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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

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.

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.

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 · 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.

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.

Applications · Chemistry, Physics, and Earth Sciences

Shuqi Lu, Xiaohong Ji, Bohang Zhang, Lin Yao, Siyuan Liu, Zhifeng Gao, Linfeng Zhang, Guolin Ke

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components:(1)grid-based space discretization; (2)grid sampling/merging; and (3)efficient 3D positional encoding.Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

Applications · Chemistry, Physics, and Earth Sciences

Chen Hao Xia, Manasa Kaniselvan, Alexandros Nikolaos Ziogas, Marko Mladenovic, Rayen Mahjoub, Alexander Maeder, Mathieu Luisier

Graph neural networks (GNNs) have shown promise in learning the ground-state electronic properties of materials, subverting *ab initio* density functional theory (DFT) calculations when the underlying lattices can be represented as small and/or repeatable unit cells (i.e., molecules and periodic crystals). Realistic systems are, however, non-ideal and generally characterized by higher structural complexity. As such, they require large (10+ Å) unit cells and thousands of atoms to be accurately described. At these scales, DFT becomes computationally prohibitive, making GNNs especially attractive. In this work, we present a strictly local equivariant GNN capable of learning the electronic Hamiltonian (**H**) of realistically extended materials. It incorporates an *augmented partitioning* approach that enables training on arbitrarily large structures while preserving local atomic environments beyond boundaries. We demonstrate its capabilities by predicting the electronic Hamiltonian of various systems with up to 3,000 nodes (atoms), 500,000+ edges, ~ 28 million orbital interactions (nonzero entries of **H**), and $\leq$0.53\% error in the eigenvalue spectra. Our work expands the applicability of current electronic property prediction methods to some of the most challenging cases encountered in computational materials science, namely systems with disorder, interfaces, and defects.

Applications · Chemistry, Physics, and Earth Sciences

Tianyu Chen, Haoyi Zhou, Ying Li, Hao Wang, Chonghan Gao, Rongye Shi, Shanghang Zhang, Jianxin Li

Foundation models have revolutionized language modeling, while whether this success is replicated in scientific computing remains unexplored. We present OmniArch, the first prototype aiming at solving multi-scale and multi-physics scientific computing problems with physical alignment. We addressed all three challenges with one unified architecture. Its pre-training stage contains a Fourier Encoder-decoder fading out the disharmony across separated dimensions and a Transformer backbone integrating quantities through temporal dynamics, and the novel PDE-Aligner performs physics-informed fine-tuning under flexible conditions. As far as we know, we first conduct 1D-2D-3D united pre-training on the PDEBench, and it sets not only new performance benchmarks for 1D, 2D, and 3D PDEs but also demonstrates exceptional adaptability to new physics via in-context and zero-shot learning approaches, which supports realistic engineering applications and foresight physics discovery.

Applications · Chemistry, Physics, and Earth Sciences

Zhang Jiasheng, Delvin Zhang, Shuang Liang, Zhengpin Li, ZHITAO YING, Jie Shao

Protein language models often struggle to capture biological functions due to their lack of factual knowledge (e.g., gene descriptions). Existing solutions leverage protein knowledge graphs (PKGs) as auxiliary pre-training objectives, but lack explicit integration of task-oriented knowledge, making them suffer from limited knowledge exploitation and catastrophic forgetting. The root cause is that they fail to align PKGs with task-specific data, forcing their knowledge modeling to adapt to the knowledge-isolated nature of downstream tasks. In this paper, we propose Knowledge-aware retrieval augmented protein language model (Kara), achieving the first task-oriented and explicit integration of PKGs and protein language models. With a knowledge retriever learning to predict linkages between PKG and task proteins, Kara unifies the knowledge integration of the pre-training and fine-tuning stages with a structure-based regularization, mitigating catastrophic forgetting. To ensure task-oriented integration, Kara uses contextualized virtual tokens to extract graph context as task-specific knowledge for new proteins. Experiments show that Kara outperforms existing knowledge-enhanced models in 6 representative tasks, achieving on average 5.1% improvements.

Applications · Chemistry, Physics, and Earth Sciences

Parshin Shojaee, Ngoc Hieu Nguyen, Kazem Meidani, Amir Barati Farimani, Khoa Doan, Chandan Reddy

Scientific equation discovery is a fundamental task in the history of scientific progress, enabling the derivation of laws governing natural phenomena. Recently, Large Language Models (LLMs) have gained interest for this task due to their potential to leverage embedded scientific knowledge for hypothesis generation. However, evaluating the true discovery capabilities of these methods remains challenging, as existing benchmarks often rely on common equations that are susceptible to memorization by LLMs, leading to inflated performance metrics that do not reflect actual discovery. In this paper, we introduce LLM-SRBench, a comprehensive benchmark with 239 challenging problems across four scientific domains specifically designed to evaluate LLM-based scientific equation discovery methods while preventing trivial memorization. Our benchmark comprises two main categories: LSR-Transform, which transforms common physical models into less common mathematical representations to test reasoning beyond memorization, and LSR-Synth, which introduces synthetic, discovery-driven problems requiring data-driven reasoning. Through extensive evaluation of several state-of-the-art methods on LLM-SRBench, using both open and closed LLMs, we find that the best-performing system so far achieves only 31.5% symbolic accuracy.These findings highlight the challenges of scientific equation discovery, positioning LLM-SRBench as a valuable resource for future research.

Applications · Chemistry, Physics, and Earth Sciences

Dapeng Jiang, Xiangzhe Kong, Jiaqi Han, Mingyu Li, Rui Jiao, Wenbing Huang, Stefano Ermon, Jianzhu Ma, Yang Liu

Cyclic peptides, characterized by geometric constraints absent in linear peptides, offer enhanced biochemical properties, presenting new opportunities to address unmet medical needs. However, designing target-specific cyclic peptides remains underexplored due to limited training data. To bridge the gap, we propose CP-Composer, a novel generative framework that enables zero-shot cyclic peptide generation via composable geometric constraints. Our approach decomposes complex cyclization patterns into unit constraints, which are incorporated into a diffusion model through geometric conditioning on nodes and edges. During training, the model learns from unit constraints and their random combinations in linear peptides, while at inference, novel constraint combinations required for cyclization are imposed as input. Experiments show that our model, despite trained with linear peptides, is capable of generating diverse target-binding cyclic peptides, reaching success rates from 38\% to 84\% on different cyclization strategies.

Applications · Chemistry, Physics, and Earth Sciences

Manwen Liao, Yan Zhu, Weitian Zhang, Yuxiang Yang

Characterizing quantum states is essential for advancing many quantum technologies. Recently, deep neural networks have been applied to learn quantum states by generating compressed implicit representations. Despite their success in predicting properties of the states, these representations remain a black box, lacking insights into strategies for experimental reconstruction. In this work, we aim to open this black box by developing explicit representations through generating surrogate state preparation circuits for property estimation. We design a reinforcement learning agent equipped with a Transformer-based architecture and a local fidelity reward function. Relying solely on measurement data from a few neighboring qubits, our agent accurately recovers properties of target states. We also theoretically analyze the global fidelity the agent can achieve when it learns a good local approximation. Extensive experiments demonstrate the effectiveness of our framework in learning various states of up to 100 qubits, including those generated by shallow Instantaneous Quantum Polynomial circuits, evolved by Ising Hamiltonians, and many-body ground states. Furthermore, the learned circuit representations can be applied to Hamiltonian learning as a downstream task utilizing a simple linear model.

Applications · Chemistry, Physics, and Earth Sciences

In Huh, Changwook Jeong, Muhammad Alam

Out-Of-Domain (OOD) generalization is a significant challenge in learning dynamical systems, especially when they exhibit bifurcation, a sudden topological transition triggered by a model parameter crossing a critical threshold. A prevailing belief is that machine learning models, unless equipped with strong priors, struggle to generalize across bifurcations due to the abrupt changes in data characteristics. Contrary to this belief, we demonstrate that context-dependent Neural Ordinary Differential Equations (NODEs), trained solely on localized, pre-bifurcation, symmetric data and without physics-based priors, can still identify post-bifurcation, symmetry-breaking behaviors, even in a zero-shot manner. We interpret this capability to the model's implicit utilization of topological invariants, particularly the Poincaré index, and offer a formal explanation based on the Poincaré–Hopf theorem. We derive the conditions under which NODEs can recover—or erroneously hallucinate—broken symmetries without explicit training. Building on this insight, we showcase a topological regularizer inspired by the Poincaré–Hopf theorem and validate it empirically on phase transitions of systems described by the Landau–Khalatnikov equation.

Applications · Chemistry, Physics, and Earth Sciences

Ning Liu, Yue Yu

Attention mechanisms have emerged as transformative tools in core AI domains such as natural language processing and computer vision. Yet, their largely untapped potential for modeling intricate physical systems presents a compelling frontier. Learning such systems often entails discovering operators that map between functional spaces using limited instances of function pairs---a task commonly framed as a severely ill-posed inverse PDE problem. In this work, we introduce Neural Interpretable PDEs (NIPS), a novel neural operator architecture that builds upon and enhances Nonlocal Attention Operators (NAO) in both predictive accuracy and computational efficiency. NIPS employs a linear attention mechanism to enable scalable learning and integrates a learnable kernel network that acts as a channel-independent convolution in Fourier space. As a consequence, NIPS eliminates the need to explicitly compute and store large pairwise interactions, effectively amortizing the cost of handling spatial interactions into the Fourier transform. Empirical evaluations demonstrate that NIPS consistently surpasses NAO and other baselines across diverse benchmarks, heralding a substantial leap in scalable, interpretable, and efficient physics learning. Our code and data accompanying this paper are available at https://github.com/fishmoon1234/Nonlocal-Attention-Operator.

Applications · Chemistry, Physics, and Earth Sciences

Ibrahim Fayad, Max Zimmer, Martin Schwartz, Fabian Gieseke, Philippe CIAIS, Gabriel Belouze, Sarah Brood, Aurélien de Truchis, Alexandre d'Aspremont

Significant efforts have been directed towards adapting self-supervised multimodal learning for Earth observation applications. However, most current methods produce coarse patch-sized embeddings, limiting their effectiveness and integration with other modalities like LiDAR. To close this gap, we present DUNIA, an approach to learn pixel-sized embeddings through cross-modal alignment between images and full-waveform LiDAR data. As the model is trained in a contrastive manner, the embeddings can be directly leveraged in the context of a variety of environmental monitoring tasks in a zero-shot setting. In our experiments, we demonstrate the effectiveness of the embeddings for seven such tasks: canopy height mapping, fractional canopy cover, land cover mapping, tree species identification, plant area index, crop type classification, and per-pixel waveform-based vertical structure mapping. The results show that the embeddings, along with zero-shot classifiers, often outperform specialized supervised models, even in low-data regimes. In the fine-tuning setting, we show strong performances near or better than the state-of-the-art on five out of six tasks.

Applications · Chemistry, Physics, and Earth Sciences

Michael Sun, Weize Yuan, Gang Liu, Wojciech Matusik, Jie Chen

Recent data-efficient molecular generation approaches exploit graph grammars to introduce interpretability into the generative models. However, grammar learning therein relies on expert annotation or unreliable heuristics for algorithmic inference. We propose Foundation Molecular Grammar (FMG), which leverages multi-modal foundation models (MMFMs) to induce an interpretable molecular language. By exploiting the chemical knowledge of an MMFM, FMG renders molecules as images, describes them as text, and aligns information across modalities using prompt learning. FMG can be used as a drop-in replacement for the prior grammar learning approaches in molecular generation and property prediction. We show that FMG not only excels in synthesizability, diversity, and data efficiency but also offers built-in chemical interpretability for automated molecular discovery workflows. Code is available at https://github.com/shiningsunnyday/induction.