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Table 2 Computational time in seconds

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

  Algorithm McCaskill CONTRAfold
1 γ-centroid with fixed γ 22 47
2 gCentroid-pMCC 36 59
3 Max-pMCC (1000) 178 303
4 Max-pMCC (10000) 1425 2391
5 Max-pMCC (100000) 13910 23291
6 Max-pMCC (1000000) 138987 232397
  1. Total computational time in seconds for predicting secondary structures of all RNA sequences in the S-151Rfam dataset. The 1st row indicates the γ-centroid estimator [10] with a fixed γ parameter (1 for McCaskill model and 2 for CONTRAfold model). The 2nd row indicates the prediction of RNA secondary structure with the γ-centroid estimator and pseudo-expected MCC (Method M2). "Max-pMCC (N)" from the 3rd to 6th rows indicate the estimator of Eq. (23), that is, RNA secondary structure prediction by maximizing pseudo-expected MCC with stochastic sampling (Method M1) where N is the number of samples.