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Table 1 SEN, PPV, MCC and F-score for each prediction algorithm

From: Prediction of RNA secondary structure by maximizing pseudo-expected accuracy

  McCaskill model CONTRAfold model
γ SEN PPV MCC F-score SEN PPV MCC F-score
gc-pMCC 0.67 0.54 0.60 0.60 0.68 0.69 0.68 0.68
gc-pF 0.67 0.54 0.60 0.59 0.69 0.68 0.68 0.69
0.03125 0.34 0.78 0.52 0.48 0.09 0.90 0.28 0.16
0.0625 0.40 0.74 0.54 0.52 0.14 0.90 0.36 0.24
0.125 0.45 0.69 0.56 0.55 0.21 0.86 0.42 0.34
0.25 0.51 0.66 0.58 0.58 0.30 0.82 0.50 0.44
0.5 0.57 0.62 0.59 0.60 0.41 0.79 0.56 0.54
1.0 0.65 0.58 0.61 0.61 0.53 0.75 0.63 0.62
2.0 0.67 0.53 0.60 0.60 0.65 0.70 0.67 0.67
4.0 0.68 0.51 0.59 0.59 0.72 0.65 0.68 0.68
6.0 0.69 0.51 0.59 0.58 0.74 0.62 0.68 0.68
8.0 0.69 0.50 0.59 0.58 0.75 0.61 0.68 0.67
16.0 0.69 0.49 0.58 0.57 0.76 0.58 0.66 0.66
32.0 0.69 0.48 0.58 0.57 0.76 0.56 0.65 0.64
64.0 0.69 0.48 0.57 0.56 0.76 0.54 0.64 0.64
128.0 0.69 0.47 0.57 0.56 0.76 0.53 0.64 0.63
256.0 0.69 0.47 0.57 0.56 0.76 0.53 0.63 0.62
512.0 0.69 0.47 0.57 0.56 0.76 0.52 0.63 0.62
1024.0 0.69 0.47 0.57 0.56 0.76 0.52 0.63 0.62
RNAfold 0.65 0.50 0.57 0.57 -
Simfold 0.64 0.51 0.57 0.57 -
Sfold 0.65 0.58 0.62 0.62 -
  1. The rows labeled "gc-pMCC" and "gc-pF" indicate RNA secondary structure prediction with the γ-centroid estimator and the pseudo-expected MCC and F-score, respectively (Method M2). The rows below the dashed line indicate the results of the γ-centroid estimator [10] with various values of the γ parameter (given in the first column). Note that Simfold and Sfold employ a similar probabilistic model (based on energy parameters) for secondary structures to the McCaskill model.