Bilevel integer programming on a Boolean network for discovering critical genetic alterations in cancer development and therapy

DOI10.1016/J.EJOR.2021.10.019zbMATH Open1495.92032OpenAlexW3206095108MaRDI QIDQ2116889FDOQ2116889

Kyungduk Moon, Steve Kwon, Kangbok Lee, Sunil Chopra

Publication date: 18 March 2022

Published in: European Journal of Operational Research (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.ejor.2021.10.019

zbMATH Keywords

bilevel programmingbioinformaticsBoolean networkbranch and bound algorithm

Mathematics Subject Classification ID

Medical applications (general) (92C50) Polyhedral combinatorics, branch-and-bound, branch-and-cut (90C57) Biochemistry, molecular biology (92C40) Integer programming (90C10) Mixed integer programming (90C11)

Cites Work

• Title not available (Why is that?)
• Links between linear bilevel and mixed 0-1 programming problems
• The Mixed Integer Linear Bilevel Programming Problem
• Modeling, inference and optimization of regulatory networks based on time series data
• Reduction of Boolean network models
• An exact algorithm for the bilevel mixed integer linear programming problem under three simplifying assumptions
• Dynamically consistent reduction of logical regulatory graphs
• Mapping multivalued onto Boolean dynamics
• A branch-and-cut algorithm for mixed integer bilevel linear optimization problems and its implementation
• Learning Boolean logic models of signaling networks with ASP
• Enhanced exact algorithms for discrete bilevel linear problems
• Minimal intervention strategies in logical signaling networks with ASP
• Intersection Cuts for Bilevel Optimization
• A New General-Purpose Algorithm for Mixed-Integer Bilevel Linear Programs
• Number of Fixed Points and Disjoint Cycles in Monotone Boolean Networks
• Logic and integer programming
• The Watermelon Algorithm for The Bilevel Integer Linear Programming Problem
• On the use of intersection cuts for bilevel optimization
• An enhanced branch-and-bound algorithm for bilevel integer linear programming
• A survey on mixed-integer programming techniques in bilevel optimization
• Algorithms and applications for a class of bilevel MILPs
• Integer Linear Programming in Computational and Systems Biology

Cited In (3)

• Tackling universal properties of minimal trap spaces of Boolean networks
• Computational complexity of minimal trap spaces in Boolean networks
• Approximation algorithms for connected maximum coverage problem for the discovery of mutated driver pathways in cancer

Uses Software

• Gurobi
• BoolNet
• Ginsim
• MaBoSS
• GitHub

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