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 GenoCanyon above SIFT in 6 of 8 comparisons; 3 of 3 other studies rank SIFT above GenoCanyon.
3 papers rank SIFT above GenoCanyon in 14 of their 16 comparisons and GenoCanyon higher in 1; 1 is a tie. Comprehensive assessment… ranks GenoCanyon above SIFT in 6 of its 10 comparisons and SIFT higher in 2; 2 are ties.
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 MutFormer above SIFT in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks SIFT above MutFormer in 3 of 4 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above SIFT in 8 of their 13 comparisons and SIFT higher in 3; 2 are ties. Of those papers, An openly licensed benchmark… ranks SIFT higher on its own (3 of 6).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks SIFT above Condel in 5 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above SIFT in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above SIFT in 7 of their 12 comparisons and SIFT higher in 5. Of those papers, Clinical likelihood ratios and balanced… ranks SIFT higher on its own (5 of 5).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks SIFT above PANTHER in 3 of 4 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks PANTHER above SIFT in 5 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank PANTHER above SIFT in 6 of their 11 comparisons and SIFT higher in 4; 1 is a tie. Of those papers, Clinical likelihood ratios and balanced… ranks SIFT higher on its own (3 of 5).