Completing networks using observed data

Authors:
Tatsuya Akutsu;Takeyuki Tamura;Katsuhisa Horimoto
Affiliations:
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan;Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan;Computational Biology Research Center, Tokyo, Japan
Venue:
ALT'09 Proceedings of the 20th international conference on Algorithmic learning theory
Year:
2009

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Abstract

This paper studies problems of completing a given Boolean network (Boolean circuit) so that the input/output behavior is consistent with given examples, where we only consider acyclic networks. These problems arise in the study of inference of signaling networks using reporter proteins. We prove that these problems are NP-complete in general and a basic version remains NP-complete even for tree structured networks. On the other hand, we show that these problems can be solved in polynomial time for partial k-trees of bounded (constant) indegree if a logarithmic number of examples are given.