Data set: Support vector machines and neural networks applied to the prediction of HIV-1 coreceptor usage

Description

Linear support vector machines (libsvm) and neural networks (R package nnet) were applied to predict usage of the coreceptors CCR5 and CXCR4 based on sequence data of the third variable loop of the HIV envelope protein.

Usage

data(ROCR.hiv)

Format

A list consisting of the SVM (ROCR.hiv$hiv.svm) and NN (ROCR.hiv$hiv.nn) classification data. Each of those is in turn a list consisting of the two elements $predictions and $labels (10 element list representing cross-validation data).

References

Sing, T. & Beerenwinkel, N. & Lengauer, T. "Learning mixtures of localized rules by maximizing the area under the ROC curve". 1st International Workshop on ROC Analysis in AI, 89-96, 2004.

Examples

data(ROCR.hiv)
attach(ROCR.hiv)
pred.svm <- prediction(hiv.svm$predictions, hiv.svm$labels)
perf.svm <- performance(pred.svm, 'tpr', 'fpr')
pred.nn <- prediction(hiv.nn$predictions, hiv.svm$labels)
perf.nn <- performance(pred.nn, 'tpr', 'fpr')
plot(perf.svm, lty=3, col="red",main="SVMs and NNs for prediction of
HIV-1 coreceptor usage")
plot(perf.nn, lty=3, col="blue",add=TRUE)
plot(perf.svm, avg="vertical", lwd=3, col="red",
     spread.estimate="stderror",plotCI.lwd=2,add=TRUE)
plot(perf.nn, avg="vertical", lwd=3, col="blue",
spread.estimate="stderror",plotCI.lwd=2,add=TRUE)
legend(0.6,0.6,c('SVM','NN'),col=c('red','blue'),lwd=3)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ROCR)
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ROCR/ROCR.hiv.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ROCR.hiv
> ### Title: Data set: Support vector machines and neural networks applied to
> ###   the prediction of HIV-1 coreceptor usage
> ### Aliases: ROCR.hiv
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(ROCR.hiv)
> attach(ROCR.hiv)
> pred.svm <- prediction(hiv.svm$predictions, hiv.svm$labels)
> perf.svm <- performance(pred.svm, 'tpr', 'fpr')
> pred.nn <- prediction(hiv.nn$predictions, hiv.svm$labels)
> perf.nn <- performance(pred.nn, 'tpr', 'fpr')
> plot(perf.svm, lty=3, col="red",main="SVMs and NNs for prediction of
+ HIV-1 coreceptor usage")
> plot(perf.nn, lty=3, col="blue",add=TRUE)
> plot(perf.svm, avg="vertical", lwd=3, col="red",
+      spread.estimate="stderror",plotCI.lwd=2,add=TRUE)
> plot(perf.nn, avg="vertical", lwd=3, col="blue",
+ spread.estimate="stderror",plotCI.lwd=2,add=TRUE)
> legend(0.6,0.6,c('SVM','NN'),col=c('red','blue'),lwd=3)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>