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Applications · Chemistry, Physics, and Earth Sciences

Shu Wei, Yanjie Li, Lina Yu, Weijun Li, Min Wu, Linjun Sun, Jingyi Liu, Hong Qin, Deng Yusong, Jufeng Han 等

The quest for analytical solutions to differential equations has traditionally been constrained by the need for extensive mathematical expertise.Machine learning methods like genetic algorithms have shown promise in this domain, but are hindered by significant computational time and the complexity of their derived solutions. This paper introduces **SSDE** (Symbolic Solver for Differential Equations), a novel reinforcement learning-based approach that derives symbolic closed-form solutions for various differential equations. Evaluations across a diverse set of ordinary and partial differential equations demonstrate that SSDE outperforms existing machine learning methods, delivering superior accuracy and efficiency in obtaining analytical solutions.

Applications · Chemistry, Physics, and Earth Sciences

Long-Kai Huang, Rongyi Zhu, Bing He, Jianhua Yao

Protein Language Models (PLMs), pre-trained on extensive evolutionary data from natural proteins, have emerged as indispensable tools for protein design. While powerful, PLMs often struggle to produce proteins with precisely specified functionalities or properties due to inherent challenges in controlling their outputs. In this work, we investigate the potential of Activation Steering, a technique originally developed for controlling text generation in Large Language Models (LLMs), to direct PLMs toward generating protein sequences with targeted properties. We propose a simple yet effective method that employs activation editing to steer PLM outputs, and extend this approach to protein optimization through a novel editing site identification module. Through comprehensive experiments on lysozyme-like sequence generation and optimization, we demonstrate that our methods can be seamlessly integrated into both auto-encoding and autoregressive PLMs without requiring additional training. These results highlight a promising direction for precise protein engineering using foundation models.

Applications · Chemistry, Physics, and Earth Sciences

Karn Tiwari, Niladri Dutta, N M Anoop Krishnan, Prathosh AP

Neural operators have emerged as powerful data-driven frameworks for solving Partial Differential Equations (PDEs), offering significant speedups over numerical methods. However, existing neural operators struggle with scalability in high-dimensional spaces, incur high computational costs, and face challenges in capturing continuous and long-range dependencies in PDE dynamics. To address these limitations, we introduce the Latent Mamba Operator (LaMO), which integrates the efficiency of state-space models (SSMs) in latent space with the expressive power of kernel integral formulations in neural operators. We also establish a theoretical connection between state-space models (SSMs) and the kernel integral of neural operators. Extensive experiments across diverse PDE benchmarks on regular grids, structured meshes, and point clouds covering solid and fluid physics datasets, LaMOs achieve consistent state-of-the-art (SOTA) performance, with a 32.3\% improvement over existing baselines in solution operator approximation, highlighting its efficacy in modeling complex PDEs solution.

Position · Methodology

Yoonsoo Nam, Seok Hyeong Lee, Clémentine Dominé, Yeachan Park, Charles London, Wonyl Choi, Niclas Göring, Seungjai Lee

In physics, complex systems are often simplified into minimal, solvable models that retain only the core principles. In machine learning, layerwise linear models (e.g., linear neural networks) act as simplified representations of neural network dynamics. These models follow the dynamical feedback principle, which describes how layers mutually govern and amplify each other's evolution. This principle extends beyond the simplified models, successfully explaining a wide range of dynamical phenomena in deep neural networks, including neural collapse, emergence, lazy and rich regimes, and grokking. In this position paper, we call for the use of layerwise linear models retaining the core principles of neural dynamical phenomena to accelerate the science of deep learning.

Applications · Everything Else

Jesse He, Helen Jenne, Herman Chau, Davis Brown, Mark Raugas, Sara Billey, Henry Kvinge

Machine learning is becoming an increasingly valuable tool in mathematics, enabling one to identify subtle patterns across collections of examples so vast that they would be impossible for a single researcher to feasibly review and analyze. In this work, we use graph neural networks to investigate quiver mutation---an operation that transforms one quiver (or directed multigraph) into another---which is central to the theory of cluster algebras with deep connections to geometry, topology, and physics. In the study of cluster algebras, the question of mutation equivalence is of fundamental concern: given two quivers, can one efficiently determine if one quiver can be transformed into the other through a sequence of mutations? In this paper, we use graph neural networks and AI explainability techniques to independently discover mutation equivalence criteria for quivers of type $\tilde{D}$. Along the way, we also show that even without explicit training to do so, our model captures structure within its hidden representation that allows us to reconstruct known criteria from type $D$, adding to the growing evidence that modern machine learning models are capable of learning abstract and general rules from mathematical data.

Deep Learning · Algorithms

Jan Blechschmidt, Tom-Christian Riemer, Max Winkler, Martin STOLL, Jan-Frederik Pietschmann

We develop a novel physics informed deep learning approach for solving nonlinear drift-diffusion equations on metric graphs. These models represent an important model class with a large number of applications in areas ranging from transport in biological cells to the motion of human crowds. While traditional numerical schemes require a large amount of tailoring, especially in the case of model design or parameter identification problems, physics informed deep operator networks (DeepONets) have emerged as a versatile tool for the solution of partial differential equations with the particular advantage that they easily incorporate parameter identification questions. We here present an approach where we first learn three DeepONet models for representative inflow, inner and outflow edges, resp., and then subsequently couple these models for the solution of the drift-diffusion metric graph problem by relying on an edge-based domain decomposition approach. We illustrate that our framework is applicable for the accurate evaluation of graph-coupled physics models and is well suited for solving optimization or inverse problems on these coupled networks.

Applications · Chemistry, Physics, and Earth Sciences

Runzhong Wang, Rui-Xi Wang, Mrunali Manjrekar, Connor Coley

Molecular machine learning has gained popularity with the advancements of geometric deep learning. In parallel, retrieval-augmented generation has become a principled approach commonly used with language models. However, the optimal integration of retrieval augmentation into molecular machine learning remains unclear. Graph neural networks stand to benefit from clever matching to understand the structural alignment of retrieved molecules to a query molecule. Neural graph matching offers a compelling solution by explicitly modeling node and edge affinities between two structural graphs while employing a noise-robust, end-to-end neural network to learn affinity metrics. We apply this approach to mass spectrum simulation and introduce MARASON, a novel model that incorporates neural graph matching to enhance a fragmentation-based neural network. Experimental results highlight the effectiveness of our design, with MARASON achieving 27% top-1 accuracy, a substantial improvement over the non-retrieval state-of-the-art accuracy of 19%. Moreover, MARASON outperforms both naive retrieval-augmented generation methods and traditional graph matching approaches. Code is publicly available at https://github.com/coleygroup/ms-pred.

Deep Learning · Attention Mechanisms

Greyson Brothers

We investigate the design of pooling methods used to summarize the outputs of transformer embedding models, primarily motivated by reinforcement learning and vision applications. This work considers problems where a subset of the input vectors contains requisite information for a downstream task (signal) while the rest are distractors (noise). By framing pooling as vector quantization with the goal of minimizing signal loss, we demonstrate that the standard methods used to aggregate transformer outputs, AvgPool, MaxPool, and ClsToken, are vulnerable to performance collapse as the signal-to-noise ratio (SNR) of inputs fluctuates. We then show that an attention-based *adaptive pooling* method can approximate the signal-optimal vector quantizer within derived error bounds for any SNR. Our theoretical results are first validated by supervised experiments on a synthetic dataset designed to isolate the SNR problem, then generalized to standard relational reasoning, multi-agent reinforcement learning, and vision benchmarks with noisy observations, where transformers with adaptive pooling display superior robustness across tasks.

Reinforcement Learning · Everything Else

Samuel Holt, Todor Davchev, Dhruva Tirumala, Ben Moran, Atil Iscen, Antoine Laurens, Yixin Lin, Erik Frey, Markus Wulfmeier, Francesco Romano 等

High-frequency control in continuous action and state spaces is essential for practical applications in the physical world. Directly applying end-to-end reinforcement learning to high-frequency control tasks struggles with assigning credit to actions across long temporal horizons, compounded by the difficulty of efficient exploration. The alternative, learning low-frequency policies that guide higher-frequency controllers (e.g., proportional-derivative (PD) controllers), can result in a limited total expressiveness of the combined control system, hindering overall performance. We introduce *EvoControl*, a novel bi-level policy learning framework for learning both a slow high-level policy (using PPO) and a fast low-level policy (using Evolution Strategies) for solving continuous control tasks. Learning with Evolution Strategies for the lower-policy allows robust learning for long horizons that crucially arise when operating at higher frequencies. This enables *EvoControl* to learn to control interactions at a high frequency, benefitting from more efficient exploration and credit assignment than direct high-frequency torque control without the need to hand-tune PD parameters. We empirically demonstrate that *EvoControl* can achieve a higher evaluation reward for continuous-control tasks compared to existing approaches, specifically excelling in tasks where high-frequency control is needed, such as those requiring safety-critical fast reactions.

Applications · Robotics

Lucy Xiaoyang Shi, brian ichter, Michael Equi, Liyiming Ke, Karl Pertsch, Quan Vuong, James Tanner, Anna Walling, Haohuan Wang, Niccolo Fusai 等

Generalist robots that can perform a range of different tasks in open-world settings must be able to not only reason about the steps needed to accomplish their goals, but also process complex instructions, prompts, and even feedback during task execution. Intricate instructions (e.g., "Could you make me a vegetarian sandwich?" or "I don't like that one") require not just the ability to physically perform the individual steps, but the ability to situate complex commands and feedback in the physical world. In this work, we describe a system that uses vision-language models in a hierarchical structure, first reasoning over complex prompts and user feedback to deduce the most appropriate next step to fulfill the task, and then performing that step with low-level actions. In contrast to direct instruction following methods that can fulfill simple commands ("pick up the cup"), our system can reason through complex prompts and incorporate situated feedback during task execution ("that's not trash"). We evaluate our system across three robotic platforms, including single-arm, dual-arm, and dual-arm mobile robots, demonstrating its ability to handle tasks such as cleaning messy tables, making sandwiches, and grocery shopping.Videos are available at https://www.pi.website/research/hirobot

Applications · Chemistry, Physics, and Earth Sciences

Jaeheun Jung, Jaehyuk Lee, ChangHae Jung, Hanyoung Kim, Bosung Jung, Donghun Lee

Shock waves caused by earthquakes can be devastating. Generating realistic earthquake-caused ground motion waveforms help reducing losses in lives and properties, yet generative models for the task tend to generate subpar waveforms. We present High-fidelity Earthquake Groundmotion Generation System (HEGGS) and demonstrate its superior performance using earthquakes from North American, East Asian, and European regions. HEGGS exploits the intrinsic characteristics of earthquake dataset and learns the waveforms using an end-to-end differentiable generator containing conditional latent diffusion model and hi-fidelity waveform construction model. We show the learning efficiency of HEGGS by training it on a single GPU machine and validate its performance using earthquake databases from North America, East Asia, and Europe, using diverse criteria from waveform generation tasks and seismology. Once trained, HEGGS can generate three dimensional E-N-Z seismic waveforms with accurate P/S phase arrivals, envelope correlation, signal-to-noise ratio, GMPE analysis, frequency content analysis, and section plot analysis.

Applications · Chemistry, Physics, and Earth Sciences

Nikita Kazeev, Wei Nong, Ignat Romanov, Ruiming Zhu, Andrey Ustyuzhanin, Shuya Yamazaki, Kedar Hippalgaonkar

Crystal symmetry plays a fundamental role in determining its physical, chemical, and electronic properties such as electrical and thermal conductivity, optical and polarization behavior, and mechanical strength. Almost all known crystalline materials have internal symmetry. However, this is often inadequately addressed by existing generative models, making the consistent generation of stable and symmetrically valid crystal structures a significant challenge. We introduce WyFormer, a generative model that directly tackles this by formally conditioning on space group symmetry. It achieves this by using Wyckoff positions as the basis for an elegant, compressed, and discrete structure representation. To model the distribution, we develop a permutation-invariant autoregressive model based on the Transformer encoder and an absence of positional encoding. Extensive experimentation demonstrates WyFormer's compelling combination of attributes: it achieves best-in-class symmetry-conditioned generation, incorporates a physics-motivated inductive bias, produces structures with competitive stability, predicts material properties with competitive accuracy even without atomic coordinates, and exhibits unparalleled inference speed.

Applications · Chemistry, Physics, and Earth Sciences

Rudy Morel, Jiequn Han, Edouard Oyallon

We address the problem of predicting the next states of a dynamical system governed by *unknown* temporal partial differential equations (PDEs) using only a short trajectory. While standard transformers provide a natural black-box solution to this task, the presence of a well-structured evolution operator in the data suggests a more tailored and efficient approach. Specifically, when the PDE is fully known, classical numerical solvers can evolve the state accurately with only a few parameters. Building on this observation, we introduce DISCO, a model that uses a large hypernetwork to process a short trajectory and generate the parameters of a much smaller operator network, which then predicts the next states through time integration. Our framework decouples dynamics estimation -- i.e., DISCovering an evolution Operator from a short trajectory -- from state prediction -- i.e., evolving this operator. Experiments show that pretraining our model on diverse physics datasets achieves state-of-the-art performance while requiring significantly fewer epochs. Moreover, it generalizes well to unseen initial conditions and remains competitive when fine-tuned on downstream tasks.

Deep Learning · Generative Models and Autoencoders

Alexander Lobashev, Dmitry Guskov, Maria Larchenko, Mikhail Tamm

This paper presents a novel method for analyzing the latent space geometry of generative models, including statistical physics models and diffusion models, by reconstructing the Fisher information metric. The method approximates the posterior distribution of latent variables given generated samples and uses this to learn the log-partition function, which defines the Fisher metric for exponential families. Theoretical convergence guarantees are provided, and the method is validated on the Ising and TASEP models, outperforming existing baselines in reconstructing thermodynamic quantities. Applied to diffusion models, the method reveals a fractal structure of phase transitions in the latent space, characterized by abrupt changes in the Fisher metric. We demonstrate that while geodesic interpolations are approximately linear within individual phases, this linearity breaks down at phase boundaries, where the diffusion model exhibits a divergent Lipschitz constant with respect to the latent space. These findings provide new insights into the complex structure of diffusion model latent spaces and their connection to phenomena like phase transitions.Our source code is available at \url{https://github.com/alobashev/hessian-geometry-of-diffusion-models}.

Applications · Chemistry, Physics, and Earth Sciences

Seung Lee, Hojoon Kim, Yutack Park, Dawoon Jeong, Seungwu Han, Yeonhong Park, Jae W. Lee

Machine Learning Interatomic Potentials (MLIPs) enable efficient molecular dynamics (MD) simulations with high accuracy. While equivariant MLIPs achieve state-of-the-art accuracy, they face significant computational bottlenecks centered around their Tensor-Product layer, which account for up to 75\% of training time and cause substantial memory overhead. We present FlashTP, a highly optimized tensor-product library that addresses these inefficiencies through kernel fusion, sparse computation, and path-aggregated execution. FlashTP achieves up to 41.6$\times$ and 60.8$\times$ kernel speedups over _e3nn_ and NVIDIA cuEquivariance, respectively. For SevenNet-l3i5, it delivers 4.2$\times$ and 3.5$\times$ speedup while reducing peak memory usage by 6.3$\times$ and 6.2$\times$ for inference and training, respectively. The code is available at https://github.com/SNU-ARC/flashTP.

Deep Learning · Algorithms

Hang Zhou, Yuezhou Ma, Haixu Wu, Haowen Wang, Mingsheng Long

Deep models have recently emerged as promising tools to solve partial differential equations (PDEs), known as neural PDE solvers. While neural solvers trained from either simulation data or physics-informed loss can solve PDEs reasonably well, they are mainly restricted to a few instances of PDEs, e.g. a certain equation with a limited set of coefficients. This limits their generalization to diverse PDEs, preventing them from being practical surrogate models of numerical solvers. In this paper, we present Unisolver, a novel Transformer model trained on diverse data and conditioned on diverse PDEs, aiming towards a universal neural PDE solver capable of solving a wide scope of PDEs. Instead of purely scaling up data and parameters, Unisolver stems from the theoretical analysis of the PDE-solving process. Inspired by the mathematical structure of PDEs that a PDE solution is fundamentally governed by a series of PDE components such as equation symbols and boundary conditions, we define a complete set of PDE components and flexibly embed them as domain-wise and point-wise deep conditions for Transformer PDE solvers. Integrating physical insights with recent Transformer advances, Unisolver achieves consistent state-of-the-art on three challenging large-scale benchmarks, showing impressive performance and generalizability. Code is available at [https://github.com/thuml/Unisolver](https://github.com/thuml/Unisolver).

Applications · Chemistry, Physics, and Earth Sciences

David K Park, Xihaier Luo, Guang Zhao, Seungjun Lee, Miruna Oprescu, Shinjae Yoo

Spatiotemporal learning is challenging due to the intricate interplay between spatial and temporal dependencies, the high dimensionality of the data, and scalability constraints. These challenges are further amplified in scientific domains, where data is often irregularly distributed (e.g., missing values from sensor failures) and high-volume (e.g., high-fidelity simulations), posing additional computational and modeling difficulties. In this paper, we present SCENT, a novel framework for scalable and continuity-informed spatiotemporal representation learning. SCENT unifies interpolation, reconstruction, and forecasting within a single architecture. Built on a transformer-based encoder-processor-decoder backbone, SCENT introduces learnable queries to enhance generalization and a query-wise cross-attention mechanism to effectively capture multi-scale dependencies. To ensure scalability in both data size and model complexity, we incorporate a sparse attention mechanism, enabling flexible output representations and efficient evaluation at arbitrary resolutions. We validate SCENT through extensive simulations and real-world experiments, demonstrating state-of-the-art performance across multiple challenging tasks while achieving superior scalability.

Deep Learning · Sequential Models, Time series

Shurui Gui, Xiner Li, Shuiwang Ji

We consider learning underlying laws of dynamical systems governed by ordinary differential equations (ODE). A key challenge is how to discover intrinsic dynamics across multiple environments while circumventing environment-specific mechanisms. Unlike prior work, we tackle more complex environments where changes extend beyond function coefficients to entirely different function forms. For example, we demonstrate the discovery of ideal pendulum's natural motion $\alpha^2 \sin{\theta_t}$ by observing pendulum dynamics in different environments, such as the damped environment $\alpha^2 \sin(\theta_t) - \rho \omega_t$ and powered environment $\alpha^2 \sin(\theta_t) + \rho \frac{\omega_t}{\left|\omega_t\right|}$. Here, we formulate this problem as an *invariant function learning* task and propose a new method, known as **D**isentanglement of **I**nvariant **F**unctions (DIF), that is grounded in causal analysis. We propose a causal graph and design an encoder-decoder hypernetwork that explicitly disentangles invariant functions from environment-specific dynamics. The discovery of invariant functions is guaranteed by our information-based principle that enforces the independence between extracted invariant functions and environments. Quantitative comparisons with meta-learning and invariant learning baselines on three ODE systems demonstrate the effectiveness and efficiency of our method. Furthermore, symbolic regression explanation results highlight the ability of our framework to uncover intrinsic laws.

Deep Learning · Large Language Models

Bohan Lyu, Yadi Cao, Duncan Watson-Parris, Leon Bergen, Taylor Berg-Kirkpatrick, Rose Yu

Large Language Models (LLMs) demonstrate promising capabilities in solving scientific problems but often suffer from the issue of hallucination. While integrating LLMs with tools can mitigate this issue, models fine-tuned on tool usage become overreliant on them and incur unnecessary costs. Inspired by how human experts assess problem complexity before selecting solutions, we propose a novel two-component fine-tuning method, *Adapting while Learning* (AWL). In the first component *World Knowledge Learning* (WKL), LLMs internalize scientific knowledge by learning from tool-generated solutions. In the second component *Tool Usage Adaptation* (TUA), we categorize problems as easy or hard based on the model's accuracy, and train it to maintain direct reasoning for easy problems while switching to tools for hard ones. We validate our method on 6 scientific benchmark datasets across climate science, epidemiology, physics, and other domains. Compared to the original instruct model (8B), models post-trained with AWL achieve 29.11\% higher answer accuracy and 12.72\% better tool usage accuracy, even surpassing state-of-the-art models including GPT-4o and Claude-3.5 on 4 custom-created datasets. Our code is open-source at \url{https://github.com/Rose-STL-Lab/Adapting-While-Learning}.

Applications · Robotics

Dantong Niu, Yuvan Sharma, Haoru Xue, Giscard Biamby, Junyi Zhang, Ziteng Ji, Trevor Darrell, Roi Herzig

Foundation models pre-trained on massive unlabeled datasets have revolutionized natural language and computer vision, exhibiting remarkable generalization capabilities, thus highlighting the importance of pre-training. Yet, efforts in robotics have struggled to achieve similar success, limited by either the need for costly robotic annotations or the lack of representations that effectively model the physical world. In this paper, we introduce ARM4R, an **A**uto-regressive **R**obotic **M**odel that leverages low-level **4**D **R**epresentations learned from human video data to yield a better pre-trained robotic model. Specifically, we focus on utilizing 3D point tracking representations from videos derived by lifting 2D representations into 3D space via monocular depth estimation across time. These 4D representations maintain a shared geometric structure between the points and robot state representations up to a linear transformation, enabling efficient transfer learning from human video data to low-level robotic control. Our experiments show that ARM4R can transfer efficiently from human video data to robotics and consistently improves performance on tasks across various robot environments and configurations.