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Table 4 Multi-location prediction results on the PROSITE-GO version of the dataset, per location, averaged over 25 runs of 5-fold cross-validation, for the combined set of single- and multi-localized proteins

From: Protein (multi-)location prediction: using location inter-dependencies in a probabilistic framework

  cyt (3785) ex (1405) nuc (2952) mem (1824) mi (870)
Pre- Std s i (SVMs) 0.84 (± 0.01) 0.87 (± 0.02) 0.79 (± 0.02) 0.93 (± 0.01) 0.90 (± 0.03)
Pre- Std s i (Our system) 0.84 (± 0.01) 0.91 (± 0.02) 0.79 (± 0.03) 0.90 (± 0.01) 0.87 (± 0.03)
Rec- Std s i (SVMs) 0.85 (± 0.01) 0.64 (± 0.02) 0.72 (± 0.02) 0.79 (± 0.02) 0.62 (± 0.03)
Rec- Std s i (Our system) 0.86 (± 0.01) 0.65 (± 0.02) 0.74 (± 0.03) 0.80 (± 0.02) 0.66 (± 0.03)
Pre s i (SVMs) 0.82 (± 0.01) 0.89 (± 0.02) 0.83 (± 0.01) 0.92 (± 0.01) 0.87 (± 0.03)
Pre s i (Our system) 0.81 (± 0.02) 0.91 (± 0.02) 0.83 (± 0.01) 0.90 (± 0.01) 0.89 (± 0.02)
Rec s i (SVMs) 0.78 (± 0.01) 0.72 (± 0.02) 0.77 (± 0.01) 0.76 (± 0.01) 0.68 (± 0.02)
Rec s i (Our system) 0.80 (± 0.01) 0.74 (± 0.02) 0.78 (± 0.02) 0.78 (± 0.01) 0.73 (± 0.02)
  1. Results are shown for the five locations s i that have the largest number of associated proteins (the number of proteins per location is given in parenthesis): cytoplasm (cyt), extracellular space (ex), nucleus (nuc), membrane (mem), and mitochondrion (mi). The table shows the per-location measures: standard precision (Pre- Std s i ), recall (Rec- Std s i ), Multilabel-Precision ( Pre s i ), and Multilabel-Recall ( Rec s i ), obtained from SVMs without using location inter-dependencies and from our system using location inter-dependencies. For each location and measure, the highest of the values obtained from the two methods is shown in boldface. Standard deviations are shown in parentheses.