Discovery of Genetic Networks Through Abduction and Qualitative Simulation

  • Authors:

  • Blaž Zupan;Ivan Bratko;Janez Demšar;Peter Juvan;Adam Kuspa;John A. Halter;Gad Shaulsky

  • Affiliations:

  • Artificial Inteligence Laboratory, Faculty of Computer and Information Science, University of Ljubljana, Slovenia and Department of Biochemistry and Molecular Biology, Baylor College of Medicine, ...;Artificial Inteligence Laboratory, Faculty of Computer and Information Science, University of Ljubljana, Slovenia and Department of Intelligent Systems, Jožef Stefan Institute, Ljubljana, Slo ...;Artificial Inteligence Laboratory, Faculty of Computer and Information Science, University of Ljubljana, Slovenia;Artificial Inteligence Laboratory, Faculty of Computer and Information Science, University of Ljubljana, Slovenia;Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA;PM&R and Division of Neuroscience, Baylor College of Medicine, Houston, Texas, USA;Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

  • Venue:
  • Computational Discovery of Scientific Knowledge
  • Year:
  • 2007

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Abstract

GenePath is an automated system for reasoning about 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 background 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, as illustrated by an example on aggregation of a soil amoeba Dictyostelium discoideum, a combination of constraint satisfaction and qualitative reasoning produces a small set of plausible networks.