Learning effective stochastic differential equations from microscopic simulations: combining stochastic numerics and deep learning

We identify effective stochastic differential equations (SDE) for coarse observables of fine-grained particleor agent-based simulations; these SDE then provide coarse surrogate models of the fine scale dynamics. We approximate the drift and diffusivity functions in these effective SDE through neural networks, which can be thought of as effective stochastic ResNets. The loss function is inspired by, and embodies, the structure of established stochastic numerical integrators (here, Euler-Maruyama and Milstein); our approximations can thus benefit from error analysis of these underlying numerical schemes. They also lend themselves naturally to “physics-informed” gray-box identification when approximate coarse models, such as mean field equations, are available. Our approach does not require long trajectories, works on scattered snapshot data, and is designed to naturally handle different time steps per snapshot. We consider both the case where the coarse collective observables are known in advance, as well as the case where they must be found in a data-driven manner.

[1]  Abhishek Kumar,et al.  Score-Based Generative Modeling through Stochastic Differential Equations , 2020, ICLR.

[2]  David Duvenaud,et al.  Neural Ordinary Differential Equations , 2018, NeurIPS.

[3]  S. Zagatti On viscosity solutions of Hamilton-Jacobi equations , 2008 .

[4]  D. Gillespie The chemical Langevin equation , 2000 .

[5]  D. Gillespie A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[6]  A. B. Bortz,et al.  A new algorithm for Monte Carlo simulation of Ising spin systems , 1975 .

[7]  Aiqing Zhu,et al.  Deep Hamiltonian networks based on symplectic integrators , 2020, ArXiv.

[8]  I.G. Kevrekidis,et al.  Continuous-time nonlinear signal processing: a neural network based approach for gray box identification , 1994, Proceedings of IEEE Workshop on Neural Networks for Signal Processing.

[9]  Bin Dong,et al.  RODE-Net: Learning Ordinary Differential Equations with Randomness from Data , 2020, ArXiv.

[10]  Jason Yosinski,et al.  Hamiltonian Neural Networks , 2019, NeurIPS.

[11]  Desmond J. Higham,et al.  An Algorithmic Introduction to Numerical Simulation of Stochastic Differential Equations , 2001, SIAM Rev..

[12]  Xiongzhi Chen Brownian Motion and Stochastic Calculus , 2008 .

[13]  D. Giannakis,et al.  Nonparametric forecasting of low-dimensional dynamical systems. , 2014, Physical review. E, Statistical, nonlinear, and soft matter physics.

[14]  Liu Yang,et al.  Generative Ensemble-Regression: Learning Stochastic Dynamics from Discrete Particle Ensemble Observations , 2020, ArXiv.

[15]  P. Lions,et al.  User’s guide to viscosity solutions of second order partial differential equations , 1992, math/9207212.

[17]  Benjamin Recht,et al.  Unsupervised Regression with Applications to Nonlinear System Identification , 2006, NIPS.

[18]  Anthony Widjaja,et al.  Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond , 2003, IEEE Transactions on Neural Networks.

[19]  A basic lattice model of an excitable medium: Kinetic Monte Carlo simulations , 2017 .

[20]  Ioannis G. Kevrekidis,et al.  Coarse bifurcation analysis of kinetic Monte Carlo simulations: A lattice-gas model with lateral interactions , 2002 .

[21]  Jian Sun,et al.  Deep Residual Learning for Image Recognition , 2015, 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).

[22]  Lucia Russo,et al.  Mathematical modeling of infectious disease dynamics , 2013, Virulence.

[23]  David Duvenaud,et al.  Scalable Gradients for Stochastic Differential Equations , 2020, AISTATS.

[24]  Ioannis G. Kevrekidis,et al.  Identification of distributed parameter systems: A neural net based approach , 1998 .

[25]  J. M. Sancho,et al.  Stochastic algorithms for discontinuous multiplicative white noise. , 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

[26]  K. C. Zygalakis,et al.  On the Existence and the Applications of Modified Equations for Stochastic Differential Equations , 2011, SIAM J. Sci. Comput..

[27]  George Em Karniadakis,et al.  Learning nonlinear operators via DeepONet based on the universal approximation theorem of operators , 2019, Nature Machine Intelligence.

[28]  Jaehoon Lee,et al.  Deep Neural Networks as Gaussian Processes , 2017, ICLR.

[29]  Timothy D. Sauer,et al.  Time-Scale Separation from Diffusion-Mapped Delay Coordinates , 2013, SIAM J. Appl. Dyn. Syst..

[30]  I. Mezić Spectral Properties of Dynamical Systems, Model Reduction and Decompositions , 2005 .

[31]  Yoshua Bengio,et al.  Generative Adversarial Nets , 2014, NIPS.

[32]  S. Brunton,et al.  Discovering governing equations from data by sparse identification of nonlinear dynamical systems , 2015, Proceedings of the National Academy of Sciences.

[33]  W. O. Kermack,et al.  A contribution to the mathematical theory of epidemics , 1927 .

[34]  Alex Graves,et al.  Generating Sequences With Recurrent Neural Networks , 2013, ArXiv.

[35]  Hod Lipson,et al.  Automated reverse engineering of nonlinear dynamical systems , 2007, Proceedings of the National Academy of Sciences.

[36]  Stéphane Lafon,et al.  Diffusion maps , 2006 .

[37]  Zhen Zhang,et al.  Learning Poisson systems and trajectories of autonomous systems via Poisson neural networks , 2020, ArXiv.

[38]  G. N. Mil’shtejn Approximate Integration of Stochastic Differential Equations , 1975 .

[39]  L. Allen,et al.  A primer on stochastic epidemic models: Formulation, numerical simulation, and analysis , 2017, Infectious Disease Modelling.

[40]  Ioannis G. Kevrekidis,et al.  On learning Hamiltonian systems from data. , 2019, Chaos.

[41]  Shihao Yang,et al.  Inference of dynamic systems from noisy and sparse data via manifold-constrained Gaussian processes , 2021, Proceedings of the National Academy of Sciences.

[42]  Ioannis G. Kevrekidis,et al.  DISCRETE- vs. CONTINUOUS-TIME NONLINEAR SIGNAL PROCESSING OF Cu ELECTRODISSOLUTION DATA , 1992 .

[43]  Stefan Klus,et al.  Data-driven approximation of the Koopman generator: Model reduction, system identification, and control , 2019 .

[44]  Carmeline J. Dsilva,et al.  Parsimonious Representation of Nonlinear Dynamical Systems Through Manifold Learning: A Chemotaxis Case Study , 2015, 1505.06118.

[45]  Ivan Kobyzev,et al.  Normalizing Flows: An Introduction and Review of Current Methods , 2020, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[46]  K. Burrage,et al.  Numerical methods for strong solutions of stochastic differential equations: an overview , 2004, Proceedings of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[47]  Alexandros G. Dimakis,et al.  The Robust Manifold Defense: Adversarial Training using Generative Models , 2017, ArXiv.

[48]  Vladas Sidoravicius,et al.  Stochastic Processes and Applications , 2007 .

[49]  Markus Heinonen,et al.  LEARNING STOCHASTIC DIFFERENTIAL EQUATIONS WITH GAUSSIAN PROCESSES WITHOUT GRADIENT MATCHING , 2018, 2018 IEEE 28th International Workshop on Machine Learning for Signal Processing (MLSP).

[50]  Ioannis G. Kevrekidis,et al.  “Coarse” stability and bifurcation analysis using stochastic simulators: Kinetic Monte Carlo examples , 2001, nlin/0111038.

[51]  Max Welling,et al.  Auto-Encoding Variational Bayes , 2013, ICLR.

[52]  Gerta Köster,et al.  Datafold: Data-driven Models for Point Clouds and Time Series on Manifolds , 2020, J. Open Source Softw..