Table 1.

ANN topologies and filtering parameters for highest observed accuracies for the various ARVs

ARVs		Topology	Number of unique sequence IDs/expanded sequences	Number of allowed combinations	Rare variant filtering	Number of outliers removed
PIs	ATV	10x8x6	995 / 13,625	< 1000	✓	1
	DRV	8 × 8	590 / 10,374	< 1000	✓	2
	FPV	8x8x8	1429 / 17,501	< 1000	x	none
	IDV	8x6x10	1459 / 16,977	< 1000	✓	1
	LPV	10x8x10	1284 / 11,019	< 300	x	none
	NFV	10x10x10	1524 / 11,929	< 300	x	none
	SQV	10x10x8	1484 / 11,509	< 300	x	none
	TPV	10x6x8	698 / 11,989	< 1000	✓	2
NRTIs	3TC	10x10x6	1342 / 33,181	< 1000	✓	none
	ABC	14	1401 / 34,016	< 1000	x	none
	AZT	19	1358 / 33,818	< 1000	✓	none
	D4T	10x4x4	1365 / 34,056	< 1000	✓	none
	DDI	10x6x6	1368 / 34,062	< 1000	✓	none
	TDF	10 × 2	1130 / 29,637	< 1000	x	none
NNRTIs	EFV	10x6x10	1400 / 33,906	< 1000	✓	none
	ETR	8x2x10	448 / 11,397	< 1000	x	2
	NVP	10x10x4	1414 / 20,348	< 300	x	none
	RPV	16	169 / 2977	< 1000	✓	none