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Table 1 Runtime in milliseconds averaged over 20 runs comparing the naive, exact, and sampled distribution computation for q = 2,3,4, and 5

From: Exact score distribution computation for ontological similarity searches

Runtime Analysis with the HPO
     runtime in milliseconds
OMIM ID |T| | T I M P L | |U| naive exact sampled*
q = 2       
264300 5 17 16 3779 4 50
613124 7 36 36 3794 6 53
113450 12 80 72 3789 6 65
129500 20 66 61 3702 15 89
q = 3       
264300 5 17 16 ~ 1.2 · 107 4 49
613124 7 36 36 ~ 1.2 · 107 6 53
113450 12 80 72 ~ 1.2 · 107 19 66
129500 20 66 61 ~ 1.2 · 107 15 79
q = 4       
264300 5 17 16 - 5 46
613124 7 36 36 - 20 55
113450 12 80 72 - 250 65
129500 20 66 61 - 135 77
q = 5       
264300 5 17 16 - 7 48
613124 7 36 36 - 141 54
113450 12 80 72 - 3896 63
129500 20 66 61 - 1776 79
  1. Four OMIM diseases with a varying number of annotated HPO terms (|T|) were used; 264300: 17-β Hydroxysteroid Dehydrogenase III deficiency, 613124: Hydrops fetalis, nonimmune, with gracile bones and dysmorphic features, 113450: Brachydactyly-distal symphalangism syndrome, 129500: Ectodermal dysplasia 2, hidrotic. Entries denoted "-" were terminated after four hours. *Sampling with 105 repetitions.