BMC Systems Biology

Table 4 Performance of the random walk model with different measures of phenotype similarity and gene similarity in the leave-one-out cross-validation experiments

From: Mimvec: a deep learning approach for analyzing the human phenome

		TOP (%)				MRR (%)				AUC (%)
		RSEQ	PSEQ	STRG	GOBP	RSEQ	PSEQ	STRG	GOBP	RSEQ	PSEQ	STRG	GOBP
Linkage Interval	Mimvec	32.33	35.88	43.54	41.69	19.62	21.22	12.72	11.97	80.67	79.07	87.65	88.41
	UMLS	30.48	34.92	42.72	41.08	20.45	21.77	13.13	12.47	79.84	78.52	87.24	87.90
	MeSH	28.72	32.42	41.65	38.99	20.97	21.93	13.29	12.72	79.32	78.35	87.08	87.66
	HPO	28.22	31.09	39.19	37.32	20.95	22.14	13.61	13.25	79.34	78.14	86.79	87.08
Nearest Neighbor	Mimvec	40.37	44.11	54.19	51.19	19.19	20.89	12.38	11.59	81.13	79.46	88.02	88.81
	UMLS	37.93	43.04	52.99	50.03	20.07	21.50	12.80	12.10	80.24	78.85	87.60	88.29
	MeSH	35.53	40.00	51.40	47.72	20.54	21.60	12.90	12.35	79.76	78.75	87.43	88.04
	HPO	34.44	37.77	48.29	44.83	20.53	21.77	13.27	12.90	79.77	78.57	87.12	87.29
Random Control	Mimvec	44.33	50.36	59.87	57.04	17.72	20.34	11.66	10.83	82.60	80.01	88.74	89.57
	UMLS	41.48	46.94	57.65	54.34	18.98	20.91	12.17	11.37	81.33	79.43	88.61	89.02
	MeSH	38.71	44.74	55.32	51.86	19.59	21.05	12.32	11.63	80.72	79.30	87.43	88.76
	HPO	37.21	41.96	52.23	44.83	19.56	21.26	12.65	12.14	80.75	79.08	87.75	88.24

Mimvec phenotype similarity derived from the vector presentation of phenotypes (100 dimension), UMLS phenotype similarity derived from the Unified Medical Language System, MeSH phenotype similarity derived from the Medical Subject Headings, HPO phenotype similarity derived from the Human Phenotype Ontology, RSEQ gene similarity derived from the RNA-seq data, PSEQ gene similarity derived from the protein sequence data, STRG gene similarity derived from the protein-protein interaction data, GOBP gene similarity derived from the gene ontology (biological process)

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