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International Conference on AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems

CPAIOR 2017: Integration of AI and OR Techniques in Constraint Programming pp 263–276Cite as

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

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10335))

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.

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Acknowledgments

M.A. was supported by the Swiss National Science Foundation through the project 205321-147138/1: Steiner trees for functional analysis in cancer system biology. M.A. (partially) and A.L. were supported by the National Institute of Health through the project U54-NS-091046 and U01-CA-184898.

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Authors and Affiliations

  1. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Murodzhon Akhmedov, Alexander LeNail & Ernest Fraenkel

  2. Dalle Molle Institute for Artificial Intelligence Research (IDSIA-USI/SUPSI), Manno, Switzerland

    Murodzhon Akhmedov, Ivo Kwee & Roberto Montemanni

  3. Institute of Oncology Research (IOR), Bellinzona, Switzerland

    Murodzhon Akhmedov, Francesco Bertoni & Ivo Kwee

Authors
  1. Murodzhon Akhmedov
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  2. Alexander LeNail
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  3. Francesco Bertoni
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  4. Ivo Kwee
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  5. Ernest Fraenkel
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  6. Roberto Montemanni
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Corresponding author

Correspondence to Roberto Montemanni .

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Editors and Affiliations

  1. University of Padua, Padua, Italy

    Domenico Salvagnin

  2. University of Bologna, Bologna, Italy

    Michele Lombardi

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Akhmedov, M., LeNail, A., Bertoni, F., Kwee, I., Fraenkel, E., Montemanni, R. (2017). A Fast Prize-Collecting Steiner Forest Algorithm for Functional Analyses in Biological Networks. In: Salvagnin, D., Lombardi, M. (eds) Integration of AI and OR Techniques in Constraint Programming. CPAIOR 2017. Lecture Notes in Computer Science(), vol 10335. Springer, Cham. https://doi.org/10.1007/978-3-319-59776-8_22

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  • DOI: https://doi.org/10.1007/978-3-319-59776-8_22

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-59775-1

  • Online ISBN: 978-3-319-59776-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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