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Classification using biological pathways as prior knowledge

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fit.rfe: Recursive Feature Elimination (RFE)

fit.rfe: Recursive Feature Elimination (RFE)
In pathClass: Classification using biological pathways as prior knowledge

Description Usage Arguments Value Note Author(s) Examples

View source: R/RecursiveFeatureElimination.R

Description

Implementation of the Recursive Feature Elimination (RFE) algorithm.

Usage

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  fit.rfe(x, y, DEBUG = FALSE,
    scale = c("center", "scale"), Cs = 10^c(-3:3),
    stepsize = 0.1)

Arguments

x

a p x n matrix of expression measurements with p samples and n genes.

y

a factor of length p comprising the class labels.

DEBUG

should debugging information be plotted.

scale

a character vector defining if the data should be centered and/or scaled. Possible values are center and/or scale. Defaults to c('center', 'scale').

Cs

soft-margin tuning parameter of the SVM. Defaults to 10^c(-3:3).

stepsize

amount of features that are discarded in each step of the feature elimination. Defaults to 10%.

Value

a RFE fit object. features = selected features error.bound = span bound of the model fit = fitted SVM model

Note

The optimal number of features is found by using the span estimate. See Chapelle, O., Vapnik, V., Bousquet, O., and Mukherjee, S. (2002). Choosing multiple parameters for support vector machines. Machine Learning, 46(1), 131-159.

Author(s)

Marc Johannes JohannesMarc@gmail.com

Examples

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## Not run: 
library(Biobase)
data(sample.ExpressionSet)
x <- t(exprs(sample.ExpressionSet))
y <- factor(pData(sample.ExpressionSet)$sex)
res.rfe <- crossval(x,y,DEBUG=TRUE,theta.fit=fit.rfe,folds=2,repeats=1,parallel=TRUE,Cs=10^(-3:3))

## End(Not run)

Example output

Loading required package: svmpath
Loaded svmpath 0.955

Loading required package: kernlab
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:BiocGenerics':

    normalize, union

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: lpSolve
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
sh: 1: wc: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Detected  NA  cores. Will use  NA  of them.

  |                                                                            
  |                                                                      |   0%Starting classification of repeat: 1 
starting Fold: 2 
500  Features left.
starting Fold: 1 
500  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Best C= 0.001 
Model Updated. Spanbound= 0.7692308 , C= 0.1 ,  500 features.
Model Updated. Spanbound= 0.3846154 , C= 0.001 ,  500 features.
450  Features left.
450  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0.3076923 , C= 0.01 ,  450 features.
405  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0.7692308 , C= 0.1 ,  450 features.
405  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 1 
Model Updated. Spanbound= 0.6153846 , C= 1 ,  405 features.
365  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0.3076923 , C= 0.01 ,  405 features.
365  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 10 
Trying C= 1 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 1 
Model Updated. Spanbound= 0.2307692 , C= 1 ,  365 features.
329  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0.3076923 , C= 0.01 ,  365 features.
329  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0.3076923 , C= 0.01 ,  329 features.
Best C= 0.1 
Model Updated. Spanbound= 0.2307692 , C= 0.1 ,  329 features.
296  Features left.
296  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0.1538462 , C= 0.1 ,  296 features.
266  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0.1538462 , C= 0.01 ,  296 features.
266  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0.1538462 , C= 0.01 ,  266 features.
239  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0.07692308 , C= 0.1 ,  266 features.
239  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0.07692308 , C= 0.01 ,  239 features.
215  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0.07692308 , C= 0.1 ,  239 features.
215  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Best C= 0.01 
Model Updated. Spanbound= 0.07692308 , C= 0.01 ,  215 features.
193  Features left.
Model Updated. Spanbound= 0.07692308 , C= 0.01 ,  215 features.
193  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Best C= 0.01 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  193 features.
174  Features left.
Model Updated. Spanbound= 0.07692308 , C= 0.01 ,  193 features.
174  Features left.
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 1 
Trying C= 0.1 
Trying C= 1 
Trying C= 10 
Trying C= 100Trying C= 10 
Trying C= 100 
 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0.07692308 , C= 0.01 ,  174 features.
157  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  174 features.
157  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0.07692308 , C= 0.01 ,  157 features.
141  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  157 features.
141  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  141 features.
127  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0.07692308 , C= 0.01 ,  141 features.
127  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0.07692308 , C= 0.01 ,  127 features.
114  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  127 features.
114  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  114 features.
103  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  114 features.
103  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  103 features.
93  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  103 features.
93  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  93 features.
84  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  93 features.
84  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  84 features.
76  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  84 features.
76  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  76 features.
68  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  76 features.
68  Features left.
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  68 features.
61  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  68 features.
61  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  61 features.
55  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  61 features.
55  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  55 features.
49  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  55 features.
49  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  49 features.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  49 features.
44  Features left.
44  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  44 features.
40  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  44 features.
40  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  40 features.
36  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  40 features.
36  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  36 features.
32  Features left.
Trying C= 0.001 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  36 features.
32  Features left.
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  32 features.
29  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  32 features.
29  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  29 features.
26  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  29 features.
26  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  26 features.
23  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  26 features.
23  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  23 features.
21  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  23 features.
21  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  21 features.
19  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  21 features.
19  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  19 features.
17  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  19 features.
17  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  17 features.
15  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  17 features.
15  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  15 features.
13  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  15 features.
13  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  13 features.
12  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  13 features.
12  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  12 features.
11  Features left.
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  12 features.
11  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  11 features.
10  Features left.
Trying C= 0.001 
Best C= 0.01 
Model Updated. Spanbound= 0 , C= 0.01 ,  11 features.
10  Features left.
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  10 features.
9  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  10 features.
9  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  9 features.
8  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  9 features.
8  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 1 
Trying C= 0.1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  8 features.
7  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  Trying C= 0.001 
8 features.
7  Features left.
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  7 features.
6  Features left.
Trying C= 0.001 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  7 features.
6  Features left.
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  6 features.
5  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  6 features.
5  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  5 features.
4  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  5 features.
4  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
3  Features left.
Best C= 0.1 
Model Updated. Spanbound= 0 , C= 0.1 ,  4 features.
3  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 1 
2  Features left.
Best C= 0.1 
2  Features left.
Trying C= 0.001 
Trying C= 0.001 
Trying C= 0.01 
Trying C= 0.01 
Trying C= 0.1 
Trying C= 0.1 
Trying C= 1 
Trying C= 1 
Trying C= 10 
Trying C= 10 
Trying C= 100 
Trying C= 100 
Trying C= 1000 
Trying C= 1000 
Best C= 0.1 
Best Model is: Spanbound= 0 , C= 0.1 , 4 features.
Best C= 10 
Best Model is: Spanbound= 0 , C= 0.1 , 5 features.
 Test AUC = 0.6666667 
Finished fold: 2 

 Test AUC = 0.325 
Finished fold: 1 


All models of repeat: 1 have been trained.

pathClass documentation built on May 29, 2017, 11:44 p.m.

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