Proving Stabilization of Biological Systems

Byron Cook, Jasmin Fisher, Elzbieta Krepska, Nir Piterman

12th International Conference on Verification, Model Checking, and Abstract Interpretation Conference VMCAI'11. R. Jhala and D. Schmidt (Eds.), LNCS |

Published by Springer Verlag

R. Jhala and D. Schmidt (Eds.), LNCS vol. 6538, pp 134-149, 2011.

We describe an efficient procedure for proving stabilization of biological systems modeled as qualitative networks or genetic regulatory networks. For scalability, our procedure uses modular proof techniques, where state-space exploration is applied only locally to small pieces of the system rather than the entire system as a whole. Our procedure exploits the observation that, in practice, the form of modular proofs can be restricted to a very limited set. For completeness, our technique falls back on a non-compositional counterexample search. Using our new procedure, we have solved a number of challenging published examples, including: a 3-D model of the mammalian epidermis; a model of metabolic networks operating in type-2 diabetes; a model of fate determination of vulval precursor cells in the C. elegans worm; and a model of pair-rule regulation during segmentation in the Drosophila embryo. Our results show many orders of magnitude speedup in cases where previous stabilization proving techniques were known to succeed, and new results in cases where tools had previously failed.