src/test/scripts/functions/builtin/NaiveBayes.R

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args <- commandArgs(TRUE)

library("Matrix")

D = as.matrix(readMM(paste(args[1], "X.mtx", sep="")))
C = as.matrix(readMM(paste(args[1], "Y.mtx", sep="")))

# reading input args
numClasses = as.integer(args[2]);
laplace_correction = as.double(args[3]);

numRows = nrow(D)
numFeatures = ncol(D)

# Compute conditionals

# Compute the feature counts for each class
classFeatureCounts = matrix(0, numClasses, numFeatures)
for (i in 1:numFeatures) {
  Col = D[,i]
  classFeatureCounts[,i] = aggregate(as.vector(Col), by=list(as.vector(C)), FUN=sum)[,2];
}

# Compute the total feature count for each class 
# and add the number of features to this sum
# for subsequent regularization (Laplace's rule)
classSums = rowSums(classFeatureCounts) + numFeatures*laplace_correction

# Compute class conditional probabilities
ones = matrix(1, 1, numFeatures)
repClassSums = classSums %*% ones;
class_conditionals = (classFeatureCounts + laplace_correction) / repClassSums;

# Compute class priors
class_counts = aggregate(as.vector(C), by=list(as.vector(C)), FUN=length)[,2]
class_prior = class_counts / numRows;

# Compute accuracy on training set
ones = matrix(1, numRows, 1)
D_w_ones = cbind(D, ones)
model = cbind(class_conditionals, class_prior)
log_probs = D_w_ones %*% t(log(model))
pred = max.col(log_probs,ties.method="last");
acc = sum(pred == C) / numRows * 100

print(paste("Training Accuracy (%): ", acc, sep=""))

# write out the model
writeMM(as(class_prior, "CsparseMatrix"), paste(args[4], "prior", sep=""));
writeMM(as(class_conditionals, "CsparseMatrix"), paste(args[4], "conditionals", sep=""));