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