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.
TraitGym official metrics: AUPRC by chromosome, weighted average (Hugging Face dataset songlab/TraitGym) ranks phyloP above GPN-MSA in 2 of 2 comparisons; 2 of 2 other studies rank GPN-MSA above phyloP.
3 papers rank GPN-MSA above phyloP in 59 of their 67 comparisons and phyloP higher in 2; 6 are ties. TraitGym official metrics ranks phyloP above GPN-MSA in all 2 of its comparisons.
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks GenoCanyon above phyloP in 3 of 3 comparisons; 2 of 2 other studies rank phyloP above GenoCanyon.
2 papers rank phyloP above GenoCanyon in 11 of their 13 comparisons and GenoCanyon higher in 1; 1 is a tie. Brandes et al. 2023 ranks GenoCanyon above phyloP in all 3 comparisons that are not ties (1 is a tie).
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks SiPhy above phyloP in 3 of 4 comparisons; 2 of 2 other studies rank phyloP above SiPhy.
2 papers rank phyloP above SiPhy in all 13 of their comparisons. Brandes et al. 2023 ranks SiPhy above phyloP in 3 of its 4 comparisons and phyloP higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above phyloP in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks phyloP above MutFormer in 4 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above phyloP in 8 of their 13 comparisons and phyloP higher in 4; 1 is a tie. Of those papers, An openly licensed benchmark… ranks phyloP higher on its own (4 of 6).