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Parameter identification of canalyzing and nested canalyzing boolean functions with ternary vectors for gene networks
Publikationstyp
Conference Paper
Date Issued
2016-07
Sprache
English
Author(s)
First published in
Number in series
676
Start Page
198
End Page
221
Citation
Advances in Intelligent Systems and Computing 676: 198-221 (2018-01-01)
Publisher DOI
Scopus ID
Publisher
Springer
In gene dynamics modeling, parameters of Boolean networks are identified from continuous data under various assumptions expressed by logical constraints. These constraints may restrict the dynamics of the network to the subclass of canalyzing or nested canalyzing functions, which are known to be appropriate for genetic networks. This paper introduces high performance algorithms, which solve the parameter identification problem by so called Zhegalkin identification and exploit the restriction to canalyzing or nested canalyzing functions resulting in reduced calculation time. The constraints are formulated in terms of orthogonal ternary vector lists, which offer an efficient representation for Boolean functions. The canalyzing constraints can be intrinsically incorporated in an existing Branch-and-Cut algorithm, which lead to a natural restriction of the search space and thus of the calculation time. For nested canalyzing constraints this is not possible. Instead, an identification algorithm based on enumeration is proposed. The algorithms are applied to mRNA micro array data from mice under different contaminant conditions and good correspondence to a known apoptotic pathway can be shown.
Subjects
Boolean functions
Gene dynamics
Networks
Parameter identification
Systems biology
Ternary logic
DDC Class
004: Informatik