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 REVEL above ClinPred in 6 of 7 comparisons; 2 of 2 other studies rank ClinPred above REVEL.
3 papers rank ClinPred above REVEL in 10 of their 12 comparisons and REVEL higher in 1; 1 is a tie. Livesey and Marsh 2025 ranks REVEL above ClinPred in 6 of its 7 comparisons and ClinPred higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaRNN above ClinPred in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks ClinPred above MetaRNN in 2 of 2 comparisons. No other study gives a verdict, so neither is the outlier.
3 papers rank ClinPred above MetaRNN in 2 of their 14 comparisons and MetaRNN higher in 7; 5 are ties. Of those papers, Livesey and Marsh 2025 ranks MetaRNN higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks VARITY above ClinPred in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks ClinPred above VARITY in 4 of 4 comparisons. No other study gives a verdict, so neither is the outlier.
3 papers rank ClinPred above VARITY in 5 of their 14 comparisons and VARITY higher in 7; 2 are ties. Of those papers, Livesey and Marsh 2025 ranks VARITY higher on its own (7 of 7).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above ClinPred in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks ClinPred above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ClinPred 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).
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).