumar, Somil Bansal

As autonomous systems become more ubiquitous in daily life, ensuring high performance with guaranteed safety is crucial. However, safety and performance could be competing objectives, which makes their co-optimization difficult. Learning-based methods, such as Constrained Reinforcement Learning (CRL), achieve strong performance but lack formal safety guarantees due to safety being enforced as soft constraints, limiting their use in safety-critical settings. Conversely, formal methods such as Hamilton-Jacobi (HJ) Reachability Analysis and Control Barrier Functions (CBFs) provide rigorous safety assurances but often neglect performance, resulting in overly conservative controllers. To bridge this gap, we formulate the co-optimization of safety and performance as a state-constrained optimal control problem, where performance objectives are encoded via a cost function and safety requirements are imposed as state constraints. We demonstrate that the resultant value function satisfies a Hamilton-Jacobi-Bellman (HJB) equation, which we approximate efficiently using a novel physics-informed machine learning framework. In addition, we introduce a conformal prediction-based verification strategy to quantify the learning errors, recovering a high-confidence safety value function, along with a probabilistic error bound on performance degradation. Through several case studies, we demonstrate the efficacy of the proposed framework in enabling scalable learning of safe and performant controllers for complex, high-dimensional autonomous systems.

Applications · Chemistry, Physics, and Earth Sciences

Henrik Schopmans, Pascal Friederich

Efficient sampling of unnormalized probability densities such as theBoltzmann distribution of molecular systems is a longstanding challenge.Next to conventional approaches like molecular dynamics or Markov chainMonte Carlo, variational approaches, such as training normalizing flows withthe reverse Kullback-Leibler divergence, have been introduced. However, suchmethods are prone to mode collapse and often do not learn to sample the fullconfigurational space. Here, we present temperature-annealed Boltzmanngenerators (TA-BG) to address this challenge. First, we demonstrate thattraining a normalizing flow with the reverse Kullback-Leibler divergence athigh temperatures is possible without mode collapse. Furthermore, weintroduce 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.

Applications · Chemistry, Physics, and Earth Sciences

Tianyi Bao, Ruizhe Zhong, Xinyu Ye, Yehui Tang, Junchi Yan

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.

Deep Learning · Foundation Models

Congcong Zhu, Xiaoyan Xu, Jiayue Han, Jingrun Chen

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}.

Applications · Chemistry, Physics, and Earth Sciences

Haorui Wang, Jeff Guo, Lingkai Kong, Rampi Ramprasad, Philippe Schwaller, Yuanqi Du, Chao Zhang

Retrosynthesis, the process of breaking down a target molecule into simpler precursors through a series of valid reactions, stands at the core of organic chemistry and drug development. Although recent machine learning (ML) research has advanced single-step retrosynthetic modeling and subsequent route searches, these solutions remain restricted by the extensive combinatorial space of possible pathways. Concurrently, large language models (LLMs) have exhibited remarkable chemical knowledge, hinting at their potential to tackle complex decision-making tasks in chemistry. In this work, we explore whether LLMs can successfully navigate the highly constrained, multi-step retrosynthesis planning problem. We introduce an efficient scheme for encoding reaction pathways and present a new route-level search strategy, moving beyond the conventional step-by-step reactant prediction. Through comprehensive evaluations, we show that our LLM-augmented approach excels at retrosynthesis planning and extends naturally to the broader challenge of synthesizable molecular design.

Optimization · Stochastic

Savelii Chezhegov, Klyukin Yaroslav, Andrei Semenov, Aleksandr Beznosikov, Alexander Gasnikov, Samuel Horváth, Martin Takac, Eduard Gorbunov

Methods with adaptive stepsizes, such as AdaGrad and Adam, are essential for training modern Deep Learning models, especially Large Language Models. Typically, the noise in the stochastic gradients is heavy-tailed for the later ones. Gradient clipping provably helps to achieve good high-probability convergence for such noises. However, despite the similarity between AdaGrad/Adam and Clip-SGD, the current understanding of the high-probability convergence of AdaGrad/Adam-type methods is limited in this case. In this work, we prove that AdaGrad/Adam (and their delayed version) can have provably bad high-probability convergence if the noise is heavy-tailed. We also show that gradient clipping fixes this issue, i.e., we derive new high-probability convergence bounds with polylogarithmic dependence on the confidence level for AdaGrad-Norm and Adam-Norm with clipping and with/without delay for smooth convex/non-convex stochastic optimization with heavy-tailed noise. We extend our results to the case of AdaGrad/Adam with delayed stepsizes. Our empirical evaluations highlight the superiority of clipped versions of AdaGrad/Adam in handling the heavy-tailed noise.

Applications · Chemistry, Physics, and Earth Sciences

Erpai Luo, Xinran Wei, Lin Huang, Yunyang Li, Han Yang, Zaishuo Xia, Zun Wang, Chang Liu, Bin Shao, Jia Zhang

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

Applications · Chemistry, Physics, and Earth Sciences

Kevin Han Huang, Ni Zhan, Elif Ertekin, Peter Orbanz, Ryan P. Adams

Incorporating group symmetries into neural networks has been a cornerstone of success in many AI-for-science applications. Diagonal groups of isometries, which describe the invariance under a simultaneous movement of multiple objects, arise naturally in many-body quantum problems. Despite their importance, diagonal groups have received relatively little attention, as they lack a natural choice of invariant maps except in special cases. We study different ways of incorporating diagonal invariance in neural network ansatze trained via variational Monte Carlo methods, and consider specifically data augmentation, group averaging and canonicalization. We show that, contrary to standard ML setups, in-training symmetrization destabilizes training and can lead to worse performance. Our theoretical and numerical results indicate that this unexpected behavior may arise from a unique computational-statistical tradeoff not found in standard ML analyses of symmetrization. Meanwhile, we demonstrate that post hoc averaging is less sensitive to such tradeoffs and emerges as a simple, flexible and effective method for improving neural network solvers.

Applications · Chemistry, Physics, and Earth Sciences

Montgomery Bohde, Mrunali Manjrekar, Runzhong Wang, Shuiwang Ji, Connor Coley

Mass spectrometry plays a fundamental role in elucidating the structures of unknown molecules and subsequent scientific discoveries. One formulation of the structure elucidation task is the conditional *de novo* generation of molecular structure given a mass spectrum. Toward a more accurate and efficient scientific discovery pipeline for small molecules, we present DiffMS, a formula-restricted encoder-decoder generative network that achieves state-of-the-art performance on this task. The encoder utilizes a transformer architecture and models mass spectra domain knowledge such as peak formulae and neutral losses, and the decoder is a discrete graph diffusion model restricted by the heavy-atom composition of a known chemical formula. To develop a robust decoder that bridges latent embeddings and molecular structures, we pretrain the diffusion decoder with fingerprint-structure pairs, which are available in virtually infinite quantities, compared to structure-spectrum pairs that number in the tens of thousands. Extensive experiments on established benchmarks show that DiffMS outperforms existing models on *de novo* molecule generation. We provide several ablations to demonstrate the effectiveness of our diffusion and pretraining approaches and show consistent performance scaling with increasing pretraining dataset size. DiffMS code is publicly available at https://github.com/coleygroup/DiffMS.

Deep Learning · Large Language Models

Xin Xu, Qiyun Xu, Tong Xiao, Tianhao Chen, Yuchen Yan, Jiaxin ZHANG, Shizhe Diao, Can Yang, Yang Wang

Large language models (LLMs) have demonstrated remarkable capabilities in solving complex reasoning tasks, particularly in mathematics. However, the domain of physics reasoning presents unique challenges that have received significantly less attention. Existing benchmarks often fall short in evaluating LLMs’ abilities on the breadth and depth of undergraduate-level physics, underscoring the need for a comprehensive evaluation. To fill this gap, we introduce UGPhysics, a large-scale and diverse benchmark specifically designed to evaluate **U**nder**G**raduate-level **Physics** (**UGPhysics**) reasoning with LLMs. UGPhysics includes 5,520 undergraduate-level physics problems in both English and Chinese across 13 subjects with seven different answer types and four distinct physics reasoning skills, all rigorously screened for data leakage. Additionally, we develop a Model-Assistant Rule-based Judgment (**MARJ**) pipeline specifically tailored for assessing physics problems, ensuring accurate evaluation. Our evaluation of 31 leading LLMs shows that the highest overall accuracy, 49.8% (achieved by OpenAI-o1-mini), emphasizes the need for models with stronger physics reasoning skills, beyond math abilities. We hope UGPhysics, along with MARJ, will drive future advancements in AI for physics reasoning. Codes and data are available at \href{https://github.com/YangLabHKUST/UGPhysics}{https://github.com/YangLabHKUST/UGPhysics}.

Applications · Chemistry, Physics, and Earth Sciences

Talal Widatalla, Richard Shuai, Brian Hie, Po-Ssu Huang

Leading deep learning-based methods for fixed-backbone protein sequence design do not model protein sidechain conformation during sequence generation despite the large role the three-dimensional arrangement of sidechain atoms play in protein conformation, stability, and overall protein function. Instead, these models implicitly reason about crucial sidechain interactions based solely on backbone geometry and amino-acid sequence. To address this, we present FAMPNN (Full-Atom MPNN), a sequence design method that explicitly models both sequence identity and sidechain conformation for each residue, where the per-token distribution of a residue’s discrete amino acid identity and its continuous sidechain conformation are learned with a combined categorical cross-entropy and diffusion loss objective. We demonstrate learning these distributions jointly is a highly synergistic task that both improves sequence recovery while achieving state-of-the-art sidechain packing. Furthermore, benefits from explicit full-atom modeling generalize from sequence recovery to practical protein design applications, such as zero-shot prediction of experimental binding and stability measurements.

Applications · Chemistry, Physics, and Earth Sciences

Qi Wang, Yuan Mi, Wang Haoyun, Yi Zhang, Ruizhi Chengze, Hongsheng Liu, Ji-Rong Wen, Hao Sun

Solving partial differential equations (PDEs) by numerical methods meet computational cost challenge for getting the accurate solution since fine grids and small time steps are required. Machine learning can accelerate this process, but struggle with weak generalizability, interpretability, and data dependency, as well as suffer in long-term prediction. To this end, we propose a PDE-embedded network with multiscale time stepping (MultiPDENet), which fuses the scheme of numerical methods and machine learning, for accelerated simulation of flows. In particular, we design a convolutional filter based on the structure of finite difference stencils with a small number of parameters to optimize, which estimates the equivalent form of spatial derivative on a coarse grid to minimize the equation's residual. A Physics Block with a 4th-order Runge-Kutta integrator at the fine time scale is established that embeds the structure of PDEs to guide the prediction. To alleviate the curse of temporal error accumulation in long-term prediction, we introduce a multiscale time integration approach, where a neural network is used to correct the prediction error at a coarse time scale. Experiments across various PDE systems, including the Navier-Stokes equations, demonstrate that MultiPDENet can accurately predict long-term spatiotemporal dynamics, even given small and incomplete training data, e.g., spatiotemporally down-sampled datasets. MultiPDENet achieves the state-of-the-art performance compared with other neural baseline models, also with clear speedup compared to classical numerical methods

Applications · Chemistry, Physics, and Earth Sciences

Fanmeng Wang, Wentao Guo, Qi Ou, Hongshuai Wang, Haitao Lin, Hongteng Xu, Zhifeng Gao

Polymer conformation generation is a critical task that enables atomic-level studies of diverse polymer materials. While significant advances have been made in designing conformation generation methods for small molecules and proteins, these methods struggle to generate polymer conformations due to their unique structural characteristics.Meanwhile, the scarcity of polymer conformation datasets further limits the progress, making this important area largely unexplored.In this work, we propose PolyConf, a pioneering tailored polymer conformation generation method that leverages hierarchical generative models to unlock new possibilities.Specifically, we decompose the polymer conformation into a series of local conformations (i.e., the conformations of its repeating units), generating these local conformations through an autoregressive model, and then generating their orientation transformations via a diffusion model to assemble them into the complete polymer conformation.Moreover, we develop the first benchmark with a high-quality polymer conformation dataset derived from molecular dynamics simulations to boost related research in this area.The comprehensive evaluation demonstrates that PolyConf consistently outperforms existing conformation generation methods, thus facilitating advancements in polymer modeling and simulation.The whole work is available at https://polyconf-icml25.github.io.

Deep Learning · Algorithms

HUAKUN LUO, Haixu Wu, Hang Zhou, Lanxiang Xing, Yichen Di, Jianmin Wang, Mingsheng Long

Although deep models have been widely explored in solving partial differential equations (PDEs), previous works are primarily limited to data only with up to tens of thousands of mesh points, far from the million-point scale required by industrial simulations that involve complex geometries. In the spirit of advancing neural PDE solvers to real industrial applications, we present Transolver++, a highly parallel and efficient neural solver that can accurately solve PDEs on million-scale geometries. Building upon previous advancements in solving PDEs by learning physical states via Transolver, Transolver++ is further equipped with an extremely optimized parallelism framework and a local adaptive mechanism to efficiently capture eidetic physical states from massive mesh points, successfully tackling the thorny challenges in computation and physics learning when scaling up input mesh size. Transolver++ increases the single-GPU input capacity to million-scale points for the first time and is capable of continuously scaling input size in linear complexity by increasing GPUs. Experimentally, Transolver++ yields 13\% relative promotion across six standard PDE benchmarks and achieves over 20\% performance gain in million-scale high-fidelity industrial simulations, whose sizes are 100$\times$ larger than previous benchmarks, covering car and 3D aircraft designs.