Related papers: Kinetically Consistent Coarse Graining using Kerne…
This paper tackles the data-driven approximation of unknown dynamical systems using Koopman-operator methods. Given a dictionary of functions, these methods approximate the projection of the action of the operator on the finite-dimensional…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
Many dimensionality and model reduction techniques rely on estimating dominant eigenfunctions of associated dynamical operators from data. Important examples include the Koopman operator and its generator, but also the Schr\"odinger…
Recent advances in graph neural networks (GNNs) have enabled more comprehensive modeling of molecules and molecular systems, thereby enhancing the precision of molecular property prediction and molecular simulations. Nonetheless, as the…
Extended dynamic mode decomposition (EDMD) is a data-driven algorithm for approximating spectral data of the Koopman operator associated to a dynamical system, combining a Galerkin method of order N and collocation method of order M.…
We introduce a general framework for deriving effective dynamics from arbitrary time-dependent generators, based on a systematic operator cumulant expansion. Unlike traditional approaches, which typically assume periodic or adiabatic…
Inference of space-time varying signals on graphs emerges naturally in a plethora of network science related applications. A frequently encountered challenge pertains to reconstructing such dynamic processes, given their values over a…
Machine learning has recently entered into the mainstream of coarse-grained (CG) molecular modeling and simulation. While a variety of methods for incorporating deep learning into these models exist, many of them involve training neural…
We present a low-rank Koopman operator formulation for accelerating deformable subspace simulation. Using a Dynamic Mode Decomposition (DMD) parameterization of the Koopman operator, our method learns the temporal evolution of deformable…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
We consider a Graph Neural Network (GNN) non-Markovian modeling framework to identify coarse-grained dynamical systems on graphs. Our main idea is to systematically determine the GNN architecture by inspecting how the leading term of the…
In this paper, we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular dynamics. The latter are ubiquitous in physicochemical and biological…
The Koopman operator and extended dynamic mode decomposition (EDMD) as a data-driven technique for its approximation have attracted considerable attention as a key tool for modeling, analysis, and control of complex dynamical systems.…
This paper provides answers to an open problem: given a nonlinear data-driven dynamical system model, e.g., kernel conditional mean embedding (CME) and Koopman operator, how can one propagate the ambiguity sets forward for multiple steps?…
We extend the unified kernel framework for transport equations and Koopman eigenfunctions, developed in previous work by the authors for deterministic systems, to stochastic differential equations (SDEs). In the deterministic setting, three…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). While Paper II successfully captured translational motions in…
Recent deep learning extensions in Koopman theory have enabled compact, interpretable representations of nonlinear dynamical systems which are amenable to linear analysis. Deep Koopman networks attempt to learn the Koopman eigenfunctions…
We address the problem of classifying trajectory data generated by some nonlinear dynamics, where each class corresponds to a distinct dynamical system. We propose Dynafit, a kernel-based method for learning a distance metric between…
The aim of this work is the description of the chain formation phenomena observed in colloidal suspensions of superparamagnetic nanoparticles under high magnetic fields. We propose a new methodology based on an on-the-fly Coarse-Grain (CG)…