J. Comput. Biol. - An improved satisfiability algorithm for nested canalyzing functions and its application to determining a singleton attractor of a Boolean network.

Tópicos

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Resumo

We study the problem of finding a 0-1 assignment to Boolean variables satisfying a given set of nested canalyzing functions, a class of Boolean functions that is known to be of interest in biology. For this problem, an extension of the satisfiability problem for a conjunctive normal form formula, an O(min(2(k), 2((k+m)/2))poly(m)) time algorithm has been known, where m and k are the number of nested canalyzing functions and variables, respectively. Here we present an improved O(min(2(k), 1.325(k+m), 2(m))poly(m)) time algorithm for this problem. We also study the problem of finding a singleton attractor of a Boolean network consisting of n nested canalyzing functions. Although an O(1.799(n)) time algorithm was proposed in a previous study, it was implicitly assumed that the network does not contain any positive self-loops. By utilizing the improved satisfiability algorithm for nested canalyzing functions, while allowing for the presence of positive self-loops, we show that the general case can be solved in O(1.871(n)) time.

Resumo Limpo

studi problem find assign boolean variabl satisfi given set nest canalyz function class boolean function known interest biolog problem extens satisfi problem conjunct normal form formula omink kmpolym time algorithm known m k number nest canalyz function variabl respect present improv omink km mpolym time algorithm problem also studi problem find singleton attractor boolean network consist n nest canalyz function although time algorithm propos previous studi implicit assum network contain posit selfloop util improv satisfi algorithm nest canalyz function allow presenc posit selfloop show general case can solv time

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