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Heterogeneous reciprocal graphical models

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  • Yang Ni
  • Peter Müller
  • Yitan Zhu
  • Yuan Ji

Abstract

We develop novel hierarchical reciprocal graphical models to infer gene networks from heterogeneous data. In the case of data that can be naturally divided into known groups, we propose to connect graphs by introducing a hierarchical prior across group†specific graphs, including a correlation on edge strengths across graphs. Thresholding priors are applied to induce sparsity of the estimated networks. In the case of unknown groups, we cluster subjects into subpopulations and jointly estimate cluster†specific gene networks, again using similar hierarchical priors across clusters. We illustrate the proposed approach by simulation studies and three applications with multiplatform genomic data for multiple cancers.

Suggested Citation

  • Yang Ni & Peter Müller & Yitan Zhu & Yuan Ji, 2018. "Heterogeneous reciprocal graphical models," Biometrics, The International Biometric Society, vol. 74(2), pages 606-615, June.
    • Handle: RePEc:bla:biomet:v:74:y:2018:i:2:p:606-615
    DOI: 10.1111/biom.12791
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    References listed on IDEAS

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    Cited by:

    1. Zhang, Junyi & Dassios, Angelos, 2023. "Truncated two-parameter Poisson-Dirichlet approximation for Pitman-Yor process hierarchical models," LSE Research Online Documents on Economics 120294, London School of Economics and Political Science, LSE Library.
    2. van Wieringen, Wessel N. & Stam, Koen A. & Peeters, Carel F.W. & van de Wiel, Mark A., 2020. "Updating of the Gaussian graphical model through targeted penalized estimation," Journal of Multivariate Analysis, Elsevier, vol. 178(C).
    3. Yang Ni & Veerabhadran Baladandayuthapani & Marina Vannucci & Francesco C. Stingo, 2022. "Bayesian graphical models for modern biological applications," Statistical Methods & Applications, Springer;Società Italiana di Statistica, vol. 31(2), pages 197-225, June.
    4. Lawless Caroline & Arbel Julyan, 2019. "A simple proof of Pitman–Yor’s Chinese restaurant process from its stick-breaking representation," Dependence Modeling, De Gruyter, vol. 7(1), pages 45-52, March.
    5. Lin Zhang & Andrew DiLernia & Karina Quevedo & Jazmin Camchong & Kelvin Lim & Wei Pan, 2021. "A random covariance model for bi‐level graphical modeling with application to resting‐state fMRI data," Biometrics, The International Biometric Society, vol. 77(4), pages 1385-1396, December.
    6. Lee, Kyoungjae & Cao, Xuan, 2022. "Bayesian joint inference for multiple directed acyclic graphs," Journal of Multivariate Analysis, Elsevier, vol. 191(C).

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