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.
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks MVP above ESM-1b in 2 of 2 comparisons; 2 of 2 other studies rank ESM-1b above MVP.
2 papers rank ESM-1b above MVP in all 13 of their comparisons. Brandes et al. 2023 ranks MVP above ESM-1b in all 2 comparisons that are not ties (2 are ties).
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks MVP above REVEL in 4 of 5 comparisons; 3 of 3 other studies rank REVEL above MVP.
3 papers rank REVEL above MVP in all 19 comparisons that are not ties (4 are ties). Clinical likelihood ratios and balanced… ranks MVP above REVEL in 4 of its 5 comparisons and REVEL higher in 1.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks PolyPhen-2 above MVP in 6 of 6 comparisons; 3 of 3 other studies rank MVP above PolyPhen-2.
3 papers rank MVP above PolyPhen-2 in 18 of their 21 comparisons and PolyPhen-2 higher in 2; 1 is a tie. Livesey and Marsh 2025 ranks PolyPhen-2 above MVP in all 6 of its comparisons.
Clinical likelihood ratios and balanced accuracy for 44 in silico tools against multiple large-scale functional assays of cancer susceptibility genes ranks MVP above Condel in 4 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above MVP in 6 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above MVP in 7 of their 12 comparisons and MVP higher in 5. Of those papers, Clinical likelihood ratios and balanced… ranks MVP higher on its own (4 of 5).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above MVP in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MVP above MutFormer in 6 of 6 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MutFormer above MVP in 7 of their 13 comparisons and MVP higher in 6. Of those papers, An openly licensed benchmark… ranks MVP higher on its own (6 of 6).