Joint estimation of multiple related biological networks
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Abstract: Graphical models are widely used to make inferences concerning interplay in multivariate systems. In many applications, data are collected from multiple related but nonidentical units whose underlying networks may differ but are likely to share features. Here we present a hierarchical Bayesian formulation for joint estimation of multiple networks in this nonidentically distributed setting. The approach is general: given a suitable class of graphical models, it uses an exchangeability assumption on networks to provide a corresponding joint formulation. Motivated by emerging experimental designs in molecular biology, we focus on time-course data with interventions, using dynamic Bayesian networks as the graphical models. We introduce a computationally efficient, deterministic algorithm for exact joint inference in this setting. We provide an upper bound on the gains that joint estimation offers relative to separate estimation for each network and empirical results that support and extend the theory, including an extensive simulation study and an application to proteomic data from human cancer cell lines. Finally, we describe approximations that are still more computationally efficient than the exact algorithm and that also demonstrate good empirical performance.
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Cited in
(18)- On Joint Estimation of Gaussian Graphical Models for Spatial and Temporal Data
- Bayesian approaches for large biological networks
- Inference and characterization of multi-attribute networks with application to computational biology
- Bayesian graphical regression
- Using Complexity for the Estimation of Bayesian Networks
- Estimation of joint directed acyclic graphs with Lasso family for gene networks
- Quantifying the multi-scale performance of network inference algorithms
- Heterogeneous reciprocal graphical models
- Exact estimation of multiple directed acyclic graphs
- Joint estimation of multiple related biological networks
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- Inferring multiple graphical structures
- Multi-way blockmodels for analyzing coordinated high-dimensional responses
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