11,898 research outputs found
Learning Bayesian Networks with the bnlearn R Package
bnlearn is an R package which includes several algorithms for learning the
structure of Bayesian networks with either discrete or continuous variables.
Both constraint-based and score-based algorithms are implemented, and can use
the functionality provided by the snow package to improve their performance via
parallel computing. Several network scores and conditional independence
algorithms are available for both the learning algorithms and independent use.
Advanced plotting options are provided by the Rgraphviz package.Comment: 22 pages, 4 picture
Structural Agnostic Modeling: Adversarial Learning of Causal Graphs
A new causal discovery method, Structural Agnostic Modeling (SAM), is
presented in this paper. Leveraging both conditional independencies and
distributional asymmetries in the data, SAM aims at recovering full causal
models from continuous observational data along a multivariate non-parametric
setting. The approach is based on a game between players estimating each
variable distribution conditionally to the others as a neural net, and an
adversary aimed at discriminating the overall joint conditional distribution,
and that of the original data. An original learning criterion combining
distribution estimation, sparsity and acyclicity constraints is used to enforce
the end-to-end optimization of the graph structure and parameters through
stochastic gradient descent. Besides the theoretical analysis of the approach
in the large sample limit, SAM is extensively experimentally validated on
synthetic and real data
Measures of Variability for Bayesian Network Graphical Structures
The structure of a Bayesian network includes a great deal of information
about the probability distribution of the data, which is uniquely identified
given some general distributional assumptions. Therefore it's important to
study its variability, which can be used to compare the performance of
different learning algorithms and to measure the strength of any arbitrary
subset of arcs.
In this paper we will introduce some descriptive statistics and the
corresponding parametric and Monte Carlo tests on the undirected graph
underlying the structure of a Bayesian network, modeled as a multivariate
Bernoulli random variable. A simple numeric example and the comparison of the
performance of some structure learning algorithm on small samples will then
illustrate their use.Comment: 19 pages, 4 figures. arXiv admin note: substantial text overlap with
arXiv:0909.168
Learning Bayesian Networks with the bnlearn R Package
bnlearn is an R package (R Development Core Team 2010) which includes several algorithms for learning the structure of Bayesian networks with either discrete or continuous variables. Both constraint-based and score-based algorithms are implemented, and can use the functionality provided by the snow package (Tierney et al. 2008) to improve their performance via parallel computing. Several network scores and conditional independence algorithms are available for both the learning algorithms and independent use. Advanced plotting options are provided by the Rgraphviz package (Gentry et al. 2010).
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
Privacy-Preserving Adversarial Networks
We propose a data-driven framework for optimizing privacy-preserving data
release mechanisms to attain the information-theoretically optimal tradeoff
between minimizing distortion of useful data and concealing specific sensitive
information. Our approach employs adversarially-trained neural networks to
implement randomized mechanisms and to perform a variational approximation of
mutual information privacy. We validate our Privacy-Preserving Adversarial
Networks (PPAN) framework via proof-of-concept experiments on discrete and
continuous synthetic data, as well as the MNIST handwritten digits dataset. For
synthetic data, our model-agnostic PPAN approach achieves tradeoff points very
close to the optimal tradeoffs that are analytically-derived from model
knowledge. In experiments with the MNIST data, we visually demonstrate a
learned tradeoff between minimizing the pixel-level distortion versus
concealing the written digit.Comment: 16 page
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