Solving Generalized Maximum-Weight Connected Subgraph Problem for Network Enrichment Analysis

  • Alexander A. Loboda
  • Maxim N. Artyomov
  • Alexey A. Sergushichev
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9838)

Abstract

Network enrichment analysis methods allow to identify active modules without being biased towards a priori defined pathways. One of mathematical formulations of such analysis is a reduction to a maximum-weight connected subgraph problem. In particular, in analysis of metabolic networks a generalized maximum-weight connected subgraph (GMWCS) problem, where both nodes and edges are scored, naturally arises. Here we present the first to our knowledge practical exact GMWCS solver. We have tested it on real-world instances and compared to similar solvers. First, the results show that on node-weighted instances GMWCS solver has a similar performance to the best solver for that problem. Second, GMWCS solver is faster compared to the closest analogue when run on GMWCS instances with edge weights.

Keywords

Network enrichment Maximum weight connected subgraph problem Exact solver Mixed integer programming 

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Alexander A. Loboda
    • 1
  • Maxim N. Artyomov
    • 2
  • Alexey A. Sergushichev
    • 1
  1. 1.Computer Technologies DepartmentITMO UniversitySaint PetersburgRussia
  2. 2.Department of Pathology and ImmunologyWashington University in St. LouisSt. LouisUSA

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