50,577 research outputs found
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
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