Abstract
Boolean network is a modeling tool that describes a dynamic system with binary variables and their logical transition formulas. Recent studies in precision medicine use a Boolean network to discover critical genetic alterations that may lead to cancer or target genes for effective therapies to individuals. In this paper, we study a logical inference problem in a Boolean network to find all such critical genetic alterations in a minimal (parsimonious) way. We propose a bilevel integer programming model to find a single minimal genetic alteration. Using the bilevel integer programming model, we develop a branch and bound algorithm that effectively finds all of the minimal alterations. Through a computational study with eleven Boolean networks from the literature, we show that the proposed algorithm finds solutions much faster than the state-of-the-art algorithms in large data sets.
Original language | English (US) |
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Pages (from-to) | 743-754 |
Number of pages | 12 |
Journal | European Journal of Operational Research |
Volume | 300 |
Issue number | 2 |
DOIs | |
State | Published - Jul 16 2022 |
Funding
This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.
Keywords
- Bilevel programming
- Bioinformatics
- Boolean network
- Branch and bound algorithm
ASJC Scopus subject areas
- General Computer Science
- Modeling and Simulation
- Management Science and Operations Research
- Information Systems and Management