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.
Comprehensive assessment of computational algorithms in predicting cancer driver mutations ranks LRT above MetaLR in 15 of 17 comparisons; 2 of 2 other studies rank MetaLR above LRT.
2 papers rank MetaLR above LRT in 12 of their 13 comparisons and LRT higher in 1. Comprehensive assessment… ranks LRT above MetaLR in 15 of its 20 comparisons and MetaLR higher in 2; 3 are ties.
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods ranks MetaLR above ESM-1b in 2 of 2 comparisons; 2 of 2 other studies rank ESM-1b above MetaLR.
2 papers rank ESM-1b above MetaLR in all 13 of their comparisons. Brandes et al. 2023 ranks MetaLR 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 MetaLR above FATHMM-MKL in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-MKL above MetaLR.
2 papers rank FATHMM-MKL above MetaLR in 18 of their 25 comparisons and MetaLR higher in 5; 2 are ties. Livesey and Marsh 2025 ranks MetaLR above FATHMM-MKL in all 7 of its comparisons.
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaLR above FATHMM-XF in 7 of 7 comparisons; 2 of 2 other studies rank FATHMM-XF above MetaLR.
2 papers rank FATHMM-XF above MetaLR in 22 of their 26 comparisons and MetaLR higher in 3; 1 is a tie. Livesey and Marsh 2025 ranks MetaLR above FATHMM-XF in all 7 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 MetaLR above SuSPect in 4 of 5 comparisons; Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks SuSPect above MetaLR in 6 of 7 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank SuSPect above MetaLR in 7 of their 13 comparisons and MetaLR higher in 5; 1 is a tie. Of those papers, Clinical likelihood ratios and balanced… ranks MetaLR higher on its own (4 of 6).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MetaLR 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 MetaLR in 4 of 5 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank LIST-S2 above MetaLR in 4 of their 13 comparisons and MetaLR higher in 8; 1 is a tie. Of those papers, Livesey and Marsh 2025 ranks MetaLR higher on its own (7 of 7).