Hierarchical Naive Bayes for genetic association studies

Malovini, Alberto; Barbarini, Nicola; Bellazzi, Riccardo; De Michelis, Francesca

doi:10.1186/1471-2105-13-S14-S6

BMC Bioinformatics

Table 2 Results from the analysis of simulated datasets

From: Hierarchical Naive Bayes for genetic association studies

				10 Folds CV		Independent Test
sim	GRR	LD thr.	Model	CA	AUC	CA	AUC
1	1.5/3.0	r² ≥ 0.6.	HNB	0.85 [0.81-0.87]	0.92 [0.91-0.95]	0.64	0.66
			NB	0.80 [0.78-0.82]	0.90 [0.89-0.90]	0.69	0.70
		r² ≥ 0.8.	HNB	0.85 [0.81-0.89]	0.93 [0.90-0.95]	0.63	0.68
			NB	0.80 [0.78-0.82]	0.90 [0.89-0.90]	0.69	0.70
2	1.5/3.0	r² ≥ 0.6.	HNB	0.87 [0.83-0.93]	0.94 [0.89-0.98]	0.63	0.68
			NB	0.83 [0.80-0.83]	0.87 [0.84-0.90]	0.59	0.63
		r² ≥ 0.8.	HNB	0.85 [0.80-0.87]	0.92 [0.88-0.94]	0.65	0.70
			NB	0.83 [0.80-0.83]	0.87 [0.84-0.90]	0.59	0.63
3	1.5/3.0	r² ≥ 0.6	HNB	0.73 [0.70-0.77]	0.82 [0.76-0.85]	0.65	0.72
			NB	0.78 [0.69-0.80]	0.86 [0.77-0.94]	0.68	0.75
		r² ≥ 0.8	HNB	0.77 [0.70-0.80]	0.85 [0.80-0.88]	0.71	0.75
			NB	0.78 [0.69-0.80]	0.86 [0.77-0.94]	0.68	0.75
4	2.0/4.0	r² ≥ 0.6	HNB	0.78 [0.72-0.84]	0.85 [0.80-0.89]	0.74	0.80
			NB	0.72 [0.64-0.81]	0.76 [0.72-0.86]	0.71	0.75
		r² ≥ 0.8	HNB	0.72 [0.64-0.81]	0.77 [0.71-0.88]	0.70	0.76
			NB	0.72 [0.64-0.81]	0.76 [0.72-0.86]	0.71	0.75
5	2.0/4.0	r² ≥ 0.6	HNB	0.82 [0.77-0.83]	0.89 [0.83-0.92]	0.73	0.80
			NB	0.78 [0.73-0.80]	0.84 [0.77-0.85]	0.76	0.83
		r² ≥ 0.8	HNB	0.82 [0.78-0.83]	0.88 [0.84-0.90]	0.76	0.86
			NB	0.78 [0.73-0.80]	0.84 [0.77-0.85]	0.76	0.83
6	2.0/4.0	r² ≥ 0.6	HNB	0.77 [0.73-0.80]	0.85 [0.83-0.87]	0.71	0.79
			NB	0.75 [0.68-0.77]	0.80 [0.76-0.82]	0.66	0.71
		r² ≥ 0.8	HNB	0.73 [0.67-0.77]	0.80 [0.79-0.82]	0.65	0.72
			NB	0.75 [0.68-0.77]	0.79 [0.76-0.82]	0.66	0.71
7	3.0/6.0	r² ≥ 0.6	HNB	0.83 [0.81-0.83]	0.91 [0.87-0.93]	0.76	0.84
			NB	0.80 [0.77-0.83]	0.85 [0.83-0.88]	0.81	0.87
		r² ≥ 0.8	HNB	0.83 [0.80-0.86]	0.94 [0.93-0.94]	0.82	0.91
			NB	0.80 [0.77-0.83]	0.85 [0.83-0.88]	0.81	0.87
8	3.0/6.0	r² ≥ 0.6	HNB	0.83 [0.78-0.87]	0.91 [0.89-0.94]	0.78	0.83
			NB	0.82 [0.80-0.86]	0.87 [0.82-0.94]	0.81	0.85
		r² ≥ 0.8	HNB	0.82 [0.77-0.86]	0.90 [0.85-0.94]	0.78	0.86
			NB	0.82 [0.78-0.86]	0.87 [0.82-0.94]	0.81	0.85
9	3.0/6.0	r² ≥ 0.6	HNB	0.92 [0.87-0.93]	0.96 [0.94-0.98]	0.86	0.92
			NB	0.83 [0.83-0.87]	0.92 [0.92-0.95]	0.84	0.86
		r² ≥ 0.8	HNB	0.87 [0.87-0.92]	0.96 [0.93-0.97]	0.89	0.92
			NB	0.83 [0.83-0.87]	0.92 [0.92-0.95]	0.84	0.86

CA, Median Classification Accuracy and 25% - 75% of the distribution; AUC, Median Area Under the Curve and 25% - 75% of the distribution. The 25% - 75% of the distribution are reported for results deriving from 10 Folds CV.
Majority Classifier CA and AUC for 10 Folds CV and Independent test sets: 0.50

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ISSN: 1471-2105

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