RDInfoTheory::InfoBitRanker Class Reference

#include <InfoBitRanker.h>

List of all members.

Public Types
enum	InfoType { ENTROPY = 1, BIASENTROPY = 2, CHISQUARE = 3, BIASCHISQUARE = 4 }
	the type of measure for information More...
Public Member Functions
	InfoBitRanker (unsigned int nBits, unsigned int nClasses, InfoType infoType=InfoBitRanker::ENTROPY)
	Constructor.
	~InfoBitRanker ()
void	accumulateVotes (const ExplicitBitVect &bv, unsigned int label)
	Accumulate the votes for all the bits turned on in a bit vector.
void	accumulateVotes (const SparseBitVect &bv, unsigned int label)
double *	getTopN (unsigned int num)
	Returns the top n bits ranked by the information metric.
unsigned int	getNumInstances () const
	return the number of labelled instances(examples) or fingerprints seen so far
unsigned int	getNumClasses () const
	return the number of classes
void	setBiasList (RDKit::INT_VECT &classList)
	Set the classes to which the entropy calculation should be biased.
void	setMaskBits (RDKit::INT_VECT &maskBits)
	Set the bits to be used as a mask.
void	writeTopBitsToStream (std::ostream *outStream) const
	Write the top N bits to a stream.
void	writeTopBitsToFile (std::string fileName) const
	Write the top bits to a file.

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Detailed Description

Definition at line 78 of file InfoBitRanker.h.

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Member Enumeration Documentation

enum RDInfoTheory::InfoBitRanker::InfoType

the type of measure for information

Enumerator:

ENTROPY
BIASENTROPY
CHISQUARE
BIASCHISQUARE

Definition at line 84 of file InfoBitRanker.h.

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Constructor & Destructor Documentation

RDInfoTheory::InfoBitRanker::InfoBitRanker	(	unsigned int	nBits,
		unsigned int	nClasses,
		InfoType	infoType = InfoBitRanker::ENTROPY
	)			[inline]

Constructor.

ARGUMENTS:

• nBits: the dimension of the bit vectors or the fingerprint length
• nClasses: the number of classes used in the classification problem (e.g. active, moderately active, inactive etc.). It is assumed that the classes are numbered from 0 to (nClasses - 1)
• infoType: the type of information metric

Definition at line 101 of file InfoBitRanker.h.

RDInfoTheory::InfoBitRanker::~InfoBitRanker

(

)

[inline]

Definition at line 117 of file InfoBitRanker.h.

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Member Function Documentation

void RDInfoTheory::InfoBitRanker::accumulateVotes	(	const SparseBitVect &	bv,
		unsigned int	label
	)

void RDInfoTheory::InfoBitRanker::accumulateVotes	(	const ExplicitBitVect &	bv,
		unsigned int	label
	)

Accumulate the votes for all the bits turned on in a bit vector.

ARGUMENTS:

• bv : bit vector that supports [] operator
• label : the class label for the bit vector. It is assumed that 0 <= class < nClasses

unsigned int RDInfoTheory::InfoBitRanker::getNumClasses

(

)

const [inline]

return the number of classes

Definition at line 155 of file InfoBitRanker.h.

unsigned int RDInfoTheory::InfoBitRanker::getNumInstances

(

)

const [inline]

return the number of labelled instances(examples) or fingerprints seen so far

Definition at line 148 of file InfoBitRanker.h.

double* RDInfoTheory::InfoBitRanker::getTopN

(

unsigned int

num

)

Returns the top n bits ranked by the information metric.

This is actually the function where most of the work of ranking is happening

Parameters:

num

the number of top ranked bits that are required

Returns:

a pointer to an information array. The client should *not* delete this

void RDInfoTheory::InfoBitRanker::setBiasList

(

RDKit::INT_VECT &

classList

)

Set the classes to which the entropy calculation should be biased.

This list contains a set of class ids used when in the BIASENTROPY mode of ranking bits. In this mode, a bit must be correllated higher with one of the biased classes than all the other classes. For example, in a two class problem with actives and inactives, the fraction of actives that hit the bit has to be greater than the fraction of inactives that hit the bit

ARGUMENTS: classList - list of class ids that we want a bias towards

void RDInfoTheory::InfoBitRanker::setMaskBits

(

RDKit::INT_VECT &

maskBits

)

Set the bits to be used as a mask.

If this function is called, only the bits which are present in the maskBits list will be used.

ARGUMENTS: maskBits - the bits to be considered

void RDInfoTheory::InfoBitRanker::writeTopBitsToFile

(

std::string

fileName

)

const

Write the top bits to a file.

void RDInfoTheory::InfoBitRanker::writeTopBitsToStream

(

std::ostream *

outStream

)

const

Write the top N bits to a stream.

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The documentation for this class was generated from the following file:

• InfoBitRanker.h