CombineSplits: ANOVA and multiple comparisons for chemmodlab objects

In jrash/chemmodlab: A Cheminformatics Modeling Laboratory for Fitting and Assessing Machine Learning Models

ANOVA and multiple comparisons for chemmodlab objects

Description

CombineSplits evaluates a specified performance measure across all splits created by ModelTrain and conducts statistical tests to determine the best performing descriptor set and model (D-M) combinations. Performance can evaluate many performance measures across all splits created by ModelTrain, then outputs a data frame for each D-M combination.

Usage

CombineSplits(cml.result, metric = "enhancement", m = NA, thresh = 0.5)

Performance(cml.result, metrics = "enhancement", m = NA, thresh = 0.5)

Arguments

cml.result	an object of class chemmodlab.
metric	the model performance measure to use. This should be one of error rate, enhancement, R2, rho, auc, sensitivity, specificity, ppv, fmeasure.
m	the number of tests to use for binary model performance measures (see Details). If m is not specified, enhancement uses floor(min(300,n/4)), where n is the number of observations. By default, all other binary performance measures are computed using all observations.
thresh	if the predicted probability that a binary response is 1 is above this threshold, an observation is classified as 1. Used to compute error rate, sensitivity, specificity, ppv, and fmeasure.
metrics	a character vector containing a subset of the performance measures above. Performance can compute several measures.

Details

CombineSplits quantifies how sensitive performance measures are to fold assignments (assignments to training and test sets). Intuitively, this assesses how much a performance measure may change if a slightly different data set is used.

ModelTrain is a designed study in that 'experimental' conditions are defined according to two factors: method (D-M combination) and split (fold assignment). The factor "split" is a blocking factor, and factor "method" is of primary interest. The design of this experiment is amenable to an analysis of variance to identify significant differences between performance measures according to factors and levels. CombineSplits outputs such an analysis of variance decomposition.

The multiple comparisons similarity (MCS) plot shows the results for tests for signficance in all pairwise differences of D-M mean performance measures. Because there can be many estimated mean performance measures for a dataset, care must be taken to adjust for multiple testing, and we do this using the Tukey-Kramer multiple comparison procedure (see Tukey (1953) and Kramer (1956)). If you are having trouble viewing all the components of the plot, make the plotting window larger.

By default, CombineSplits uses initial enhancement proposed by Kearsley et al. (1996) to assess model performance. Enhancement at m tests is the hit rate at m tests (accumulated actives at m tests divided by m) divided by the proportion of actives in the entire collection. It is a relative measure of hit rate improvement offered by the new method beyond what can be expected under random selection, and values much larger than one are desired. Initial enhancement is typically taken to be enhancement at m=300 tests.

Root mean squared error (RMSE), despite its popularity in statistics, may be inappropriate for continuous chemical assay responses because it assumes losses are equal for both under-predicting and over-predicting biological activity. A suitable alternative may be initial enhancement. Other options are the coeffcient of determination (R2) and Spearman's rho.

For binary chemical assay responses, alternatives to misclassification rate (error rate) (which may be inappropriate because it assigns equal weights to false positives and false negatives) include sensitivity, specificity, area under the receiver operating characteristic curve (auc), positive predictive value, also known as precision (ppv), F1 measure (fmeasure), and initial enhancement.

Functions

• Performance: outputs a data frame with performance measures for each D-M combination.

Author(s)

Jacqueline Hughes-Oliver, Jeremy Ash, Atina Brooks

References

Kearsley, S.K., Sallamack, S., Fluder, E.M., Andose, J.D., Mosley, R.T., and Sheridan, R.P. (1996). Chemical similarity using physiochemical property descriptors, J. Chem. Inf. Comput. Sci. 36, 118-127.

Kramer, C. Y. (1956). Extension of multiple range tests to group means with unequal numbers of replications. Biometrics 12, 307-310.

Tukey, J. W. (1953). The problem of multiple comparisons. Unpublished manuscript. In The Collected Works of John W. Tukey VIII. Multiple Comparisons: 1948-1983, Chapman and Hall, New York.

See Also

chemmodlab, ModelTrain

Examples

## Not run: 
# A data set with  binary response and multiple descriptor sets
data(aid364)

cml <- ModelTrain(aid364, ids = TRUE, xcol.lengths = c(24, 147),
                  des.names = c("BurdenNumbers", "Pharmacophores"))
CombineSplits(cml)

## End(Not run)

# A continuous response
cml <- ModelTrain(USArrests, nsplits = 2, nfolds = 2,
                  models = c("KNN", "Lasso", "Tree"))
CombineSplits(cml)

jrash/chemmodlab documentation built on May 18, 2023, 8:42 p.m.