GeNICE: A Novel Framework for Gene Network Inference by Clustering, Exhaustive Search, and Multivariate Analysis

A framework to shift basins of attraction of gene regulatory networks through batch reinforcement learning

A major challenge in gene regulatory networks (GRN) of biological systems is to discover when and what interventions should be applied to shift them to healthy phenotypes. A set of gene activity profiles, called basin of attraction (BOA), takes this network to a specific phenotype; therefore, a healthy BOA leads the GRN to a healthy phenotype. However, without the complete observability of the genes, it is not possible to identify whether the current BOA is healthy. In this article we investigate external interventions in GRN with partial observability aiming to bring it to healthy BOAs. We propose a new batch reinforcement learning method (BRL), called mSFQI, to define intervention strategies based on the probabilities of the gene activity profiles being in healthy BOAs, which are calculated from a set of previous observed experiences. BRL uses approximation functions and repeated applications of previous experiences to accelerate learning. Results demonstrate that our proposal can quickly shift a partially observable GRN to healthy BOAs, while reducing the number of interventions. In addition, when observability is poor, mSFQI produces better results when the probabilities for a greater amount of previous observations are available.