A new Bayesian piecewise linear regression model for dynamic network reconstruction

Abstract

Abstract Background Linear regression models are important tools for learning regulatory networks from gene expression time series. A conventional assumption for non-homogeneous regulatory processes on a short time scale is that the network structure stays constant across time, while the network parameters are time-dependent. The objective is then to learn the network structure along with changepoints that divide the time series into time segments. An uncoupled model learns the parameters separately for each segment, while a coupled model enforces the parameters of any segment to stay similar to those of the previous segment. In this paper, we propose a new consensus model that infers for each individual time segment whether it is coupled to (or uncoupled from) the previous segment. Results The results show that the new consensus model is superior to the uncoupled and the coupled model, as well as superior to a recently proposed generalized coupled model. Conclusions The newly proposed model has the uncoupled and the coupled model as limiting cases, and it is able to infer the best trade-off between them from the data.

Keywords

• Bayesian piece-wise linear regression
• Gene regulatory networks
• Network reconstruction
• Segment-wise parameter coupling