Bayesian Data Fusion of Gene Expression and Histone Modification Profiles for Inference of Gene Regulatory Network

BIC-LP: A Hybrid Higher-Order Dynamic Bayesian Network Score Function for Gene Regulatory Network Reconstruction

Reconstructing gene regulatory networks(GRNs) is an increasingly hot topic in bioinformatics. Dynamic Bayesian network(DBN) is a stochastic graph model commonly used as a vital model for GRN reconstruction. But probabilistic characteristics of biological networks and the existence of data noise bring great challenges to GRN reconstruction and always lead to many false positive/negative edges. ScoreLasso is a hybrid DBN score function combining DBN and linear regression with good performance. Its performance is, however, limited by first-order assumption and ignorance of the initial network of DBN. In this article, an integrated model based on higher-order DBN model, higher-order Lasso linear regression model and Pearson correlation model is proposed. Based on this, a hybrid higher-order DBN score function for GRN reconstruction is proposed, namely BIC-LP. BIC-LP score function is constructed by adding terms based on Lasso linear regression coefficients and Pearson correlation coefficients on classical BIC score function. Therefore, it could capture more information from dataset and curb information loss, compared with both many existing Bayesian family score functions and many state-of-the-art methods for GRN reconstruction. Experimental results show that BIC-LP can reasonably eliminate some false positive edges while retaining most true positive edges, so as to achieve better GRN reconstruction performance.

A New Total Uncertainty Measure from A Perspective of Maximum Entropy Requirement

The Dempster-Shafer theory (DST) is an information fusion framework and widely used in many fields. However, the uncertainty measure of a basic probability assignment (BPA) is still an open issue in DST. There are many methods to quantify the uncertainty of BPAs. However, the existing methods have some limitations. In this paper, a new total uncertainty measure from a perspective of maximum entropy requirement is proposed. The proposed method can measure both dissonance and non-specificity in BPA, which includes two components. The first component is consistent with Yager's dissonance measure. The second component is the non-specificity measurement with different functions. We also prove the desirable properties of the proposed method. Besides, numerical examples and applications are provided to illustrate the effectiveness of the proposed total uncertainty measure.