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Table 4 Binary classification result of task Ia

From: Development of Natural Compound Molecular Fingerprint (NC-MFP) with the Dictionary of Natural Products (DNP) for natural product-based drug development

Performance of each molecular fingerprint obtained by averaging ten external validation tasksa,b
Molecular fingerprintNatural compound classificationSynthetic compound classification
Avg. TPAvg. FNAvg. Sensitivityc (%)Avg. TNAvg. FPAvg. Specificityd (%)
NC-MFP1831492.651138756.50
MACCS1693084.601465373.35
PubChem
FP
1653482.601544677.00
GraphFP1613880.751435671.80
APFP1534676.551415870.70
  1. aThe result of performance about the binary classification task I. The external validation data set was randomly selected 10 times by a proportion of 20% from the data set. “NC-MFP” stands for Natural Compound Molecular Fingerprints and “APFP” for AtomPairs2DFingerprint and “GraphFP” for GraphOnlyFingerprint. “MACCS” reports Molecular Access System keys fingerprints and “PubChemFP” stands for PubChem fingerprint
  2. bThe performance index consist of Sensitivity and specificity. “TP” stands for True positive and “FN” stands for False negative and “TN” standards for True negative and “FP” standard for False negative
  3. cThe sensitivity is the proportion of positive class that was correctly identified
  4. dThe specificity is the proportion of negative class that was correctly identified