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Applications · Robotics

Yucheng Hu, Yanjiang Guo, Pengchao Wang, Xiaoyu Chen, Yen-Jen Wang, Jianke Zhang, Koushil Sreenath, Chaochao Lu, Jianyu Chen

Visual representations play a crucial role in developing generalist robotic policies. Previous vision encoders, typically pre-trained with single-image reconstruction or two-image contrastive learning, tend to capture static information, often neglecting the dynamic aspects vital for embodied tasks. Recently, video diffusion models (VDMs) demonstrate the ability to predict future frames and showcase a strong understanding of physical world. We hypothesize that VDMs inherently produce visual representations that encompass both current static information and predicted future dynamics, thereby providing valuable guidance for robot action learning. Based on this hypothesis, we propose the Video Prediction Policy (VPP), which learns implicit inverse dynamics model conditioned on predicted future representations inside VDMs. To predict more precise future, we fine-tune pre-trained video foundation model on robot datasets along with internet human manipulation data.In experiments, VPP achieves a 18.6\% relative improvement on the Calvin ABC-D generalization benchmark compared to the previous state-of-the-art, and demonstrates a 31.6\% increase in success rates for complex real-world dexterous manipulation tasks. For your convenience, videos can be found at https://video-prediction-policy.github.io/

Applications · Chemistry, Physics, and Earth Sciences

Anas Jnini, Lorenzo Breschi, Flavio Vella

Divergence-free symmetric tensors (DFSTs) are fundamental in continuum mechanics, encoding conservation laws such as mass and momentum conservation. We introduce Riemann Tensor Neural Networks (RTNNs), a novel neural architecture that inherently satisfies the DFST condition to machine precision, providing a strong inductive bias for enforcing these conservation laws. We prove that RTNNs can approximate any sufficiently smooth DFST with arbitrary precision and demonstrate their effectiveness as surrogates for conservative PDEs, achieving improved accuracy across benchmarks. This work is the first to use DFSTs as an inductive bias in neural PDE surrogates and to explicitly enforce the conservation of both mass and momentum within a physics-constrained neural architecture.

Applications · Everything Else

Vint Lee, Minh Nguyen, Leena Elzeiny, Chun Deng, Pieter Abbeel, Wawrzynek

Macro placement is a vital step in digital circuit design that defines the physical location of large collections of components, known as macros, on a 2D chip. Because key performance metrics of the chip are determined by the placement, optimizing it is crucial. Existing learning-based methods typically fall short because of their reliance on reinforcement learning (RL), which is slow and struggles to generalize, requiring online training on each new circuit. Instead, we train a diffusion model capable of placing new circuits zero-shot, using guided sampling in lieu of RL to optimize placement quality. To enable such models to train at scale, we designed a capable yet efficient architecture for the denoising model, and propose a novel algorithm to generate large synthetic datasets for pre-training. To allow zero-shot transfer to real circuits, we empirically study the design decisions of our dataset generation algorithm, and identify several key factors enabling generalization. When trained on our synthetic data, our models generate high-quality placements on unseen, realistic circuits, achieving competitive performance on placement benchmarks compared to state-of-the-art methods.

Applications · Chemistry, Physics, and Earth Sciences

Peter Eckmann, Dongxia Wu, Germano Heinzelmann, Michael Gilson, Rose Yu

Current generative models for drug discovery primarily use molecular docking as an oracle to guide the generation of active compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show real-world experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. To address this challenge, we propose Multi-Fidelity Latent space Active Learning (MF-LAL), a generative modeling framework that integrates a set of oracles with varying cost-accuracy tradeoffs. Using active learning, we train a surrogate model for each oracle and use these surrogates to guide generation of compounds with high predicted activity. Unlike previous approaches that separately learn the surrogate model and generative model, MF-LAL combines the generative and multi-fidelity surrogate models into a single framework, allowing for more accurate activity prediction and higher quality samples. Our experiments on two disease-relevant proteins show that MF-LAL produces compounds with significantly better binding free energy scores than other single and multi-fidelity approaches (~50% improvement in mean binding free energy score). The code is available at https://github.com/Rose-STL-Lab/MF-LAL.

Applications · Chemistry, Physics, and Earth Sciences

Makoto Takamoto, Viktor Zaverkin, Mathias Niepert

Machine learning is playing an increasingly important role in computational chemistry and materials science, complementing expensive ab initio and first-principles methods. However, machine-learned interatomic potentials (MLIPs) often struggle with generalization and robustness, leading to unphysical energy and force predictions in atomistic simulations. To address this, we propose a physics-informed, weakly supervised training framework for MLIPs. Our method introduces two novel loss functions: one based on Taylor expansions of the potential energy and another enforcing conservative force constraints. This approach enhances accuracy, particularly in low-data regimes, and reduces the reliance on large, expensive training datasets. Extensive experiments across benchmark datasets show up to 2× reductions in energy and force errors for multiple baseline models. Additionally, our method improves the stability of molecular dynamics simulations and facilitates effective fine-tuning of ML foundation models on sparse, high-accuracy ab initio data. An implementation of our method and scripts for executing experiments are available at \url{https://github.com/nec-research/PICPS-ML4Sci}.

Applications · Chemistry, Physics, and Earth Sciences

Koen Minartz, Tim d'Hondt, Leon Hillmann, Jörn Starruß, Lutz Brusch, Vlado Menkovski

The cellular Potts model (CPM) is a powerful computational method for simulating collective spatiotemporal dynamics of biological cells.To drive the dynamics, CPMs rely on physics-inspired Hamiltonians. However, as first principles remain elusive in biology, these Hamiltonians only approximate the full complexity of real multicellular systems.To address this limitation, we propose NeuralCPM, a more expressive cellular Potts model that can be trained directly on observational data.At the core of NeuralCPM lies the Neural Hamiltonian, a neural network architecture that respects universal symmetries in collective cellular dynamics.Moreover, this approach enables seamless integration of domain knowledge by combining known biological mechanisms and the expressive Neural Hamiltonian into a hybrid model.Our evaluation with synthetic and real-world multicellular systems demonstrates that NeuralCPM is able to model cellular dynamics that cannot be accounted for by traditional analytical Hamiltonians.

Applications · Chemistry, Physics, and Earth Sciences

Dong-Hee Shin, Young-Han Son, Hyun Jung Lee, Deok-Joong Lee, Tae-Eui Kam

Molecular discovery has attracted significant attention in scientific fields for its ability to generate novel molecules with desirable properties. Although numerous methods have been developed to tackle this problem, most rely on an online setting that requires repeated online evaluation of candidate molecules using the oracle. However, in real-world molecular discovery, the oracle is often represented by wet-lab experiments, making this online setting impractical due to the significant time and resource demands. To fill this gap, we propose the Molecular Stitching (MolStitch) framework, which utilizes a fixed offline dataset to explore and optimize molecules without the need for repeated oracle evaluations. Specifically, MolStitch leverages existing molecules from the offline dataset to generate novel `stitched molecules' that combine their desirable properties. These stitched molecules are then used as training samples to fine-tune the generative model using preference optimization techniques. Experimental results on various offline multi-objective molecular optimization problems validate the effectiveness of MolStitch. The source code is available online.

Applications · Chemistry, Physics, and Earth Sciences

Ye Liu, Yuntian Chen

Automotive drag coefficient ($C_d$) is pivotal to energy efficiency, fuel consumption, and aerodynamic performance. However, costly computational fluid dynamics (CFD) simulations and wind tunnel tests struggle to meet the rapid-iteration demands of automotive design. We present DragSolver, a Transformer-based framework for rapid and accurate $C_d$ estimation from large-scale, diverse 3D vehicle models.DragSolver tackles four key real-world challenges: (1) multi-scale feature extraction to capture both global shape and fine local geometry; (2) heterogeneous scale normalization to handle meshes with varying sizes and densities;(3) surface-guided gating to suppress internal structures irrelevant to external aerodynamics;and (4) epistemic uncertainty estimation via Monte Carlo dropout for risk-aware design. Extensive evaluations on three industrial-scale datasets (DrivaerNet, DrivaerNet++, and DrivaerML) show that DragSolver outperforms existing approaches in accuracy and generalization, achieving an average reduction of relative $L_2$ error by 58.7% across real-world datasets. Crucially, DragSolver is the first to achieve reliable, real-time $C_d$ inference on production-level automotive geometries.

Applications · Chemistry, Physics, and Earth Sciences

Louis Serrano, Armand Kassaï Koupaï, Thomas Wang, Pierre ERBACHER, patrick gallinari

Solving time-dependent parametric partial differential equations (PDEs) is challenging for data-driven methods, as these models must adapt to variations in parameters such as coefficients, forcing terms, and initial conditions. State-of-the-art neural surrogates perform adaptation through gradient-based optimization and meta-learning to implicitly encode the variety of dynamics from observations. This often comes with increased inference complexity. Inspired by the in-context learning capabilities of large language models (LLMs), we introduce Zebra, a novel generative auto-regressive transformer designed to solve parametric PDEs without requiring gradient adaptation at inference. By leveraging in-context information during both pre-training and inference, Zebra dynamically adapts to new tasks by conditioning on input sequences that incorporate context example trajectories. As a generative model, Zebra can be used to generate new trajectories and allows quantifying the uncertainty of the predictions. We evaluate Zebra across a variety of challenging PDE scenarios, demonstrating its adaptability, robustness, and superior performance compared to existing approaches.

Applications · Chemistry, Physics, and Earth Sciences

Mingquan Feng, Weixin Liao, Yixin Huang, Yifan Fu, Qifu Zheng, Junchi Yan

Neural operators have emerged as a promising approach for solving high-dimensional partial differential equations (PDEs). However, existing neural operators often have difficulty in dealing with constrained PDEs, where the solution must satisfy additional equality or inequality constraints beyond the governing equations. To close this gap, we propose a novel neural operator, Hyper Extended Adaptive PDHG (HEAP) for constrained high-dim PDEs, where the learned operator evolves in the parameter space of PDEs. We first show that the evolution operator learning can be formulated as a quadratic programming (QP) problem, then unroll the adaptive primal-dual hybrid gradient (APDHG) algorithm as the QP-solver into the neural operator architecture. This allows us to improve efficiency while retaining theoretical guarantees of the constrained optimization. Empirical results on a variety of high-dim PDEs show that HEAP outperforms the state-of-the-art neural operator model.

Applications · Chemistry, Physics, and Earth Sciences

Ruocheng Wang, Zhuo Xia, Ge Yan, Junchi Yan

Differential equations are essential and popular in science and engineering. Learning-based methods including neural operators, have emerged as a promising paradigm. We explore its quantum counterpart, and propose QuanONet -- a quantum neural operator which has not been well studied in literature compared with their counterparts in other machine learning areas. We design a novel architecture as a hardware-efficient ansatz, in the era of noisy intermediate-scale quantum (NISQ). Its circuit is pure quantum. By lying its ground on the operator approximation theorem for its quantum counterpart, QuanONet in theory can fit various differential equation operators. We also propose its modified version TF-QuanONet with ability to adaptively fit the dominant frequency of the problem. The real-device empirical results on problems including anti-derivative operators, Diffusion-reaction Systems demonstrate that QuanONet outperforms peer quantum methods when their model sizes are set akin to QuanONet.

Applications · Chemistry, Physics, and Earth Sciences

Seungbeom Lee, Munsun Jo, Jungseul Ok, Dongwoo Kim

Deep learning-based Structure-based drug design aims to generate ligand molecules with desirable properties for protein targets. While existing models have demonstrated competitive performance in generating ligand molecules, they primarily focus on learning the chemical distribution of training datasets, often lacking effective steerability to ensure the desired chemical quality of generated molecules. To address this issue, we propose a multi-reward optimization framework that fine-tunes generative models for attributes, such as binding affinity, validity, and drug-likeness, together. Specifically, we derive direct preference optimization for a Bayesian flow network, used as a backbone for molecule generation, and integrate a reward normalization scheme to adopt multiple objectives. Experimental results show that our method generates more realistic ligands than baseline models while achieving higher binding affinity, expanding the Pareto front empirically observed in previous studies.

Applications · Chemistry, Physics, and Earth Sciences

Shilong Tao, Zhe Feng, Haonan Sun, Zhanxing Zhu, Yunhuai Liu

Multi-solid systems are foundational to a wide range of real-world applications, yet modeling their complex interactions remains challenging. Existing deep learning methods predominantly rely on implicit modeling, where the factors influencing solid deformation are not explicitly represented but are instead indirectly learned. However, as the number of solids increases, these methods struggle to accurately capture intricate physical interactions. In this paper, we introduce a novel explicit modeling paradigm that incorporates factors influencing solid deformation through structured modules. Specifically, we present Unisoma, a unified and flexible Transformer-based model capable of handling variable numbers of solids. Unisoma directly captures physical interactions using contact modules and adaptive interaction allocation mechanism, and learns the deformation through a triplet relationship. Compared to implicit modeling techniques, explicit modeling is more well-suited for multi-solid systems with diverse coupling patterns, as it enables detailed treatment of each solid while preventing information blending and confusion. Experimentally, Unisoma achieves consistent state-of-the-art performance across seven well-established datasets and two complex multi-solid tasks. Code is avaiable at [https://github.com/therontau0054/Unisoma](https://github.com/therontau0054/Unisoma).

Applications · Chemistry, Physics, and Earth Sciences

Zelin Xu, Yupu Zhang, Tingsong Xiao, Maitane Lizaso, Jose Gonzalez-Ondina, Zibo Liu, Shigang Chen, Zhe Jiang

Over 40\% of the global population lives within 100 kilometers of the coast, which contributes more than \$8 trillion annually to the global economy. Unfortunately, coastal ecosystems are increasingly vulnerable to more frequent and intense extreme weather events and rising sea levels. Coastal scientists use numerical models to simulate complex physical processes, but these models are often slow and expensive. In recent years, deep learning has become a promising alternative to reduce the cost of numerical models. However, progress has been hindered by the lack of a large-scale, high-resolution coastal simulation dataset to train and validate deep learning models. Existing studies often focus on relatively small datasets and simple processes. To fill this gap, we introduce a decade-long, high-resolution (<100m) coastal circulation modeling dataset on a real-world 3D mesh in southwest Florida with around 6 million cells. The dataset contains key oceanography variables (e.g., current velocities, free surface level, temperature, salinity) alongside external atmospheric and river forcings. We evaluated a customized Vision Transformer model that takes initial and boundary conditions and external forcings and predicts ocean variables at varying lead times. The dataset provides an opportunity to benchmark novel deep learning models for high-resolution coastal simulations (e.g., physics-informed machine learning, neural operator learning).The code and dataset can be accessed at https://github.com/spatialdatasciencegroup/CoastalBench.

Applications · Chemistry, Physics, and Earth Sciences

Chen Wang, Siyu Hu, Guangming Tan, Weile Jia

Pre-trained interatomic potentials have become a new paradigm for atomistic materials simulations, enabling accurate and efficient predictions across diverse chemical systems. Despite their promise, fine-tuning is often required for complex tasks to achieve high accuracy. Traditional parameter-efficient fine-tuning approaches are effective in NLP and CV. However, when applied to SO(3) equivariant pre-trained interatomic potentials, these methods will inevitably break equivariance—a critical property for preserving physical symmetries. In this paper, we introduce ELoRA (Equivariant Low-Rank Adaptation), a novel fine-tuning method designed specifically for SO(3) equivariant Graph Neural Networks (GNNs), the backbones in multiple pre-trained interatomic potentials. ELoRA adopts a path-dependent decomposition for weights updating which offers two key advantages: (1) it preserves SO(3) equivariance throughout the fine-tuning process, ensuring physically consistent predictions, and (2) it leverages low-rank adaptations to significantly improve data efficiency. We prove that ELoRA maintains equivariance and demonstrate its effectiveness through comprehensive experiments. On the rMD17 organic dataset, ELoRA achieves a 25.5\% improvement in energy prediction accuracy and a 23.7\% improvement in force prediction accuracy compared to full-parameter fine-tuning. Similarly, across 10 inorganic datasets, ELoRA achieves average improvements of 12.3\% and 14.4\% in energy and force predictions, respectively. Code will be made publicly available at https://github.com/hyjwpk/ELoRA.

Probabilistic Methods · Monte Carlo and Sampling Methods

Dongze Wu, Yao Xie

Sampling from high-dimensional, multi-modal distributions remains a fundamental challenge across domains such as statistical Bayesian inference and physics-based machine learning. In this paper, we propose Annealing Flow (AF), a method built on Continuous Normalizing Flows (CNFs) for sampling from high-dimensional and multi-modal distributions. AF is trained with a dynamic Optimal Transport (OT) objective incorporating Wasserstein regularization, and guided by annealing procedures, facilitating effective exploration of modes in high-dimensional spaces. Compared to recent NF methods, AF significantly improves training efficiency and stability, with minimal reliance on MC assistance. We demonstrate the superior performance of AF compared to state-of-the-art methods through extensive experiments on various challenging distributions and real-world datasets, particularly in high-dimensional and multi-modal settings. We also highlight AF’s potential for sampling the least favorable distributions.

Deep Learning · Graph Neural Networks

Artem Moskalev, Mangal Prakash, Junjie Xu, Tianyu Cui, Rui Liao, Tommaso Mansi

Processing global geometric context while preserving equivariance is crucial when modeling biological, chemical, and physical systems. Yet, this is challenging due to the computational demands of equivariance and global context at scale. Standard methods such as equivariant self-attention suffer from quadratic complexity, while local methods such as distance-based message passing sacrifice global information. Inspired by the recent success of state-space and long-convolutional models, we introduce Geometric Hyena, the first equivariant long-convolutional model for geometric systems. Geometric Hyena captures global geometric context at sub-quadratic complexity while maintaining equivariance to rotations and translations. Evaluated on all-atom property prediction of large RNA molecules and full protein molecular dynamics, Geometric Hyena outperforms existing equivariant models while requiring significantly less memory and compute that equivariant self-attention. Notably, our model processes the geometric context of $30k$ tokens $20 \times$ faster than the equivariant transformer and allows $72 \times$ longer context within the same budget.

Applications · Neuroscience, Cognitive Science

Luca M. Schulze Buschoff, Konstantinos Voudouris, Elif Akata, Matthias Bethge, Josh Tenenbaum, Eric Schulz

Pre-trained vision language models still fall short of human visual cognition. In an effort to improve visual cognition and align models with human behavior, we introduce visual stimuli and human judgments on visual cognition tasks, allowing us to systematically evaluate performance across cognitive domains under a consistent environment. We fine-tune models on ground truth data for intuitive physics and causal reasoning and find that this improves model performance in the respective fine-tuning domain. Furthermore, it can improve model alignment with human behavior. However, we find that task-specific fine-tuning does not contribute to robust human-like generalization to data with other visual characteristics or to tasks in other cognitive domains.

Applications · Chemistry, Physics, and Earth Sciences

Da Long, Zhitong Xu, Guang Yang, Akil Narayan, Shandian Zhe

Modern physics simulation often involves multiple functions of interests, and traditional numerical approaches are known to be complex and computationally costly. While machine learning-based surrogate models can offer significant cost reductions, most focus on a single task, such as forward prediction, and typically lack uncertainty quantification --- an essential component in many applications. To overcome these limitations, we propose Arbitrarily-Conditioned Multi-Functional Diffusion (ACM-FD), a versatile probabilistic surrogate model for multi-physics emulation. ACM-FD can perform a wide range of tasks within a single framework, including forward prediction, various inverse problems, and simulating data for entire systems or subsets of quantities conditioned on others. Specifically, we extend the standard Denoising Diffusion Probabilistic Model (DDPM) for multi-functional generation by modeling noise as Gaussian processes (GP). We propose a random-mask based, zero-regularized denoising loss to achieve flexible and robust conditional generation. We induce a Kronecker product structure in the GP covariance matrix, substantially reducing the computational cost and enabling efficient training and sampling. We demonstrate the effectiveness of ACM-FD across several fundamental multi-physics systems.

Applications · Chemistry, Physics, and Earth Sciences

Jinho Chang, Jong Chul YE

With the emergence of diffusion models as a frontline generative model, many researchers have proposed molecule generation techniques with conditional diffusion models. However, the unavoidable discreteness of a molecule makes it difficult for a diffusion model to connect raw data with highly complex conditions like natural language. To address this, here we present a novel latent diffusion model dubbed LDMol for text-conditioned molecule generation. By recognizing that the suitable latent space design is the key to the diffusion model performance, we employ a contrastive learning strategy to extract novel feature space from text data that embeds the unique characteristics of the molecule structure. Experiments show that LDMol outperforms the existing autoregressive baselines on the text-to-molecule generation benchmark, being one of the first diffusion models that outperforms autoregressive models in textual data generation with a better choice of the latent domain.Furthermore, we show that LDMol can be applied to downstream tasks such as molecule-to-text retrieval and text-guided molecule editing, demonstrating its versatility as a diffusion model.