How to perform feature selection (i.e. pick important variables) using Boruta Package in R ?

guest_blog 26 Aug, 2021 • 8 min read

Introduction

Variable selection is an important aspect of model building which every analyst must learn. After all, it helps in building predictive models free from correlated variables, biases and unwanted noise.

A lot of novice analysts assume that keeping all (or more) variables will result in the best model as you are not losing any information. Sadly, that is not true!

How many times has it happened that removing a variable from the model has increased your model accuracy ?

At least, it has happened to me. Such variables are often found to be correlated and hinder achieving higher model accuracy. Today, we’ll learn one of the ways of how to get rid of such variables in R. I must say, R has an incredible CRAN repository. Out of all packages, one such available package for variable selection is Boruta Package.

In this article, we’ll focus on understanding the theory and practical aspects of using Boruta Package. I’ve followed a step wise approach to help you understand better.

I’ve also drawn a comparison of boruta with other traditional feature selection algorithms. Using this, you can arrive at a more meaningful set of features which can pave the way for a robust prediction model. The terms “features”, “variables” and “attributes” have been used interchangeably, so don’t get confused!

tutorial on using boruta package in R

 

What is Boruta algorithm and why such a strange name ?

Boruta is a feature selection algorithm. Precisely, it works as a wrapper algorithm around Random Forest. This package derive its name from a demon in Slavic mythology who dwelled in pine forests.

We know that feature selection is a crucial step in predictive modeling. This technique achieves supreme importance when a data set comprised of several variables is given for model building.

Boruta can be your algorithm of choice to deal with such data sets. Particularly when one is interested in understanding the mechanisms related to the variable of interest, rather than just building a black box predictive model with good prediction accuracy.

 

How does it work?

Below is the step wise working of boruta algorithm:

  1. Firstly, it adds randomness to the given data set by creating shuffled copies of all features (which are called shadow features).
  2. Then, it trains a random forest classifier on the extended data set and applies a feature importance measure (the default is Mean Decrease Accuracy) to evaluate the importance of each feature where higher means more important.
  3. At every iteration, it checks whether a real feature has a higher importance than the best of its shadow features (i.e. whether the feature has a higher Z score than the maximum Z score of its shadow features) and constantly removes features which are deemed highly unimportant.
  4. Finally, the algorithm stops either when all features gets confirmed or rejected or it reaches a specified limit of random forest runs.

 

What makes it different from traditional feature selection algorithms?

Boruta follows an all-relevant feature selection method where it captures all features which are in some circumstances relevant to the outcome variable. In contrast, most of the traditional feature selection algorithms follow a minimal optimal method where they rely on a small subset of features which yields a minimal error on a chosen classifier.

While fitting a random forest model on a data set, you can recursively get rid of features in each iteration which didn’t perform well in the process. This will eventually lead to a minimal optimal subset of features as the method minimizes the error of random forest model. This happens by selecting an over-pruned version of the input data set, which in turn, throws away some relevant features.

On the other hand, boruta find all features which are either strongly or weakly relevant to the decision variable. This makes it well suited for biomedical applications where one might be interested to determine which human genes (features) are connected in some way to a particular medical condition (target variable).

 

Boruta in Action in R (Practical)

Till here, we have understood the theoretical aspects of Boruta Package. But, that isn’t enough. The real challenge starts now. Let’s learn to implement this package in R.

First things first. Let’s install and call this package for use.

> install.packages("Boruta")
> library(Boruta)

Now, we’ll load the data set. For this tutorial I’ve taken the data set from Practice Problem Loan Prediction

> setwd("../Data/Loan_Prediction")
> traindata <- read.csv("train.csv", header = T, stringsAsFactors = F)

Let’s have a look at the data.

> str(traindata)
> names(traindata) <- gsub("_", "", names(traindata))

gsub() function is used to replace an expression with other one. In this case, I’ve replaced the underscore(_) with blank(“”).

Let’s check if this data set has missing values.

> summary(traindata)

We find that many variables have missing values. It’s important to treat missing values prior to implementing boruta package. Moreover, this data set also has blank values. Let’s clean this data set.

Now we’ll replace blank cells with NA. This will help me treat all NA’s at once.

> traindata[traindata == ""] <- NA

Here, I’m following the simplest method of missing value treatment i.e. list wise deletion. More sophisticated methods & packages of missing value imputation can be found here.

> traindata <- traindata[complete.cases(traindata),]

Let’s convert the categorical variables into factor data type.

> convert <- c(2:6, 11:13)
> traindata[,convert] <- data.frame(apply(traindata[convert], 2, as.factor))

Now is the time to implement and check the performance of boruta package. The syntax of boruta is almost similar to regression (lm) method.

> set.seed(123)
> boruta.train <- Boruta(LoanStatus~.-LoanID, data = traindata, doTrace = 2)
> print(boruta.train)

Boruta performed 99 iterations in 18.80749 secs.
5 attributes confirmed important: ApplicantIncome, CoapplicantIncome,
CreditHistory, LoanAmount, LoanAmountTerm.
4 attributes confirmed unimportant: Dependents, Education, Gender, SelfEmployed.
2 tentative attributes left: Married, PropertyArea.

Boruta gives a crystal clear call on the significance of variables in a data set. In this case, out of 11 attributes, 4 of them are rejected and 5 are confirmed. 2 attributes are designated as tentative. Tentative attributes have importance so close to their best shadow attributes that Boruta is not able to make a decision with the desired confidence in default number of random forest runs.

Now, we’ll plot the boruta variable importance chart.

By default, plot function in Boruta adds the attribute values to the x-axis horizontally where all the attribute values are not dispayed due to lack of space.

Here I’m adding the attributes to the x-axis vertically.

> plot(boruta.train, xlab = "", xaxt = "n")
> lz<-lapply(1:ncol(boruta.train$ImpHistory),function(i)
boruta.train$ImpHistory[is.finite(boruta.train$ImpHistory[,i]),i])

> names(lz) <- colnames(boruta.train$ImpHistory)
> Labels <- sort(sapply(lz,median))
> axis(side = 1,las=2,labels = names(Labels),
at = 1:ncol(boruta.train$ImpHistory), cex.axis = 0.7)

variable importance boruta package in R

Blue boxplots correspond to minimal, average and maximum Z score of a shadow attribute. Red, yellow and green boxplots represent Z scores of rejected, tentative and confirmed attributes respectively.

Now is the time to take decision on tentative attributes.  The tentative attributes will be classified as confirmed or rejected by comparing the median Z score of the attributes with the median Z score of the best shadow attribute. Let’s do it.

> final.boruta <- TentativeRoughFix(boruta.train)
> print(final.boruta)

Boruta performed 99 iterations in 18.399 secs.
Tentatives roughfixed over the last 99 iterations.
6 attributes confirmed important: ApplicantIncome, CoapplicantIncome,
CreditHistory, LoanAmount, LoanAmountTerm and 1 more.
5 attributes confirmed unimportant: Dependents, Education, Gender, PropertyArea,
SelfEmployed.

Boruta result plot after the classification of tentative attributes

boruta tentative importance plot

It’s time for results now. Let’s obtain the list of confirmed attributes

> getSelectedAttributes(final.boruta, withTentative = F)
[1] "Married"           "ApplicantIncome"   "CoapplicantIncome" "LoanAmount"
[5] "LoanAmountTerm"    "CreditHistory"

We’ll create a data frame of the final result derived from Boruta.

> boruta.df <- attStats(final.boruta)
> class(boruta.df)
[1] "data.frame"
> print(boruta.df)

                     meanImp   medianImp   minImp    maxImp   normHits    decision

Gender             1.04104738  0.9181620 -1.9472672  3.767040 0.01010101  Rejected

Married            2.76873080  2.7843600 -1.5971215  6.685000 0.56565657  Confirmed

Dependents         1.15900910  1.0383850 -0.7643617  3.399701 0.01010101  Rejected

Education          0.64114702  0.4747312 -1.0773928  3.745441 0.03030303  Rejected

SelfEmployed      -0.02442418 -0.1511711 -0.9536783  1.495992 0.00000000  Rejected

ApplicantIncome    6.05487791  6.0311639  2.9801751  9.197305 0.94949495  Confirmed

CoapplicantIncome  5.76704389  5.7920332  1.9322989 10.184245 0.97979798  Confirmed

LoanAmount         5.19167613  5.3606935  1.7489061  8.855464 0.88888889  Confirmed

LoanAmountTerm     5.50553498  5.3938036  2.0361781  9.025020 0.90909091  Confirmed

CreditHistory     59.57931404 60.2352549 51.7297906 69.721650 1.00000000  Confirmed

PropertyArea       2.77155525  2.4715892 -1.2486696  8.719109 0.54545455  Rejected

 

Let’s understand the parameters used in Boruta as follows:

  • maxRuns: maximal number of random forest runs. You can consider increasing this parameter if tentative attributes are left. Default is 100.
  • doTrace: It refers to verbosity level. 0 means no tracing. 1 means reporting attribute decision as soon as it is cleared. 2 means all of 1 plus additionally reporting each iteration. Default is 0.
  • holdHistory: The full history of importance runs is stored if set to TRUE (Default). Gives a plot of Classifier run vs. Importance when the plotImpHistory function is called.

For more complex parameters, please refer to the package documentation of Boruta.

 

Boruta vs Traditional Feature Selection Algorithm

Till here, we have learnt about the concept and steps to implement boruta package in R.

What if we used a traditional feature selection algorithm such as recursive feature elimination on the same data set. Do we end up with the same set of important features? Let us find out.

Now, we’ll learn the steps used to implement recursive feature elimination (RFE). In R, RFE algorithm can be implemented using caret package.

Let’s start by defining a control function to be used with RFE algorithm. We’ll load the required libraries:

> library(caret)
> library(randomForest)
> set.seed(123)
> control <- rfeControl(functions=rfFuncs, method="cv", number=10)

Here we have specified a random forest selection function through rfFuncs option (which is also the underlying algorithm in Boruta)

Let’s implement the RFE algorithm now. 

> rfe.train <- rfe(traindata[,2:12], traindata[,13], sizes=1:12, rfeControl=control)

I’m sure this is self explanatory. traindata[,2:12] refers to selecting all independent variables except the ID variable. traindata[,13] selects only the dependent variable. It might take some time to run.

We can also check the outcome of this algorithm.

> rfe.train

Recursive feature selection
Outer resampling method: Cross-Validated (10 fold)
Resampling performance over subset size:

Variables  Accuracy   Kappa   AccuracySD   KappaSD Selected
     1      0.8083    0.4702   0.03810     0.1157     *
     2      0.8041    0.4612   0.03575     0.1099
     3      0.8021    0.4569   0.04201     0.1240
     4      0.7896    0.4378   0.03991     0.1249
     5      0.7978    0.4577   0.04557     0.1348
     6      0.7957    0.4471   0.04422     0.1315
     7      0.8061    0.4754   0.04230     0.1297
     8      0.8083    0.4767   0.04055     0.1203
     9      0.7897    0.4362   0.05044     0.1464
    10      0.7918    0.4453   0.05549     0.1564
    11      0.8041    0.4751   0.04419     0.1336

The top 1 variables (out of 1):
CreditHistory

This algorithm gives highest weightage to Credit History. Now, we’ll plot the result of RFE algorithm and obtain a variable importance chart.

> plot(rfe.train, type=c("g", "o"), cex = 1.0, col = 1:11)

importance2

Let’s extract the chosen features. I am confident it would result in Credit History.

predictors(rfe.train)
[1] "CreditHistory"

Hence, we see that recursive feature elimination algorithm has selected “CreditHistory” as the only important feature among the 11 features in the dataset.

As compared to this traditional feature selection algorithm, boruta returned a much better result of variable importance which was easy to interpret as well ! I find it awesome to work on R where one has access to so many amazing packages. I’m sure there would be many other packages for feature selection. I’d love to read about them.

 

End notes

Boruta is an easy to use package as there aren’t many parameters to tune / remember. You shouldn’t use a data set with missing values to check important variables using Boruta. It’ll blatantly throw errors. You can use this algorithm on any classification / regression problem in hand to come up with a subset of meaningful features.

In this article, I’ve used a quick method to impute missing value because the scope of this article was to understand boruta (theory & practical). I’d suggest you to use advanced methods of missing value imputation. After all, information available in data is all we look for !  Keep going.

Did you like reading this article ? What other methods of variable selection do you use? Do share your suggestions / opinions in the comments section below.

About the Author

Debarati_DuttaDebarati Dutta is MA Econometrics graduate from University of Madras. She has more than 3 years of experience in data analytics and predictive modeling across multiple domains. She has worked in companies such as Amazon, Antuit, Netlink. Currently, she’s based out of Montreal, Canada.

Debarati is the first winner of Blogathon. She won amazon voucher worth INR 5000.

 

You can test your skills and knowledge. Check out Live Competitions and compete with best Data Scientists from all over the world.

guest_blog 26 Aug 2021

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Responses From Readers

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Sreenivas Kalahasti
Sreenivas Kalahasti 23 Mar, 2016

Gr8 Share Debrati. I was looking for the same kind of info. Keep sharing. Thanks.

Dr.D.K.Samuel
Dr.D.K.Samuel 23 Mar, 2016

Beautiful, meaningful info, thanks a lot

Vlad
Vlad 23 Mar, 2016

Hi, This is not the best package for the determination of the importance of predictors. See this article.https://www.mql5.com/en/articles/2029

geneseo2000
geneseo2000 23 Mar, 2016

Great tutorial! Thanks!

Mathew
Mathew 23 Mar, 2016

Hi Debrati, Has this model of feature selection helped in improving the predictions.

Hunaidkhan Pathan
Hunaidkhan Pathan 23 Mar, 2016

Really useful package and thanks Debarati really helpful article .only one Comment for the readers please do change Loan_status to LoandStatus and Loan_ID to LoanID , otherwise it will throw an error

joo
joo 23 Mar, 2016

thanks for this info , please can you send me the traindata thanks

michael.suelzer@gmail.com
[email protected] 23 Mar, 2016

It would be nice to obtain a decent print of this and other articles.

Pallavi
Pallavi 23 Mar, 2016

Hi, Nice article! This seems to be computationally very expensive. I have a dataset which has 80K rows and 150 columns and Boruta feature selection is taking over 3 hours... Is there any way to optimize the calculations?

Michael
Michael 24 Mar, 2016

Really nice article thanks. Donyou know if the algorithm can be implemented in Python?

james
james 25 Mar, 2016

I've DATE data in my csv file. Boruta can diffentiate them, but RFE cannot take in DATE format ?it seems RFE can take in only numerical variables ?Eg mydate is "3/10/2016"

venugopal rao
venugopal rao 28 Mar, 2016

Good one

karthika
karthika 30 Mar, 2016

thanks for sharing this nice information.wonderful explanation.your way of explanation is good.,it was more impressive to read ,which helps to design more in effective ways

Anu
Anu 03 Apr, 2016

Really good article. when I tried the same approach on my data, I received a bit different result. I found 4 variables through Boruta and 5 through the variables, even the 4 variables are not subset of the 5 variables. I am wondering what could be the reason of this.

Debarshi
Debarshi 04 Apr, 2016

Thanks Debarati for sharing this. Though I have not tested this, but have few questions: 1. If my ultimate aim is to use a GLM (Generalized Linear Model), do you think it's useful to use a random forest based feature analysis, or should I try something else which are based on GLM methods? 2. What's the 'importance' criterion in this model based on (e.g. Goodness of fit, information criterion,...) 3. Do you think it's useful for regression analysis where the predicted value is a continuous variable?

astrude
astrude 08 Apr, 2016

Have you tried Gradient Boosting based Feature Importance? It's a very powerful technique. It gave superior results to Random Forest results on all my datasets

Sivaji
Sivaji 12 Apr, 2016

Hi,Thanks for sharing the information.Although you explained it clearly the logic behind the Boruta package, I still surprised that most of the features shown as confirmed are not significant in simple glm. Here my analysis is not to improve the accuracy of the model but towards understanding the relationships within the data. I also tried with simple t-test/chi square on the confirmed features and found all numeric features are not significant. As you pointed Boruta is a wrapper algorithm around random forest and looks like it is biased towards numeric features.My analysis suggests cforest from party package is providing reasonable features which are aligned with my EDA like t-test/chi square test .Even for finding strong relationship with target variable, not sure this package is doing justice to it.

Amit
Amit 30 Jun, 2016

Great Share

KISHORE
KISHORE 08 Dec, 2016

Hello #Debarathi Dutta , This really helped to improve my model. Thank you very much for sharing .

Sam
Sam 13 May, 2017

Thank you for the article. Appreciate it What benefit this package adds on top of Random Forest if I were to directly use Random Forest? Thank you for your help

SEO YOUNG JAE
SEO YOUNG JAE 26 May, 2017

Good information!But I have a question.In result of Boruta, what is the normHits? Can you explain formulation???In Boruta PDF, only explain what is the normHits shortly. But I want to know formulation.

Kishor
Kishor 14 Jun, 2017

Hello Debrati,Thank you for sharing such a informative post.I have couple of questions:How good is this in dealing with outilers? Should we treat them before applying Boruta? For categorical variables, should we create dummy variables and run Boruta or before creating any dummy variables should we run?Thanks,

Babu R
Babu R 27 Jun, 2017

Good article. Wanted to run this code and play around, but could not find the data set for download. Could you share the data set in anyway?

Enrique Solarte
Enrique Solarte 16 Jul, 2017

Hi everybody, I was trying to download the dataset used in this tutorial but I couldn't find it. Could someone help me, please? On another hand, I don´t know if it is right to ask you by this way, but I was working on a dataset which has many features related each other, it is a data set of cutting tools machines, I aim to get a model to predict some cutting parameters, thus I was trying to apply something to analyze the importance of each feature, not only to reduce them, also to understand their impact to my results. I am quite sure if random forest or Boruta could they help me because I m not looking for a tree decision. Could someone give an advice about this? Thank so much

Stephen
Stephen 25 Jul, 2017

This appears to be just what I need. Thanks so much. Any updates or other packages that may have come over the past year? Thanks again, Stephen

Ran k
Ran k 02 Aug, 2017

Hello, Great articles. Thanks for sharing!

cheeku
cheeku 06 Sep, 2017

Can't find the dataset in the link provided. Can you please share the dataset so that I can do this hands on ?

John Petroda
John Petroda 26 Sep, 2017

How do you compare this with the one done by RandomForest? Thank you

Faiz
Faiz 26 Sep, 2017

Great write up Debarthi... Found the article very informative and lucid explanation. Though I have one question.. I am working on problem set having 2489 attributes. I am planning to use nnets to predict the output variable. If I have to apply Boruta on the dataset ( for which underlying algo is random forest) , how will the model behave. Though i will be trying it out , but wanted to know if you can throw some light on it . Any help is appreciated. Thanks

Faiz
Faiz 26 Sep, 2017

Great write up Debarthi... Found the article very informative and lucid explanation. Though I have one question.. I am working on problem set having 2489 attributes. I am planning to use nnets to predict the output variable. If I have to apply Boruta on the dataset ( for which underlying algo is random forest) , how will the model behave. Though i will be trying it out , but wanted to know if you can throw some light on it . Your help is appreciated. Thanks

Sayan Banerjee
Sayan Banerjee 04 Nov, 2017

Can anyone please describe what the upper and lower bar correspond for in that plot? And also what is the bold line within each box?

Sundararaman
Sundararaman 24 Nov, 2017

I used both Boruta and rfe feature selection method on the kaggle titanic dataset. To my surprise Boruta declared all the predictors as important while rfe picked up only 4 out of 8 variables. I built a rf model using both suggestions and the rfe method gave me a better model compared to boruta. Is there any reason for such behaviour ?

Kaan Yilmaz
Kaan Yilmaz 06 May, 2018

Thank you for this great explanation of two different feature selection algorithms. However, just because RFE selected only 1 feature out of 11 while boruta selected 6 features, doesn't mean that boruta is superior. I wished you developed two different models using both RFE's and boruta's features then compared their accuracy or another metric in order to see which is better.Best regards,

Ibrahem Kandel
Ibrahem Kandel 13 May, 2018

Dear Debarati; Great article, really helpful but the data link isn't working anymore, can you please upload another link, again thank you Debarati

Ashay Jain
Ashay Jain 21 May, 2018

Can somebody send the training data for this problem!

damiannelus
damiannelus 21 May, 2018

Wow, great wrap up. Probably all the needed to jump start knowledge in the one place and served in a comprehensive way. Many thanks!

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