论文检索

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

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.

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

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.