KINETIC MODELS AND QUALITATIVE ABSTRACTION FOR RELATIONAL LEARNING IN SYSTEMS BIOLOGY

Gabriel Synnaeve, Katsumi Inoue, Andrei Doncescu, Hidetomo Nabeshima, Yoshitaka Kameya, Masakazu Ishihata, Taisuke Sato

2011

Abstract

This paper presents a method for enabling the relational learning or inductive logic programming (ILP) framework 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 interpretation 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 results in a large number of hypotheses, they are ranked with an expectation maximization algorithm working on binary decision diagrams.

Paper Citation

in Harvard Style

Synnaeve G., Inoue K., Doncescu A., Nabeshima H., Kameya Y., Ishihata M. and Sato T. (2011). KINETIC MODELS AND QUALITATIVE ABSTRACTION FOR RELATIONAL LEARNING IN SYSTEMS BIOLOGY . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011) ISBN 978-989-8425-36-2, pages 47-54. DOI: 10.5220/0003166300470054

in Bibtex Style

@conference{bioinformatics11,
author={Gabriel Synnaeve and Katsumi Inoue and Andrei Doncescu and Hidetomo Nabeshima and Yoshitaka Kameya and Masakazu Ishihata and Taisuke Sato},
title={KINETIC MODELS AND QUALITATIVE ABSTRACTION FOR RELATIONAL LEARNING IN SYSTEMS BIOLOGY},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)},
year={2011},
pages={47-54},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003166300470054},
isbn={978-989-8425-36-2},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2011)
TI - KINETIC MODELS AND QUALITATIVE ABSTRACTION FOR RELATIONAL LEARNING IN SYSTEMS BIOLOGY
SN - 978-989-8425-36-2
AU - Synnaeve G.
AU - Inoue K.
AU - Doncescu A.
AU - Nabeshima H.
AU - Kameya Y.
AU - Ishihata M.
AU - Sato T.
PY - 2011
SP - 47
EP - 54
DO - 10.5220/0003166300470054