rdkit.ML.Neural.CrossValidate

Package rdkit :: Package ML :: Package Neural :: Module CrossValidate |
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# Source Code for Module rdkit.ML.Neural.CrossValidate

      1  #
      2  #  Copyright (C) 2000  greg Landrum
      3  #
      4  """ handles doing cross validation with neural nets
      5
      6  This is, perhaps, a little misleading.  For the purposes of this module,
      7  cross validation == evaluating the accuracy of a net.
      8
      9  """
     10  from __future__ import print_function
     11  from rdkit.ML.Neural import Network,Trainers
     12  from rdkit.ML.Data import SplitData
     13  import math
     14
     15 -def CrossValidate(net,testExamples,tolerance,appendExamples=0):
     16    """ Determines the classification error for the testExamples
     17      **Arguments**
     18
     19        - tree: a decision tree (or anything supporting a _ClassifyExample()_ method)
     20
     21        - testExamples: a list of examples to be used for testing
     22
     23        - appendExamples: a toggle which is ignored, it's just here to maintain
     24           the same API as the decision tree code.
     25
     26      **Returns**
     27
     28        a 2-tuple consisting of:
     29
     30          1) the percent error of the net
     31
     32          2) a list of misclassified examples
     33
     34     **Note**
     35       At the moment, this is specific to nets with only one output
     36    """
     37    nTest = len(testExamples)
     38    nBad = 0
     39    badExamples = []
     40    for i in range(nTest):
     41      testEx = testExamples[i]
     42      trueRes = testExamples[i][-1]
     43      res = net.ClassifyExample(testEx)
     44      if math.fabs(trueRes-res) > tolerance:
     45        badExamples.append(testEx)
     46        nBad = nBad + 1
     47
     48    return float(nBad)/nTest,badExamples
     49
     50 -def CrossValidationDriver(examples,attrs=[],nPossibleVals=[],holdOutFrac=.3,silent=0,
     51                            tolerance=0.3,calcTotalError=0,hiddenSizes=None,
     52                            **kwargs):
     53    """
     54      **Arguments**
     55
     56        - examples: the full set of examples
     57
     58        - attrs: a list of attributes to consider in the tree building
     59           *This argument is ignored*
     60
     61        - nPossibleVals: a list of the number of possible values each variable can adopt
     62           *This argument is ignored*
     63
     64        - holdOutFrac: the fraction of the data which should be reserved for the hold-out set
     65           (used to calculate the error)
     66
     67        - silent: a toggle used to control how much visual noise this makes as it goes.
     68
     69        - tolerance: the tolerance for convergence of the net
     70
     71        - calcTotalError: if this is true the entire data set is used to calculate
     72             accuracy of the net
     73
     74        - hiddenSizes: a list containing the size(s) of the hidden layers in the network.
     75             if _hiddenSizes_ is None, one hidden layer containing the same number of nodes
     76             as the input layer will be used
     77
     78      **Returns**
     79
     80         a 2-tuple containing:
     81
     82           1) the net
     83
     84           2) the cross-validation error of the net
     85
     86      **Note**
     87        At the moment, this is specific to nets with only one output
     88
     89    """
     90    nTot = len(examples)
     91    if not kwargs.get('replacementSelection',0):
     92      testIndices,trainIndices = SplitData.SplitIndices(nTot,holdOutFrac,
     93                                                        silent=1,legacy=1,
     94                                                        replacement=0)
     95    else:
     96      testIndices,trainIndices = SplitData.SplitIndices(nTot,holdOutFrac,
     97                                                        silent=1,legacy=0,
     98                                                        replacement=1)
     99    trainExamples = [examples[x] for x in trainIndices]
    100    testExamples = [examples[x] for x in testIndices]
    101
    102    nTrain = len(trainExamples)
    103    if not silent:
    104      print('Training with %d examples'%(nTrain))
    105
    106    nInput = len(examples[0])-1
    107    nOutput = 1
    108    if  hiddenSizes is None:
    109      nHidden = nInput
    110      netSize = [nInput,nHidden,nOutput]
    111    else:
    112      netSize = [nInput] + hiddenSizes + [nOutput]
    113    net = Network.Network(netSize)
    114    t = Trainers.BackProp()
    115    t.TrainOnLine(trainExamples,net,errTol=tolerance,useAvgErr=0,silent=silent)
    116
    117
    118    nTest = len(testExamples)
    119    if not silent:
    120      print('Testing with %d examples'%nTest)
    121    if not calcTotalError:
    122      xValError,badExamples = CrossValidate(net,testExamples,tolerance)
    123    else:
    124      xValError,badExamples = CrossValidate(net,allExamples,tolerance)
    125    if not silent:
    126      print('Validation error was %%%4.2f'%(100*xValError))
    127    net._trainIndices=trainIndices
    128    return net,xValError
    129