bnlearn-package {bnlearn} R Documentation

Bayesian network structure learning, parameter learning and inference

Description

Bayesian network structure learning (via constraint-based, score-based and hybrid algorithms), parameter learning (via ML and Bayesian estimators) and inference (via approximate inference algorithms).

Details

Package: bnlearn
Type: Package
Version: 4.6-20190819
Date: 2019-08-19
License: GPLv2 or later

bnlearn implements key algorithms covering all stages of Bayesian network modelling: data preprocessing, structure learning combining data and expert/prior knowledge, parameter learning, and inference (including causal inference via do-calculus). bnlearn aims to be a one-stop shop for Bayesian networks in R, providing the tools needed for learning and working with discrete Bayesian networks, Gaussian Bayesian networks and conditional linear Gaussian Bayesian networks on real-world data. Incomplete data with missing values are also supported. Furthermore the modular nature of bnlearn makes it easy to use it for simulation studies.

Implemented structure learning algorithms include:

  • Constraint-based algorithms, which use conditional independence tests to learn conditional independence constraints from data. The constraints in turn are used to learn the structure of the Bayesian network under the assumption that conditional independence implies graphical separation (so, two variables that are independent cannot be connected by an arc).

  • Score-based algorithms, which are general-purpose optimization algorithms that rank network structures with respect to a goodness-of-fit score.

  • Hybrid algorithms combine aspects of both constraint-based and score-based algorithms, as they use conditional independence tests (usually to reduce the search space) and network scores (to find the optimal network in the reduced space) at the same time.

For more details about structure learning algorithms see structure learning; available conditional independence tests are described in independence tests and available network scores are described in network scores. Specialized algorithms to learn the structure of Bayesian network classifiers are described in network classifiers. All algorithms support the use of whitelists and blacklists to include and exclude arcs from the networks (see whitelists and blacklists); and many have parallel implementation built on the parallel package. Bayesian network scores support the use of graphical priors.

Parameter learning approaches include both frequentist and Bayesian estimators. Inference is implemented using approximate algorithms via particle filters approaches such as likelihood weighting, and covers conditional probability queries, prediction and imputation.

Additional facilities include support for bootstrap and cross-validation; advanced plotting capabilities implemented on top of Rgraphviz and lattice; model averaging; random graphs and random samples generation; import/export functions to integrate bnlearn with software such as Hugin and GeNIe; an associated Bayesian network repository of golden-standard networks at http://www.bnlearn.com/bnrepository.

Use citation("bnlearn") to find out how to cite bnlearn in publications and other materials; and visit http://www.bnlearn.com for more examples and code from publications using bnlearn.

Author(s)

Marco Scutari
Istituto Dalle Molle di Studi sull'Intelligenza Artificiale (IDSIA)

Maintainer: Marco Scutari

References

reference books:

Koller D, Friedman N (2009). Probabilistic Graphical Models: Principles and Techniques. MIT Press.

Korb K, Nicholson AE (2010). Bayesian Artificial Intelligence. Chapman & Hall/CRC, 2nd edition.

Pearl J (1988). Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference. Morgan Kaufmann.

from the author:

Nagarajan R, Scutari M, Lebre S (2013). "Bayesian Networks in R with Applications in Systems Biology". Springer.

Scutari M (2010). "Learning Bayesian Networks with the bnlearn R Package". Journal of Statistical Software, 35(3):1–22.

Scutari M (20107). "Bayesian Network Constraint-Based Structure Learning Algorithms: Parallel and Optimized Implementations in the bnlearn R Package". Journal of Statistical Software, 77(2):1–20.

Examples

## the workflow of Bayesian network modelling in bnlearn:
# choose the data set to work on...
data(learning.test)
# ... choose an algorithm and learn the structure of the network from the data...
net = hc(learning.test)
# ... plot it...
## Not run: graphviz.plot(net)
# ... learn the parameters of the network...
bn = bn.fit(net, learning.test)
# ... explore the network with a classic barchart...
## Not run: graphviz.chart(bn)
# ... and perform inference to answer any question that interests you!
cpquery(bn, event = (A == "a"), evidence = (C == "a"))