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Model-checking sign...
Model-checking signal transduction networks through decreasing reachability sets
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- Lindström Claessen, Koen, 1975 (author)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Fisher, J.P. (author)
- Microsoft Research
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- Ishtiaq, S.S. (author)
- Microsoft Research
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- Piterman, N. (author)
- University Of Leicester
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- Wang, Q. (author)
- Carnegie Mellon University (CMU)
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(creator_code:org_t)
- ISBN 9783642397981
- Berlin, Heidelberg : Springer Berlin Heidelberg, 2013
- 2013
- English.
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In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - Berlin, Heidelberg : Springer Berlin Heidelberg. - 1611-3349 .- 0302-9743. - 9783642397981 ; 0302-9743, s. 85-100
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- We consider model checking of Qualitative Networks, a popular formalism for modeling signal transduction networks in biology. One of the unique features of qualitative networks, due to them lacking initial states, is that of "reducing reachability sets". Simply put, a state that is not visited after i steps will not be visited after i′ steps for every i′ > i. We use this feature to create a compact representation of all the paths of a qualitative network of a certain structure. Combining this compact path representation with LTL model checking leads to significant acceleration in performance. In particular, for a recent model of Leukemia, our approach works at least 5 times faster than the standard approach and up to 100 times faster in some cases. Our approach enhances the iterative hypothesis-driven experimentation process used by biologists, enabling fast turn-around of executable biological models.
Subject headings
- NATURVETENSKAP -- Data- och informationsvetenskap -- Programvaruteknik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Software Engineering (hsv//eng)
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- ref (subject category)
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