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.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks FATHMM-XF above CADD in 10 of 10 comparisons; 2 of 2 other studies rank CADD above FATHMM-XF.
2 papers rank CADD above FATHMM-XF in all 12 comparisons that are not ties (1 is a tie). Comprehensive assessment… ranks FATHMM-XF above CADD in all 10 of its comparisons.
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 MetaLR above FATHMM-XF in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above MetaLR.
2 papers rank FATHMM-XF above MetaLR in 22 of their 26 comparisons and MetaLR higher in 3; 1 is a tie. Livesey and Marsh 2025 ranks MetaLR above FATHMM-XF in all 7 of its comparisons.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaSVM above FATHMM-XF in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above MetaSVM.
2 papers rank FATHMM-XF above MetaSVM in 22 of their 26 comparisons and MetaSVM higher in 4. Livesey and Marsh 2025 ranks MetaSVM above FATHMM-XF in all 7 of its comparisons.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutationAssessor above FATHMM-XF in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above MutationAssessor.
2 papers rank FATHMM-XF above MutationAssessor in 21 of their 26 comparisons and MutationAssessor higher in 5. Livesey and Marsh 2025 ranks MutationAssessor above FATHMM-XF in all 7 of its comparisons.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks SIFT above FATHMM-XF in 6 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above SIFT.
2 papers rank FATHMM-XF above SIFT in 25 of their 26 comparisons and SIFT higher in 1. Livesey and Marsh 2025 ranks SIFT above FATHMM-XF in 6 of its 7 comparisons and FATHMM-XF higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks PolyPhen-2 above FATHMM-XF in 6 of 6 comparisons; 2 of 2 other studies rank FATHMM-XF above PolyPhen-2.
2 papers rank FATHMM-XF above PolyPhen-2 in 20 of their 26 comparisons and PolyPhen-2 higher in 1; 5 are ties. Livesey and Marsh 2025 ranks PolyPhen-2 above FATHMM-XF in all 6 of its comparisons.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above FATHMM-XF in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks FATHMM-XF above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank FATHMM-XF above MutFormer in 6 of their 13 comparisons and MutFormer higher in 7. Of those papers, Livesey and Marsh 2025 ranks MutFormer higher on its own (7 of 7).