Abductive Inference of Genetic Networks

GenePath is an automated system for reasoning on genetic networks, wherein a set of genes have various influences on one another and on a biological outcome, and a combination of constraint satisfaction and qualitative reasoning produces a small set of plausible networks.

Abstract

GenePath is an automated system for reasoning on genetic networks, wherein a set of genes have various influences on one another and on a biological outcome. It acts on a set of experiments in which genes are knocked out or overexpressed, and the outcome of interest is evaluated. Implemented in Prolog, GenePath uses abductive inference to elucidate network constraints based on prior knowledge and experimental results. Two uses of the system are demonstrated: synthesis of a consistent network from abduced constraints, and qualitative reasoning-based approach that generates a set of networks consistent with the data. In practice, illustrated by an example using Dictyostelium aggregation, a combination of constraint satisfaction and qualitative reasoning produces a small set of plausible networks.