Ranking vertices for active module recovery problem

Javlon E. Isomurodov, Alexander A. Loboda, Alexey A. Sergushichev

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations


Selecting a connected subnetwork enriched in individually important vertices is an approach commonly used in many areas of bioinformatics, including analysis of gene expression data, mutations, metabolomic profiles and others. It can be formulated as a recovery of an active module from which an experimental signal is generated. Commonly, methods for solving this problem result in a single subnetwork that is considered to be a good candidate. However, it is usually useful to consider not one but multiple candidate modules at different significance threshold levels. Therefore, in this paper we suggest to consider a problem of finding a vertex ranking instead of finding a single module. We also propose two algorithms for solving this problem: one that we consider to be optimal but computationally expensive for real-world networks and one that works close to the optimal in practice and is also able to work with big networks.

Original languageEnglish
Title of host publicationAlgorithms for Computational Biology - 4th International Conference, AlCoB 2017, Proceedings
EditorsMiguel A. Vega-Rodriguez, Daniel Figueiredo, Diogo Pratas, Carlos Martin-Vide
PublisherSpringer Verlag
Number of pages10
ISBN (Print)9783319581620
StatePublished - 2017
Event4th International Conference on Algorithms for Computational Biology, AlCoB 2017 - Aveiro, Portugal
Duration: Jun 5 2017Jun 6 2017

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10252 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Conference4th International Conference on Algorithms for Computational Biology, AlCoB 2017


  • Active module
  • Connected subgraphs
  • Dynamic programming
  • Integer linear programming
  • Interaction networks
  • Vertex ranking


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