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.
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MutationAssessor above MutFormer in 5 of 5 comparisons; other studies rank MutFormer above MutationAssessor in 7 of 7.
Livesey and Marsh 2025 ranks MutFormer above MutationAssessor in all 7 of its comparisons. An openly licensed benchmark… ranks MutationAssessor above MutFormer in all 5 comparisons that are not ties (1 is a tie).
ProteinGym AMFR assay-level Spearman comparison ranks Tranception above ESM-1v in 14 of 17 comparisons; other studies rank ESM-1v above Tranception in 7 of 7.
Livesey and Marsh 2025 ranks ESM-1v above Tranception in all 7 of its comparisons. ProteinGym AMFR assay-level Spearman… ranks Tranception above ESM-1v in 14 of its 19 comparisons and ESM-1v higher in 3; 2 are ties.
An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MutPred above MutFormer in 6 of 6 comparisons; other studies rank MutFormer above MutPred in 6 of 7.
Livesey and Marsh 2025 ranks MutFormer above MutPred in 6 of its 7 comparisons and MutPred higher in 1. An openly licensed benchmark… ranks MutPred above MutFormer in all 6 of its comparisons.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks LRT above M-CAP in 16 of 20 comparisons; other studies rank M-CAP above LRT in 9 of 11.
2 papers rank M-CAP above LRT in 9 of their 11 comparisons and LRT higher in 2. Comprehensive assessment… ranks LRT above M-CAP in 16 of its 20 comparisons and M-CAP higher in 4.
A benchmarking study of individual somatic variant callers and voting-based ensembles for whole-exome sequencing ranks MuSE above NeuSomatic in 3 of 3 comparisons; other studies rank NeuSomatic above MuSE in 86 of 100.
2 papers rank NeuSomatic above MuSE in 86 of their 101 comparisons and MuSE higher in 14; 1 is a tie. A benchmarking study of individual… ranks MuSE above NeuSomatic in all 3 comparisons that are not ties (3 are ties).
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; other studies rank MutFormer above BayesDel in 6 of 7.
Livesey and Marsh 2025 ranks MutFormer above BayesDel in 6 of its 7 comparisons and BayesDel higher in 1. An openly licensed benchmark… ranks BayesDel above MutFormer in all 6 of its comparisons.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks FATHMM above CADD in 10 of 10 comparisons; other studies rank CADD above FATHMM in 11 of 13.
3 papers rank CADD above FATHMM in 11 of their 13 comparisons and FATHMM higher in 2. Comprehensive assessment… ranks FATHMM above CADD in all 10 of its comparisons.