Package rdkit :: Package ML :: Package Scoring :: Module Scoring

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# Source Code for Module rdkit.ML.Scoring.Scoring

      1  """
      2  $Id$
      3
      4  Scoring - Calculate rank statistics
      5
      6  Created by Sereina Riniker, October 2012
      7  after a file from Peter Gedeck, Greg Landrum
      8
      9  """
     10
     11  import math, exceptions
     12
     13  """
     14  \param scores: ordered list with descending similarity containing
     15                 active/inactive information
     16  \param col: column index in scores where active/inactive information is stored
     17  \param fractions: list of fractions at which the value shall be calculated
     18  \param alpha: exponential weight
     19  """
     20
     21 -def CalcROC(scores, col):
     22      """ Determines a ROC curve """
     23      numMol = len(scores)
     24      if numMol == 0: raise ValueError('score list is empty')
     25      TPR = [0]*numMol # True positive rate: TP/(TP+FP)
     26      TNR = [0]*numMol # True negative rate: TN/(TN+FN)
     27      numActives = 0
     28      numInactives = 0
     29
     30      # loop over score list
     31      for i in range(numMol):
     32          if scores[i][col]:
     33              numActives += 1
     34          else:
     35              numInactives +=1
     36          TPR[i] = numActives # TP
     37          TNR[i] = numInactives # TN
     38
     39      # normalize, check that there are actives and inactives
     40      if numActives > 0:
     41          TPR = [1.0*i / numActives for i in TPR]
     42      if numInactives > 0:
     43          TNR = [1.0*i / numInactives for i in TNR]
     44
     45      return [TNR, TPR]
     46
     47 -def CalcAUC(scores, col):
     48      """ Determines the area under the ROC curve """
     49      # determine the ROC curve
     50      roc = CalcROC(scores, col)
     51      TNR = roc[0]
     52      TPR = roc[1]
     53
     54      numMol = len(scores)
     55      AUC = 0
     56
     57      # loop over score list
     58      for i in range(0, numMol-1):
     59          AUC += (TNR[i+1]-TNR[i]) * (TPR[i+1]+TPR[i])
     60
     61      return 0.5*AUC
     62
     63 -def _RIEHelper(scores, col, alpha):
     64      numMol = len(scores)
     65      alpha = float(alpha)
     66      if numMol == 0: raise ValueError('score list is empty')
     67      if alpha <= 0.0: raise ValueError('alpha must be greater than zero')
     68
     69      denom = 1.0/numMol * ((1-math.exp(-alpha)) / (math.exp(alpha/numMol) -1))
     70      numActives = 0
     71      sum_exp = 0
     72
     73      # loop over score list
     74      for i in range(numMol):
     75          active = scores[i][col]
     76          if active:
     77              numActives += 1
     78              sum_exp += math.exp(-(alpha*(i+1)) / numMol)
     79
     80      if numActives > 0: # check that there are actives
     81          RIE = sum_exp / (numActives * denom)
     82      else:
     83          RIE = 0.0
     84
     85      return RIE, numActives
     86
     87 -def CalcRIE(scores, col, alpha):
     88      """ RIE original definded here:
     89      Sheridan, R.P., Singh, S.B., Fluder, E.M. & Kearsley, S.K.
     90      Protocols for Bridging the Peptide to Nonpeptide Gap in Topological Similarity Searches.
     91      J. Chem. Inf. Comp. Sci. 41, 1395-1406 (2001).
     92      """
     93      RIE, numActives = _RIEHelper(scores, col, alpha)
     94      return RIE
     95
     96 -def CalcBEDROC(scores, col, alpha):
     97      """ BEDROC original defined here:
     98      Truchon, J. & Bayly, C.I.
     99      Evaluating Virtual Screening Methods: Good and Bad Metric for the "Early Recognition"
    100      Problem. J. Chem. Inf. Model. 47, 488-508 (2007).
    101      """
    102      # calculate RIE
    103      RIE, numActives = _RIEHelper(scores, col, alpha)
    104
    105      if numActives > 0:
    106          numMol = len(scores)
    107          ratio = 1.0*numActives / numMol
    108          RIEmax = (1-math.exp(-alpha*ratio)) / (ratio*(1-math.exp(-alpha)))
    109          RIEmin = (1-math.exp(alpha*ratio)) / (ratio*(1-math.exp(alpha)))
    110
    111          if RIEmax != RIEmin:
    112              BEDROC = (RIE - RIEmin) / (RIEmax - RIEmin)
    113          else: # numActives = numMol
    114              BEDROC = 1.0
    115      else:
    116          BEDROC = 0.0
    117
    118      return BEDROC
    119
    120 -def CalcEnrichment(scores, col, fractions):
    121      """ Determines the enrichment factor for a set of fractions """
    122      numMol = len(scores)
    123      if numMol == 0: raise ValueError('score list is empty')
    124      if len(fractions) == 0: raise ValueError('fraction list is empty')
    125      for i in fractions:
    126          if i > 1 or i < 0: raise ValueError('fractions must be between [0,1]')
    127
    128      numPerFrac = [math.ceil(numMol*f) for f in fractions]
    129      numPerFrac.append(numMol)
    130      numActives = 0
    131      enrich = []
    132
    133      # loop over score list
    134      for i in range(numMol):
    135          if i > (numPerFrac[0]-1) and i > 0:
    136              enrich.append(1.0*numActives*numMol / i)
    137              numPerFrac.pop(0)
    138          active = scores[i][col]
    139          if active: numActives += 1
    140
    141      if numActives > 0: # check that there are actives
    142          enrich = [e / numActives for e in enrich]
    143      else:
    144          enrich = [0.0]*len(fractions)
    145      return enrich
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