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Table 2 Explanation ratios of the MIPS yeast datasets

From: A domain-based approach to predict protein-protein interactions

No of Parameters Training set PPI Explanation Ratio (%)a Accuracy Precision
867 Inclusive Positive 95.6 96.4 38.9
   Negative 96.1   
344 Closed Positive 99.3 98.7 90.6
   Negative 98.7   
2466 Inclusive Positive 96.2 95.7 24.3
   Negative 95.7   
1216 Closed Positive 99.0 96.6 60.8
   Negative 96.4   
5095 Inclusive Positive 97.3 95.6 19.3
   Negative 95.6   
3060 Closed Positive 99.3 95.9 56.5
   Negative 95.6   
Deng et al. with Inclusive Positive 95–98 93–95 24–30
867 pmts b   Negative 93–95   
  Closed Positive 91–93 89–90 54–55
   Negative 89–90   
Random with Inclusive Positive 61.0 36.0 2.2
867 pmts   Negative 35.4   
  1. a Explanation ratio is the ratio of successful predictions to the overall number of entries in a particular list. We note that the explanation ratios for the positive and negative PPI lists respectively correspond to the sensitivity and specificity with Lin et al. definitions.
  2. b Calculated performance metrics depend on the false positive and negative prediction rates used in the MLE algorithm as well as on the cutoff for positive and negative PPI assignments. Therefore, we report the range of obtained percentages that were obtained when various prediction rates were used in the MLE algorithm. Whole set of results can be found in Supplementary Table 1 [see Additional file].