| | 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 |
- 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.
