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 PolyPhen-2 above MVP in 6 of 6 comparisons; 3 of 3 other studies rank MVP above PolyPhen-2.
3 papers rank MVP above PolyPhen-2 in 18 of their 21 comparisons and PolyPhen-2 higher in 2; 1 is a tie. Livesey and Marsh 2025 ranks PolyPhen-2 above MVP in all 6 of its comparisons.
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 PolyPhen-2 in 6 of 6 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks PolyPhen-2 above MutFormer in 5 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above PolyPhen-2 in 7 of their 12 comparisons and PolyPhen-2 higher in 5. Of those papers, An openly licensed benchmark… ranks PolyPhen-2 higher on its own (5 of 6).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks PolyPhen-2 above Condel in 4 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above PolyPhen-2 in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above PolyPhen-2 in 7 of their 12 comparisons and PolyPhen-2 higher in 4; 1 is a tie. Of those papers, Clinical likelihood ratios and balanced… ranks PolyPhen-2 higher on its own (4 of 6).