Analyzing pathways using ASP-based approaches

Authors:
Oliver Ray;Takehide Soh;Katsumi Inoue
Affiliations:
University of Bristol, Bristol, United Kingdom;Graduate University for Advanced Studies, Chiyoda-ku, Tokyo, Japan;National Institute of Informatics, Chiyoda-ku, Tokyo, Japan
Venue:
ANB'10 Proceedings of the 4th international conference on Algebraic and Numeric Biology
Year:
2010

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Abstract

This paper contributes to a line of research which aims to combine numerical information with logical inference in order to find the most likely states of a biological system under various (actual or hypothetical) constraints. To this end, we build upon a state-of-the-art approach that employs weighted Boolean constraints to represent and reason about biochemical reaction networks. Our first contribution is to show how this existing method fails to deal satisfactorily with networks that contain cycles. Our second contribution is to define a new method which correctly handles such cases by exploiting the formalism of Answer Set Programming (ASP). We demonstrate the significance of our results on two case-studies previously studied in the literature.