score: Score of the Bayesian network

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/frontend-score.R


Compute the score of the Bayesian network.


score(x, data, type = NULL, ..., by.node = FALSE, debug = FALSE)

## S3 method for class 'bn'
logLik(object, data, ...)
## S3 method for class 'bn'
AIC(object, data, ..., k = 1)
## S3 method for class 'bn'
BIC(object, data, ...)


x, object

an object of class bn.


a data frame containing the data the Bayesian network was learned from.


a character string, the label of a network score. If none is specified, the default score is the Bayesian Information Criterion for both discrete and continuous data sets. See bnlearn-package for details.


a boolean value. If TRUE and the score is decomposable, the function returns the individual node contributions to the score; otherwise it returns their sum (the overall score of x).


a boolean value. If TRUE a lot of debugging output is printed; otherwise the function is completely silent.


extra arguments from the generic method (for the AIC and logLik functions, currently ignored) or additional tuning parameters (for the score function).


a numeric value, the penalty coefficient to be used; the default k = 1 gives the expression used to compute the AIC in the context of scoring Bayesian networks.


Additional arguments of the score function:

  • iss: the imaginary sample size, used by the Bayesian Dirichlet equivalent score (both the bde and mbde) and the Bayesian Gaussian score (bge). It is also known as “equivalent sample size”. The default value is equal to 10 for both the bde/mbde scores and bge.

  • exp: a list of indexes of experimental observations (those that have been artificially manipulated). Each element of the list must be named after one of the nodes, and must contain a numeric vector with indexes of the observations whose value has been manipulated for that node.

  • k: the penalty coefficient to be used by the AIC and BIC scores. The default value is 1 for AIC and log(nrow(data))/2 for BIC.

  • phi: the prior phi matrix formula to use in the Bayesian Gaussian equivalent (bge) score. Possible values are heckerman (default) and bottcher (the one used by default in the deal package.)

  • prior: the prior distribution to be used with the various Bayesian Dirichlet scores (bde, mbde, bds) and the Bayesian Gaussian score (bge). Possible values are uniform (the default), vsp (the Bayesian variable selection prior, which puts a probability of inclusion on parents) and cs (the Castelo & Siebes prior, which puts an independent prior probability on each arc and direction).

  • beta: the parameter associated with prior. If prior is uniform, beta is ignored. If prior is vsp, beta is the probability of inclusion of an additional parent (the default is 1/ncol(data)). If prior is cs, beta is a data frame with columns from, to and prob specifying the prior probability for a set of arcs. A uniform probability distribution is assumed for the remaining arcs.


For score with by.node = TRUE, a vector of numeric values, the individual node contributions to the score of the Bayesian network. Otherwise, a single numeric value, the score of the Bayesian network.


AIC and BIC are computed as logLik(x) - k * nparams(x), that is, the classic definition rescaled by -2. Therefore higher values are better, and for large sample sizes BIC converges to log(BDe).

When using the Castelo & Siebes prior in structure learning, the prior probabilties associated with an arc are bound away from zero and one by shrinking them towards the uniform distribution as per Hausser and Strimmer (2009) with a lambda equal to 3 * sqrt(.Machine$double.eps). This dramatically improves structure learning, which is less likely to get stuck when starting from an empty graph. As an alternative to prior probabilities, a blacklist can be used to prevent arcs from being included in the network, and a whitelist can be used to force the inclusion of particular arcs. beta is not modified when the prior is used from functions other than those implementing score-based and hybrid structure learning.


Marco Scutari


Castelo R, Siebes A (2000). "Priors on Network Structures. Biasing the Search for Bayesian Networks". International Journal of Approximate Reasoning, 24(1), 39-57.

Chickering DM (1995). "A Transformational Characterization of Equivalent Bayesian Network Structures". In "UAI '95: Proceedings of the Eleventh Annual Conference on Uncertainty in Artificial Intelligence", pp. 87-98. Morgan Kaufmann.

Cooper GF, Yoo C (1999). "Causal Discovery from a Mixture of Experimental and Observational Data". In "UAI '99: Proceedings of the Fifteenth Annual Conference on Uncertainty in Artificial Intelligence", pp. 116-125. Morgann Kaufmann.

Geiger D, Heckerman D (1994). "Learning Gaussian Networks". In "UAI '94: Proceedings of the Tenth Annual Conference on Uncertainty in Artificial Intelligence", pp. 235-243. Morgann Kaufmann. Available as Technical Report MSR-TR-94-10.

Hausser J, Strimmer K (2009). "Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks". Statistical Applications in Genetics and Molecular Biology, 10, 1469-1484.

Heckerman D, Geiger D, Chickering DM (1995). "Learning Bayesian Networks: The Combination of Knowledge and Statistical Data". Machine Learning, 20(3), 197-243. Available as Technical Report MSR-TR-94-09.

See Also

choose.direction, arc.strength,


res = set.arc(gs(learning.test), "A", "B")
score(res, learning.test, type = "bde")

## let's see score equivalence in action!
res2 = set.arc(gs(learning.test), "B", "A")
score(res2, learning.test, type = "bde")

## K2 score on the other hand is not score equivalent.
score(res, learning.test, type = "k2")
score(res2, learning.test, type = "k2")

## BDe with a prior.
beta = data.frame(from = c("A", "D"), to = c("B", "F"),
         prob = c(0.2, 0.5), stringsAsFactors = FALSE)
score(res, learning.test, type = "bde", prior = "cs", beta = beta)

## equivalent to logLik(res, learning.test)
score(res, learning.test, type = "loglik")

## equivalent to AIC(res, learning.test)
score(res, learning.test, type = "aic")

bnlearn documentation built on May 19, 2017, 11:55 p.m.

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