Literature DB >> 31330605

Learning moment closure in reaction-diffusion systems with spatial dynamic Boltzmann distributions.

Oliver K Ernst1, Thomas M Bartol, Terrence J Sejnowski2, Eric Mjolsness3.   

Abstract

Many physical systems are described by probability distributions that evolve in both time and space. Modeling these systems is often challenging due to their large state space and analytically intractable or computationally expensive dynamics. To address these problems, we study a machine-learning approach to model reduction based on the Boltzmann machine. Given the form of the reduced model Boltzmann distribution, we introduce an autonomous differential equation system for the interactions appearing in the energy function. The reduced model can treat systems in continuous space (described by continuous random variables), for which we formulate a variational learning problem using the adjoint method to determine the right-hand sides of the differential equations. This approach can be used to enforce a reduced physical model by a suitable parametrization of the differential equations. The parametrization we employ uses the basis functions from finite-element methods, which can be used to model any physical system. One application domain for such physics-informed learning algorithms is to modeling reaction-diffusion systems. We study a lattice version of the Rössler chaotic oscillator, which illustrates the accuracy of the moment closure approximation made by the method and its dimensionality reduction power.

Entities:  

Year:  2019        PMID: 31330605      PMCID: PMC6852890          DOI: 10.1103/PhysRevE.99.063315

Source DB:  PubMed          Journal:  Phys Rev E        ISSN: 2470-0045            Impact factor:   2.529


  19 in total

1.  Statistical properties of dynamical chaos.

Authors:  Vadim S Anishchenko; Tatjana E Vadivasova; Galina I Strelkova; George A Okrokvertskhov
Journal:  Math Biosci Eng       Date:  2004-06       Impact factor: 2.080

2.  Efficient statistical inference for stochastic reaction processes.

Authors:  Andreas Ruttor; Manfred Opper
Journal:  Phys Rev Lett       Date:  2009-12-02       Impact factor: 9.161

3.  The finite state projection algorithm for the solution of the chemical master equation.

Authors:  Brian Munsky; Mustafa Khammash
Journal:  J Chem Phys       Date:  2006-01-28       Impact factor: 3.488

4.  Prediction of spatiotemporal patterns of neural activity from pairwise correlations.

Authors:  O Marre; S El Boustani; Y Frégnac; A Destexhe
Journal:  Phys Rev Lett       Date:  2009-04-02       Impact factor: 9.161

5.  Prospects for Declarative Mathematical Modeling of Complex Biological Systems.

Authors:  Eric Mjolsness
Journal:  Bull Math Biol       Date:  2019-06-07       Impact factor: 1.758

6.  A high-bias, low-variance introduction to Machine Learning for physicists.

Authors:  Pankaj Mehta; Ching-Hao Wang; Alexandre G R Day; Clint Richardson; Marin Bukov; Charles K Fisher; David J Schwab
Journal:  Phys Rep       Date:  2019-03-14       Impact factor: 25.600

7.  Learning dynamic Boltzmann distributions as reduced models of spatial chemical kinetics.

Authors:  Oliver K Ernst; Thomas Bartol; Terrence Sejnowski; Eric Mjolsness
Journal:  J Chem Phys       Date:  2018-07-21       Impact factor: 3.488

8.  Rigorous elimination of fast stochastic variables from the linear noise approximation using projection operators.

Authors:  Philipp Thomas; Ramon Grima; Arthur V Straube
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2012-10-08

9.  FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES.

Authors:  Rex A Kerr; Thomas M Bartol; Boris Kaminsky; Markus Dittrich; Jen-Chien Jack Chang; Scott B Baden; Terrence J Sejnowski; Joel R Stiles
Journal:  SIAM J Sci Comput       Date:  2008-10-13       Impact factor: 2.373

10.  Model reduction for stochastic CaMKII reaction kinetics in synapses by graph-constrained correlation dynamics.

Authors:  Todd Johnson; Tom Bartol; Terrence Sejnowski; Eric Mjolsness
Journal:  Phys Biol       Date:  2015-06-18       Impact factor: 2.583

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