Nested canalyzing, unate cascade, and polynomial functions

DOI10.1016/J.PHYSD.2007.06.022zbMATH Open1126.06004arXivq-bio/0606013OpenAlexW1994094326WikidataQ42161170 ScholiaQ42161170MaRDI QIDQ2383555FDOQ2383555

Abdul Salam Jarrah, Reinhard Laubenbacher, Blessilda P. Raposa

Publication date: 19 September 2007

Published in: Physica D (Search for Journal in Brave)

Abstract: This paper focuses on the study of certain classes of Boolean functions that have appeared in several different contexts. Nested canalyzing functions have been studied recently in the context of Boolean network models of gene regulatory networks. In the same context, polynomial functions over finite fields have been used to develop network inference methods for gene regulatory networks. Finally, unate cascade functions have been studied in the design of logic circuits and binary decision diagrams. This paper shows that the class of nested canalyzing functions is equal to that of unate cascade functions. Furthermore, it provides a description of nested canalyzing functions as a certain type of Boolean polynomial function. Using the polynomial framework one can show that the class of nested canalyzing functions, or, equivalently, the class of unate cascade functions, forms an algebraic variety which makes their analysis amenable to the use of techniques from algebraic geometry and computational algebra. As a corollary of the functional equivalence derived here, a formula in the literature for the number of unate cascade functions provides such a formula for the number of nested canalyzing functions.

Full work available at URL: https://arxiv.org/abs/q-bio/0606013

zbMATH Keywords

algebraic varietyparametrizationBoolean functionpolynomial functionnested canalyzing functionunate cascade function

Mathematics Subject Classification ID

Genetics and epigenetics (92D10) Boolean functions (06E30)

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Cited In (26)

• Certificate complexity and symmetry of nested canalizing functions
• Deciding atomicity of subword-closed languages
• Boolean dynamics revisited through feedback interconnections
• The influence of canalization on the robustness of Boolean networks
• Regulatory patterns in molecular interaction networks
• Modular construction of Boolean networks
• Maximal sensitivity of Boolean nested canalizing functions
• Dimension reduction of large sparse AND-NOT network models
• Multistate nested canalizing functions and their networks
• Stratification and enumeration of Boolean functions by canalizing depth
• Functional pearl: folding polynomials of polynomials
• Deciding atomicity of subword-closed languages
• Limit cycle structure for dynamic bi-threshold systems
• Linear read-once and related Boolean functions
• The polynomial hierarchy of functions and its levels
• Stability structures of conjunctive Boolean networks
• Inferring biologically relevant models: nested canalyzing functions
• An Improved Algorithm for Detecting a Singleton Attractor in a Boolean Network Consisting of AND/OR Nodes
• The number of multistate nested canalyzing functions
• Analysis of discrete bioregulatory networks using symbolic steady states
• Revealing the canalizing structure of Boolean functions: algorithms and applications
• Extracting Boolean and probabilistic rules from trained neural networks
• Boolean nested canalizing functions: a comprehensive analysis
• Nested canalyzing depth and network stability
• Algebraic Models and Their Use in Systems Biology
• The number of fixed points of AND-OR networks with chain topology

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