Analyzing Pathways Using ASP-Based Approaches

  • Oliver Ray
  • Takehide Soh
  • Katsumi Inoue
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6479)

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.

Keywords

Metabolic Network Logic Programming Biological Network Reaction Network Stable Model 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Oliver Ray
    • 1
  • Takehide Soh
    • 2
  • Katsumi Inoue
    • 3
  1. 1.University of BristolBristolUnited Kingdom
  2. 2.Graduate University for Advanced StudiesChiyoda-kuJapan
  3. 3.National Institute of InformaticsChiyoda-kuJapan

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