#!/usr/bin/env perl
use lib '../blib/lib', '../blib/arch';
### boosting_for_bulk_classificaiton.pl
## Call syntax example:
## boosting_for_bulk_classification.pl training6.csv test6.csv out6.csv
## This script demonstrates how a boosted decision-tree classifier can be used
## to carry out bulk classification of all your test samples in a file.
use strict;
use warnings;
use Algorithm::BoostedDecisionTree;
die "This script must be called with exactly three command-line arguments:\n" .
" 1st arg: name of the training datafile\n" .
" 2nd arg: name of the test data file\n" .
" 3rd arg: the name of the output file to which class labels will be written\n"
unless @ARGV == 3;
my $debug = 0;
my ($training_datafile, $test_datafile, $outputfile) = @ARGV;
my $training_file_class_name_in_column = 1;
my $training_file_columns_for_feature_values = [2,3];
my $how_many_stages = 4;
my (@all_class_names, @feature_names, %class_for_sample_hash, %feature_values_for_samples_hash,
%features_and_values_hash, %features_and_unique_values_hash,
%numeric_features_valuerange_hash, %feature_values_how_many_uniques_hash);
my $boosted = Algorithm::BoostedDecisionTree->new(
training_datafile => $training_datafile,
csv_class_column_index => $training_file_class_name_in_column,
csv_columns_for_features => $training_file_columns_for_feature_values,
entropy_threshold => 0.01,
max_depth_desired => 8,
symbolic_to_numeric_cardinality_threshold => 10,
how_many_stages => $how_many_stages,
);
print "Reading and processing training data...\n";
$boosted->get_training_data_for_base_tree();
## UNCOMMENT THE FOLLOWING STATEMENT if you want to see the training data used for
## just the base tree:
$boosted->show_training_data_for_base_tree();
# This is a required call:
print "Calculating first-order probabilities...\n";
$boosted->calculate_first_order_probabilities_and_class_priors();
# This is a required call:
print "Constructing base decision tree...\n";
$boosted->construct_base_decision_tree();
# UNCOMMENT THE FOLLOWING TWO STATEMENTS if you would like to see the base decision
# tree displayed in your terminal window:
#print "\n\nThe Decision Tree:\n\n";
#$boosted->display_base_decision_tree();
# This is a required call:
print "Constructing the rest of the decision trees....\n";
$boosted->construct_cascade_of_trees();
# UNCOMMENT the following statement if you wish to see the class labels for the
# samples misclassified by any particular stage. The integer argument in the call
# you see below is the stage index. Whe set to 0, that means the base classifier.
$boosted->show_class_labels_for_misclassified_samples_in_stage(0);
## UNCOMMENT the next statement if you want to see the decision trees constructed
## for each stage of the cascade:
print "\nDisplaying the decision trees for all stages:\n\n";
$boosted->display_decision_trees_for_different_stages();
### NOW YOU ARE READY TO CLASSIFY THE FILE-BASED TEST DATA:
get_test_data_from_csv();
open FILEOUT, ">$outputfile"
or die "Unable to open file $outputfile for writing out classification results: $!";
my $class_names = join ",", sort @{$boosted->get_all_class_names()};
my $output_string = "sample_index,$class_names\n";
print FILEOUT $output_string;
foreach my $item (sort {sample_index($a) <=> sample_index($b)} keys %feature_values_for_samples_hash) {
my $test_sample = $feature_values_for_samples_hash{$item};
$boosted->classify_with_boosting($test_sample);
my $classification = $boosted->trust_weighted_majority_vote_classifier();
my $output_string = sample_index($item);
# $output_string .= "," + $classification[11:]
$output_string .= ",$classification";
print FILEOUT "$output_string\n";
}
print "Majority vote classifications using boosting written out to $outputfile\n";
############################ Utility Routines #################################
sub get_test_data_from_csv {
open FILEIN, $test_datafile or die "Unable to open $test_datafile: $!";
die("Aborted. get_test_data_csv() is only for CSV files")
unless $test_datafile =~ /\.csv$/;
my $class_name_in_column = $training_file_class_name_in_column - 1;
my @all_data = <FILEIN>;
my %data_hash = ();
foreach my $record (@all_data) {
my @fields = map {$_ =~ s/^\s*|\s*$//; $_} split /,/, $record;
my @fields_after_first = @fields[1..$#fields];
$data_hash{$fields[0]} = \@fields_after_first;
}
die 'Aborted. The first row of CSV file must begin with "" and then list the feature names and class names' unless exists $data_hash{'""'};
my @field_names = map {$_ =~ s/^\s*\"|\"\s*$//g;$_} @{$data_hash{'""'}};
my $class_column_heading = $field_names[$class_name_in_column];
@feature_names = map {$field_names[$_-1]} @{$training_file_columns_for_feature_values};
$class_column_heading =~ s/^\s*\"|\"\s*$//g;
%class_for_sample_hash = ();
%feature_values_for_samples_hash = ();
foreach my $key (keys %data_hash) {
next if $key =~ /^\"\"$/;
my $cleanedup = $key;
$cleanedup =~ s/^\s*\"|\"\s*$//g;
my $which_class = $data_hash{$key}[$class_name_in_column];
$which_class =~ s/^\s*\"|\"\s*$//g;
$class_for_sample_hash{"sample_$cleanedup"} = "$class_column_heading=$which_class";
my @features_and_values_list = ();
foreach my $i (@{$training_file_columns_for_feature_values}) {
my $feature_column_header = $field_names[$i-1];
my $feature_val = $data_hash{$key}->[$i-1];
$feature_val =~ s/^\s*\"|\"\s*$//g;
$feature_val = sprintf("%.1f",$feature_val) if $feature_val =~ /^\d+$/;
push @features_and_values_list, "$feature_column_header=$feature_val";
}
$feature_values_for_samples_hash{"sample_" . $cleanedup} = \@features_and_values_list;
}
%features_and_values_hash = ();
foreach my $i (@{$training_file_columns_for_feature_values}) {
my $feature = $data_hash{'""'}[$i-1];
$feature =~ s/^\s*\"|\"\s*$//g;
my @feature_values = ();
foreach my $key (keys %data_hash) {
next if $key =~ /^\"\"$/;
my $feature_val = $data_hash{$key}[$i-1];
$feature_val =~ s/^\s*\"|\"\s*$//g;
$feature_val = sprintf("%.1f",$feature_val) if $feature_val =~ /^\d+$/;
push @feature_values, $feature_val;
}
$features_and_values_hash{$feature} = \@feature_values;
}
my %seen = ();
@all_class_names = grep {$_ if !$seen{$_}++} values %class_for_sample_hash;
print "\n All class names: @all_class_names\n" if $debug;
%numeric_features_valuerange_hash = ();
my %feature_values_how_many_uniques_hash = ();
%features_and_unique_values_hash = ();
foreach my $feature (keys %features_and_values_hash) {
my %seen1 = ();
my @unique_values_for_feature = sort grep {$_ if $_ ne 'NA' && !$seen1{$_}++}
@{$features_and_values_hash{$feature}};
$feature_values_how_many_uniques_hash{$feature} = scalar @unique_values_for_feature;
my $not_all_values_float = 0;
map {$not_all_values_float = 1 if $_ !~ /^\d*\.\d+$/} @unique_values_for_feature;
if ($not_all_values_float == 0) {
my @minmaxvalues = minmax(\@unique_values_for_feature);
$numeric_features_valuerange_hash{$feature} = \@minmaxvalues;
}
$features_and_unique_values_hash{$feature} = \@unique_values_for_feature;
}
if ($debug) {
print "\nAll class names: @all_class_names\n";
print "\nEach sample data record:\n";
foreach my $sample (sort {sample_index($a) <=> sample_index($b)} keys %feature_values_for_samples_hash) {
print "$sample => @{$feature_values_for_samples_hash{$sample}}\n";
}
print "\nclass label for each data sample:\n";
foreach my $sample (sort {sample_index($a) <=> sample_index($b)} keys %class_for_sample_hash) {
print "$sample => $class_for_sample_hash{$sample}\n";
}
print "\nFeatures used: @feature_names\n\n";
print "\nfeatures and the values taken by them:\n";
foreach my $feature (sort keys %features_and_values_hash) {
print "$feature => @{$features_and_values_hash{$feature}}\n";
}
print "\nnumeric features and their ranges:\n";
foreach my $feature (sort keys %numeric_features_valuerange_hash) {
print "$feature => @{$numeric_features_valuerange_hash{$feature}}\n";
}
print "\nnumber of unique values in each feature:\n";
foreach my $feature (sort keys %feature_values_how_many_uniques_hash) {
print "$feature => $feature_values_how_many_uniques_hash{$feature}\n";
}
}
}
sub minmax {
my $arr = shift;
my ($min, $max);
foreach my $i (0..@{$arr}-1) {
if ( (!defined $min) || ($arr->[$i] < $min) ) {
$min = $arr->[$i];
}
if ( (!defined $max) || ($arr->[$i] > $max) ) {
$max = $arr->[$i];
}
}
return ($min, $max);
}
sub sample_index {
my $arg = shift;
$arg =~ /_(.+)$/;
return $1;
}