Source Code for Module ML.InfoTheory.BitClusterer

 1  #
 
 2  #  Copyright (C) 2000,2003  Rational Discovery LLC
 
 3  #
 
 4  
 
 5  from SimDivFilters import rdSimDivPickers as rdsimdiv 
 6  import DataStructs 
 7  from Numeric import * 
 8 -class BitClusterer(object): 
 9      """ Class to cluster a set of bits based on their correllation
 
10  
 
11      The correlation matrix is first built using by reading the fingerprints
 
12      from a database or a list of fingerprints
 
13      """ 
14  
 
15 -    def __init__(self, idList, nCluster, type=rdsimdiv.ClusterMethod.WARD): 
16          self._clusters = [] 
17          self._bidList = idList 
18          #self._matGen = BitCorrelationMatGenerator(idList)
 
19          self._nClusters = nCluster 
20          self._type = type 
21  
 
22 -    def ClusterBits(self, corrMat) : 
23          # clutering code actually needs distances so, take 1/val for each element in corMat
 
24          distMat = 1/corrMat 
25  
 
26          pkr = rdsimdiv.HierarchicalClusterPicker(self._type) 
27          
 
28          cls = pkr.Cluster(distMat, len(self._bidList), self._nClusters) 
29          # map the clusters to the actual bit ids
 
30          self._clusters = [] 
31          for cl in cls : 
32              bcls = [] 
33              for i in cl : 
34                  bid = self._bidList[i] 
35                  bcls.append(bid) 
36              self._clusters.append(bcls) 
37  
 
38 -    def SetClusters(self, clusters): 
39          assert len(clusters) == self._nClusters 
40          self._clusters = clusters 
41          
 
42 -    def GetClusters(self) : 
43          return self._clusters 
44  
 
45 -    def MapToClusterScores(self, fp) : 
46          """ Map the fingerprint to a real valued vector of score based on the bit clusters
 
47  
 
48          The dimension of the vector is same as the number of clusters. Each value in the 
 
49          vector corresponds to the number of bits in the corresponding cluster
 
50          that are turned on in the fingerprint
 
51  
 
52          ARGUMENTS:
 
53           - fp : the fingerprint 
 
54          """ 
55      
 
56          scores = [0]*self._nClusters 
57  
 
58          i = 0 
59          for cls in self._clusters: 
60              for bid in cls : 
61                  if fp[bid] : 
62                      scores[i] += 1 
63  
 
64              i += 1 
65  
 
66          return scores 
67  
 
68 -    def MapToClusterFP(self, fp) : 
69          """ Map the fingerprint to a smaller sized (= number of clusters) fingerprint
 
70  
 
71          Each cluster get a bit in the new fingerprint and is turned on if any of the bits in
 
72          the cluster are turned on in the original fingerprint""" 
73  
 
74          ebv = DataStructs.ExplicitBitVect(self._nClusters) 
75          i = 0 
76  
 
77          for cls in self._clusters: 
78              for bid in cls : 
79                  if fp[bid] : 
80                      ebv.SetBit(i) 
81                      break 
82              i += 1 
83          
 
84          return ebv 
85