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Physical Models · Climate

Salva Rühling Cachay, Brian Henn, Oliver Watt-Meyer, Christopher S. Bretherton, Rose Yu

Data-driven deep learning models are transforming global weather forecasting. It is an open question if this success can extend to climate modeling, where the complexity of the data and long inference rollouts pose significant challenges. Here, we present the first conditional generative model that produces accurate and physically consistent global climate ensemble simulations by emulating a coarse version of the United States' primary operational global forecast model, FV3GFS.Our model integrates the dynamics-informed diffusion framework (DYffusion) with the Spherical Fourier Neural Operator (SFNO) architecture, enabling stable 100-year simulations at 6-hourly timesteps while maintaining low computational overhead compared to single-step deterministic baselines.The model achieves near gold-standard performance for climate model emulation, outperforming existing approaches and demonstrating promising ensemble skill.This work represents a significant advance towards efficient, data-driven climate simulations that can enhance our understanding of the climate system and inform adaptation strategies. Code is available at [https://github.com/Rose-STL-Lab/spherical-dyffusion](https://github.com/Rose-STL-Lab/spherical-dyffusion).

Miscellaneous Aspects of Machine Learning · General Machine Learning Techniques

Samuel Holt, Zhaozhi Qian, Tennison Liu, Jim Weatherall, Mihaela van der Schaar

The discovery of dynamical systems is crucial across a range of fields, including pharmacology, epidemiology, and physical sciences. *Accurate* and *interpretable* modeling of these systems is essential for understanding complex temporal processes, optimizing interventions, and minimizing adverse effects. In pharmacology, for example, precise modeling of drug dynamics is vital to maximize therapeutic efficacy while minimizing patient harm, as in chemotherapy. However, current models, often developed by human experts, are limited by high cost, lack of scalability, and restriction to existing human knowledge. In this paper, we present the **Data-Driven Discovery (D3)** framework, a novel approach leveraging Large Language Models (LLMs) to iteratively discover and refine interpretable models of dynamical systems, demonstrated here with pharmacological applications. Unlike traditional methods, D3 enables the LLM to propose, acquire, and integrate new features, validate, and compare dynamical systems models, uncovering new insights into pharmacokinetics. Experiments on a pharmacokinetic Warfarin dataset reveal that D3 identifies a new plausible model that is well-fitting, highlighting its potential for precision dosing in clinical applications.

Miscellaneous Aspects of Machine Learning · General Machine Learning Techniques

William Redman, Juan Bello-Rivas, Maria Fonoberova, Ryan Mohr, Yannis Kevrekidis, Igor Mezic

Study of the nonlinear evolution deep neural network (DNN) parameters undergo during training has uncovered regimes of distinct dynamical behavior. While a detailed understanding of these phenomena has the potential to advance improvements in training efficiency and robustness, the lack of methods for identifying when DNN models have equivalent dynamics limits the insight that can be gained from prior work. Topological conjugacy, a notion from dynamical systems theory, provides a precise definition of dynamical equivalence, offering a possible route to address this need. However, topological conjugacies have historically been challenging to compute. By leveraging advances in Koopman operator theory, we develop a framework for identifying conjugate and non-conjugate training dynamics. To validate our approach, we demonstrate that comparing Koopman eigenvalues can correctly identify a known equivalence between online mirror descent and online gradient descent. We then utilize our approach to: (a) identify non-conjugate training dynamics between shallow and wide fully connected neural networks; (b) characterize the early phase of training dynamics in convolutional neural networks; (c) uncover non-conjugate training dynamics in Transformers that do and do not undergo grokking. Our results, across a range of DNN architectures, illustrate the flexibility of our framework and highlight its potential for shedding new light on training dynamics.

Robotics

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

Diffusion models have demonstrated remarkable capabilities in image generation tasks, including image editing and video creation, representing a good understanding of the physical world. On the other line, diffusion models have also shown promise in robotic control tasks by denoising actions, known as diffusion policy. Although the diffusion generative model and diffusion policy exhibit distinct capabilities—image prediction and robotic action, respectively—they technically follow similar denoising process. In robotic tasks, the ability to predict future images and generate actions is highly correlated since they share the same underlying dynamics of the physical world. Building on this insight, we introduce \textbf{PAD}, a novel visual policy learning framework that unifies image \textbf{P}rediction and robot \textbf{A}ction within a joint \textbf{D}enoising process. Specifically, PAD utilizes Diffusion Transformers (DiT) to seamlessly integrate images and robot states, enabling the simultaneous prediction of future images and robot actions. Additionally, PAD supports co-training on both robotic demonstrations and large-scale video datasets and can be easily extended to other robotic modalities, such as depth images. PAD outperforms previous methods, achieving a significant 38.9\% relative improvement on the full Metaworld benchmark, by utilizing a single text-conditioned visual policy within a data-efficient imitation learning setting. Furthermore, PAD demonstrates superior generalization to unseen tasks in real-world robot manipulation settings with 28.0\% success rate increase compared to the strongest baseline. Videos of PAD can be found at https://sites.google.com/view/pad-paper

Deep Learning · Robustness

ZAITANG LI, Pin-Yu Chen, Tsung-Yi Ho

Current studies on adversarial robustness mainly focus on aggregating \textit{local} robustness results from a set of data samples to evaluate and rank different models. However, the local statistics may not well represent the true \textit{global} robustness of the underlying unknown data distribution. To address this challenge, this paper makes the first attempt to present a new framework, called \textit{GREAT Score}, for global robustness evaluation of adversarial perturbation using generative models. Formally, GREAT Score carries the physical meaning of a global statistic capturing a mean certified attack-proof perturbation level over all samples drawn from a generative model. For finite-sample evaluation, we also derive a probabilistic guarantee on the sample complexity and the difference between the sample mean and the true mean. GREAT Score has several advantages: (1) Robustness evaluations using GREAT Score are efficient and scalable to large models, by sparing the need of running adversarial attacks. In particular, we show high correlation and significantly reduced computation cost of GREAT Score when compared to the attack-based model ranking on RobustBench \cite{croce2021robustbench}. (2) The use of generative models facilitates the approximation of the unknown data distribution. In our ablation study with different generative adversarial networks (GANs), we observe consistency between global robustness evaluation and the quality of GANs. (3) GREAT Score can be used for remote auditing of privacy-sensitive black-box models, as demonstrated by our robustness evaluation on several online facial recognition services.

Physical Models · Physics

Jiahe Huang, Guandao Yang, Zichen Wang, Jeong Joon Park

We introduce a general framework for solving partial differential equations (PDEs) using generative diffusion models. In particular, we focus on the scenarios where we do not have the full knowledge of the scene necessary to apply classical solvers. Most existing forward or inverse PDE approaches perform poorly when the observations on the data or the underlying coefficients are incomplete, which is a common assumption for real-world measurements. In this work, we propose DiffusionPDE that can simultaneously fill in the missing information and solve a PDE by modeling the joint distribution of the solution and coefficient spaces. We show that the learned generative priors lead to a versatile framework for accurately solving a wide range of PDEs under partial observation, significantly outperforming the state-of-the-art methods for both forward and inverse directions.

Deep Learning · Theory

Jeongjin Park, Nicole Yang, Nisha Chandramoorthy

Conventional notions of generalization often fail to describe the ability of learned models to capture meaningful information from dynamical data. A neural network that learns complex dynamics with a small test error may still fail to reproduce its \emph{physical} behavior, including associated statistical moments and Lyapunov exponents. To address this gap, we propose an ergodic theoretic approach to generalization of complex dynamical models learned from time series data. Our main contribution is to define and analyze generalization of a broad suite of neural representations of classes of ergodic systems, including chaotic systems, in a way that captures emulating underlying invariant, physical measures. Our results provide theoretical justification for why regression methods for generators of dynamical systems (Neural ODEs) fail to generalize, and why their statistical accuracy improves upon adding Jacobian information during training. We verify our results on a number of ergodic chaotic systems and neural network parameterizations, including MLPs, ResNets, Fourier Neural layers, and RNNs.

Physical Models · Physics

Philipp Schleich, Marta Skreta, Lasse Kristensen, Rodrigo Vargas-Hernandez, Alan Aspuru-Guzik

The feasibility of variational quantum algorithms, the most popular correspondent of neural networks on noisy, near-term quantum hardware, is highly impacted by the circuit depth of the involved parametrized quantum circuits (PQCs). Higher depth increases expressivity, but also results in a detrimental accumulation of errors. Furthermore, the number of parameters involved in the PQC significantly influences the performance through the necessary number of measurements to evaluate gradients, which scales linearly with the number of parameters. Motivated by this, we look at deep equilibrium models (DEQs), which mimic an infinite-depth, weight-tied network using a fraction of the memory by employing a root solver to find the fixed points of the network. In this work, we present Quantum Deep Equilibrium Models (QDEQs): a training paradigm that learns parameters of a quantum machine learning model given by a PQC using DEQs. To our knowledge, no work has yet explored the application of DEQs to QML models. We apply QDEQs to find the parameters of a quantum circuit in two settings: the first involves classifying MNIST-4 digits with 4 qubits; the second extends it to 10 classes of MNIST, FashionMNIST and CIFAR. We find that QDEQ is not only competitive with comparable existing baseline models, but also achieves higher performance than a network with 5 times more layers. This demonstrates that the QDEQ paradigm can be used to develop significantly more shallow quantum circuits for a given task, something which is essential for the utility of near-term quantum computers. Our code is available at \url{https://github.com/martaskrt/qdeq}.

Computational Biology

Leon Klein, Frank Noe

The generation of equilibrium samples of molecular systems has been a long-standing problem in statistical physics. Boltzmann Generators are a generative machine learning method that addresses this issue by learning a transformation via a normalizing flow from a simple prior distribution to the target Boltzmann distribution of interest. Recently, flow matching has been employed to train Boltzmann Generators for small molecular systems in Cartesian coordinates. We extend this work and propose a first framework for Boltzmann Generators that are transferable across chemical space, such that they predict zero-shot Boltzmann distributions for test molecules without being retraining for these systems. These transferable Boltzmann Generators allow approximate sampling from the target distribution of unseen systems, as well as efficient reweighting to the target Boltzmann distribution. The transferability of the proposed framework is evaluated on dipeptides, where we show that it generalizes efficiently to unseen systems.Furthermore, we demonstrate that our proposed architecture enhances the efficiency of Boltzmann Generators trained on single molecular systems.

Statistical Methods

Hamidreza Hashempoorikderi, Wan Choi

This paper advances temporal reasoning within dynamically changing high-dimensional noisy observations, focusing on a latent space that characterizes the nonlinear dynamics of objects in their environment. We introduce the *Gated Inference Network* (GIN), an efficient approximate Bayesian inference algorithm for state space models (SSMs) with nonlinear state transitions and emissions. GIN disentangles two latent representations: one representing the object derived from a nonlinear mapping model, and another representing the latent state describing its dynamics. This disentanglement enables direct state estimation and missing data imputation as the world evolves. To infer the latent state, we utilize a deep extended Kalman filter (EKF) approach that integrates a novel compact RNN structure to compute both the Kalman Gain (KG) and smoothing gain (SG), completing the data flow. This design results in a computational cost per step that is linearly faster than EKF but introduces issues such as the exploding gradient problem. To mitigate the exploding gradients caused by the compact RNN structure in our model, we propose a specialized learning method that ensures stable training and inference. The model is then trained end-to-end on videos depicting a diverse range of simulated and real-world physical systems, and outperforms its ounterparts —RNNs, autoregressive models, and variational approaches— in state estimation and missing data imputation tasks.

Applications

Keying Kuang, Frances Dean, Jack B. Jedlicki, David Ouyang, Anthony Philippakis, David Sontag, Ahmed Alaa

A digital twin is a virtual replica of a real-world physical phenomena that uses mathematical modeling to characterize and simulate its defining features. By constructing digital twins for disease processes, we can perform in-silico simulations that mimic patients' health conditions and counterfactual outcomes under hypothetical interventions in a virtual setting. This eliminates the need for invasive procedures or uncertain treatment decisions. In this paper, we propose a method to identify digital twin model parameters using only noninvasive patient health data. We approach the digital twin modeling as a composite inverse problem, and observe that its structure resembles pretraining and finetuning in self-supervised learning (SSL). Leveraging this, we introduce a physics-informed SSL algorithm that initially pretrains a neural network on the pretext task of learning a differentiable simulator of a physiological process. Subsequently, the model is trained to reconstruct physiological measurements from noninvasive modalities while being constrained by the physical equations learned in pretraining. We apply our method to identify digital twins of cardiac hemodynamics using noninvasive echocardiogram videos, and demonstrate its utility in unsupervised disease detection and in-silico clinical trials.

Haixu Wu, Huakun Luo, Yuezhou Ma, Jianmin Wang, Mingsheng Long

Physics-informed neural networks (PINNs) have been widely applied to solve partial differential equations (PDEs) by enforcing outputs and gradients of deep models to satisfy target equations. Due to the limitation of numerical computation, PINNs are conventionally optimized on finite selected points. However, since PDEs are usually defined on continuous domains, solely optimizing models on scattered points may be insufficient to obtain an accurate solution for the whole domain. To mitigate this inherent deficiency of the default scatter-point optimization, this paper proposes and theoretically studies a new training paradigm as region optimization. Concretely, we propose to extend the optimization process of PINNs from isolated points to their continuous neighborhood regions, which can theoretically decrease the generalization error, especially for hidden high-order constraints of PDEs. A practical training algorithm, Region Optimized PINN (RoPINN), is seamlessly derived from this new paradigm, which is implemented by a straightforward but effective Monte Carlo sampling method. By calibrating the sampling process into trust regions, RoPINN finely balances optimization and generalization error. Experimentally, RoPINN consistently boosts the performance of diverse PINNs on a wide range of PDEs without extra backpropagation or gradient calculation. Code is available at this repository: https://github.com/thuml/RoPINN.

Physical Models · Geoscience

Joel Oskarsson, Tomas Landelius, Marc Deisenroth, Fredrik Lindsten

In recent years, machine learning has established itself as a powerful tool for high-resolution weather forecasting. While most current machine learning models focus on deterministic forecasts, accurately capturing the uncertainty in the chaotic weather system calls for probabilistic modeling. We propose a probabilistic weather forecasting model called Graph-EFM, combining a flexible latent-variable formulation with the successful graph-based forecasting framework. The use of a hierarchical graph construction allows for efficient sampling of spatially coherent forecasts. Requiring only a single forward pass per time step, Graph-EFM allows for fast generation of arbitrarily large ensembles. We experiment with the model on both global and limited area forecasting. Ensemble forecasts from Graph-EFM achieve equivalent or lower errors than comparable deterministic models, with the added benefit of accurately capturing forecast uncertainty.

Theory · Active Learning and Interactive Learning

Felix Teufel, Carsten Stahlhut, Jesper Ferkinghoff-Borg

Bayesian optimization (BO) is an attractive machine learning framework for performing sample-efficient global optimization of black-box functions. The optimization process is guided by an acquisition function that selects points to acquire in each round of BO. In batched BO, when multiple points are acquired in parallel, commonly used acquisition functions are often high-dimensional and intractable, leading to the use of sampling-based alternatives. We propose a statistical physics inspired acquisition function that can natively handle batches. Batched Energy-Entropy acquisition for BO (BEEBO) enables tight control of the explore-exploit trade-off of the optimization process and generalizes to heteroskedastic black-box problems. We demonstrate the applicability of BEEBO on a range of problems, showing competitive performance to existing acquisition functions.

Computer Vision · Stereo

Liqiang Lin, Wenpeng Wu, Chi-Wing Fu, Hao Zhang, Hui Huang

We introduce camera ray matching (CRAYM) into the joint optimization of camera poses and neural fields from multi-view images. The optimized field, referred to as a feature volume, can be “probed” by the camera rays for novel view synthesis (NVS) and 3D geometry reconstruction. One key reason for matching camera rays, instead of pixels as in prior works, is that the camera rays can be parameterized by the feature volume to carry both geometric and photometric information. Multi-view consistencies involving the camera rays and scene rendering can be naturally integrated into the joint optimization and network training, to impose physically meaningful constraints to improve the final quality of both the geometric reconstruction and photorealistic rendering. We formulate our per-ray optimization and matched ray coherence by focusing on camera rays passing through keypoints in the input images to elevate both the efficiency and accuracy of scene correspondences. Accumulated ray features along the feature volume provide a means to discount the coherence constraint amid erroneous ray matching. We demonstrate the effectiveness of CRAYM for both NVS and geometry reconstruction, over dense- or sparse-view settings, with qualitative and quantitative comparisons to state-of-the-art alternatives.

Optimization · Convex

Artem Agafonov, Petr Ostroukhov, Roman Mozhaev, Konstantin Yakovlev, Eduard Gorbunov, Martin Takac, Alexander Gasnikov, Dmitry Kamzolov

Variational inequalities represent a broad class of problems, including minimization and min-max problems, commonly found in machine learning. Existing second-order and high-order methods for variational inequalities require precise computation of derivatives, often resulting in prohibitively high iteration costs. In this work, we study the impact of Jacobian inaccuracy on second-order methods. For the smooth and monotone case, we establish a lower bound with explicit dependence on the level of Jacobian inaccuracy and propose an optimal algorithm for this key setting. When derivatives are exact, our method converges at the same rate as exact optimal second-order methods. To reduce the cost of solving the auxiliary problem, which arises in all high-order methods with global convergence, we introduce several Quasi-Newton approximations. Our method with Quasi-Newton updates achieves a global sublinear convergence rate. We extend our approach with a tensor generalization for inexact high-order derivatives and support the theory with experiments.

Physical Models

Hanqing Zhu, Wenyan Cong, Guojin Chen, Shupeng Ning, Ray Chen, Jiaqi Gu, David Z. Pan

Electromagnetic field simulation is central to designing, optimizing, and validating photonic devices and circuits. However, costly computation associated with numerical simulation poses a significant bottleneck, hindering scalability and turnaround time in the photonic circuit design process.Neural operators offer a promising alternative, but existing SOTA approaches, Neurolight, struggle with predicting high-fidelity fields for real-world complicated photonic devices, with the best reported 0.38 normalized mean absolute error in Neurolight.The interplays of highly complex light-matter interaction, e.g., scattering and resonance, sensitivity to local structure details, non-uniform learning complexity for full-domain simulation, and rich frequency information, contribute to the failure of existing neural PDE solvers.In this work, we boost the prediction fidelity to an unprecedented level for simulating complex photonic devices with a novel operator design driven by the above challenges.We propose a novel cross-axis factorized PACE operator with a strong long-distance modeling capacity to connect the full-domain complex field pattern with local device structures.Inspired by human learning, we further divide and conquer the simulation task for extremely hard cases into two progressively easy tasks, with a first-stage model learning an initial solution refined by a second model.On various complicated photonic device benchmarks, we demonstrate one sole PACE model is capable of achieving 73% lower error with 50% fewer parameters compared with various recent ML for PDE solvers.The two-stage setup further advances high-fidelity simulation for even more intricate cases.In terms of runtime, PACE demonstrates 154-577x and 11.8-12x simulation speedup over numerical solver using scipy or highly-optimized pardiso solver, respectively.We open-sourced the code and *complicated* optical device dataset at [PACE-Light](https://github.com/zhuhanqing/PACE-Light).

Deep Learning · Theory

Alessandro Betti, Marco Gori

The spectacular results achieved in machine learning, including the recent advances in generative AI, rely on large data collections. On the opposite, intelligent processes in nature arises without the need for such collections, but simply by on-line processing of the environmental information. In particular, natural learning processes rely on mechanisms where data representation and learning are intertwined in such a way to respect spatiotemporal locality. This paper shows that such a feature arises from a pre-algorithmic view of learning that is inspired by related studies in Theoretical Physics. We show that the algorithmic interpretation of the derived “laws of learning”, which takes the structure of Hamiltonian equations, reduces to Backpropagation when the speed of propagation goes to infinity. This opens the doors to machine learning studies based on full on-line information processing that are based on the replacement of Backpropagation with the proposed spatiotemporal local algorithm.

Tycho van der Ouderaa, Mark van der Wilk, Pim de Haan

Symmetries have proven useful in machine learning models, improving generalisation and overall performance. At the same time, recent advancements in learning dynamical systems rely on modelling the underlying Hamiltonian to guarantee the conservation of energy.These approaches can be connected via a seminal result in mathematical physics: Noether's theorem, which states that symmetries in a dynamical system correspond to conserved quantities.This work uses Noether's theorem to parameterise symmetries as learnable conserved quantities. We then allow conserved quantities and associated symmetries to be learned directly from train data through approximate Bayesian model selection, jointly with the regular training procedure. As training objective, we derive a variational lower bound to the marginal likelihood. The objective automatically embodies an Occam's Razor effect that avoids collapse of conversation laws to the trivial constant, without the need to manually add and tune additional regularisers. We demonstrate a proof-of-principle on n-harmonic oscillators and n-body systems. We find that our method correctly identifies the correct conserved quantities and U(n) and SE(n) symmetry groups, improving overall performance and predictive accuracy on test data.

Jiaxian Yan, ZAIXI ZHANG, Jintao Zhu, Kai Zhang, Jianfeng Pei, Qi Liu

Molecular docking, a technique for predicting ligand binding poses, is crucial in structure-based drug design for understanding protein-ligand interactions. Recent advancements in docking methods, particularly those leveraging geometric deep learning (GDL), have demonstrated significant efficiency and accuracy advantages over traditional sampling methods. Despite these advancements, current methods are often tailored for specific docking settings, and limitations such as the neglect of protein side-chain structures, difficulties in handling large binding pockets, and challenges in predicting physically valid structures exist. To accommodate various docking settings and achieve accurate, efficient, and physically reliable docking, we propose a novel two-stage docking framework, DeltaDock, consisting of pocket prediction and site-specific docking. We innovatively reframe the pocket prediction task as a pocket-ligand alignment problem rather than direct prediction in the first stage. Then we follow a bi-level coarse-to-fine iterative refinement process to perform site-specific docking. Comprehensive experiments demonstrate the superior performance of DeltaDock. Notably, in the blind docking setting, DeltaDock achieves a 31\% relative improvement over the docking success rate compared with the previous state-of-the-art GDL model DiffDock. With the consideration of physical validity, this improvement increases to about 300\%.