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AI-NeuralNet-Kohonen

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lib/AI/NeuralNet/Kohonen.pm view on Meta::CPAN

package AI::NeuralNet::Kohonen;

use vars qw/$VERSION/;
$VERSION = 0.142;	# 08 August 2006 test lost input file

=head1 NAME

AI::NeuralNet::Kohonen - Kohonen's Self-organising Maps

=cut

use strict;
use warnings;
use Carp qw/croak cluck confess/;

use AI::NeuralNet::Kohonen::Node;
use AI::NeuralNet::Kohonen::Input;

=head1 SYNOPSIS

	$_ = AI::NeuralNet::Kohonen->new(
		map_dim_x => 39,
		map_dim_y => 19,
		epochs    => 100,
		table     =>
	"3
	1 0 0 red
	0 1 0 yellow
	0 0 1 blue
	0 1 1 cyan
	1 1 0 yellow
	1 .5 0 orange
	1 .5 1 pink"
	);

	$_->train;
	$_->save_file('mydata.txt');
	exit;

=head1 DESCRIPTION

An illustrative implimentation of Kohonen's Self-organising Feature Maps (SOMs)
in Perl. It's not fast - it's illustrative. In fact, it's slow: but it is illustrative....

Have a look at L<AI::NeuralNet::Kohonen::Demo::RGB> for an example of
visualisation of the map.

I'll maybe add some more text here later.

=head1 DEPENDENCIES

	AI::NeuralNet::Kohonen::Node
	AI::NeuralNet::Kohonen::Input

=head1 EXPORTS

None

=head1 CONSTRUCTOR new

Instantiates object fields:

=over 4

=item input_file

A I<SOM_PAK> training file to load. This does not prevent
other input methods (C<input>, C<table>) being processed, but
it does over-ride any specifications (C<weight_dim>) which may
have been explicitly handed to the constructor.

See also L</FILE FORMAT> and L</METHOD load_input>.

=item input

A reference to an array of training vectors, within which each vector
is represented by an array:

	[ [v1a, v1b, v1c], [v2a,v2b,v2c], ..., [vNa,vNb,vNc] ]

See also C<table>.

=item table

The contents of a file of the format that could be supplied to
the C<input_file> field.

=item input_names

A name for each dimension of the input vectors.

=item map_dim_x

=item map_dim_y

The dimensions of the feature map to create - defaults to a toy 19.
(note: this is Perl indexing, starting at zero).

=item epochs

Number of epochs to run for (see L<METHOD train>).
Minimum number is C<1>.

=item learning_rate

The initial learning rate.

=item train_start

Reference to code to call at the begining of training.

=item epoch_start

Reference to code to call at the begining of every epoch
(such as a colour calibration routine).

=item epoch_end

Reference to code to call at the end of every epoch
(such as a display routine).

=item train_end

Reference to code to call at the end of training.

=item targeting

If undefined, random targets are chosen; otherwise
they're iterated over. Just for experimental purposes.

=item smoothing

The amount of smoothing to apply by default when C<smooth>
is applied (see L</METHOD smooth>).

=item neighbour_factor

When working out the size of the neighbourhood of influence,
the average of the dimensions of the map are divided by this variable,
before the exponential function is applied: the default value is 2.5,
but you may with to use 2 or 4.

=item missing_mask

Used to signify data is missing in an input vector. Defaults
to C<x>.

=back

Private fields:

=over 4

=item time_constant

The number of iterations (epochs) to be completed, over the log of the map radius.

=item t

The current epoch, or moment in time.

=item l

The current learning rate.

=item map_dim_a

Average of the map dimensions.

=back

=cut

sub new {
	my $class					= shift;
	my %args					= @_;
	my $self 					= bless \%args,$class;

	$self->{missing_mask}		= 'x' unless defined $self->{missing_mask};
	$self->_process_table if defined $self->{table};	# Creates {input}
	$self->load_input($self->{input_file}) if defined $self->{input_file};	# Creates {input}
	if (not defined $self->{input}){
		cluck "No {input} supplied!";
		return undef;
	}

	$self->{map_dim_x}			= 19 unless defined $self->{map_dim_x};
	$self->{map_dim_y}			= 19 unless defined $self->{map_dim_y};
	# Legacy from...yesterday
	if ($self->{map_dim}){
		$self->{map_dim_x} 		= $self->{map_dim_y} = $self->{map_dim}
	}
	if (not defined $self->{map_dim_x} or $self->{map_dim_x}==0
	 or not defined $self->{map_dim_y} or $self->{map_dim_y}==0){
		 confess "No map dimensions in the input!";
	 }
	if ($self->{map_dim_x}>$self->{map_dim_y}){
		$self->{map_dim_a} 		= $self->{map_dim_y} + (($self->{map_dim_x}-$self->{map_dim_y})/2)
	} else {
		$self->{map_dim_a} 		= $self->{map_dim_x} + (($self->{map_dim_y}-$self->{map_dim_x})/2)
	}
	$self->{neighbour_factor}	= 2.5 unless $self->{neighbour_factor};
	$self->{epochs}				= 99 unless defined $self->{epochs};
	$self->{epochs}				= 1 if $self->{epochs}<1;
	$self->{time_constant}		= $self->{epochs} / log($self->{map_dim_a}) unless $self->{time_constant};	# to base 10?

lib/AI/NeuralNet/Kohonen.pm view on Meta::CPAN

=head1 METHOD load_input

Loads a SOM_PAK-format file of input vectors.

This method is automatically accessed if the constructor is supplied
with an C<input_file> field.

Requires: a path to a file.

Returns C<undef> on failure.

See L</FILE FORMAT>.

=cut

sub load_input { my ($self,$path) = (shift,shift);
	local *IN;
	if (not open IN,$path){
		warn "Could not open file <$path>: $!";
		return undef;
	}
	@_ = <IN>;
	close IN;
	$self->_process_input_text(\@_);
	return 1;
}


=head1 METHOD save_file

Saves the map file in I<SOM_PAK> format (see L<METHOD load_input>)
at the path specified in the first argument.

Return C<undef> on failure, a true value on success.

=cut

sub save_file { my ($self,$path) = (shift,shift);
	local *OUT;
	if (not open OUT,">$path"){
		warn "Could not open file for writing <$path>: $!";
		return undef;
	}
	#- Dimensionality of the vectors (integer, compulsory).
	print OUT ($self->{weight_dim}+1)," ";	# Perl indexing
	#- Topology type, either hexa or rect (string, optional, case-sensitive).
	if (not defined $self->{display}){
		print OUT "rect ";
	} else { # $self->{display} eq 'hex'
		print OUT "hexa ";
	}
	#- Map dimension in x-direction (integer, optional).
	print OUT $self->{map_dim_x}." ";
	#- Map dimension in y-direction (integer, optional).
	print OUT $self->{map_dim_y}." ";
	#- Neighborhood type, either bubble or gaussian (string, optional, case-sen- sitive).
	print OUT "gaussian ";
	# End of header
	print OUT "\n";

	# Format input data
	foreach (@{$self->{input}}){
		print OUT join("\t",@{$_->{values}});
		if ($_->{class}){
			print OUT " $_->{class} " ;
		}
		print OUT "\n";
	}
	# EOF
	print OUT chr 26;
	close OUT;
	return 1;
}


#
# Process ASCII from table field or input file
# Accepts: ASCII as array or array ref
#
sub _process_input_text { my ($self) = (shift);
	if (not defined $_[1]){
		if (ref $_[0] eq 'ARRAY'){
			@_ = @{$_[0]};
		} else {
			@_ = split/[\n\r\f]+/,$_[0];
		}
	}
	chomp @_;
	my @specs = split/\s+/,(shift @_);
	#- Dimensionality of the vectors (integer, compulsory).
	$self->{weight_dim} = shift @specs;
	$self->{weight_dim}--; # Perl indexing
	#- Topology type, either hexa or rect (string, optional, case-sensitive).
	my $display		    = shift @specs;
	if (not defined $display and exists $self->{display}){
		# Intentionally blank
	} elsif (not defined $display){
		$self->{display} = undef;
	} elsif ($display eq 'hexa'){
		$self->{display} = 'hex'
	} elsif ($display eq 'rect'){
		$self->{display} = undef;
	}
	#- Map dimension in x-direction (integer, optional).
	$_				      = shift @specs;
	$self->{map_dim_x}    = $_ if defined $_;
	#- Map dimension in y-direction (integer, optional).
	$_				      = shift @specs;
	$self->{map_dim_y}    = $_ if defined $_;
	#- Neighborhood type, either bubble or gaussian (string, optional, case-sen- sitive).
	# not implimented

	# Format input data
	foreach (@_){
		$self->_add_input_from_str($_);
	}
	return 1;
}


=head1 PRIVATE METHOD _select_target

Return a random target from the training set in the C<input> field,
unless the C<targeting> field is defined, when the targets are
iterated over.

=cut

sub _select_target { my $self=shift;
	if (not $self->{targeting}){
		return $self->{input}->[
			(int rand(scalar @{$self->{input}}))
		];
	}
	else {
		$self->{tar}++;
		if ($self->{tar}>$#{ $self->{input} }){
			$self->{tar} = 0;
		}
		return $self->{input}->[$self->{tar}];
	}
}


=head1 PRIVATE METHOD _adjust_neighbours_of

Accepts: a reference to an array containing
the distance of the BMU from the target, as well
as the x and y co-ordinates of the BMU in the map;
a reference to the target, which is an
C<AI::NeuralNet::Kohonen::Input> object.

Returns: true.

=head2 FINDING THE NEIGHBOURS OF THE BMU

	                        (      t   )
	sigma(t) = sigma(0) exp ( - ------ )
	                        (   lambda )

Where C<sigma> is the width of the map at any stage
in time (C<t>), and C<lambda> is a time constant.

Lambda is our field C<time_constant>.

The map radius is naturally just half the map width.

=head2 ADJUSTING THE NEIGHBOURS OF THE BMU

	W(t+1) = W(t) + THETA(t) L(t)( V(t)-W(t) )

Where C<L> is the learning rate, C<V> the target vector,
and C<W> the weight. THETA(t) represents the influence

lib/AI/NeuralNet/Kohonen.pm view on Meta::CPAN

the second, C<sigma>, specifies the width of the mask.

Returns the gaussian weight.

See also L<_decay_learning_rate>.

=cut

sub _gauss_weight { my ($r, $sigma) = (shift,shift);
	return exp( -($r**2) / (2 * $sigma**2) );
}


=head1 PUBLIC METHOD quantise_error

Returns the quantise error for either the supplied points,
or those in the C<input> field.

=cut


sub quantise_error { my ($self,$targets) = (shift,shift);
	my $qerror=0;
	if (not defined $targets){
		$targets = $self->{input};
	} else {
		foreach (@$targets){
			if (not ref $_ or ref $_ ne 'ARRAY'){
				croak "Supplied target parameter should be an array of arrays!"
			}
			$_ = new AI::NeuralNet::Kohonen::Input(values=>$_);
		}
	}

	# Recieves an array of ONE element,
	# should be an array of an array of elements
	my @bmu = $self->get_results($targets);

	# Check input and output dims are the same
	if ($#{$self->{map}->[0]->[1]->{weight}} != $targets->[0]->{dim}){
		confess "target input and map dimensions differ";
	}

	for my $i (0..$#bmu){
		foreach my $w (0..$self->{weight_dim}){
			$qerror += $targets->[$i]->{values}->[$w]
			- $self->{map}->[$bmu[$i]->[1]]->[$bmu[$i]->[2]]->{weight}->[$w];
		}
	}
	$qerror /= scalar @$targets;
	return $qerror;
}


=head1 PRIVATE METHOD _add_input_from_str

Adds to the C<input> field an input vector in SOM_PAK-format
whitespace-delimited ASCII.

Returns C<undef> on failure to add an item (perhaps because
the data passed was a comment, or the C<weight_dim> flag was
not set); a true value on success.

=cut

sub _add_input_from_str { my ($self) = (shift);
	$_ = shift;
	s/#.*$//g;
	return undef if /^$/ or not defined $self->{weight_dim};
	my @i = split /\s+/,$_;
	return undef if $#i < $self->{weight_dim}; # catch bad lines
	# 'x' in files signifies unknown: we prefer undef?
#	@i[0..$self->{weight_dim}] = map{
#		$_ eq 'x'? undef:$_
#	} @i[0..$self->{weight_dim}];
	my %args = (
		dim 	=> $self->{weight_dim},
		values	=> [ @i[0..$self->{weight_dim}] ],
	);
	$args{class} = $i[$self->{weight_dim}+1] if $i[$self->{weight_dim}+1];
	$args{enhance} = $i[$self->{weight_dim}+1] if $i[$self->{weight_dim}+2];
	$args{fixed} = $i[$self->{weight_dim}+1] if $i[$self->{weight_dim}+3];
	push @{$self->{input}}, new AI::NeuralNet::Kohonen::Input(%args);

	return 1;
}


#
# Processes the 'table' paramter to the constructor
#
sub _process_table { my $self = shift;
	$_ = $self->_process_input_text( $self->{table} );
	undef $self->{table};
	return $_;
}


__END__
1;

=head1 FILE FORMAT

This module has begun to attempt the I<SOM_PAK> format:
I<SOM_PAK> file format version 3.1 (April 7, 1995),
Helsinki University of Technology, Espoo:

=over 4

The input data is stored in ASCII-form as a list of entries, one line
...for each vectorial sample.

The first line of the file is reserved for status knowledge of the
entries; in the present version it is used to define the following
items (these items MUST occur in the indicated order):

   - Dimensionality of the vectors (integer, compulsory).
   - Topology type, either hexa or rect (string, optional, case-sensitive).
   - Map dimension in x-direction (integer, optional).
   - Map dimension in y-direction (integer, optional).
   - Neighborhood type, either bubble or gaussian (string, optional, case-sen-
      sitive).

...

Subsequent lines consist of n floating-point numbers followed by an
optional class label (that can be any string) and two optional
qualifiers (see below) that determine the usage of the corresponding
data entry in training programs.  The data files can also contain an
arbitrary number of comment lines that begin with '#', and are
ignored. (One '#' for each comment line is needed.)

If some components of some data vectors are missing (due to data
collection failures or any other reason) those components should be
marked with 'x'...[in processing, these] are ignored.

...

Each data line may have two optional qualifiers that determine the
usage of the data entry during training. The qualifiers are of the
form codeword=value, where spaces are not allowed between the parts of
the qualifier. The optional qualifiers are the following:

=over 4

=item -

Enhancement factor: e.g. weight=3.  The training rate for the
corresponding input pattern vector is multiplied by this
parameter so that the reference vectors are updated as if this
input vector were repeated 3 times during training (i.e., as if
the same vector had been stored 2 extra times in the data file).

=item -

Fixed-point qualifier: e.g. fixed=2,5.  The map unit defined by
the fixed-point coordinates (x = 2; y = 5) is selected instead of
the best-matching unit for training. (See below for the definition
of coordinates over the map.) If several inputs are forced to
known locations, a wanted orientation results in the map.

=back

=back

Not (yet) implimented in file format:

=over 4

=item *

hexa/rect is only visual, and only in the ::Demo::RGB package atm

=item *

I<neighbourhood type> is always gaussian.

=item *

i<x> for missing data.

=item *

the two optional qualifiers

=back

=cut

=head1 SEE ALSO

See L<AI::NeuralNet::Kohonen::Node/distance_from>;
L<AI::NeuralNet::Kohonen::Demo::RGB>.

L<The documentation for C<SOM_PAK>|ftp://cochlea.hut.fi/pub/som_pak>,
which has lots of advice on map building that may or may not be applicable yet.

A very nice explanation of Kohonen's algorithm:
L<AI-Junkie SOM tutorial part 1|http://www.fup.btinternet.co.uk/aijunkie/som1.html>

=head1 AUTHOR AND COYRIGHT

This implimentation Copyright (C) Lee Goddard, 2003-2006.
All Rights Reserved.

Available under the same terms as Perl itself.

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