Publications

The randomized singular value decomposition (SVD) has become a popular approach to computing cheap, yet accurate, low-rank approximations to matrices due to its efficiency and strong theoretical guarantees. Recent work by Boullé and Townsend [Found. Comput. Math., 23 (2023), pp. 709–739] presents an infinite-dimensional analogue of the randomized SVD to approximate Hilbert–Schmidt operators. However, many applications involve computing low-rank approximations to symmetric positive semi-definite matrices. In this setting, it is well established that the randomized Nyström approximation is usually preferred over the randomized SVD. This paper explores an infinite-dimensional analogue of the Nyström approximation to compute low-rank approximations to non-negative self-adjoint trace-class operators. We present an analysis of the method and, along the way, improve the existing infinite-dimensional bounds for the randomized SVD. Our analysis yields bounds on the expected value and tail bounds for the Nyström approximation error in the operator, trace, and Hilbert–Schmidt norms. Numerical experiments on integral operators arising from Gaussian process sampling and Bayesian inverse problems are used to validate the proposed infinite-dimensional Nyström algorithm.

We introduce a Fourier-based fast algorithm for Gaussian process regression in low dimensions. It approximates a translationally invariant covariance kernel by complex exponentials on an equispaced Cartesian frequency grid of \(M\) nodes. This results in a weight-space \(M\times M\) system matrix with Toeplitz structure, which can thus be applied to a vector in \({\mathcal O}(M \log{M})\) operations via the fast Fourier transform (FFT), independent of the number of data points \(N\). The linear system can be set up in \({\mathcal O}(N+M \log{M})\) operations using nonuniform FFTs. This enables efficient massive-scale regression via an iterative solver, even for kernels with fat-tailed spectral densities (large \(M\)). We provide bounds on both kernel approximation and posterior mean errors. Numerical experiments for squared-exponential and Matérn kernels in one, two, and three dimensions often show 1–2 orders of magnitude acceleration over state-of-the-art rank-structured solvers at comparable accuracy. Our method allows two-dimensional Matérn-\(\frac{3}{2}\) regression from \(N=10^9\) data points to be performed in two minutes on a standard desktop, with posterior mean accuracy \(10^{-3}\). This opens up spatial statistics applications 100 times larger than previously possible.

Extracting conformational heterogeneity from cryo-electron microscopy (cryo-EM) images is particularly challenging for flexible biomolecules, where traditional 3D classification approaches often fail. Over the past few decades, advancements in experimental and computational techniques have been made to tackle this challenge, especially Bayesian-based approaches that provide physically interpretable insights into cryo-EM heterogeneity. To reduce the computational cost for Bayesian approaches, and building upon previously developed Fourier–Bessel image-representation methods, we created CryoLike, computationally efficient software for evaluating image-to-structure (or image-to-volume) likelihoods across large image data sets, packaged in a user-friendly Python workflow.

Notwithstanding the evidence against them, classical variational phase-field models continue to be used and pursued in an attempt to describe fracture nucleation in elastic brittle materials. In this context, the main objective of this paper is to provide a comprehensive review of the existing evidence against such a class of models as descriptors of fracture nucleation. To that end, a review is first given of the plethora of experimental observations of fracture nucleation in nominally elastic brittle materials under quasi-static loading conditions, as well as of classical variational phase-field models, without and with energy splits. These models are then confronted with the experimental observations. The conclusion is that they cannot possibly describe fracture nucleation in general. This because classical variational phase-field models cannot account for material strength as an independent macroscopic material property. The last part of the paper includes a brief summary of a class of phase-field models that can describe fracture nucleation. It also provides a discussion of how pervasively material strength has been overlooked in the analysis of fracture at large, as well as an outlook into the modeling of fracture nucleation beyond the basic setting of elastic brittle materials.

Extracting conformational heterogeneity from cryo-electron microscopy (cryo-EM) images is particularly challenging for flexible biomolecules, where traditional 3D classification approaches often fail. Over the past few decades, advancements in experimental and computational techniques have been made to tackle this challenge, especially Bayesian-based approaches that provide physically interpretable insights into cryo-EM heterogeneity. To reduce the computational cost for Bayesian approaches, and building upon previously developed Fourier–Bessel image-representation methods, we created CryoLike, computationally efficient software for evaluating image-to-structure (or image-to-volume) likelihoods across large image data sets, packaged in a user-friendly Python workflow.

Notwithstanding the evidence against them, classical variational phase-field models continue to be used and pursued in an attempt to describe fracture nucleation in elastic brittle materials. In this context, the main objective of this paper is to provide a comprehensive review of the existing evidence against such a class of models as descriptors of fracture nucleation. To that end, a review is first given of the plethora of experimental observations of fracture nucleation in nominally elastic brittle materials under quasi-static loading conditions, as well as of classical variational phase-field models, without and with energy splits. These models are then confronted with the experimental observations. The conclusion is that they cannot possibly describe fracture nucleation in general. This because classical variational phase-field models cannot account for material strength as an independent macroscopic material property. The last part of the paper includes a brief summary of a class of phase-field models that can describe fracture nucleation. It also provides a discussion of how pervasively material strength has been overlooked in the analysis of fracture at large, as well as an outlook into the modeling of fracture nucleation beyond the basic setting of elastic brittle materials.

The two-dimensional (2D) homogeneous electron gas (HEG) is a fundamental model in quantum many-body physics. It is important to theoretical and computational studies, where exchange-correlation energies computed in it serve as the foundation for density-functional calculations. It is also of direct relevance to a variety of experimental settings, especially with the rapid recent growth in 2D materials and moiré systems. In these experiments, metallic gates are often present, which screen the Coulomb interaction between electrons. The effect of the screening can qualitatively change the behavior of the 2D HEG, and requires accurate many-body computations to capture. In this work, we perform state-of-the-art diffusion Monte Carlo (DMC) calculations in the 2D HEG subjected to symmetric dual-gate screening. We systematically compute the correlation energy across a range of densities and gate separations for both spin unpolarized and fully polarized systems. A global fit is obtained for the correlation energy, using these data and imposing various limiting behaviors obtained from perturbation analysis. The new functional will allow density-functional calculations to be performed for a variety of realistic experimental setups which can accurately account for the presence of gates. We also investigate how the gate screening affects the bulk modulus, pair correlation function, and the structure factor of the 2D HEG, which can potentially be probed in experiments.

The two-dimensional (2D) homogeneous electron gas (HEG) is a fundamental model in quantum many-body physics. It is important to theoretical and computational studies, where exchange-correlation energies computed in it serve as the foundation for density-functional calculations. It is also of direct relevance to a variety of experimental settings, especially with the rapid recent growth in 2D materials and moiré systems. In these experiments, metallic gates are often present, which screen the Coulomb interaction between electrons. The effect of the screening can qualitatively change the behavior of the 2D HEG, and requires accurate many-body computations to capture. In this work, we perform state-of-the-art diffusion Monte Carlo (DMC) calculations in the 2D HEG subjected to symmetric dual-gate screening. We systematically compute the correlation energy across a range of densities and gate separations for both spin unpolarized and fully polarized systems. A global fit is obtained for the correlation energy, using these data and imposing various limiting behaviors obtained from perturbation analysis. The new functional will allow density-functional calculations to be performed for a variety of realistic experimental setups which can accurately account for the presence of gates. We also investigate how the gate screening affects the bulk modulus, pair correlation function, and the structure factor of the 2D HEG, which can potentially be probed in experiments.

In recent years, neuroscience has made significant progress in building large-scale artificial neural network (ANN) models of brain activity and behavior. However, there is no consensus on the most efficient ways to collect data and design experiments to develop the next generation of models. This article explores the controversial opinions that have emerged on this topic in the domain of vision and language. Specifically, we address two critical points. First, we weigh the pros and cons of using qualitative insights from empirical results versus raw experimental data to train models. Second, we consider model-free (intuition-based) versus model-based approaches for data collection, specifically experimental design and stimulus selection, for optimal model development. Finally, we consider the challenges of developing a synergistic approach to experimental design and model building, including encouraging data and model sharing and the implications of iterative additions to existing models. The goal of the paper is to discuss decision points and propose directions for both experimenters and model developers in the quest to understand the brain.

Tensor network contractions are widely used in statistical physics, quantum computing, and computer science. We introduce a method to efficiently approximate tensor network contractions using low-rank approximations, where each intermediate tensor generated during the contractions is approximated as a low-rank binary tree tensor network. The proposed algorithm has the flexibility to incorporate a large portion of the environment when performing low-rank approximations, which can lead to high accuracy for a given rank. Here, the environment refers to the remaining set of tensors in the network, and low-rank approximations with larger environments can generally provide higher accuracy. For contracting tensor networks defined on lattices, the proposed algorithm can be viewed as a generalization of the standard boundary-based algorithms. In addition, the algorithm includes a cost-efficient density matrix algorithm for approximating a tensor network with a general graph structure into a tree structure, whose computational cost is asymptotically upper-bounded by that of the standard algorithm that uses canonicalization. Experimental results indicate that the proposed technique outperforms previously proposed approximate tensor network contraction algorithms for multiple problems in terms of both accuracy and efficiency.