A Fast Prize-Collecting Steiner Forest Algorithm for Functional Analyses in Biological Networks

Author(s)
Bertoni, Francesco; Kwee, Ivo; Montemanni, Roberto; Akhmedov, Murodzhon; Lenail, Alexander; ... Show more
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Abstract
The Prize-collecting Steiner Forest (PCSF) problem is NP-hard, requiring extreme computational effort to find exact solutions for large inputs. We introduce a new heuristic algorithm for PCSF which preserves the quality of solutions obtained by previous heuristic approaches while reducing the runtime by a factor of 10 for larger graphs. By decreasing the draw on computational resources, this algorithm affords systems biologists the opportunity to analyze larger biological networks faster and narrow their analyses to individual patients. Keywords: Prize-collecting Steiner Forest, Biological networks
Date issued
2017-05
URI
http://hdl.handle.net/1721.1/118381
Department
Massachusetts Institute of Technology. Department of Biological Engineering
Journal
Integration of AI and OR Techniques in Constraint Programming
Publisher
Springer International Publishing
Citation
Akhmedov, Murodzhon, et al. “A Fast Prize-Collecting Steiner Forest Algorithm for Functional Analyses in Biological Networks.” Integration of AI and OR Techniques in Constraint Programming, edited by Domenico Salvagnin and Michele Lombardi, vol. 10335, Springer International Publishing, 2017, pp. 263–76.
Version: Author's final manuscript
ISBN
978-3-319-59775-1
978-3-319-59776-8
ISSN
0302-9743
1611-3349
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