×

Hybrid metabolic network completion. (English) Zbl 1491.92061

Balduccini, Marcello (ed.) et al., Logic programming and nonmonotonic reasoning. 14th international conference, LPNMR 2017, Espoo, Finland, July 3–6, 2017. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 10377, 308-321 (2017).
Summary: Metabolic networks play a crucial role in biology since they capture all chemical reactions in an organism. While there are networks of high quality for many model organisms, networks for less studied organisms are often of poor quality and suffer from incompleteness. To this end, we introduced in previous work an ASP-based approach to metabolic network completion. Although this qualitative approach allows for restoring moderately degraded networks, it fails to restore highly degraded ones. This is because it ignores quantitative constraints capturing reaction rates. To address this problem, we propose a hybrid approach to metabolic network completion that integrates our qualitative ASP approach with quantitative means for capturing reaction rates. We begin by formally reconciling existing stoichiometric and topological approaches to network completion in a unified formalism. With it, we develop a hybrid ASP encoding and rely upon the theory reasoning capacities of the ASP system Clingo for solving the resulting logic program with linear constraints over reals. We empirically evaluate our approach by means of the metabolic network of Escherichia coli. Our analysis shows that our novel approach yields greatly superior results than obtainable from purely qualitative or quantitative approaches.
For the entire collection see [Zbl 1367.68005].

MSC:

92C42 Systems biology, networks
92C40 Biochemistry, molecular biology
68N17 Logic programming
PDF BibTeX XML Cite
Full Text: DOI arXiv