Dynamical systems are found in innumerable forms across the physical and biological sciences, yet all these systems fall naturally into equivalence classes: conservative or dissipative, stable or unstable, compressible or incompressible. Predicting these classes from data remains an essential open challenge in computational physics on which existing time-series classification methods struggle. Here, we propose, phase2vec, an embedding method that learns high-quality, physically-meaningful representations of low-dimensional dynamical systems without supervision. Our embeddings are produced by a convolutional backbone that extracts geometric features from flow data and minimizes a physically-informed vector field reconstruction loss. The trained architecture can not only predict the equations of unseen data, but also produces embeddings that encode meaningful physical properties of input data (e.g. stability of fixed points, conservation of energy, and the incompressibility of flows) more faithfully than standard blackbox classifiers and state-of-the-art time series classification techniques. We additionally apply our embeddings to the analysis of meteorological data, showing we can detect climatically meaningful features. Collectively, our results demonstrate the viability of embedding approaches for the discovery of dynamical features in physical systems.

We present a data-driven, space-time continuous framework to learn surrogate models for complex physical systems described by advection-dominated partial differential equations. Those systems have slow-decaying Kolmogorov n-width that hinders standard methods, including reduced order modeling, from producing high-fidelity simulations at low cost. In this work, we construct hypernetwork-based latent dynamical models directly on the parameter space of a compact representation network. We leverage the expressive power of the network and a specially designed consistency-inducing regularization to obtain latent trajectories that are both low-dimensional and smooth. These properties render our surrogate models highly efficient at inference time. We show the efficacy of our framework by learning models that generate accurate multi-step rollout predictions at much faster inference speed compared to competitors, for several challenging examples.

Weather and climate simulations produce petabytes of high-resolution data that are later analyzed by researchers in order to understand climate change or severe weather. We propose a new method of compressing this multidimensional weather and climate data: a coordinate-based neural network is trained to overfit the data, and the resulting parameters are taken as a compact representation of the original grid-based data. While compression ratios range from 300x to more than 3,000x, our method outperforms the state-of-the-art compressor SZ3 in terms of weighted RMSE, MAE. It can faithfully preserve important large scale atmosphere structures and does not introduce significant artifacts.When using the resulting neural network as a 790x compressed dataloader to train the WeatherBench forecasting model, its RMSE increases by less than 2%. The three orders of magnitude compression democratizes access to high-resolution climate data and enables numerous new research directions.

Kohn-Sham Density Functional Theory (KS-DFT) has been traditionally solved by the Self-Consistent Field (SCF) method. Behind the SCF loop is the physics intuition of solving a system of non-interactive single-electron wave functions under an effective potential. In this work, we propose a deep learning approach to KS-DFT. First, in contrast to the conventional SCF loop, we propose to directly minimize the total energy by reparameterizing the orthogonal constraint as a feed-forward computation. We prove that such an approach has the same expressivity as the SCF method, yet reduces the computational complexity from O(N^4) to O(N^3). Second, the numerical integration which involves a summation over the quadrature grids can be amortized to the optimization steps. At each step, stochastic gradient descent (SGD) is performed with a sampled minibatch of the grids. Extensive experiments are carried out to demonstrate the advantage of our approach in terms of efficiency and stability. In addition, we show that our approach enables us to explore more complex neural-based wave functions.

Antibody design is valuable for therapeutic usage and biological research. Existing deep-learning-based methods encounter several key issues: 1) incomplete context for Complementarity-Determining Regions (CDRs) generation; 2) incapability of capturing the entire 3D geometry of the input structure; 3) inefficient prediction of the CDR sequences in an autoregressive manner. In this paper, we propose Multi-channel Equivariant Attention Network (MEAN) to co-design 1D sequences and 3D structures of CDRs. To be specific, MEAN formulates antibody design as a conditional graph translation problem by importing extra components including the target antigen and the light chain of the antibody. Then, MEAN resorts to E(3)-equivariant message passing along with a proposed attention mechanism to better capture the geometrical correlation between different components. Finally, it outputs both the 1D sequences and 3D structure via a multi-round progressive full-shot scheme, which enjoys more efficiency and precision against previous autoregressive approaches. Our method significantly surpasses state-of-the-art models in sequence and structure modeling, antigen-binding CDR design, and binding affinity optimization. Specifically, the relative improvement to baselines is about 23\% in antigen-binding CDR design and 34\% for affinity optimization.

Despite their widespread success in various domains, Transformer networks have yet to perform well across datasets in the domain of 3D atomistic graphs such as molecules even when 3D-related inductive biases like translational invariance and rotational equivariance are considered. In this paper, we demonstrate that Transformers can generalize well to 3D atomistic graphs and present Equiformer, a graph neural network leveraging the strength of Transformer architectures and incorporating SE(3)/E(3)-equivariant features based on irreducible representations (irreps). First, we propose a simple and effective architecture by only replacing original operations in Transformers with their equivariant counterparts and including tensor products. Using equivariant operations enables encoding equivariant information in channels of irreps features without complicating graph structures. With minimal modifications to Transformers, this architecture has already achieved strong empirical results. Second, we propose a novel attention mechanism called equivariant graph attention, which improves upon typical attention in Transformers through replacing dot product attention with multi-layer perceptron attention and including non-linear message passing. With these two innovations, Equiformer achieves competitive results to previous models on QM9, MD17 and OC20 datasets.

The long runtime of high-fidelity partial differential equation (PDE) solvers makes them unsuitable for time-critical applications. We propose to accelerate PDE solvers using reduced-order modeling (ROM). Whereas prior ROM approaches reduce the dimensionality of discretized vector fields, our continuous reduced-order modeling (CROM) approach builds a low-dimensional embedding of the continuous vector fields themselves, not their discretization. We represent this reduced manifold using continuously differentiable neural fields, which may train on any and all available numerical solutions of the continuous system, even when they are obtained using diverse methods or discretizations. We validate our approach on an extensive range of PDEs with training data from voxel grids, meshes, and point clouds. Compared to prior discretization-dependent ROM methods, such as linear subspace proper orthogonal decomposition (POD) and nonlinear manifold neural-network-based autoencoders, CROM features higher accuracy, lower memory consumption, dynamically adaptive resolutions, and applicability to any discretization. For equal latent space dimension, CROM exhibits 79$\times$ and 49$\times$ better accuracy, and 39$\times$ and 132$\times$ smaller memory footprint, than POD and autoencoder methods, respectively. Experiments demonstrate 109$\times$ and 89$\times$ wall-clock speedups over unreduced models on CPUs and GPUs, respectively. Videos and codes are available on the project page: https://crom-pde.github.io