Neural network aided approximation and parameter inference of stochastic models of gene expression

• Published in: bioRxiv
• Main Authors: Jiang, Qingchao, Fu, Xiaoming, Yan, Shifu, Li, Runlai, Du, Wenli, Cao, Zhixing, Qian, Feng, Grima, Ramon
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 15.12.2020
• Subjects: Approximation; Gene expression; Markov chains; Neural networks; Stochastic models; Stochasticity; Timing; Transcription
• DOI: 10.1101/2020.12.15.422883

Abstract Non-Markov models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models, as well as the inference of their parameters from data, are fraught with difficulties because the dynamics depends on the system’s history. Here we use an artificial neural network to approximate the time-dependent distributions of non-Markov models by the solutions of much simpler time-inhomogeneous Markov models; the approximation does not increase the dimensionality of the model and simultaneously leads to inference of the kinetic parameters. The training of the neural network uses a relatively small set of noisy measurements generated by experimental data or stochastic simulations of the non-Markov model. We show using a variety of models, where the delays stem from transcriptional processes and feedback control, that the Markov models learnt by the neural network accurately reflect the stochastic dynamics across parameter space. Competing Interest Statement The authors have declared no competing interest.