Kinetic Models and Qualitative Abstraction for Relational Learning in Systems Biology

Gabriel Synnaeve (1, 2) , Katsumi Inoue (3) , Andrei Doncescu (4) , Hidetomo Nabeshima (5) , Yoshitaka Kameya (6) , Masakazu Ishihata (6) , Taisuke Sato (6)

1 LIG - Laboratoire d'Informatique de Grenoble
2 E-MOTION - Geometry and Probability for Motion and Action
3 NII - National Institute of Informatics
4 LAAS - Laboratoire d'analyse et d'architecture des systèmes
5 Yamanashi University
6 TITECH - Tokyo Institute of Technology [Tokyo]

This paper presents a method for enabling the relational learning or inductive logic programming (ILP) frame- work to deal with quantitative information from experimental data in systems biology. The study of systems biology through ILP aims at improving the understanding of the physiological state of the cell and the interpre- tation of the interactions between metabolites and signaling networks. A logical model of the glycolysis and pentose phosphate pathways of E. Coli is proposed to support our method description. We explain our original approach to building a symbolic model applied to kinetics based on Michaelis-Menten equation, starting with the discretization of the changes in concentration of some of the metabolites over time into relevant levels. We can then use them in our ILP-based model. Logical formulae on concentrations of some metabolites, which could not be measured during the dynamic state, are produced through logical abduction. Finally, as this re- sults in a large number of hypotheses, they are ranked with an expectation maximization algorithm working on binary decision diagrams.

Mots clés: bioinformatics; inductive logic programming; HMM; discretization; metabolic pathways; cell biology

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Logique en informatique [cs.LO]

Gabriel Synnaeve, Katsumi Inoue, Andrei Doncescu, Hidetomo Nabeshima, Yoshitaka Kameya, et al.. Kinetic Models and Qualitative Abstraction for Relational Learning in Systems Biology. BIOSTEC Bioinformatics 2011, Jan 2011, Rome, Italy. ⟨hal-00607296⟩