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