Classification of drug molecules considering their IC50 values using mixed-integer linear programming based hyper-boxes method

Armutlu, Pelin; Ozdemir, Muhittin E; Uney-Yuksektepe, Fadime; Kavakli, I Halil; Turkay, Metin

doi:10.1186/1471-2105-9-411

Table 3 Comparison of classification accuracies of best WEKA classifiers with the MILP based hyper-boxes classification.

From: Classification of drug molecules considering their IC₅₀ values using mixed-integer linear programming based hyper-boxes method

	% accuracy				% accuracy
ACHE	7-attribute	10-attribute	15-attribute	BZR	7-attribute	10-attribute	15-attribute
MILP based hyper-boxes method	100	91.89	89.19	MILP based hyper-boxes method	96.36	94.55	92.73
Bayes Network	79.28	77.48	78.38	Bayes Network	77.91	77.3	73.62
Naive Bayes	80.18	80.18	81.08	Naive Bayes	80.37	77.91	66.26
Naive Bayes Simple	81.08	80.18	81.98	Naive Bayes Simple	79.14	77.3	68.71
Naive Bayes Updatable	80.18	80.18	81.08	Naive Bayes Updatable	80.37	77.91	66.26
Lojistic	79.28	*84.68*	80.18	Lojistic	*83.44*	80.98	80.98
Multilayer Perceptron	82.88	81.08	81.08	Multilayer Perceptron	79.75	80.98	79.14
SimpleLogistic	*83.78*	82.88	79.28	SimpleLogistic	80.98	*82.82*	79.14
SMO (WEKA SVM)	79.28	80.18	80.18	SMO (WEKA SVM)	79.14	77.91	77.91
IB1	70.27	80.18	77.48	IB1	72.39	74.85	75.46
Ibk	70.27	80.18	77.48	IBk	72.39	74.85	75.46
Logit Boost	82.88	81.08	*82.88*	Logit Boost	78.53	77.3	77.91
Multi Class Classifier	79.28	*84.68*	80.18	Multi Class Classifier	*83.44*	80.98	*80.98*
Threshold Selector	47.75	68.47	60.36	Threshold Selector	78.53	76.69	75.46
LMT	*83.78*	82.88	79.28	LMT	80.98	*82.82*	79.14
RandomForest	80.18	80.18	81.98	RandomForest	77.3	79.75	*80.98*
OneR	81.08	72.97	72.97	OneR	74.85	74.23	79.14
	% accuracy				% accuracy
DHFR_TG	7-attribute	10-attribute	15-attribute	COX-2	7-attribute	10-attribute	15-attribute
MILP based hyper-boxes method	97.74	96.24	97.74	MILP based hyper-boxes method	98.13	97.2	90.65
Bayes Network	77.33	78.09	73.05	Bayes Network	67.2	67.2	66.88
Naive Bayes	76.57	*79.35*	72.54	Naive Bayes	71.66	70.06	64.65
Naive Bayes Simple	75.57	78.84	67	Naive Bayes Simple	72.29	70.06	64.65
Naive Bayes Updatable	76.57	*79.35*	72.54	Naive Bayes Updatable	71.66	70.06	64.65
Lojistic	75.82	78.84	75.57	Lojistic	72.29	70.38	70.06
Multilayer Perceptron	76.32	77.08	75.06	Multilayer Perceptron	*72.61*	72.29	*75.16*
SimpleLogistic	74.56	77.83	75.31	SimpleLogistic	72.29	71.97	68.47
SMO (WEKA SVM)	72.54	79.09	72.54	SMO (WEKA SVM)	71.02	69.43	69.43
IB1	75.31	79.09	75.82	IB1	69.11	71.02	70.06
Ibk	75.31	79.09	75.82	IBk	69.11	71.02	70.06
Logit Boost	77.33	78.34	78.34	Logit Boost	71.66	70.06	70.7
Multi Class Classifier	75.82	78.84	75.57	Multi Class Classifier	72.29	70.38	70.06
Threshold Selector	69.77	74.81	73.55	Threshold Selector	68.47	65.29	64.65
LMT	76.07	76.57	77.83	LMT	71.34	71.02	68.15
RandomForest	*77.58*	79.09	*80.35*	RandomForest	71.97	*74.2*	70.06
OneR	69.77	69.77	70.53	OneR	70.7	70.38	70.06
	% accuracy				% accuracy
DHFR_RL	7-attribute	10-attribute	15-attribute	DHFR_PC	7-attribute	10-attribute	15-attribute
MILP based hyper-boxes method	96.99	97.74	94.73	MILP based hyper-boxes method	97.62	98.41	93.65
Bayes Network	63.72	71.78	70.5	Bayes Network	80.42	80.42	78.04
Naive Bayes	63.97	68.76	71.7	Naive Bayes	82.54	81.48	80.95
Naive Bayes Simple	63.97	67.75	71	Naive Bayes Simple	82.8	79.89	81.22
Naive Bayes Updatable	63.98	68.77	71.78	Naive Bayes Updatable	82.54	81.48	80.95
Lojistic	*69.52*	73.8	78.58	Lojistic	81.75	83.33	81.75
Multilayer Perceptron	62.72	76.57	77.58	Multilayer Perceptron	82.8	82.8	84.13
SimpleLogistic	66.75	73.55	78.33	SimpleLogistic	80.42	*84.13*	81.22
SMO (WEKA SVM)	64.99	73.05	79.59	SMO (WEKA SVM)	82.28	83.33	79.1
IB1	62.97	75.06	81.11	IB1	82.28	80.16	81.75
Ibk	62.97	75.06	*81.11*	IBk	82.28	80.16	81.75
Logit Boost	64.99	75.06	77.33	Logit Boost	83.33	81.48	81.48
Multi Class Classifier	69.52	73.8	78.59	Multi Class Classifier	81.75	83.33	81.75
Threshold Selector	64.99	69.52	78.59	Threshold Selector	83.33	79.1	81.22
LMT	65.24	*77.33*	77.83	LMT	*83.6*	83.07	*85.19*
RandomForest	68.51	77.08	77.83	RandomForest	82.8	80.95	83.07
OneR	61.46	66	62.72	OneR	79.89	79.89	80.16

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ISSN: 1471-2105

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