7,019 research outputs found
Approximate Decentralized Bayesian Inference
This paper presents an approximate method for performing Bayesian inference
in models with conditional independence over a decentralized network of
learning agents. The method first employs variational inference on each
individual learning agent to generate a local approximate posterior, the agents
transmit their local posteriors to other agents in the network, and finally
each agent combines its set of received local posteriors. The key insight in
this work is that, for many Bayesian models, approximate inference schemes
destroy symmetry and dependencies in the model that are crucial to the correct
application of Bayes' rule when combining the local posteriors. The proposed
method addresses this issue by including an additional optimization step in the
combination procedure that accounts for these broken dependencies. Experiments
on synthetic and real data demonstrate that the decentralized method provides
advantages in computational performance and predictive test likelihood over
previous batch and distributed methods.Comment: This paper was presented at UAI 2014. Please use the following BibTeX
citation: @inproceedings{Campbell14_UAI, Author = {Trevor Campbell and
Jonathan P. How}, Title = {Approximate Decentralized Bayesian Inference},
Booktitle = {Uncertainty in Artificial Intelligence (UAI)}, Year = {2014}
Bayesian Network Structure Learning with Permutation Tests
In literature there are several studies on the performance of Bayesian
network structure learning algorithms. The focus of these studies is almost
always the heuristics the learning algorithms are based on, i.e. the
maximisation algorithms (in score-based algorithms) or the techniques for
learning the dependencies of each variable (in constraint-based algorithms). In
this paper we investigate how the use of permutation tests instead of
parametric ones affects the performance of Bayesian network structure learning
from discrete data. Shrinkage tests are also covered to provide a broad
overview of the techniques developed in current literature.Comment: 13 pages, 4 figures. Presented at the Conference 'Statistics for
Complex Problems', Padova, June 15, 201
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
Partition MCMC for inference on acyclic digraphs
Acyclic digraphs are the underlying representation of Bayesian networks, a
widely used class of probabilistic graphical models. Learning the underlying
graph from data is a way of gaining insights about the structural properties of
a domain. Structure learning forms one of the inference challenges of
statistical graphical models.
MCMC methods, notably structure MCMC, to sample graphs from the posterior
distribution given the data are probably the only viable option for Bayesian
model averaging. Score modularity and restrictions on the number of parents of
each node allow the graphs to be grouped into larger collections, which can be
scored as a whole to improve the chain's convergence. Current examples of
algorithms taking advantage of grouping are the biased order MCMC, which acts
on the alternative space of permuted triangular matrices, and non ergodic edge
reversal moves.
Here we propose a novel algorithm, which employs the underlying combinatorial
structure of DAGs to define a new grouping. As a result convergence is improved
compared to structure MCMC, while still retaining the property of producing an
unbiased sample. Finally the method can be combined with edge reversal moves to
improve the sampler further.Comment: Revised version. 34 pages, 16 figures. R code available at
https://github.com/annlia/partitionMCM
Learning to Discover Sparse Graphical Models
We consider structure discovery of undirected graphical models from
observational data. Inferring likely structures from few examples is a complex
task often requiring the formulation of priors and sophisticated inference
procedures. Popular methods rely on estimating a penalized maximum likelihood
of the precision matrix. However, in these approaches structure recovery is an
indirect consequence of the data-fit term, the penalty can be difficult to
adapt for domain-specific knowledge, and the inference is computationally
demanding. By contrast, it may be easier to generate training samples of data
that arise from graphs with the desired structure properties. We propose here
to leverage this latter source of information as training data to learn a
function, parametrized by a neural network that maps empirical covariance
matrices to estimated graph structures. Learning this function brings two
benefits: it implicitly models the desired structure or sparsity properties to
form suitable priors, and it can be tailored to the specific problem of edge
structure discovery, rather than maximizing data likelihood. Applying this
framework, we find our learnable graph-discovery method trained on synthetic
data generalizes well: identifying relevant edges in both synthetic and real
data, completely unknown at training time. We find that on genetics, brain
imaging, and simulation data we obtain performance generally superior to
analytical methods
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).
Recommended from our members
Genomics analysis on the responses of E. coli cells to varying environmental conditions
The natural living environments of E. coli cells are diverse, varying from
mammalian gastrointestinal tracts and soil. Each environment might require
distinct metabolic pathways and transporter systems, and long-term evolution
has established elaborate regulatory system for E. coli cells to quickly adapt to
the changing conditions. Sensing outside stresses and then adopting a different
phenotype enable them to take advantage of any possible nutrients and defend
against hostile environment. A lot of regulatory mechanisms have been identified
by genetic, biochemical and molecular biology methods, and our study aim to
build a systematic view on the response of the whole genome to four different
environmental conditions. We used statistical tests including Pearson’s tests and
Spearman’s tests and multiple testing adjustments to identify feature genes that
are induced or repressed significantly across treatment levels. The feature genes
identified were partially supported by previous literatures, and some of the novel
genes not found in any previous studies may infer a potential research blind spot.
Additionally, we compared the correlation tests to the implementation of machine
learning algorithms, and discussed the advantage and drawbacks of each
method.Statistic
- …