On the efficacy of per-relation basis performance evaluation for PPI extraction and a high-precision rule-based approach

Lee, Junkyu; Kim, Seongsoon; Lee, Sunwon; Lee, Kyubum; Kang, Jaewoo

doi:10.1186/1472-6947-13-S1-S7

BMC Medical Informatics and Decision Making

Table 4 Performance of the two-tier extraction system: our rule-based system in the first tier

From: On the efficacy of per-relation basis performance evaluation for PPI extraction and a high-precision rule-based approach

Min #Inst. per Relation	#Uniq. Relation		#Instances		Methods	Per-Relation					Per-Instance
	Pos	Neg	Pos	Neg		TP	FP	Precision	Recall	F-Score	TP	FP	Precision	Recall	F-Score
					ours	132	7	0.950	0.214	0.349	153	10	0.939	0.153	0.263
					+hybrid	477	326	0.594	0.772	0.671	701	555	0.558	0.701	0.621
					+SST-PT	231	112	0.673	0.374	0.481	287	167	0.632	0.287	0.395
1	618	2,312	1,000	4,834	+SVM	152	44	0.776	0.246	0.374	172	67	0.720	0.172	0.278
					+NB	247	254	0.493	0.400	0.442	285	410	0.410	0.285	0.336
					+DT	155	40	0.795	0.251	0.382	180	67	0.729	0.180	0.289
					+kNN	215	226	0.488	0.348	0.406	242	310	0.438	0.242	0.312
					ours	80	3	0.964	0.406	0.571	101	5	0.953	0.174	0.294
					+hybrid	183	151	0.548	0.929	0.689	395	310	0.560	0.682	0.615
					+SST-PT	127	62	0.672	0.645	0.658	186	102	0.646	0.321	0.429
2	197	695	579	2,827	+SVM	94	36	0.723	0.477	0.575	116	63	0.648	0.200	0.306
					+NB	113	110	0.507	0.574	0.538	151	196	0.435	0.261	0.326
					+DT	90	21	0.811	0.457	0.585	112	45	0.713	0.193	0.304
					+kNN	129	138	0.483	0.655	0.556	163	235	0.410	0.282	0.334
					ours	51	2	0.962	0.573	0.718	67	3	0.957	0.185	0.310
					+hybrid	88	94	0.484	0.989	0.650	257	222	0.537	0.708	0.611
					+SST-PT	70	38	0.648	0.787	0.711	129	58	0.690	0.355	0.469
3	89	314	363	1,835	+SVM	58	22	0.725	0.652	0.687	78	32	0.709	0.215	0.330
					+NB	59	54	0.522	0.663	0.584	86	89	0.491	0.237	0.320
					+DT	53	5	0.914	0.596	0.722	70	8	0.897	0.193	0.318
					+kNN	66	85	0.437	0.742	0.550	97	153	0.388	0.267	0.316
					ours	35	2	0.946	0.686	0.795	50	3	0.943	0.201	0.331
					+hybrid	51	63	0.447	1	0.618	171	150	0.533	0.687	0.600
					+SST-PT	45	27	0.625	0.882	0.732	92	43	0.681	0.369	0.479
4	51	181	249	1,349	+SVM	38	15	0.717	0.745	0.731	55	25	0.688	0.221	0.335
					+NB	42	43	0.494	0.824	0.618	67	86	0.438	0.269	0.333
					+DT	36	5	0.878	0.706	0.783	54	8	0.871	0.217	0.347
					+kNN	44	56	0.440	0.863	0.583	74	104	0.416	0.297	0.347
					ours	23	1	0.958	0.821	0.884	37	1	0.974	0.236	0.380
					+hybrid	28	40	0.412	1	0.584	108	88	0.551	0.688	0.612
					+SST-PT	25	14	0.641	0.893	0.746	57	22	0.722	0.363	0.483
5	28	107	157	984	+SVM	25	12	0.676	0.893	0.769	40	18	0.690	0.255	0.372
					+NB	24	21	0.533	0.857	0.657	40	40	0.500	0.255	0.338
					+DT	23	4	0.852	0.821	0.836	37	8	0.822	0.236	0.367
					+kNN	26	31	0.456	0.929	0.612	45	51	0.469	0.287	0.356

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ISSN: 1472-6947

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