4,273 research outputs found
Learning Large-Scale Bayesian Networks with the sparsebn Package
Learning graphical models from data is an important problem with wide
applications, ranging from genomics to the social sciences. Nowadays datasets
often have upwards of thousands---sometimes tens or hundreds of thousands---of
variables and far fewer samples. To meet this challenge, we have developed a
new R package called sparsebn for learning the structure of large, sparse
graphical models with a focus on Bayesian networks. While there are many
existing software packages for this task, this package focuses on the unique
setting of learning large networks from high-dimensional data, possibly with
interventions. As such, the methods provided place a premium on scalability and
consistency in a high-dimensional setting. Furthermore, in the presence of
interventions, the methods implemented here achieve the goal of learning a
causal network from data. Additionally, the sparsebn package is fully
compatible with existing software packages for network analysis.Comment: To appear in the Journal of Statistical Software, 39 pages, 7 figure
Ancestral Causal Inference
Constraint-based causal discovery from limited data is a notoriously
difficult challenge due to the many borderline independence test decisions.
Several approaches to improve the reliability of the predictions by exploiting
redundancy in the independence information have been proposed recently. Though
promising, existing approaches can still be greatly improved in terms of
accuracy and scalability. We present a novel method that reduces the
combinatorial explosion of the search space by using a more coarse-grained
representation of causal information, drastically reducing computation time.
Additionally, we propose a method to score causal predictions based on their
confidence. Crucially, our implementation also allows one to easily combine
observational and interventional data and to incorporate various types of
available background knowledge. We prove soundness and asymptotic consistency
of our method and demonstrate that it can outperform the state-of-the-art on
synthetic data, achieving a speedup of several orders of magnitude. We
illustrate its practical feasibility by applying it on a challenging protein
data set.Comment: In Proceedings of Advances in Neural Information Processing Systems
29 (NIPS 2016
Advances in Learning Bayesian Networks of Bounded Treewidth
This work presents novel algorithms for learning Bayesian network structures
with bounded treewidth. Both exact and approximate methods are developed. The
exact method combines mixed-integer linear programming formulations for
structure learning and treewidth computation. The approximate method consists
in uniformly sampling -trees (maximal graphs of treewidth ), and
subsequently selecting, exactly or approximately, the best structure whose
moral graph is a subgraph of that -tree. Some properties of these methods
are discussed and proven. The approaches are empirically compared to each other
and to a state-of-the-art method for learning bounded treewidth structures on a
collection of public data sets with up to 100 variables. The experiments show
that our exact algorithm outperforms the state of the art, and that the
approximate approach is fairly accurate.Comment: 23 pages, 2 figures, 3 table
Connectionist Theory Refinement: Genetically Searching the Space of Network Topologies
An algorithm that learns from a set of examples should ideally be able to
exploit the available resources of (a) abundant computing power and (b)
domain-specific knowledge to improve its ability to generalize. Connectionist
theory-refinement systems, which use background knowledge to select a neural
network's topology and initial weights, have proven to be effective at
exploiting domain-specific knowledge; however, most do not exploit available
computing power. This weakness occurs because they lack the ability to refine
the topology of the neural networks they produce, thereby limiting
generalization, especially when given impoverished domain theories. We present
the REGENT algorithm which uses (a) domain-specific knowledge to help create an
initial population of knowledge-based neural networks and (b) genetic operators
of crossover and mutation (specifically designed for knowledge-based networks)
to continually search for better network topologies. Experiments on three
real-world domains indicate that our new algorithm is able to significantly
increase generalization compared to a standard connectionist theory-refinement
system, as well as our previous algorithm for growing knowledge-based networks.Comment: See http://www.jair.org/ for any accompanying file
Learning a bayesian network from ordinal data
Bayesian networks are graphical models that represent the joint distributionof a set of variables using directed acyclic graphs. When the dependence structure is unknown (or partially known) the network can be learnt from data. In this paper, we propose a constraint-based method to perform Bayesian networks structural learning in presence of ordinal variables. The new procedure, called OPC, represents a variation of the PC algorithm. A nonparametric test, appropriate for ordinal variables, has been used. It will be shown that, in some situation, the OPC algorithm is a solution more efficient than the PC algorithm.Structural Learning, Monotone Association, Nonparametric Methods
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