Where one study disagrees with what other studies report for the same models, and what we are doing to resolve each case.
These are automatic leads, not findings of error. Each release, a check compares how every study ranks the models it shares with other studies. It flags a study that reverses the order the others agree on, or whose gap to a shared reference model lies well outside theirs. Different tasks, populations or metrics often explain a flag.
A flag never hides a result. Flagged results stay in every table, page and download, marked Contested. A result is withheld only when a reviewer marks it disputed.
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks ESM3 above ESM-2 in 18 of 18 comparisons; pfmbench primary benchmark evidence ranks ESM-2 above ESM3 in 9 of 12 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM-2 above ESM3 in 9 of their 31 comparisons and ESM3 higher in 21; 1 is a tie. Of those papers, ProteinGym ranks ESM3 higher on its own (18 of 19).
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks ESM-1b above EVE in 6 of 6 comparisons; 2 of 2 other studies rank EVE above ESM-1b.
2 papers rank EVE above ESM-1b in 22 of their 26 comparisons and ESM-1b higher in 1; 3 are ties. Brandes et al. 2023 ranks ESM-1b above EVE in all 6 comparisons that are not ties (2 are ties).