A classification algorithm based on dynamic ensemble selection to predict mutational patterns of the envelope protein in HIV-infected patients

Fili, Mohammad; Hu, Guiping; Han, Changze; Kort, Alexa; Trettin, John; Haim, Hillel

doi:10.1186/s13015-023-00228-0

Algorithms for Molecular Biology

Table 2 Prediction of variability at Env positions in the high-mannose patch by KBC and other algorithms

From: A classification algorithm based on dynamic ensemble selection to predict mutational patterns of the envelope protein in HIV-infected patients

Position	Method ^a	Balanced Accuracy ^b,c	Accuracy	Precision	Recall	F1 Score
289	KBC	0.88 (± 0.13)	0.92 (± 0.08)	0.94 (± 0.07)	0.80 (± 0.26)	0.83 (± 0.20)
	QDA	0.83 (± 0.01)	0.88 (± 0.01)	0.90 (± 0.07)	0.71 (± 0.05)	0.79 (± 0.01)
	LDA	0.87 (± 0.02)	0.91 (± 0.01)	0.93 (± 0.05)	0.76 (± 0.05)	0.84 (± 0.03)
	NB	0.71 (± 0.18)	0.69 (± 0.26)	0.66 (± 0.26)	0.76 (± 0.05)	0.67 (± 0.16)
	ADA	0.86 (± 0.01)	0.90 (± 0.01)	0.91 (± 0.07)	0.76 (± 0.05)	0.83 (± 0.02)
	LogReg	0.86 (± 0.01)	0.90 (± 0.01)	0.91 (± 0.07)	0.76 (± 0.05)	0.83 (± 0.02)
	SVM	0.83 (± 0.01)	0.88 (± 0.01)	0.90 (± 0.07)	0.71 (± 0.05)	0.79 (± 0.01)
339	KBC	0.75 (± 0.12)	0.74 (± 0.12)	0.71 (± 0.12)	0.81 (± 0.13)	0.75 (± 0.11)
	QDA	0.59 (± 0.07)	0.59 (± 0.07)	0.56 (± 0.09)	0.72 (± 0.09)	0.63 (± 0.07)
	LDA	0.57 (± 0.03)	0.57 (± 0.03)	0.55 (± 0.05)	0.64 (± 0.13)	0.59 (± 0.06)
	NB	0.65 (± 0.08)	0.65 (± 0.07)	0.64 (± 0.00)	0.68 (± 0.16)	0.66 (± 0.19)
	ADA	0.60 (± 0.02)	0.60 (± 0.02)	0.59 (± 0.03)	0.62 (± 0.06)	0.59 (± 0.02)
	LogReg	0.59 (± 0.06)	0.58 (± 0.07)	0.54 (± 0.05)	0.94 (± 0.05)	0.69 (± 0.03)
	SVM	0.65 (± 0.04)	0.66 (± 0.05)	1.00 (± 0.09)	0.30 (± 0.04)	0.48 (± 0.02)
332	KBC	0.85 (± 0.07)	0.85 (± 0.07)	0.86 (± 0.12)	0.80 (± 0.08)	0.83 (± 0.08)
	QDA	0.84 (± 0.05)	0.84 (± 0.06)	0.84 (± 0.12)	0.83 (± 0.11)	0.82 (± 0.06)
	LDA	0.87 (± 0.03)	0.88 (± 0.03)	0.89 (± 0.05)	0.83 (± 0.06)	0.85 (± 0.04)
	NB	0.61 (± 0.16)	0.57 (± 0.21)	0.59 (± 0.23)	0.91 (± 0.13)	0.67 (± 0.10)
	ADA	0.87 (± 0.03)	0.88 (± 0.03)	0.89 (± 0.05)	0.83 (± 0.06)	0.85 (± 0.04)
	LogReg	0.82 (± 0.09)	0.81 (± 0.12)	0.80 (± 0.18)	0.87 (± 0.11)	0.81 (± 0.08)
	SVM	0.88 (± 0.02)	0.89 (± 0.02)	0.89 (± 0.05)	0.85 (± 0.03)	0.87 (± 0.03)

^aCalculations were performed using data from 109 patients infected by HIV-1 clade C
^bStandard deviation values are indicated in parentheses
^cValues in bold font indicate the highest point estimation value for each metric

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ISSN: 1748-7188

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