binomialRF Feature Selection Vignette
In binomialRF: Binomial Random Forest Feature Selection

  library('randomForest')
  library('data.table')
  library('stats')
  library('binomialRF')

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

The $\textit{binomialRF}$ is a $\textit{randomForest}$ feature selection wrapper (Zaim 2019) that treats the random forest as a binomial process where each tree represents an iid bernoulli random variable for the event of selecting $X_j$ as the main splitting variable at a given tree. The algorithm below describes the technical aspects of the algorithm.

\begin{algorithm} \caption{binomialRF Feature Selection Algorithm } \label{alg1} \begin{algorithmic} \For{i=1:N} \State Grow $T_{i}$ \State $S_{ij} = \left{ \begin{array}{ll} 1 & X_j \text{ is splitting variable at root node by } T_i \ 0 & \text{otherwise} \ \end{array} \right. $ \State $S \gets S_{ij}$ \EndFor \State $S_j = \sum_{i=1}^N S_{ij}= \sum_{i=1}^N I[X_j \in root(T_i)]$ \State $S_j \sim \text{binomial}(N,p_0), \hspace{6mm} \text{where } p_0=\bigg(1 - \prod_{i=1}^m\frac{L-i}{L-(i-1)} \bigg)\frac{1}{m}$. \State Test for Significance \State Adjust for Multiple Comparisons

\end{algorithmic} \end{algorithm}

binomialRF Algorithm.

Simulating Data

Since $\textit{binomialRF}$ is a wrapper algorithm that internally calls and grows a randomForest object based on the inputted parameters. First we generate a simple simulated logistic data as follows:

$X_{10}\sim MNV(0, I_{10})$,
$p(x) = \frac{1}{1+e^{-X\beta}}$, and
$y \sim Binom(10,p)$.

where $\beta$ is a vector of coefficients where the first 2 coefficients are set to 3, and the rest are 0.

$$\beta = \begin{bmatrix} 3 & 3 & 0 & \cdots & 0 \end{bmatrix}^T$$

Simulated Data

set.seed(324)

### Generate multivariate normal data in R10
X = matrix(rnorm(1000), ncol=10)

### let half of the coefficients be 0, the other be 10
trueBeta= c(rep(3,2), rep(0,8))

### do logistic transform and generate the labels
z = 1 + X %*% trueBeta    
pr = 1/(1+exp(-z))        
y = rbinom(100,1,pr)

To generate data looking like this:

knitr::kable(head(cbind(round(X,2),y), 10))

Generating the Stable Correlated Binomial Distribution

Since the binomialRF requires a correlation adjustment to adjust for the tree-to-tree sampling correlation, we first generate the appropriately-parameterized stable correlated binomial distribution. Note, the correlbinom function call can take a while to execute for large number trials (i.e., trials > 1000).

require(correlbinom)
rho = 0.33
ntrees = 250

cbinom = correlbinom(rho, successprob =  1/ncol(X), trials = ntrees, 
                                  precision = 1024, model = 'kuk')

binomialRF Function Call

Then we can run the binomialRF function call as below:

binom.rf <- binomialRF::binomialRF(X,factor(y), fdr.threshold = .05,
                     ntrees = ntrees,percent_features = .6,
                     fdr.method = 'BY', user_cbinom_dist = cbinom, 
                     sampsize = round(nrow(X)*.33))
print(binom.rf)

Tuning Parameters

Percent_features

Note that since the binomial exact test is contingent on a test statistic measuring the likelihood of selecting a feature, if there is a dominant feature, then it will render all remaining 'important' features useless as it will always be selected as the splitting variable. So it is important to set the $percent_features$ parameter < 1. The results below show how setting the parameter to a fraction between .6 to 1 can allow other features to stand out as important.

# set.seed(324)

binom.rf <- binomialRF::binomialRF(X,factor(y), fdr.threshold = .05,
                     ntrees = ntrees,percent_features = 1,
                     fdr.method = 'BY', user_cbinom_dist = cbinom, sampsize = round(nrow(X)*.33))

cat('\n\nbinomialRF 100%\n\n')
print(binom.rf)

binom.rf <- binomialRF::binomialRF(X,factor(y), fdr.threshold = .05,
                     ntrees = ntrees,percent_features = .8,
                     fdr.method = 'BY', user_cbinom_dist = cbinom, sampsize = round(nrow(X)*.33))

cat('\n\nbinomialRF 80%\n\n')
print(binom.rf)

binom.rf <- binomialRF::binomialRF(X,factor(y), fdr.threshold = .05,
                     ntrees = ntrees,percent_features = .6,
                     fdr.method = 'BY', user_cbinom_dist = cbinom, sampsize = round(nrow(X)*.33))

cat('\n\nbinomialRF 60%\n\n')
print(binom.rf)

ntrees

We recommend growing at least 500 to 1,000 trees at a minimum so that the algorithm has a chance to stabilize, but also recommend choosing ntrees as a function of the number of features in your dataset. The ntrees tuning parameter must be set in conjunction with the percent_features as these two are inter-connectedm as well as the number of true features in the model. Since the correlbinom function call is slow to execute for ntrees > 1000, we recommend growing random forests with only 500-1000 trees.

set.seed(324)

binom.rf1000 <- binomialRF::binomialRF(X,factor(y), fdr.threshold = .05,
                     ntrees = ntrees,percent_features = .5,
                     fdr.method = 'BY', user_cbinom_dist = cbinom, sampsize = round(nrow(X)*.33))



rho = 0.33
ntrees = 500

cbinom = correlbinom(rho, successprob =  1/ncol(X), trials = ntrees, precision = 1024, model = 'kuk')

binom.rf500 <- binomialRF::binomialRF(X,factor(y), fdr.threshold = .05,
                     ntrees = ntrees,percent_features = .5,
                     fdr.method = 'BY', user_cbinom_dist = cbinom, sampsize = round(nrow(X)*.33))




cat('\n\nbinomialRF 250 trees\n\n')
print(binom.rf500)

cat('\n\nbinomialRF 500 trees \n\n')
print(binom.rf1000)