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 MetaSVM above ESM-1b in 2 of 2 comparisons; 2 of 2 other studies rank ESM-1b above MetaSVM.
2 papers rank ESM-1b above MetaSVM in all 13 of their comparisons. Brandes et al. 2023 ranks MetaSVM above ESM-1b in all 2 comparisons that are not ties (2 are ties).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaSVM above FATHMM-XF in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above MetaSVM.
2 papers rank FATHMM-XF above MetaSVM in 22 of their 26 comparisons and MetaSVM higher in 4. Livesey and Marsh 2025 ranks MetaSVM above FATHMM-XF in all 7 of its comparisons.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks LRT above MetaSVM in 16 of 20 comparisons; 2 of 2 other studies rank MetaSVM above LRT.
2 papers rank MetaSVM above LRT in 12 of their 13 comparisons and LRT higher in 1. Comprehensive assessment… ranks LRT above MetaSVM in 16 of its 20 comparisons and MetaSVM higher in 4.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks GenoCanyon above MetaSVM in 6 of 8 comparisons; 2 of 2 other studies rank MetaSVM above GenoCanyon.
2 papers rank MetaSVM above GenoCanyon in 12 of their 13 comparisons and GenoCanyon higher in 1. Comprehensive assessment… ranks GenoCanyon above MetaSVM in 6 of its 10 comparisons and MetaSVM higher in 2; 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 MetaSVM above Condel in 4 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks Condel above MetaSVM in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank Condel above MetaSVM in 8 of their 13 comparisons and MetaSVM higher in 4; 1 is a tie. Of those papers, Clinical likelihood ratios and balanced… ranks MetaSVM 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 MetaSVM above SuSPect in 5 of 6 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks SuSPect above MetaSVM in 7 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank SuSPect above MetaSVM in 8 of their 13 comparisons and MetaSVM higher in 5. Of those papers, Clinical likelihood ratios and balanced… ranks MetaSVM higher on its own (5 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutFormer above MetaSVM in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks MetaSVM above MutFormer in 4 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank MetaSVM above MutFormer in 4 of their 13 comparisons and MutFormer higher in 8; 1 is a tie. 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 MetaSVM above LIST-S2 in 7 of 7 comparisons; An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers ranks LIST-S2 above MetaSVM in 3 of 4 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank LIST-S2 above MetaSVM in 3 of their 13 comparisons and MetaSVM higher in 8; 2 are ties. Of those papers, Livesey and Marsh 2025 ranks MetaSVM higher on its own (7 of 7).