Discovering causal interactions using Bayesian network scoring and information gain

Zexian Zeng, Xia Jiang, Richard Neapolitan*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    20 Scopus citations

    Abstract

    Background: The problem of learning causal influences from data has recently attracted much attention. Standard statistical methods can have difficulty learning discrete causes, which interacting to affect a target, because the assumptions in these methods often do not model discrete causal relationships well. An important task then is to learn such interactions from data. Motivated by the problem of learning epistatic interactions from datasets developed in genome-wide association studies (GWAS), researchers conceived new methods for learning discrete interactions. However, many of these methods do not differentiate a model representing a true interaction from a model representing non-interacting causes with strong individual affects. The recent algorithm MBS-IGain addresses this difficulty by using Bayesian network learning and information gain to discover interactions from high-dimensional datasets. However, MBS-IGain requires marginal effects to detect interactions containing more than two causes. If the dataset is not high-dimensional, we can avoid this shortcoming by doing an exhaustive search. Results: We develop Exhaustive-IGain, which is like MBS-IGain but does an exhaustive search. We compare the performance of Exhaustive-IGain to MBS-IGain using low-dimensional simulated datasets based on interactions with marginal effects and ones based on interactions without marginal effects. Their performance is similar on the datasets based on marginal effects. However, Exhaustive-IGain compellingly outperforms MBS-IGain on the datasets based on 3 and 4-cause interactions without marginal effects. We apply Exhaustive-IGain to investigate how clinical variables interact to affect breast cancer survival, and obtain results that agree with judgements of a breast cancer oncologist. Conclusions: We conclude that the combined use of information gain and Bayesian network scoring enables us to discover higher order interactions with no marginal effects if we perform an exhaustive search. We further conclude that Exhaustive-IGain can be effective when applied to real data.

    Original languageEnglish (US)
    Article number221
    JournalBMC bioinformatics
    Volume17
    Issue number1
    DOIs
    StatePublished - May 26 2016

    Keywords

    • Bayesian network
    • Breast cancer survival
    • Cause
    • Epistasis
    • Information gain
    • Interaction
    • Low-dimensional

    ASJC Scopus subject areas

    • Structural Biology
    • Biochemistry
    • Molecular Biology
    • Computer Science Applications
    • Applied Mathematics

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