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

• Main Authors: Bertoni, Francesco (Author), Kwee, Ivo (Author), Montemanni, Roberto (Author), Akhmedov, Murodzhon (Contributor), Lenail, Alexander (Contributor), Fraenkel, Ernest (Contributor)
• Other Authors: Massachusetts Institute of Technology. Department of Biological Engineering (Contributor)
• Format: Article
• Language: English
• Published: Springer International Publishing, 2018-10-09T13:46:44Z.
• Subjects: Article
• Online Access: Get fulltext

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
National Institutes of Health (U.S.) (U54-NS-091046)
National Institutes of Health (U.S.) (U01-CA184898)
Swiss National Science Foundation (205321-147138)