Related papers: Multiscale Gaussian network model (mGNM) and multi…

Machine learning methods on graphs have proven useful in many applications due to their ability to handle generally structured data. The framework of Gaussian Markov Random Fields (GMRFs) provides a principled way to define Gaussian models…

Quantum mechanical methods like Density Functional Theory (DFT) are used with great success alongside efficient search algorithms for studying kinetics of reactive systems. However, DFT is prohibitively expensive for large scale…

Geometric Graph Neural Networks (GNNs) and Transformers have become state-of-the-art for learning from 3D protein structures. However, their reliance on message passing prevents them from capturing the hierarchical interactions that govern…

Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico…

Predicting quantum wavefunction probability distributions is crucial for computational chemistry and materials science, yet machine learning (ML) models often face a trade-off between accuracy and interpretability. This study compares…

We study the power of query access for the task of agnostic learning under the Gaussian distribution. In the agnostic model, no assumptions are made on the labels and the goal is to compute a hypothesis that is competitive with the {\em…

Lagrangian and Hamiltonian neural networks (LNNs and HNNs, respectively) encode strong inductive biases that allow them to outperform other models of physical systems significantly. However, these models have, thus far, mostly been limited…

Graph neural network (GNN) potentials such as SchNet improve the accuracy and transferability of molecular dynamics (MD) simulation by learning many-body interactions, but remain slower than classical force fields due to fragmented kernels…

The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…

Deep Learners (DLs) are the state-of-art predictive mechanism with applications in many fields requiring complex high dimensional data processing. Although conventional DLs get trained via gradient descent with back-propagation, Kalman…

By chaining a sequence of differentiable invertible transformations, normalizing flows (NF) provide an expressive method of posterior approximation, exact density evaluation, and sampling. The trend in normalizing flow literature has been…

Ensembles of neural network weight matrices are studied through the training process for the MNIST classification problem, testing the efficacy of matrix models for representing their distributions, under assumptions of Gaussianity and…

Several Tensor Basis Neural Network (TBNN) frameworks aimed at enhancing turbulence RANS modeling have recently been proposed in the literature as data-driven constitutive models for systems with known invariance properties. However,…

The GMM (generalized min-max) kernel was recently proposed (Li, 2016) as a measure of data similarity and was demonstrated effective in machine learning tasks. In order to use the GMM kernel for large-scale datasets, the prior work resorted…

We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…

Fiber nonlinear interference (NLI) modeling and monitoring are the key building blocks to support elastic optical networks (EONs). In the past, they were normally developed and investigated separately. Moreover, the accuracy of the…

We propose a criterion for optimal parameter selection in coarse-grained models of proteins, and develop a refined elastic network model (ENM) of bovine trypsinogen. The unimodal density-of-states distribution of the trypsinogen ENM…

Accurate prediction of permeability in porous media is essential for modeling subsurface flow. While pure data-driven models offer computational efficiency, they often lack generalization across scales and do not incorporate explicit…

A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…

This article introduces a nonlinear generalized matrix factor model (GMFM) that allows for mixed-type variables, extending the scope of linear matrix factor models (LMFM) that are so far limited to handling continuous variables. We…