Source Code for Module rdkit.ML.DecTree.BuildSigTree

  1  ## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c 
  2   
  3  # $Id: BuildSigTree.py 997 2009-02-25 06:12:43Z glandrum $ 
  4  # 
  5  #  Copyright (C) 2003-2008  Greg Landrum and Rational Discovery LLC 
  6  #    All Rights Reserved 
  7  # 
  8  """  
  9   
 10  """ 
 11   
 12  import numpy 
 13  from rdkit.ML.DecTree import SigTree 
 14  from rdkit.ML import InfoTheory 
 15  from rdkit.ML.FeatureSelect import CMIM 
 16  from rdkit.DataStructs.VectCollection import VectCollection 
 17  import copy 
 18  import random 
 19 -def _GenerateRandomEnsemble(nToInclude,nBits): 
 20    """  Generates a random subset of a group of indices 
 21   
 22    **Arguments** 
 23   
 24      - nToInclude: the size of the desired set 
 25   
 26      - nBits: the maximum index to be included in the set 
 27   
 28     **Returns** 
 29   
 30       a list of indices 
 31   
 32    """ 
 33    # Before Python 2.3 added the random.sample() function, this was 
 34    # way more complicated: 
 35    res = random.sample(range(nBits),nToInclude) 
 36    return res 
 37   
 38 -def BuildSigTree(examples,nPossibleRes,ensemble=None,random=0, 
 39                   metric=InfoTheory.InfoType.BIASENTROPY, 
 40                   biasList=[1], 
 41                   depth=0,maxDepth=-1, 
 42                   useCMIM=0,allowCollections=False, 
 43                   verbose=0,**kwargs): 
 44    """  
 45      **Arguments** 
 46       
 47        - examples: the examples to be classified.  Each example 
 48          should be a sequence at least three entries long, with 
 49          entry 0 being a label, entry 1 a BitVector and entry -1 
 50          an activity value 
 51   
 52        - nPossibleRes: the number of result codes possible 
 53   
 54        - ensemble: (optional) if this argument is provided, it 
 55          should be a sequence which is used to limit the bits 
 56          which are actually considered as potential descriptors. 
 57          The default is None (use all bits). 
 58           
 59        - random: (optional) If this argument is nonzero, it 
 60          specifies the number of bits to be randomly selected 
 61          for consideration at this node (i.e. this toggles the 
 62          growth of Random Trees). 
 63          The default is 0 (no random descriptor selection) 
 64   
 65        - metric: (optional) This is an _InfoTheory.InfoType_ and 
 66          sets the metric used to rank the bits. 
 67          The default is _InfoTheory.InfoType.BIASENTROPY_ 
 68   
 69        - biasList: (optional) If provided, this provides a bias 
 70          list for the bit ranker. 
 71          See the _InfoTheory.InfoBitRanker_ docs for an explanation 
 72          of bias. 
 73          The default value is [1], which biases towards actives. 
 74   
 75        - maxDepth: (optional) the maximum depth to which the tree 
 76                     will be grown 
 77          The default is -1 (no depth limit). 
 78   
 79        - useCMIM: (optional) if this is >0, the CMIM algorithm 
 80            (conditional mutual information maximization) will be 
 81            used to select the descriptors used to build the trees. 
 82            The value of the variable should be set to the number 
 83            of descriptors to be used.  This option and the 
 84            ensemble option are mutually exclusive (CMIM will not be 
 85            used if the ensemble is set), but it happily coexsts 
 86            with the random argument (to only consider random subsets 
 87            of the top N CMIM bits) 
 88          The default is 0 (do not use CMIM) 
 89           
 90        - depth: (optional) the current depth in the tree 
 91          This is used in the recursion and should not be set 
 92          by the client. 
 93   
 94      **Returns** 
 95       
 96       a SigTree.SigTreeNode with the root of the decision tree 
 97   
 98    """ 
 99    if verbose: print '  '*depth,'Build' 
100    tree=SigTree.SigTreeNode(None,'node',level=depth) 
101    tree.SetData(-666) 
102    #tree.SetExamples(examples) 
103     
104    # counts of each result code: 
105    #resCodes = map(lambda x:int(x[-1]),examples) 
106    resCodes = [int(x[-1]) for x in examples] 
107    #print 'resCodes:',resCodes 
108    counts = [0]*nPossibleRes 
109    for res in resCodes: 
110      counts[res] += 1 
111    #print '    '*depth,'counts:',counts 
112   
113    nzCounts = numpy.nonzero(counts)[0] 
114    if verbose: print '  '*depth,'\tcounts:',counts 
115    if len(nzCounts) == 1: 
116      # bottomed out because there is only one result code left 
117      #  with any counts (i.e. there's only one type of example 
118      #  left... this is GOOD!). 
119      res = nzCounts[0] 
120      tree.SetLabel(res) 
121      tree.SetName(str(res)) 
122      tree.SetTerminal(1) 
123    elif maxDepth>=0 and depth>maxDepth: 
124      # Bottomed out: max depth hit 
125      #  We don't really know what to do here, so 
126      #  use the heuristic of picking the most prevalent 
127      #  result 
128      v =  numpy.argmax(counts) 
129      tree.SetLabel(v) 
130      tree.SetName('%d?'%v) 
131      tree.SetTerminal(1) 
132    else: 
133      # find the variable which gives us the best improvement 
134      #  We do this with an InfoBitRanker: 
135      fp = examples[0][1] 
136      nBits = fp.GetNumBits() 
137      ranker = InfoTheory.InfoBitRanker(nBits,nPossibleRes,metric) 
138      if biasList: ranker.SetBiasList(biasList) 
139      if useCMIM > 0 and not ensemble: 
140        ensemble = CMIM.SelectFeatures(examples,useCMIM,bvCol=1) 
141      if random: 
142        if ensemble: 
143          if len(ensemble)>random: 
144            picks = _GenerateRandomEnsemble(random,len(ensemble)) 
145            availBits = list(take(ensemble,picks)) 
146          else: 
147            availBits = range(len(ensemble)) 
148        else: 
149          availBits = _GenerateRandomEnsemble(random,nBits) 
150      else: 
151        availBits=None 
152      if availBits: 
153        ranker.SetMaskBits(availBits) 
154      #print '  2:'*depth,availBits 
155   
156      useCollections=isinstance(examples[0][1],VectCollection) 
157      for example in examples: 
158        #print '  '*depth,example[1].ToBitString(),example[-1] 
159        if not useCollections: 
160          ranker.AccumulateVotes(example[1],example[-1]) 
161        else: 
162          example[1].Reset() 
163          ranker.AccumulateVotes(example[1].orVect,example[-1]) 
164           
165      try: 
166        bitInfo = ranker.GetTopN(1)[0] 
167        best = int(bitInfo[0]) 
168        gain = bitInfo[1] 
169      except: 
170        import traceback 
171        traceback.print_exc() 
172        print 'get top n failed' 
173        gain = -1.0 
174      if gain <= 0.0: 
175        v =  numpy.argmax(counts) 
176        tree.SetLabel(v) 
177        tree.SetName('?%d?'%v) 
178        tree.SetTerminal(1) 
179        return tree 
180      best = int(bitInfo[0]) 
181      #print '  '*depth,'\tbest:',bitInfo 
182      if verbose: print '  '*depth,'\tbest:',bitInfo 
183      # set some info at this node 
184      tree.SetName('Bit-%d'%(best)) 
185      tree.SetLabel(best) 
186      #tree.SetExamples(examples) 
187      tree.SetTerminal(0) 
188       
189      # loop over possible values of the new variable and 
190      #  build a subtree for each one 
191      onExamples = [] 
192      offExamples = [] 
193      for example in examples: 
194        if example[1][best]: 
195          if allowCollections and useCollections: 
196            sig = copy.copy(example[1]) 
197            sig.DetachVectsNotMatchingBit(best) 
198            ex = [example[0],sig] 
199            if len(example)>2: 
200              ex.extend(example[2:]) 
201            example = ex 
202          onExamples.append(example) 
203        else: 
204          offExamples.append(example) 
205      #print '    '*depth,len(offExamples),len(onExamples) 
206      for ex in (offExamples,onExamples): 
207        if len(ex) == 0: 
208          v =  numpy.argmax(counts) 
209          tree.AddChild('%d??'%v,label=v,data=0.0,isTerminal=1) 
210        else: 
211          child = BuildSigTree(ex,nPossibleRes,random=random, 
212                               ensemble=ensemble, 
213                               metric=metric,biasList=biasList, 
214                               depth=depth+1,maxDepth=maxDepth, 
215                               verbose=verbose) 
216          if child is None: 
217            v =  numpy.argmax(counts) 
218            tree.AddChild('%d???'%v,label=v,data=0.0,isTerminal=1) 
219          else: 
220            tree.AddChildNode(child) 
221    return tree 
222   
223   
224 -def SigTreeBuilder(examples,attrs,nPossibleVals,initialVar=None,ensemble=None, 
225                     randomDescriptors=0, 
226                     **kwargs): 
227    nRes = nPossibleVals[-1] 
228    return BuildSigTree(examples,nRes,random=randomDescriptors,**kwargs) 
229