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.
mRNABench: A curated benchmark for mature mRNA property and function prediction ranks DNABERT-2 above RNA-FM in 7 of 7 comparisons; 2 of 2 other studies rank RNA-FM above DNABERT-2.
2 papers rank RNA-FM above DNABERT-2 in all 30 comparisons that are not ties (4 are ties). MRNABench ranks DNABERT-2 above RNA-FM in all 7 comparisons that are not ties (3 are ties).
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) ranks MutationAssessor above Eigen in 6 of 7 comparisons; 3 of 3 other studies rank Eigen above MutationAssessor.
3 papers rank Eigen above MutationAssessor in 17 of their 22 comparisons and MutationAssessor higher in 1; 4 are ties. Livesey and Marsh 2025 ranks MutationAssessor above Eigen in 6 of its 7 comparisons and Eigen higher in 1.
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning ranks AIDO.RNA above RNAErnie in 36 of 36 comparisons; RNAGym fitness leaderboard (v0.1.1), leaderboard/fitness/README.md ranks RNAErnie above AIDO.RNA in 3 of 4 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank RNAErnie above AIDO.RNA in 3 of their 40 comparisons and AIDO.RNA higher in 37. Of those papers, Zero-shot benchmarking of RNA language… ranks AIDO.RNA higher on its own (36 of 36).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks ESM-IF1 above ProteinMPNN in 19 of 19 comparisons; proteinbench primary benchmark evidence ranks ProteinMPNN above ESM-IF1 in 10 of 10 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM-IF1 above ProteinMPNN in 19 of their 29 comparisons and ProteinMPNN higher in 10. Of those papers, proteinbench primary benchmark evidence ranks ProteinMPNN higher on its own (10 of 10).
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design ranks ESM3 above ProteinMPNN in 18 of 19 comparisons; proteinbench primary benchmark evidence ranks ProteinMPNN above ESM3 in 10 of 10 comparisons. No other study gives a verdict, so neither is the outlier.
2 papers rank ESM3 above ProteinMPNN in 18 of their 29 comparisons and ProteinMPNN higher in 11. Of those papers, proteinbench primary benchmark evidence ranks ProteinMPNN higher on its own (10 of 10).