Bayesian learning of multiple directed networks from observational data

Federico Castelletti, Guido Consonni, Stefano Peluso, Luca La Rocca, Francesco C. Stingo

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)

Abstract

Graphical modeling represents an established methodology for identifying complex dependencies in biological networks, as exemplified in the study of co-expression, gene regulatory, and protein interaction networks. The available observations often exhibit an intrinsic heterogeneity, which impacts on the network structure through the modification of specific pathways for distinct groups, such as disease subtypes. We propose to infer the resulting multiple graphs jointly in order to benefit from potential similarities across groups; on the other hand our modeling framework is able to accommodate group idiosyncrasies. We consider directed acyclic graphs (DAGs) as network structures, and develop a Bayesian method for structural learning of multiple DAGs. We explicitly account for Markov equivalence of DAGs, and propose a suitable prior on the collection of graph spaces that induces selective borrowing strength across groups. The resulting inference allows in particular to compute the posterior probability of edge inclusion, a useful summary for representing flow directions within the network. Finally, we detail a simulation study addressing the comparative performance of our method, and present an analysis of two protein networks together with a substantive interpretation of our findings.
Original languageEnglish
Pages (from-to)4745-4766
Number of pages22
JournalStatistics in Medicine
Volume39
DOIs
Publication statusPublished - 2020

Keywords

  • Markov equivalence
  • Markov random field
  • essential graph
  • objective Bayes
  • protein network

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