knitr::opts_chunk$set( fig.width = 5 , fig.height = 3.5, fig.align = 'center' ) oldpar <- list(mar = par()$mar, mfrow = par()$mfrow)
This vignette visualizes classification results from a random forest, using tools from the package.
We use the Instagram data to illustrate the visualization of a random forest classification. The data is on the identification of genuine/fake (spam) accounts on Instagram. The original data source is: https://www.kaggle.com/free4ever1/instagram-fake-spammer-genuine-accounts from Bardiya Bakhshandeh.
First we load and inspect the data.
data("data_instagram") traindata <- data_instagram[which(data_instagram$dataType == "train"), -13] str(traindata) # The variable names and their interpretation are colnames(traindata) # profile.pic: binary, indicates whether profile has picture # nums.length.username: ratio of number of numerical chars in username to its length # fullname.words: number of words in full name # nums.length.fullname: ratio of number of numerical characters in full name to its length # name..username: binary, indicates whether name == username of the profile # description.length: length of the description/biography of the profile (in number of characters) # external.URL: binary, indicates whether profile has external url # private: binary, indicates whether profile is private or not # X.posts: number of posts made by profile # X.followers: number of followers # X.follows: numbers of follows # y: whether profile is fake or not. x_train <- traindata[, -12] y_train <- traindata[, 12] dim(traindata) table(traindata$y) # 50/50 split of genuine/fake accounts:
Now we train a random forest. We set the seed as it is not deterministic.
set.seed(71) rfout <- randomForest(y ~ ., data = traindata, keep.forest = TRUE)
Now we create a list called mytype which describes the types of the variables in the data. The variables that are not listed will be interval-scaled by default. The Instagram data contains mostly numeric variables and 4 symmetric binary variables.
mytype <- list(symm = c(1, 5, 7, 8))
Now we prepare for the visualization of the random forest classification.
vcrtrain <- vcr.forest.train(X = x_train, y = y_train, trainfit = rfout, type = mytype) names(vcrtrain) vcrtrain$predint[c(1:10, 301:310)] # prediction as integer vcrtrain$pred[c(1:10, 301:310)] # prediction as label vcrtrain$altint[c(1:10, 301:310)] # alternative label as integer vcrtrain$altlab[c(1:10, 301:310)] # alternative label # Probability of Alternative Class (PAC) of each object: vcrtrain$PAC[1:3] # summary(vcrtrain$PAC) # f(i, g) is the distance from case i to class g: vcrtrain$fig[1:3, ] # for the first 3 objects: # The farness of an object i is the f(i, g) to its own class: vcrtrain$farness[1:3] # summary(vcrtrain$farness) # The "overall farness" of an object is defined as the # lowest f(i, g) it has to any class g (including its own): summary(vcrtrain$ofarness) sum(vcrtrain$ofarness > 0.99, na.rm = TRUE) # With the default cutoff = 0.99 we find 6 outliers, # also shown in the last column of the confusion matrix: confmat.vcr(vcrtrain) # If we do not want to show the outliers: confmat.vcr(vcrtrain, showOutliers = FALSE) # Note that the accuracy is computed before any objects # are flagged, so it does not depend on the cutoff. # Here the accuracy is `perfect' due to overfitting. # The out-of-box prediction accuracy is about 92%. cols <- c("blue", "red3")
Now we can use the visualization tools from this package.
stackedplot(vcrtrain, classCols = cols, main = "Instagram training data") # Silhouette plot: silplot(vcrtrain, classCols = cols) # Here all the s(i) are nonnegative (due to overfitting). # Class maps: classmap(vcrtrain, "genuine", classCols = cols) #, identify = TRUE) # farness outliers from furthest to closer: 45, 25, 41 x_train[c(45, 25, 41), ] # they have huge numbers of followers. classmap(vcrtrain, "fake", classCols = cols) #, identify = TRUE) # only case 261 is borderline far.
The classification of the training data is not very realistic due to overfitting, so let us look at the test data.
Now we consider the test data. First we load the data.
testdata <- data_instagram[which(data_instagram$dataType == "test"), -13] Xnew <- testdata[, -12] ynew <- testdata[, 12]
We can now prepare for visualization:
vcrtest <- vcr.forest.newdata(Xnew, ynew, vcrtrain) confmat.vcr(vcrtest)
First we visualize using the stacked plot and the silhouette plot:
stackedplot(vcrtest, classCols = cols, main = "RF on Instagram test data") # Silhouette plot: silplot(vcrtest, classCols = cols, main = "Silhouettes of RF on Instagram test data") # now some s(i) are negative
Now we make the class maps
## Class of genuine accounts: classmap(vcrtest, "genuine", classCols = cols) #, identify = TRUE) # one farness outlier: Xnew[c(30), ] # has very lengthy bio/description # has large number of X.posts # has very large number of followers and follows # genuine misclassified as fake: from highest PAC to lowest Xnew[c(21, 29, 51), ] # and 2 more borderline cases # They have some unusual characteristics for their class: # * 21, 29 have a (very) high nums.length.username, i.e. the # percentage of numerical characters in the username. # * 21, 29 have a full name of only 1 word. # * 21, 29 and 51 have description.length = 0, i.e. no # description/biography of their profile. # * they all have low X.posts (even 0 for case 21), i.e. # relatively few previous posts. # All of these characteristics are more common for fake profiles # than for genuine profiles, as we can see below: trcols <- cols[as.numeric(y_train)] plot(x_train[, 1], col = trcols, main = "profile.pic") # fakes are less likely to have a profile picture plot(x_train[, 2], col = trcols, main = "nums.length.username") # is higher for fakes plot(x_train[, 3], col = trcols, main = "fullname.words") # is lower for fakes plot(x_train[, 4], col = trcols, main = "nums.length.fullname") # is a bit higher for fakes plot(x_train[, 5], col = trcols, main = "name..username") # mostly 0 for genuine; fakes have a few values 1 plot(x_train[, 6], col = trcols, main = "description.length") # fakes are typically lower, and more often zero plot(x_train[, 7], col = trcols, main = "external.URL") # fakes never had them, genuines sometimes did plot(x_train[, 8], col = trcols, main = "private") # no visible difference plot((x_train[, 9])^0.1, col = trcols, main = "X.posts") # fakes have fewer posts, and often none plot((x_train[, 10])^0.1, col = trcols, main = "X.followers") # fakes have fewer followers, sometimes none plot((x_train[, 11])^0.1, col = trcols, main = "X.follows") # fakes follow a bit fewer, but the difference is small. ## Class of fake accounts: classmap(vcrtest, "fake", classCols = cols) #, identify = TRUE) # Fake identified as genuine, from highest PAC to lower: # c(27, 51, 34, 23, 58) Xnew[which(ynew == "fake")[c(27, 34, 51, 23, 58)], ] # These have a number of characteristics which are more common # for genuine profiles: # # all have profile pictures # none have numerical characters in username # none have numerical characters in fullname # 27 has a lengthy bio description # all have a relatively high number of followers # all have a relatively high number of follows.
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