10,035 research outputs found
Maximizing Activity in Ising Networks via the TAP Approximation
A wide array of complex biological, social, and physical systems have
recently been shown to be quantitatively described by Ising models, which lie
at the intersection of statistical physics and machine learning. Here, we study
the fundamental question of how to optimize the state of a networked Ising
system given a budget of external influence. In the continuous setting where
one can tune the influence applied to each node, we propose a series of
approximate gradient ascent algorithms based on the Plefka expansion, which
generalizes the na\"{i}ve mean field and TAP approximations. In the discrete
setting where one chooses a small set of influential nodes, the problem is
equivalent to the famous influence maximization problem in social networks with
an additional stochastic noise term. In this case, we provide sufficient
conditions for when the objective is submodular, allowing a greedy algorithm to
achieve an approximation ratio of . Additionally, we compare the
Ising-based algorithms with traditional influence maximization algorithms,
demonstrating the practical importance of accurately modeling stochastic
fluctuations in the system
Hierarchical relational models for document networks
We develop the relational topic model (RTM), a hierarchical model of both
network structure and node attributes. We focus on document networks, where the
attributes of each document are its words, that is, discrete observations taken
from a fixed vocabulary. For each pair of documents, the RTM models their link
as a binary random variable that is conditioned on their contents. The model
can be used to summarize a network of documents, predict links between them,
and predict words within them. We derive efficient inference and estimation
algorithms based on variational methods that take advantage of sparsity and
scale with the number of links. We evaluate the predictive performance of the
RTM for large networks of scientific abstracts, web documents, and
geographically tagged news.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS309 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Detection of regulator genes and eQTLs in gene networks
Genetic differences between individuals associated to quantitative phenotypic
traits, including disease states, are usually found in non-coding genomic
regions. These genetic variants are often also associated to differences in
expression levels of nearby genes (they are "expression quantitative trait
loci" or eQTLs for short) and presumably play a gene regulatory role, affecting
the status of molecular networks of interacting genes, proteins and
metabolites. Computational systems biology approaches to reconstruct causal
gene networks from large-scale omics data have therefore become essential to
understand the structure of networks controlled by eQTLs together with other
regulatory genes, and to generate detailed hypotheses about the molecular
mechanisms that lead from genotype to phenotype. Here we review the main
analytical methods and softwares to identify eQTLs and their associated genes,
to reconstruct co-expression networks and modules, to reconstruct causal
Bayesian gene and module networks, and to validate predicted networks in
silico.Comment: minor revision with typos corrected; review article; 24 pages, 2
figure
- …