Journal of Biomedical Semantics

Table 4 Evaluation of performance increase of TAP-10

From: Ranking relations between diseases, drugs and genes for a curation task

PharmGKB data set
setting	mean	sd	Δ	Δabs	Δrel	p value	ΔCI_l	Δrel_bs
t-e0-r0-m0-n0-c0-s0	0.27	0.010
t-e1-r0-m0-n0-c0-s0	0.32	0.010	e1	+0.042	+15.3	9.8_-4	+0.039	+15.3
t-e1-r0-m1-n0-c0-s0	0.35	0.010	m1	+0.030	+9.6	9.8_-4	+0.028	+26.4
t-e1-r0-m1-n0-c1-s0	0.37	0.012	c1	+0.019	+5.5	9.8_-4	+0.017	+33.4
t-e1-r1-m1-n0-c1-s0	0.39	0.012	r1	+0.028	+7.6	9.8_-4	+0.025	+43.6
tmc-e1-r1-m1-n0-c1-s0	0.41	0.012	tmc	+0.016	+4.2	9.8_-4	+0.011	+49.6
tmc-e1-r1-m1-n2-c1-s0	0.41	0.011	n2	+0.003	+0.7	9.8_-4	+0.001	+50.6
tmc-e1-r1-m1-n2-c6-s1	0.42	0.009	c6-s1	+0.005	+1.1	9.8_-4	+0.002	+52.3
tmc-e1-r1-m1-n3-c6-s1	0.42	0.009	n3	+0.002	+0.5	2.9_-3	+0.001	+53.0
CTD data set
setting	mean	sd	Δ	Δabs	Δrel	p value	ΔCI _l	Δrel _bs
t-r0-m0-n0-c0-s0	0.15	0.006
t-r0-m1-n0-c0-s0	0.22	0.004	m1	+0.074	+49.5	9.8_-4	+0.072	+49.5
t-r0-m1-n0-c1-s0	0.28	0.007	c1	+0.055	+24.7	9.8_-4	+0.052	+86.5
tmc-r0-m1-n0-c1-s0	0.31	0.021	tmc	+0.029	+10.2	2.0_-3	+0.030	+105.6
tmc-r1-m1-n0-c1-s0	0.32	0.021	r1	+0.014	+4.6	9.8_-4	+0.013	+115.0
tmc-r1-m1-n3-c1-s0	0.34	0.005	n3	+0.019	+5.8	2.0_-₃	+0.010	+127.5
tmc-r1-m1-n3-c3-s1	0.35	0.005	c3-s1	+0.010	+3.0	9.8 _-4	+0:007	+134.4

These tables show the amount of performance increase by exchanging one experimental parameter by another parameter (or a parameter combination, if no single parameter exchange increases the performance). From one row of the table to the following row we select the parameter(s) that gives the highest performance increase as measured by the mean TAP-10 from the cross validation runs. The absolute performance increase (Δabs) and the relative increase (Δrel) between two adjacent rows are reported in the corresponding columns. A Wilcoxon signed rank test for dependent pairs is used to assess whether the improvement is significant or due to chance. The last column shows the relative increase compared to the baseline setting (Δrel_bs).

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ISSN: 2041-1480

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