Topological Evaluation of Methods for Reconstruction of Genetic Regulatory Networks

Jakub Olczak, Narsis A. Kiani*, Hector Zenil, Jesper Tegner

*Corresponding author for this work

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

Abstract

Network inference is advancing rapidly, and new methods are proposed on a regular basis. Understanding the advantages and limitations of different network inference methods is key to their effective application in different circumstances. The common structural properties shared by diverse networks naturally pose a challenge when it comes to devising accurate inference methods, but surprisingly, there is a paucity of comparison and evaluation methods. Historically, every new methodology has only been tested against "gold standard" purpose-designed synthetic and real-world (validated) biological networks. In this paper we aim to assess the impact of taking into consideration topological aspects on the evaluation of the final accuracy of an inference procedure. Specifically, we will compare the best inference methods, in statistical terms, for preserving the topological properties of synthetic and biological networks. A new method for performance comparison is introduced by borrowing ideas from gene set enrichment analysis. Experimental results show that no individual algorithm stands out among the three inference tasks assessed, and the challenging nature of network inference is evident in the struggle of some of the algorithms to turn in a performance that's better than random guesswork. Therefore care should be taken to suit the method used to the specific purpose.

Original languageEnglish (US)
Title of host publicationProceedings - 11th International Conference on Signal-Image Technology and Internet-Based Systems, SITIS 2015
EditorsKokou Yetongnon, Albert Dipanda, Richard Chbeir
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages468-473
Number of pages6
ISBN (Electronic)9781467397216
DOIs
StatePublished - Feb 5 2016
Event11th International Conference on Signal-Image Technology and Internet-Based Systems, SITIS 2015 - Bangkok, Thailand
Duration: Nov 23 2015Nov 27 2015

Publication series

NameProceedings - 11th International Conference on Signal-Image Technology and Internet-Based Systems, SITIS 2015

Other

Other11th International Conference on Signal-Image Technology and Internet-Based Systems, SITIS 2015
CountryThailand
CityBangkok
Period11/23/1511/27/15

Keywords

  • evaluating measure
  • inference methods evaluation
  • network reconstruction
  • topological properties

ASJC Scopus subject areas

  • Signal Processing
  • Computer Networks and Communications
  • Information Systems

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