Exploring non-linear distance metrics in the structure–activity space: QSAR models for human estrogen receptor

Balabin, Ilya A.; Judson, Richard S.

doi:10.1186/s13321-018-0300-0

Journal of Cheminformatics

Table 1 Accuracy metrics for agonist, antagonist, and binding activity cross-validation

From: Exploring non-linear distance metrics in the structure–activity space: QSAR models for human estrogen receptor

Activity	# chemicals	Model and parameters	Sensitivity	Specificity	Bal accuracy	Accuracy	ROC AUC	Score
Agonist	1538	Morgan kNN arithm k = 10	0.63	0.98	0.80	0.96	0.91	0.70
Agonist	1538	Morgan kNN geom k = 2	0.40	0.99	0.70	0.96	0.73	0.49
Agonist	1538	Morgan kNN exp k = 10 X = 1.5	0.69	0.97	0.83	0.96	0.92	0.73
Agonist	1538	Morgan GkNN k = 10 X = 1 Y = 1	0.63	0.98	0.80	0.96	0.92	0.70
Agonist	1538	Morgan GkNN k = 10 X = 1 Y = 3	0.66	0.97	0.82	0.96	0.92	0.72
Agonist	1538	Morgan GkNN k = 10 X = 1.5 Y = 3	0.74	0.95	0.84	0.94	0.92	0.72
Agonist	1538	Morgan GkNN k = 20 X = 1.5 Y = 5	0.75	0.95	0.85	0.94	0.91	0.73
Antagonist	1645	Morgan kNN arithm k = 3	0.44	1.00	0.72	1.00	0.70	0.51
Antagonist	1645	Morgan kNN geom k = 3	0.00	1.00	0.50	0.99	0.50	0.25
Antagonist	1645	Morgan kNN exp k = 3 X = 1.5	0.44	1.00	0.72	1.00	0.70	0.51
Antagonist	1645	Indigo kNN arithm k = 10	0.22	1.00	0.61	0.99	0.73	0.44
Antagonist	1645	Indigo kNN geom k = 10	0.00	1.00	0.50	0.99	0.50	0.25
Antagonist	1645	Indigo kNN exp k = 10 X = 1.5	0.44	1.00	0.72	0.99	0.73	0.53
Antagonist	1645	Indigo GkNN k = 10 X = 3 Y = 7	0.56	0.98	0.77	0.98	0.73	0.55
Antagonist	1645	Indigo GkNN k = 10 X = 5 Y = 15	0.56	0.98	0.77	0.98	0.73	0.55
Binding	1529	Morgan kNN arithm k = 10	0.63	0.98	0.80	0.96	0.90	0.69
Binding	1529	Morgan kNN geom k = 2	0.43	0.99	0.71	0.96	0.74	0.50
Binding	1529	Morgan kNN exp k = 10 X = 1.5	0.69	0.97	0.83	0.95	0.90	0.71
Binding	1529	Morgan GkNN k = 10 X = 1 Y = 1	0.63	0.98	0.80	0.96	0.90	0.69
Binding	1529	Morgan GkNN k = 10 X = 1 Y = 3	0.66	0.97	0.82	0.95	0.90	0.70
Binding	1529	Morgan GkNN k = 10 X = 1.5 Y = 3	0.73	0.94	0.84	0.93	0.90	0.70
Binding	1529	Morgan GkNN k = 20 X = 1.5 Y = 5	0.75	0.95	0.85	0.94	0.89	0.71

“kNN arithm”, “kNN geom”, and “kNN exp” indicate the kNN models with the arithmetic, geometric, and exponential averaging, respectively. The cumulative score shown in the last column is the product of balanced accuracy, accuracy, and ROC AUC. Italic font indicates accuracy metric values that exceed those for the CERAPP consensus model

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