Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes

<b>Method:</b> Dynamic Bayesian networks (DBNs) have been applied widely to reconstruct the structure of regulatory processes from time series data, and they have established themselves as a standard modelling tool in computational systems biology. The conventional approach is based on the assumption of a homogeneous Markov chain, and many recent research efforts have focused on relaxing this restriction. An approach that enjoys particular popularity is based on a combination of a DBN with a multiple changepoint process, and the application of a Bayesian inference scheme via reversible jump Markov chain Monte Carlo (RJMCMC). In the present article, we expand this approach in two ways. First, we show that a dynamic programming scheme allows the changepoints to be sampled from the correct conditional distribution, which results in improved convergence over RJMCMC. Second, we introduce a novel Bayesian clustering and information sharing scheme among nodes, which provides a mechanism for automatic model complexity tuning. <b>Results:</b> We evaluate the dynamic programming scheme on expression time series for Arabidopsis thaliana genes involved in circadian regulation. In a simulation study we demonstrate that the regularization scheme improves the network reconstruction accuracy over that obtained with recently proposed inhomogeneous DBNs. For gene expression profiles from a synthetically designed Saccharomyces cerevisiae strain under switching carbon metabolism we show that the combination of both: dynamic programming and regularization yields an inference procedure that outperforms two alternative established network reconstruction methods from the biology literature

Graph Regularized Tensor Sparse Coding for Image Representation

Sparse coding (SC) is an unsupervised learning scheme that has received an increasing amount of interests in recent years. However, conventional SC vectorizes the input images, which destructs the intrinsic spatial structures of the images. In this paper, we propose a novel graph regularized tensor sparse coding (GTSC) for image representation. GTSC preserves the local proximity of elementary structures in the image by adopting the newly proposed tubal-tensor representation. Simultaneously, it considers the intrinsic geometric properties by imposing graph regularization that has been successfully applied to uncover the geometric distribution for the image data. Moreover, the returned sparse representations by GTSC have better physical explanations as the key operation (i.e., circular convolution) in the tubal-tensor model preserves the shifting invariance property. Experimental results on image clustering demonstrate the effectiveness of the proposed scheme