Package rdkit :: Package ML :: Package InfoTheory :: Module BitRank

Module BitRank

Functionality for ranking bits using info gains

**Definitions used in this module**

   - *sequence*: an object capable of containing other objects which supports
     __getitem__() and __len__().  Examples of these include lists, tuples, and
     Numeric arrays.

   - *IntVector*: an object containing integers which supports __getitem__() and
      __len__(). Examples include lists, tuples, Numeric Arrays, and BitVects.


**NOTE**: Neither *sequences* nor *IntVectors* need to support item assignment.
  It is perfectly acceptable for them to be read-only, so long as they are
  random-access.

Functions

[hide private]

FormCounts(bitVects, actVals, whichBit, nPossibleActs, nPossibleBitVals=2)
generates the counts matrix for a particular bit

source code

CalcInfoGains(bitVects, actVals, nPossibleActs, nPossibleBitVals=2)
Calculates the information gain for a set of points and activity values

source code

RankBits(bitVects, actVals, nPossibleBitVals=2, metricFunc=CalcInfoGains)
Rank a set of bits according to a metric function

source code

AnalyzeSparseVects(bitVects, actVals)
#DOC

source code

SparseRankBits(bitVects, actVals, metricFunc=AnalyzeSparseVects)
Rank a set of bits according to a metric function

source code

Imports: numpy, entropy

Function Details

[hide private]

FormCounts(bitVects, actVals, whichBit, nPossibleActs, nPossibleBitVals=2)

source code

generates the counts matrix for a particular bit

**Arguments**

  - bitVects: a *sequence* containing *IntVectors*

  - actVals: a *sequence*

  - whichBit: an integer, the bit number to use.

  - nPossibleActs: the (integer) number of possible activity values.

  - nPossibleBitVals: (optional) if specified, this integer provides the maximum
    value attainable by the (increasingly inaccurately named) bits in _bitVects_.

**Returns**

  a Numeric array with the counts

**Notes**

  This is really intended for internal use.

CalcInfoGains(bitVects, actVals, nPossibleActs, nPossibleBitVals=2)

source code

Calculates the information gain for a set of points and activity values

**Arguments**

  - bitVects: a *sequence* containing *IntVectors*

  - actVals: a *sequence*

  - nPossibleActs: the (integer) number of possible activity values.

  - nPossibleBitVals: (optional) if specified, this integer provides the maximum
    value attainable by the (increasingly inaccurately named) bits in _bitVects_.

 **Returns**   

   a list of floats

RankBits(bitVects, actVals, nPossibleBitVals=2, metricFunc=CalcInfoGains)

source code

Rank a set of bits according to a metric function

**Arguments**

  - bitVects: a *sequence* containing *IntVectors*

  - actVals: a *sequence*

  - nPossibleBitVals: (optional) if specified, this integer provides the maximum
    value attainable by the (increasingly inaccurately named) bits in _bitVects_.

  - metricFunc: (optional) the metric function to be used.  See _CalcInfoGains()_
    for a description of the signature of this function.

 **Returns**

   A 2-tuple containing:

     - the relative order of the bits (a list of ints)

     - the metric calculated for each bit (a list of floats)

AnalyzeSparseVects(bitVects, actVals)

source code

#DOC 

**Arguments**

  - bitVects: a *sequence* containing SBVs

  - actVals: a *sequence*

 **Returns**   

   a list of floats

 **Notes**

    - these need to be bit vects and binary activities

SparseRankBits(bitVects, actVals, metricFunc=AnalyzeSparseVects)

source code

Rank a set of bits according to a metric function

**Arguments**

  - bitVects: a *sequence* containing SBVs

  - actVals: a *sequence*

  - metricFunc: (optional) the metric function to be used.  See _SparseCalcInfoGains()_
    for a description of the signature of this function.

 **Returns**

   A 2-tuple containing:

     - the relative order of the bits (a list of ints)

     - the metric calculated for each bit (a list of floats)

  **Notes**

    - these need to be bit vects and binary activities