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).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks ESM3 above ProteinMPNN in 18 of 19 comparisons; proteinbench primary benchmark evidence ranks ProteinMPNN above ESM3 in 10 of 10 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM3 above ProteinMPNN in 18 of their 29 comparisons and ProteinMPNN higher in 11. Of those papers, proteinbench primary benchmark evidence ranks ProteinMPNN higher on its own (10 of 10).