On 1/1/19 5:31 PM, Priyanka Purkayastha wrote:
Thankyou David.. I tried the same, I gave x as the data matrix and y as the class label. But it returned an empty "featureRankedList". I get no output when I try the code.
If you want people to spend time on this you should post a reproducible example. See the Posting Guide ... and learn to post in plain text.
-- David
On Tue, 1 Jan 2019 at 11:42 PM, David Winsemius <dwinsem...@comcast.net <mailto:dwinsem...@comcast.net>> wrote:On 1/1/19 4:40 AM, Priyanka Purkayastha wrote: > I have a dataset (data) with 700 rows and 7000 columns. I am trying to do > recursive feature selection with the SVM model. A quick google search > helped me get a code for a recursive search with SVM. However, I am unable > to understand the first part of the code, How do I introduce my dataset in > the code? Generally the "labels" is given to such a machine learning device as the y argument, while the "features" are passed as a matrix to the x argument.--David. > > If the dataset is a matrix, named data. Please give me an example for > recursive feature selection with SVM. Bellow is the code I got for > recursive feature search. > > svmrfeFeatureRanking = function(x,y){ > > #Checking for the variables > stopifnot(!is.null(x) == TRUE, !is.null(y) == TRUE) > > n = ncol(x) > survivingFeaturesIndexes = seq_len(n) > featureRankedList = vector(length=n) > rankedFeatureIndex = n > > while(length(survivingFeaturesIndexes)>0){ > #train the support vector machine > svmModel = svm(x[, survivingFeaturesIndexes], y, cost = 10, > cachesize=500, > scale=FALSE, type="C-classification", kernel="linear" ) > > #compute the weight vector > w = t(svmModel$coefs)%*%svmModel$SV > > #compute ranking criteria > rankingCriteria = w * w > > #rank the features > ranking = sort(rankingCriteria, index.return = TRUE)$ix > > #update feature ranked list > featureRankedList[rankedFeatureIndex] = > survivingFeaturesIndexes[ranking[1]] > rankedFeatureIndex = rankedFeatureIndex - 1 > > #eliminate the feature with smallest ranking criterion > (survivingFeaturesIndexes = survivingFeaturesIndexes[-ranking[1]])} > return (featureRankedList)} > > > > I tried taking an idea from the above code and incorporate the idea in my > code as shown below > > library(e1071) > library(caret) > > data<- read.csv("matrix.csv", header = TRUE) > > x <- data > y <- as.factor(data$Class) > > svmrfeFeatureRanking = function(x,y){ > > #Checking for the variables > stopifnot(!is.null(x) == TRUE, !is.null(y) == TRUE) > > n = ncol(x) > survivingFeaturesIndexes = seq_len(n) > featureRankedList = vector(length=n) > rankedFeatureIndex = n > > while(length(survivingFeaturesIndexes)>0){ > #train the support vector machine > svmModel = svm(x[, survivingFeaturesIndexes], y, cross=10,cost = > 10, type="C-classification", kernel="linear" ) > > #compute the weight vector > w = t(svmModel$coefs)%*%svmModel$SV > > #compute ranking criteria > rankingCriteria = w * w > > #rank the features > ranking = sort(rankingCriteria, index.return = TRUE)$ix > > #update feature ranked list > featureRankedList[rankedFeatureIndex] = > survivingFeaturesIndexes[ranking[1]] > rankedFeatureIndex = rankedFeatureIndex - 1 > > #eliminate the feature with smallest ranking criterion > (survivingFeaturesIndexes = survivingFeaturesIndexes[-ranking[1]])} > > return (featureRankedList)} > > But couldn't do anything at the stage "update feature ranked list" > Please guide > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org <mailto:R-help@r-project.org> mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Regards, Priyanka Purkayastha, M.Tech, Ph.D., SERB National Postdoctoral Researcher Genomics and Systems Biology Lab, Department of Chemical Engineering, Indian Institute of Technology Bombay (IITB), Powai, Mumbai- 400076
______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
