2010 · 163 citations · 35 references
ComputingBiologyGene Regulatory NetworksMachine LearningTime Series AnalysisBayesian InferenceBayesian LearningBayesian Model BuildingBayesian StatisticsMarkov Chain Monte CarloTime Series ModelingBayesian Network Structure LearningBayesian NetworksConditional Dependence EstimationConditional StructureDependence StructureGraphical Model Structure LearningTranscriptional Regulation NetworksTranscriptional Regulatory Networks
Dynamic Bayesian network structure learning identifies conditional dependencies in time‑series data, but assumes stationarity, which is often violated in evolving systems such as developmental gene regulation, learning neural pathways, and daily traffic patterns. The authors propose non‑stationary dynamic Bayesian networks, a new graphical model that allows the conditional dependence structure to evolve over time. They define the non‑stationary DBN model, develop an MCMC sampling algorithm for learning its structure from time‑series data under various assumptions, and validate the approach on simulated and biological datasets. The algorithm successfully learns evolving network structures, as shown by improved performance on both simulated and biological data.
Learning dynamic Bayesian network structures provides a principled mechanism for identifying conditional dependencies in time-series data. An important assumption of traditional DBN structure learning is that the data are generated by a stationary process, an assumption that is not true in many important settings. In this paper, we introduce a new class of graphical model called a non-stationary dynamic Bayesian network, in which the conditional dependence structure of the underlying data-generation process is permitted to change over time. Non-stationary dynamic Bayesian networks represent a new framework for studying problems in which the structure of a network is evolving over time. Some examples of evolving networks are transcriptional regulatory networks during an organism's development, neural pathways during learning, and traffic patterns during the day. We define the non-stationary DBN model, present an MCMC sampling algorithm for learning the structure of the model from time-series data under different assumptions, and demonstrate the effectiveness of the algorithm on both simulated and biological data.
35
Using Bayesian Networks to Analyze Expression Data
Nir Friedman, Michal Linial, Iftach Nachman et al. · Journal of Computational Biology · 2000 · 3.3K citations
Genomic analysis of regulatory network dynamics reveals large topological changes
Nicholas M. Luscombe, M. Madan Babu, Haiyuan Yu et al. · Nature · 2004 · 994 citations
Gene Expression During the Life Cycle of <i>Drosophila melanogaster</i>
Michelle N Arbeitman, Eileen E. M. Furlong, Farhad Imam et al. · Science · 2002 · 946 citations