Related papers: Entrograms and coarse graining of dynamics on comp…
Representation of large data sets became a key question of many scientific disciplines in the last decade. Several approaches for network visualization, data ordering and coarse-graining accomplished this goal. However, there was no…
We introduce a definition of coarse-grained entropy that unifies measurement-based (observational entropy) and max-entropy-based (Jaynes) approaches to coarse-graining, by identifying physical constraints with information theoretic priors.…
Large ensembles of stochastically evolving interacting particles describe phenomena in diverse fields including statistical physics, neuroscience, biology, and engineering. In such systems, the infinitesimal evolution of each particle…
Systems out of equilibrium exhibit a net production of entropy. We study the dynamics of a stochastic system represented by a Master Equation that can be modeled by a Fokker-Planck equation in a coarse-grained, mesoscopic description. We…
There are several applications in computational biophysics which require the optimization of discrete interacting states; e.g., amino acid titration states, ligand oxidation states, or discrete rotamer angles. Such optimization can be very…
The general method of graph coarsening or graph reduction has been a remarkably useful and ubiquitous tool in scientific computing and it is now just starting to have a similar impact in machine learning. The goal of this paper is to take a…
We present a data-driven machine-learning approach for modeling space-time socioeconomic dynamics. Through coarse-graining fine-scale observations, our modeling framework simplifies these complex systems to a set of tractable mechanistic…
Real-world graphs, such as social networks, financial transactions, and recommendation systems, often demonstrate dynamic behavior. This phenomenon, known as graph stream, involves the dynamic changes of nodes and the emergence and…
Stochastic modelling of complex systems plays an essential, yet often computationally intensive role across the quantitative sciences. Recent advances in quantum information processing have elucidated the potential for quantum simulators to…
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…
Many well-known, real-world problems involve dynamic data which describe the relationship among the entities. Hypergraphs are powerful combinatorial structures that are frequently used to model such data. For many of today's data-centric…
We extend the analysis of the thermodynamics of the climate system by investigating the role played by processes taking place at various spatial and temporal scales through a procedure of coarse graining. The coarser is the graining of the…
Lumping a Markov process introduces a coarser level of description that is useful in many contexts and applications. The dynamics on the coarse grained states is often approximated by its Markovian component. In this letter we derive…
Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…
We propose and illustrate an approach to coarse-graining the dynamics of evolving networks (networks whose connectivity changes dynamically). The approach is based on the equation-free framework: short bursts of detailed network evolution…
We investigate fundamental connections between thermodynamics and quantum information theory. First, we show that the operational framework of thermal operations is nonequivalent to the framework of Gibbs-preserving maps, and we comment on…
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…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
The structure of the network can be described by motifs, which are subgraphs that often repeat themselves. In order to understand the structure of network motifs, it is of great importance to study subgraphs from the perspective of…
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently limited by the molecular mechanics force field employed.…