Application of new probabilistic graphical models in the genetic regulatory networks studies

This paper introduces two new probabilistic graphical models for reconstruction of genetic regulatory networks using DNA microarray data. One is an Independence Graph (IG) model with either a forward or a backward search algorithm and the other one is a Gaussian Network (GN) model with a novel greedy search method. The performances of both models were evaluated on four MAPK pathways in yeast and three simulated data sets. Generally, an IG model provides a sparse graph but a GN model produces a dense graph where more information about gene-gene interactions is preserved. Additionally, we found two key limitations in the prediction of genetic regulatory networks using DNA microarray data, the first is the sufficiency of sample size and the second is the complexity of network structures may not be captured without additional data at the protein level. Those limitations are present in all prediction methods which used only DNA microarray data.Comment: 38 pages, 3 figure

A Model of Consistent Node Types in Signed Directed Social Networks

Signed directed social networks, in which the relationships between users can be either positive (indicating relations such as trust) or negative (indicating relations such as distrust), are increasingly common. Thus the interplay between positive and negative relationships in such networks has become an important research topic. Most recent investigations focus upon edge sign inference using structural balance theory or social status theory. Neither of these two theories, however, can explain an observed edge sign well when the two nodes connected by this edge do not share a common neighbor (e.g., common friend). In this paper we develop a novel approach to handle this situation by applying a new model for node types. Initially, we analyze the local node structure in a fully observed signed directed network, inferring underlying node types. The sign of an edge between two nodes must be consistent with their types; this explains edge signs well even when there are no common neighbors. We show, moreover, that our approach can be extended to incorporate directed triads, when they exist, just as in models based upon structural balance or social status theory. We compute Bayesian node types within empirical studies based upon partially observed Wikipedia, Slashdot, and Epinions networks in which the largest network (Epinions) has 119K nodes and 841K edges. Our approach yields better performance than state-of-the-art approaches for these three signed directed networks.Comment: To appear in the IEEE/ACM International Conference on Advances in Social Network Analysis and Mining (ASONAM), 201