BMC Bioinformatics

Table 5 Overall performance measured on all single drugs and outcomes in OMOP gold standard

From: Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature

GEA	7–10			4.5–7			1–5.5			2nd level
Threshold	0.1	0.05	0.005	0.1	0.05	0.005	0.1	0.05	0.005	0.1	0.05	0.005
TP	121	119	113	112	110	100	116	113	104	116	115	102
TN	182	188	205	191	195	205	159	164	178	186	193	198
FP	33	27	10	24	20	10	56	51	37	29	22	17
FN	38	40	46	47	49	59	43	46	55	43	44	57
Precision	0.79	0.82	0.92	0.82	0.85	0.91	0.67	0.69	0.74	0.80	0.84	0.86
Recall	0.76	0.75	0.71	0.70	0.69	0.63	0.73	0.71	0.65	0.73	0.72	0.64
F1-Measure	0.77	0.78	0.80	0.76	0.76	0.74	0.70	0.70	0.69	0.76	0.78	0.73
PRR	7–10			4.5–7			1–5.5			2nd level
Threshold	1	1.5	5	1	1.5	5	1	1.5	5	1	1.5	5
TP	112	96	48	110	93	39	111	83	6	109	90	27
TN	126	144	197	150	172	208	152	176	211	166	184	211
FP	89	71	18	65	43	7	63	39	4	49	31	4
FN	47	63	111	49	66	120	48	76	153	50	69	132
Precision	0.56	0.57	0.73	0.63	0.68	0.85	0.64	0.68	0.60	0.69	0.74	0.87
Recall	0.70	0.60	0.30	0.69	0.58	0.25	0.70	0.52	0.04	0.69	0.57	0.17
F1-Measure	0.62	0.59	0.43	0.66	0.63	0.38	0.67	0.59	0.07	0.69	0.64	0.28

Performance with GEA (top) and PRR (bottom) using different abstraction levels and thresholds. Bold numbers indicate best performance throughout all configurations (individually for GEA and PRR-based configurations)

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com