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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