Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization)

BMC Bioinformatics

Table 2 Computational cost of the NMF multiplicative-update algorithm.

NMF Rank k	Number of iterations			CPU Time (seconds)			Millions of ops. per iteration
	50TG	BGM	NatRev	50TG	BGM	NatRev	50TG	BGM	NatRev
10	86	130	92	3.57	14.40	8.20	4	13	14
20	114	133	106	11.55	28.96	15.88	8	26	29
30	162	154	119	28.34	46.57	23.91	13	39	43
40	166	165	147	36.27	70.40	40.59	18	51	57
50	634	171	180	197.96	94.70	61.33	22	64	72

The number of terms (m) for the 50TG, BGM, and NatRev datasets are 8, 750, 12, 590, and 13, 038, respectively. The number of gene documents (n) for the 50TG, BGM, and NatRev datasets are 50, 102, and 110, respectively.

ISSN: 1471-2105