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Recent advances in deep learning have inspired numerous works on data-driven solutions to partial differential equation (PDE) problems. These neural PDE solvers can often be much faster than their numerical counterparts; however, each presents its unique limitations and generally balances training cost, numerical accuracy, and ease of applicability to different problem setups. To address these limitations, we introduce several methods to apply latent diffusion models to physics simulation. Firstly, we introduce a mesh autoencoder to compress arbitrarily discretized PDE data, allowing for efficient diffusion training across various physics. Furthermore, we investigate full spatio-temporal solution generation to mitigate autoregressive error accumulation. Lastly, we investigate conditioning on initial physical quantities, as well as conditioning solely on a text prompt to introduce text2PDE generation. We show that language can be a compact, interpretable, and accurate modality for generating physics simulations, paving the way for more usable and accessible PDE solvers. Through experiments on both uniform and structured grids, we show that the proposed approach is competitive with current neural PDE solvers in both accuracy and efficiency, with promising scaling behavior up to $\sim$3 billion parameters. By introducing a scalable, accurate, and usable physics simulator, we hope to bring neural PDE solvers closer to practical use., Comment: 25 pages, 7 figures

Accurate weather forecasting is crucial in various sectors, impacting decision-making processes and societal events. Data-driven approaches based on machine learning models have recently emerged as a promising alternative to numerical weather prediction models given their potential to capture physics of different scales from historical data and the significantly lower computational cost during the prediction stage. Renowned for its state-of-the-art performance across diverse domains, the Transformer model has also gained popularity in machine learning weather prediction. Yet applying Transformer architectures to weather forecasting, particularly on a global scale is computationally challenging due to the quadratic complexity of attention and the quadratic increase in spatial points as resolution increases. In this work, we propose a factorized-attention-based model tailored for spherical geometries to mitigate this issue. More specifically, it utilizes multi-dimensional factorized kernels that convolve over different axes where the computational complexity of the kernel is only quadratic to the axial resolution instead of overall resolution. The deterministic forecasting accuracy of the proposed model on $1.5^\circ$ and 0-7 days' lead time is on par with state-of-the-art purely data-driven machine learning weather prediction models. We also showcase the proposed model holds great potential to push forward the Pareto front of accuracy-efficiency for Transformer weather models, where it can achieve better accuracy with less computational cost compared to Transformer based models with standard attention., Comment: Preprint

Neural networks have shown promising potential in accelerating the numerical simulation of systems governed by partial differential equations (PDEs). Different from many existing neural network surrogates operating on high-dimensional discretized fields, we propose to learn the dynamics of the system in the latent space with much coarser discretizations. In our proposed framework - Latent Neural PDE Solver (LNS), a non-linear autoencoder is first trained to project the full-order representation of the system onto the mesh-reduced space, then a temporal model is trained to predict the future state in this mesh-reduced space. This reduction process simplifies the training of the temporal model by greatly reducing the computational cost accompanying a fine discretization. We study the capability of the proposed framework and several other popular neural PDE solvers on various types of systems including single-phase and multi-phase flows along with varying system parameters. We showcase that it has competitive accuracy and efficiency compared to the neural PDE solver that operates on full-order space.

Fluid data completion is a research problem with high potential benefit for both experimental and computational fluid dynamics. An effective fluid data completion method reduces the required number of sensors in a fluid dynamics experiment, and allows a coarser and more adaptive mesh for a Computational Fluid Dynamics (CFD) simulation. However, the ill-posed nature of the fluid data completion problem makes it prohibitively difficult to obtain a theoretical solution and presents high numerical uncertainty and instability for a data-driven approach (e.g., a neural network model). To address these challenges, we leverage recent advancements in computer vision, employing the vector quantization technique to map both complete and incomplete fluid data spaces onto discrete-valued lower-dimensional representations via a two-stage learning procedure. We demonstrated the effectiveness of our approach on Kolmogorov flow data (Reynolds number: 1000) occluded by masks of different size and arrangement. Experimental results show that our proposed model consistently outperforms benchmark models under different occlusion settings in terms of point-wise reconstruction accuracy as well as turbulent energy spectrum and vorticity distribution., Comment: 20 pages, 9 figures

We propose a mask pretraining method for Graph Neural Networks (GNNs) to improve their performance on fitting potential energy surfaces, particularly in water systems. GNNs are pretrained by recovering spatial information related to masked-out atoms from molecules, then transferred and finetuned on atomic forcefields. Through such pretraining, GNNs learn meaningful prior about structural and underlying physical information of molecule systems that are useful for downstream tasks. From comprehensive experiments and ablation studies, we show that the proposed method improves the accuracy and convergence speed compared to GNNs trained from scratch or using other pretraining techniques such as denoising. On the other hand, our pretraining method is suitable for both energy-centric and force-centric GNNs. This approach showcases its potential to enhance the performance and data efficiency of GNNs in fitting molecular force fields.

Numerically solving partial differential equations typically requires fine discretization to resolve necessary spatiotemporal scales, which can be computationally expensive. Recent advances in deep learning have provided a new approach to solving partial differential equations that involves the use of neural operators. Neural operators are neural network architectures that learn mappings between function spaces and have the capability to solve partial differential equations based on data. This study utilizes a novel neural operator called Hyena, which employs a long convolutional filter that is parameterized by a multilayer perceptron. The Hyena operator is an operation that enjoys sub-quadratic complexity and state space model to parameterize long convolution that enjoys a global receptive field. This mechanism enhances the model's comprehension of the input's context and enables data-dependent weight for different partial differential equations instances. To measure how effective the layers are in solving partial differential equations, we conduct experiments on Diffusion-Reaction equation and Navier Stokes equation. Our findings indicate Hyena Neural operator can serve as an efficient and accurate model for learning partial differential equations solution operator. The data and code used can be found at: https://github.com/Saupatil07/Hyena-Neural-Operator

Transformer has shown state-of-the-art performance on various applications and has recently emerged as a promising tool for surrogate modeling of partial differential equations (PDEs). Despite the introduction of linear-complexity attention, applying Transformer to problems with a large number of grid points can be numerically unstable and computationally expensive. In this work, we propose Factorized Transformer (FactFormer), which is based on an axial factorized kernel integral. Concretely, we introduce a learnable projection operator that decomposes the input function into multiple sub-functions with one-dimensional domain. These sub-functions are then evaluated and used to compute the instance-based kernel with an axial factorized scheme. We showcase that the proposed model is able to simulate 2D Kolmogorov flow on a $256\times 256$ grid and 3D smoke buoyancy on a $64\times64\times64$ grid with good accuracy and efficiency. The proposed factorized scheme can serve as a computationally efficient low-rank surrogate for the full attention scheme when dealing with multi-dimensional problems.

Solving Partial Differential Equations (PDEs) is the core of many fields of science and engineering. While classical approaches are often prohibitively slow, machine learning models often fail to incorporate complete system information. Over the past few years, transformers have had a significant impact on the field of Artificial Intelligence and have seen increased usage in PDE applications. However, despite their success, transformers currently lack integration with physics and reasoning. This study aims to address this issue by introducing PITT: Physics Informed Token Transformer. The purpose of PITT is to incorporate the knowledge of physics by embedding partial differential equations (PDEs) into the learning process. PITT uses an equation tokenization method to learn an analytically-driven numerical update operator. By tokenizing PDEs and embedding partial derivatives, the transformer models become aware of the underlying knowledge behind physical processes. To demonstrate this, PITT is tested on challenging 1D and 2D PDE neural operator prediction tasks. The results show that PITT outperforms popular neural operator models and has the ability to extract physically relevant information from governing equations., Comment: 23 pages, 5 figures

Recent advances in equivariant graph neural networks (GNNs) have made deep learning amenable to developing fast surrogate models to expensive ab initio quantum mechanics (QM) approaches for molecular potential predictions. However, building accurate and transferable potential models using GNNs remains challenging, as the data is greatly limited by the expensive computational costs and level of theory of QM methods, especially for large and complex molecular systems. In this work, we propose denoise pretraining on nonequilibrium molecular conformations to achieve more accurate and transferable GNN potential predictions. Specifically, atomic coordinates of sampled nonequilibrium conformations are perturbed by random noises and GNNs are pretrained to denoise the perturbed molecular conformations which recovers the original coordinates. Rigorous experiments on multiple benchmarks reveal that pretraining significantly improves the accuracy of neural potentials. Furthermore, we show that the proposed pretraining approach is model-agnostic, as it improves the performance of different invariant and equivariant GNNs. Notably, our models pretrained on small molecules demonstrate remarkable transferability, improving performance when fine-tuned on diverse molecular systems, including different elements, charged molecules, biomolecules, and larger systems. These results highlight the potential for leveraging denoise pretraining approaches to build more generalizable neural potentials for complex molecular systems., Comment: Published in Journal of Chemical Theory and Computation. 32 pages, 5 figures, 2 tables

Machine learning models are gaining increasing popularity in the domain of fluid dynamics for their potential to accelerate the production of high-fidelity computational fluid dynamics data. However, many recently proposed machine learning models for high-fidelity data reconstruction require low-fidelity data for model training. Such requirement restrains the application performance of these models, since their data reconstruction accuracy would drop significantly if the low-fidelity input data used in model test has a large deviation from the training data. To overcome this restraint, we propose a diffusion model which only uses high-fidelity data at training. With different configurations, our model is able to reconstruct high-fidelity data from either a regular low-fidelity sample or a sparsely measured sample, and is also able to gain an accuracy increase by using physics-informed conditioning information from a known partial differential equation when that is available. Experimental results demonstrate that our model can produce accurate reconstruction results for 2d turbulent flows based on different input sources without retraining.

Graph neural networks (GNNs), which are capable of learning representations from graphical data, are naturally suitable for modeling molecular systems. This review introduces GNNs and their various applications for small organic molecules. GNNs rely on message-passing operations, a generic yet powerful framework, to update node features iteratively. Many researches design GNN architectures to effectively learn topological information of 2D molecule graphs as well as geometric information of 3D molecular systems. GNNs have been implemented in a wide variety of molecular applications, including molecular property prediction, molecular scoring and docking, molecular optimization and de novo generation, molecular dynamics simulation, etc. Besides, the review also summarizes the recent development of self-supervised learning for molecules with GNNs., Comment: A chapter for the book "Machine Learning in Molecular Sciences". 31 pages, 4 figures

Data-driven learning of partial differential equations' solution operators has recently emerged as a promising paradigm for approximating the underlying solutions. The solution operators are usually parameterized by deep learning models that are built upon problem-specific inductive biases. An example is a convolutional or a graph neural network that exploits the local grid structure where functions' values are sampled. The attention mechanism, on the other hand, provides a flexible way to implicitly exploit the patterns within inputs, and furthermore, relationship between arbitrary query locations and inputs. In this work, we present an attention-based framework for data-driven operator learning, which we term Operator Transformer (OFormer). Our framework is built upon self-attention, cross-attention, and a set of point-wise multilayer perceptrons (MLPs), and thus it makes few assumptions on the sampling pattern of the input function or query locations. We show that the proposed framework is competitive on standard benchmark problems and can flexibly be adapted to randomly sampled input.

Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive. In each MD step, numerous iterative computations are performed to calculate energy based on different types of interaction and their corresponding spatial gradients. These repetitive computations can be learned and surrogated by a deep learning model like a Graph Neural Network (GNN). In this work, we developed a GNN Accelerated Molecular Dynamics (GAMD) model that directly predicts forces given the state of the system (atom positions, atom types), bypassing the evaluation of potential energy. By training the GNN on a variety of data sources (simulation data derived from classical MD and density functional theory), we show that GAMD can predict the dynamics of two typical molecular systems, Lennard-Jones system and Water system, in the NVT ensemble with velocities regulated by a thermostat. We further show that GAMD's learning and inference are agnostic to the scale, where it can scale to much larger systems at test time. We also perform a comprehensive benchmark test comparing our implementation of GAMD to production-level MD softwares, showing GAMD's competitive performance on the large-scale simulation., Comment: preprint