Comparison between pseudo-expected accuracy and expected accuracy. Comparison between the pseudo-expected SEN, PPV, MCC and F-score (the horizontal axes) and the expected SEN, PPV, MCC and F-score that are computed by stochastic sampling with a sample size of n = 1 M (the vertical axes). We used the McCaskill model (top row) and the CONTRAfold model (bottom row). The 1st, 2nd, 3rd and 4th columns indicate SEN, PPV, F-score and MCC, respectively. See Additional file 1, Figure S1 and Figure S2 for other sample sizes.