INVITED SPEAKER

Analysis of ODEs models of bio-pathways using statistical model checking

P. S. Thiagarajan
National University of Singapore

The dynamics of biochemical networks often called bio-pathways govern a variety of cellular functions. Their malfunctioning can lead to major diseases. Thus it is important to understand their behavior using mathematical models. Ordinary differential equations (ODEs) are a well-established formalism for modeling biochemical networks in which the time evolution of the concentration levels of each molecular species in the network is captured by a differential equation that captures the kinetics of the reactions that this species participates in. In the study of such ODEs systems it is important to take into account cell-to-cell variability in the values of the initial conditions as well as the rate constants that govern the kinetics of the various reactions in the network. We do so by using probability distributions to model a set of initial concentrations and kinetic rate values. We then develop a statistical model checking (SMC) procedure for verifying the dynamical properties of an ODE system accompanied by such prior distributions. In our specification logic both qualitative properties of the pathway and experimental data can be encoded. This enables us to develop SMC based parameter estimation and sensitivity analysis procedures. We have validated our method on large pathway models. We are currently extending this technique to handle multi-mode ODEs models of bio-pathways.

Brief bio

P.S. Thiagarajan is a Professor in the Department of Computer Science, National University of Singapore and a Senior Faculty Member of the NUS Graduate School of Integrative Science and Engineering (NGS). He received a B.Tech (Electronics) degree from the Indian Institute of Technology, Madras, India (1970) and a PhD degree (Computer Science) from Rice University, Houston, Texas, USA (1973). Before coming to NUS his research had been devoted to various aspects of the theory of distributed systems including Petri nets, temporal logics and supervisory control. After moving to NUS, he has focused mainly on real time, hybrid and embedded computing systems. In recent years, his interest has shifted to computational systems biology. He has given invited talks in most of the leading conferences in his areas of research. He is a Fellow of the Indian Academy of Sciences and a Fellow of the Indian National Academy of Sciences and has served on the Governing Council of the European association for Theoretical Computer Science (1997-2003). He is currently a member of the Academic Council of the Chennai Mathematical Institute. He also serves on the editorial boards of The Real-Time Systems journal and Transactions on Petri nets and Other Models of Concurrency.

Last Modified on: 16 Aug 2013