The relationship between Precision-Recall and ROC curves
ICML '06 Proceedings of the 23rd international conference on Machine learning
Recovering temporally rewiring networks: a model-based approach
Proceedings of the 24th international conference on Machine learning
Modeling changing dependency structure in multivariate time series
Proceedings of the 24th international conference on Machine learning
Learning Non-Stationary Dynamic Bayesian Networks
The Journal of Machine Learning Research
Non-homogeneous dynamic Bayesian networks for continuous data
Machine Learning
Joint Bayesian model selection and estimation of noisy sinusoidsvia reversible jump MCMC
IEEE Transactions on Signal Processing
Bayesian curve fitting using MCMC with applications to signalsegmentation
IEEE Transactions on Signal Processing
Time Varying Dynamic Bayesian Network for Nonstationary Events Modeling and Online Inference
IEEE Transactions on Signal Processing
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The proper functioning of any living cell relies on complex networks of gene regulation. These regulatory interactions are not static but respond to changes in the environment and evolve during the life cycle of an organism. A challenging objective in computational systems biology is to infer these time-varying gene regulatory networks from typically short time series of transcriptional profiles. While homogeneous models, like conventional dynamic Bayesian networks, lack the flexibility to succeed in this task, fully flexible models suffer from inflated inference uncertainty due to the limited amount of available data. In the present paper we explore a semi-flexible model based on a piecewise homogeneous dynamic Bayesian network regularized by gene-specific inter-segment information sharing. We explore different choices of prior distribution and information coupling and evaluate their performance on synthetic data. We apply our method to gene expression time series obtained during the life cycle of Drosophila melanogaster, and compare the predicted segmentation with other state-of-the-art techniques. We conclude our evaluation with an application to synthetic biology, where the objective is to predict an in vivo regulatory network of five genes in Saccharomyces cerevisiae subjected to a changing environment.