RDInfoTheory Namespace Reference

Class used to rank bits based on a specified measure of information. More...

Classes
class	BitCorrMatGenerator
class	InfoBitRanker

Typedefs
typedef std::vector< RDKit::USHORT >	USHORT_VECT
typedef std::vector< USHORT_VECT >	VECT_USHORT_VECT

Functions
template<class T >
double	ChiSquare (T *dMat, long int dim1, long int dim2)
template<class T >
double	InfoEntropy (T *tPtr, long int dim)
template<class T >
double	InfoEntropyGain (T *dMat, long int dim1, long int dim2)

Detailed Description

Class used to rank bits based on a specified measure of information.

Basically a primitive mimic of the CombiChem "signal" functionality To use:

• create an instance of this class
• loop over the fingerprints in the dataset by calling accumulateVotes method
• call getTopN to get the top n ranked bits

Sample usage and results from the python wrapper: Here's a small set of vectors:

‍for i,bv in enumerate(bvs): print bv.ToBitString(),acts[i] ... 0001 0 0101 0 0010 1 1110 1

Default ranker, using infogain:

‍ranker = InfoBitRanker(4,2) for i,bv in enumerate(bvs): ranker.AccumulateVotes(bv,acts[i]) ... for bit,gain,n0,n1 in ranker.GetTopN(3): print

int(bit),'%.3f'gain,int(n0),int(n1) ... 3 1.000 2 0 2 1.000 0 2 0 0.311 0 1

Using the biased infogain:

‍ranker = InfoBitRanker(4,2,InfoTheory.InfoType.BIASENTROPY) ranker.SetBiasList((1,)) for i,bv in enumerate(bvs): ranker.AccumulateVotes(bv,acts[i]) ... for bit,gain,n0,n1 in ranker.GetTopN(3): print

int(bit),'%.3f'gain,int(n0),int(n1) ... 2 1.000 0 2 0 0.311 0 1 1 0.000 1 1

A chi squared ranker is also available:

‍ranker = InfoBitRanker(4,2,InfoTheory.InfoType.CHISQUARE) for i,bv in enumerate(bvs): ranker.AccumulateVotes(bv,acts[i]) ... for bit,gain,n0,n1 in ranker.GetTopN(3): print

int(bit),'%.3f'gain,int(n0),int(n1) ... 3 4.000 2 0 2 4.000 0 2 0 1.333 0 1

As is a biased chi squared:

‍ranker = InfoBitRanker(4,2,InfoTheory.InfoType.BIASCHISQUARE) ranker.SetBiasList((1,)) for i,bv in enumerate(bvs): ranker.AccumulateVotes(bv,acts[i]) ... for bit,gain,n0,n1 in ranker.GetTopN(3): print

int(bit),'%.3f'gain,int(n0),int(n1) ... 2 4.000 0 2 0 1.333 0 1 1 0.000 1 1

Typedef Documentation

USHORT_VECT

typedef std::vector<RDKit::USHORT> RDInfoTheory::USHORT_VECT

Definition at line 84 of file InfoBitRanker.h.

VECT_USHORT_VECT

typedef std::vector<USHORT_VECT> RDInfoTheory::VECT_USHORT_VECT

Definition at line 85 of file InfoBitRanker.h.

Function Documentation

ChiSquare()

template<class T >

double RDInfoTheory::ChiSquare	(	T *	dMat,
		long int	dim1,
		long int	dim2
	)

Definition at line 15 of file InfoGainFuncs.h.

InfoEntropy()

template<class T >

double RDInfoTheory::InfoEntropy	(	T *	tPtr,
		long int	dim
	)

Definition at line 68 of file InfoGainFuncs.h.

Referenced by InfoEntropyGain().

InfoEntropyGain()

template<class T >

double RDInfoTheory::InfoEntropyGain	(	T *	dMat,
		long int	dim1,
		long int	dim2
	)

Definition at line 89 of file InfoGainFuncs.h.

References InfoEntropy().