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. 2020 Nov 30;16(11):e1008085. doi: 10.1371/journal.pcbi.1008085

Fig 7. Pseudolikelihood maximization does not fully recapitulate the pairwise correlation structure of input alignments.

Fig 7

(A) Average value of the Potts Hamiltonian at intermediate iterations of the Markov chain Monte Carlo sequence emission algorithm across 1000 synthetic sequences. Error bars represent standard deviation. We accept sequences after 5000 iterations. (B-C) Comparison of single-site (A) and pairwise (B) Potts model terms of a ground truth HPM (“training HPM”) versus in an HPM trained on aligned sequences emitted from the ground truth HPM (“synthetic HPM”). (D-F) Comparisons of marginal single-site probabilities (D), marginal pairwise probabilities (E), and mutual information (F) for the posterior sequence distributions sampled from the training HPM (statistics estimated from MSA2) against the synthetic HPM (statistics estimated from MSA3).