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.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks M-CAP above FATHMM-XF in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above M-CAP.
2 papers rank FATHMM-XF above M-CAP in 22 of their 26 comparisons and M-CAP higher in 3; 1 is a tie. Livesey and Marsh 2025 ranks M-CAP above FATHMM-XF in all 7 of its comparisons.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above M-CAP in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks M-CAP above MutFormer in 4 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank M-CAP above MutFormer in 4 of their 13 comparisons and MutFormer higher in 8; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks M-CAP above LIST-S2 in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks LIST-S2 above M-CAP in 5 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank LIST-S2 above M-CAP in 5 of their 13 comparisons and M-CAP higher in 8. Of those papers, Livesey and Marsh 2025 ranks M-CAP higher on its own (7 of 7).