Machine learning for discovering missing or wrong protein function annotations

Nakano, Felipe Kenji; Lietaert, Mathias; Vens, Celine

doi:10.1186/s12859-019-3060-6

BMC Bioinformatics

Table 11 Pooled AUPRC of the evaluated methods

From: Machine learning for discovering missing or wrong protein function annotations

	Method	Cellcycle	Derisi	Expr	Eisen	Gasch1	Gasch2	Seq	Spo	Struc	Hom
FunCat 2007	Clus-Ensemble	0.222	0.187	0.257	0.268	0.258	0.226	0.257	0.211	0.198	0.293
	HMC-GA	0.131 ±0.002	0.111 ±0.012	0.145 ±0.027	0.141 ±0.018	0.146 ±0.011	0.135 ±0.01	0.142 ±0.03	0.135 ±0.01	-	-
	HMC-LMLP	0.110 ±0.004	0.107 ±0.002	0.104 ±0.007	0.110 ±0.003	0.105 ±0.002	0.108 ±0.003	0.105 ±0.004	0.107 ±0.002	-	-
	AWX	0.119 ±0.001	0.032 ±0.004	0.023 ±0.003	0.161 ±0.002	0.162 ±0.001	0.125 ±0.001	0.03 ±0.002	0.032 ±0.005	0.118 ±0.005	0.09 ±0.007
FunCat 2018	Clus-Ensemble	0.356	0.361	0.410	0.380	0.411	0.392	0.414	0.370	0.225	0.363
	HMC-GA	0.128 ±0.013	0.120 ±0.014	0.165 ±0.013	0.153 ±0.009	0.134 ±0.013	0.129 ±0.012	0.128 ±0.017	0.115 ±0.011	-	-
	HMC-LMLP	0.188 ±0.003	0.167 ±0.002	0.219 ±0.003	0.241 ±0.002	0.216 ±0.005	0.194 ±0.004	0.228 ±0.002	0.173 ±0.000	-	-
	AWX	0.137 ±0.002	0.034 ±0.004	0.026 ±0.004	0.185 ±0.001	0.178 ±0.002	0.148 ±0.001	0.032 ±0.01	0.036 ±0.002	0.145 ±0.017	0.06 ±0.006
Gene Ontology 2007	Clus-Ensemble	0.236	0.205	0.266	0.284	0.264	0.243	0.282	0.230	0.372	0.431
	HMC-GA	0.304 ±0.015	0.250 ±0.042	0.335 ±0.018	0.317 ±0.026	0.317 ±0.016	0.324 ±0.011	0.311 ±0.044	0.273 ±0.024	-	-
	HMC-LMLP	0.334 ±0.002	0.334 ±0.002	0.343 ±0.003	0.376 ±0.003	0.348 ±0.005	0.343 ±0.001	0.340 ±0.003	0.313 ±0.002	-	-
	AWX	0.205 ±0.028	0.048 ±0.001	0.033 ±0.017	0.200 ±0.026	0.160 ±0.002	0.240 ±0.018	0.060 ±0.007	0.052 ±0.009	0.261 ±0.006	0.122 ±0.052
Gene Ontology 2018	Clus-Ensemble	0.384	0.368	0.406	0.425	0.409	0.391	0.437	0.374	0.348	0.429
	HMC-GA	0.296 ±0.013	0.273 ±0.043	0.326 ±0.017	0.328 ±0.025	0.307 ±0.031	0.310 ±0.018	0.338 ±0.016	0.298 ±0.002	-	-
	HMC-LMLP	0.349 ±0.000	0.339 ±0.000	0.357 ±0.000	0.395 ±0.000	0.365 ±0.000	0.361 ±0.000	0.375 ±0.000	0.337 ±0.000	-	-
	AWX	0.204 ±0.028	0.066 ±0.003	0.026 ±0.009	0.197 ±0.026	0.161 ±0.015	0.235 ±0.01	0.071 ±0.01	0.059 ±0.006	0.164 ±0.023	0.039 ±0.002

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ISSN: 1471-2105

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