Bootstrapping the FEDHC and FEDTABU Bayesian network learning algorithms {pchc}

Bootstrapping the FEDHC and FEDTABU Bayesian network learning algorithms

Description

Bootstrapping the FEDHC and FEDTABU Bayesian network learning algorithms.

Usage

fedhc.boot(x, method = "pearson", alpha = 0.05, ini.stat = NULL, R = NULL,
restart = 10, score = "bic-g", blacklist = NULL, whitelist = NULL, B = 200, ncores = 1)

fedtabu.boot(x, method = "pearson", alpha = 0.05, ini.stat = NULL, R = NULL,
tabu = 10, score = "bic-g", blacklist = NULL, whitelist = NULL, B = 200, ncores = 1)

Arguments

x

A numerical matrix with the variables. If you have a data.frame (i.e. categorical data) turn them into a matrix using data.frame.to_matrix. Note, that for the categorical case data, the numbers must start from 0. No missing data are allowed.

method

If you have continuous data, you can choose either "pearson" or "spearman". If you have categorical data though, this must be "cat". In this case, make sure the minimum value of each variable is zero. The g2test and the relevant functions work that way.

alpha

The significance level for assessing the p-values.

ini.stat

If the initial test statistics (univariate associations) are available, pass them through this parameter.

R

If the correlation matrix is available, pass it here.

restart

An integer, the number of random restarts.

tabu

An integer, the length of the tabu list used in the tabu function.

score

A character string, the label of the network score to be used in the algorithm. If none is specified, the default score is the Bayesian Information Criterion for both discrete and continuous data sets. The available score for continuous variables are: "bic-g" (default), "loglik-g", "aic-g", "bic-g" or "bge". The available score categorical variables are: "bde", "loglik" or "bic".

blacklist

A data frame with two columns (optionally labeled "from" and "to"), containing a set of arcs not to be included in the graph.

whitelist

A data frame with two columns (optionally labeled "from" and "to"), containing a set of arcs to be included in the graph.

B

The number of bootstrap resamples to draw. The algorithm is performed in each bootstrap sample. In the end, the adjacency matrix on the observed data is returned, along with another adjacency matrix produced by the bootstrap. The latter one contains values from 0 to 1 indicating the proportion of times an edge between two nodes was present.

ncores

The number of cores to use, in case of parallel computing.

Details

The FEDHC algorithm is implemented. The FBED algortihm (Borboudakis and Tsamardinos, 2019), without the backward phase, is implemented during the skeleton identification phase. Next, the Hill Climbing greedy search or the Tabu search is employed to score the network.

Value

A list including:

mod

A list including the output of the pchc or the pctabu function.

Gboot

The bootstrapped adjancency matrix of the Bayesian network.

runtime

The duration of the algorithm.

Author(s)

Michail Tsagris.

R implementation and documentation: Michail Tsagris [e-mail].

References

Tsagris M. (2022). The FEDHC Bayesian Network Learning Algorithm. Mathematics 2022, 10(15): 2604.

Borboudakis G. and Tsamardinos I. (2019). Forward-backward selection with early dropping. Journal of Machine Learning Research, 20(8): 1-39.

Tsamardinos I., Brown E.L. and Aliferis F.C. (2006). The max-min hill-climbing Bayesian network structure learning algorithm. Machine Learning, 65(1):31-78.

See Also

pchc, mmhc, fedhc, fedhc.skel

Examples

# simulate a dataset with continuous data
x <- matrix( rnorm(200 * 20, 1, 10), nrow = 200 )
a <- fedhc.boot(x, B = 50)