Contested result

DNABERT-2 and Evo: GENEB leaderboard (leaderboard.json, 13 task-type aggregates) reverses the order

Low severity
Not yet reviewed
Ordering reversal
Different tasks across studies

GENEB leaderboard (leaderboard.json, 13 task-type aggregates) ranks DNABERT-2 above Evo in 35 of 45 comparisons; other studies rank Evo above DNABERT-2 in 6 of 6.

An automatic lead, not a finding of error. The results below are shown as published, everywhere on the site, until a reviewer decides otherwise.

Which studies agree

Zero-shot benchmarking of RNA language… ranks Evo above DNABERT-2 in all 6 of its comparisons. GENEB leaderboard ranks DNABERT-2 above Evo in 35 of its 45 comparisons and Evo higher in 10.

Rank Evo higher (1): Zero-shot benchmarking of RNA language…
Rank DNABERT-2 higher (1): GENEB leaderboard (disagrees)
Mixed (0): none

Each paper sits where at least two thirds of its comparisons point; Mixed means neither model reaches two thirds. The larger, outlined dot is the paper that disagrees.

Evo higherTieDNABERT-2 higherNumbers are counts of comparisons; the outlined bar is the paper that disagrees.

Papers compared (2)
Paper	Role	Ranks Evo higher	Ranks DNABERT-2 higher	Ties
GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · Repository	Disagrees	10	35	0
Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning and 1 more record · DOI	Agrees	6	0	0

Comparisons in GENEB leaderboard (45)

Protocol	Dataset	Metric	Evo	DNABERT-2	Higher
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'Chromatin Acc.'), unitless	0.289	0.32	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'Coding/NC'), unitless	0.539	0.582	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'DNA Methyl.'), unitless	0.0458	0.0414	Evo
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'Enhancers'), unitless	0.288	0.332	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'Histone Mod.'), unitless	0.258	0.265	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'Mouse Enh.'), unitless	0.12	0.0982	Evo
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'Promoters'), unitless	0.436	0.471	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'Regulatory'), unitless	0.125	0.216	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'Species Clf.'), unitless	0.207	0.402	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'Splice Sites'), unitless	0.0657	0.218	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'TF Binding'), unitless	0.0386	0.147	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'Virus/Phage'), unitless	0.0941	0.134	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; category 'lncRNA'), unitless	0.0189	0.0627	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; macro average: unweighted mean of the 13 category MCCs), unitless	0.194	0.253	DNABERT-2
GENEB leaderboard, 10-shot, MCC aggregates	GENEB 100 tasks	MCC (10-shot; micro average: mean over all 100 tasks), unitless	0.232	0.272	DNABERT-2
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'Chromatin Acc.'), unitless	0.14	0.156	DNABERT-2
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'Coding/NC'), unitless	0.293	0.162	Evo
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'DNA Methyl.'), unitless	0.0208	0.00287	Evo
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'Enhancers'), unitless	0.165	0.134	Evo
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'Histone Mod.'), unitless	0.108	0.112	DNABERT-2
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'Mouse Enh.'), unitless	0.0568	0.0188	Evo
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'Promoters'), unitless	0.279	0.24	Evo
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'Regulatory'), unitless	0.0788	0.0709	Evo
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'Species Clf.'), unitless	0.103	0.177	DNABERT-2
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'Splice Sites'), unitless	0.0643	0.0789	DNABERT-2
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'TF Binding'), unitless	0.0084	0.0663	DNABERT-2
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'Virus/Phage'), unitless	-0.00343	0.0421	DNABERT-2
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; category 'lncRNA'), unitless	0.00964	0.0163	DNABERT-2
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; macro average: unweighted mean of the 13 category MCCs), unitless	0.102	0.0982	Evo
GENEB leaderboard, 1-shot, MCC aggregates	GENEB 100 tasks	MCC (1-shot; micro average: mean over all 100 tasks), unitless	0.126	0.119	Evo
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'Chromatin Acc.'), unitless	0.284	0.57	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'Coding/NC'), unitless	0.719	0.82	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'DNA Methyl.'), unitless	0.0732	0.18	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'Enhancers'), unitless	0.37	0.483	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'Histone Mod.'), unitless	0.397	0.469	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'Mouse Enh.'), unitless	0.287	0.527	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'Promoters'), unitless	0.537	0.708	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'Regulatory'), unitless	0.269	0.435	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'Species Clf.'), unitless	0.285	0.625	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'Splice Sites'), unitless	0.16	0.491	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'TF Binding'), unitless	0.173	0.574	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'Virus/Phage'), unitless	0.205	0.492	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; category 'lncRNA'), unitless	0.119	0.265	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; macro average: unweighted mean of the 13 category MCCs), unitless	0.298	0.511	DNABERT-2
GENEB leaderboard, full training data, MCC aggregates	GENEB 100 tasks	MCC (full training data; micro average: mean over all 100 tasks), unitless	0.342	0.506	DNABERT-2

Comparisons in Zero-shot benchmarking of RNA language… (6)

Protocol	Dataset	Metric	Evo	DNABERT-2	Higher
Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (mean over assays)	RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	AUROC (PLL-D; mean over assays), unitless	0.588	0.543	Evo
Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (median over assays)	RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	AUROC (PLL-D; median over assays), unitless	0.586	0.542	Evo
Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (mean over assays)	RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	MCC (PLL-D; mean over assays), unitless	0.132	0.069	Evo
Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (median over assays)	RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	MCC (PLL-D; median over assays), unitless	0.13	0.061	Evo
Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (mean over assays)	RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Absolute spearman correlation (PLL-D; mean over assays), unitless	0.179	0.085	Evo
Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (median over assays)	RNAGym ncRNA DMS assays (31 assays) (Wang et al. 2026)	Absolute spearman correlation (PLL-D; median over assays), unitless	0.178	0.086	Evo

What disagrees

Other studies: rank Evo above DNABERT-2 in 6 of 6 comparisons
This study: ranks DNABERT-2 above Evo in 35 of 45 comparisons

Compared: DNABERT-2, Evo
Study that disagrees: GENEB leaderboard (leaderboard.json, 13 task-type aggregates)
Other studies: Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning, Zero-shot benchmarking of RNA language models: Supplementary Information
Rule: Ordering reversal; different tasks across studies
Model identity: Matched across studies partly through links not yet reviewed

The compared numbers

Each value links to its result record and source. Compare values within one protocol; the rule compares rankings, not raw values across protocols.

In the study that disagrees (90)
Study	Tool	Protocol or benchmark	Metric	Value
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Chromatin Acc.')	0.32
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Coding/NC')	0.582
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'DNA Methyl.')	0.0414
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Enhancers')	0.332
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Histone Mod.')	0.265
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'lncRNA')	0.0627
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; macro average: unweighted mean of the 13 category MCCs)	0.253
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; micro average: mean over all 100 tasks)	0.272
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Mouse Enh.')	0.0982
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Promoters')	0.471
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Regulatory')	0.216
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Species Clf.')	0.402
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Splice Sites')	0.218
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'TF Binding')	0.147
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Virus/Phage')	0.134
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Chromatin Acc.')	0.156
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Coding/NC')	0.162
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'DNA Methyl.')	0.00287
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Enhancers')	0.134
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Histone Mod.')	0.112
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'lncRNA')	0.0163
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; macro average: unweighted mean of the 13 category MCCs)	0.0982
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; micro average: mean over all 100 tasks)	0.119
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Mouse Enh.')	0.0188
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Promoters')	0.24
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Regulatory')	0.0709
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Species Clf.')	0.177
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Splice Sites')	0.0789
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'TF Binding')	0.0663
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Virus/Phage')	0.0421
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Chromatin Acc.')	0.57
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Coding/NC')	0.82
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'DNA Methyl.')	0.18
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Enhancers')	0.483
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Histone Mod.')	0.469
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'lncRNA')	0.265
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; macro average: unweighted mean of the 13 category MCCs)	0.511
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; micro average: mean over all 100 tasks)	0.506
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Mouse Enh.')	0.527
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Promoters')	0.708
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Regulatory')	0.435
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Species Clf.')	0.625
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Splice Sites')	0.491
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'TF Binding')	0.574
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	dnabert2 (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Virus/Phage')	0.492
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Chromatin Acc.')	0.289
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Coding/NC')	0.539
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'DNA Methyl.')	0.0458
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Enhancers')	0.288
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Histone Mod.')	0.258
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'lncRNA')	0.0189
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; macro average: unweighted mean of the 13 category MCCs)	0.194
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; micro average: mean over all 100 tasks)	0.232
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Mouse Enh.')	0.12
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Promoters')	0.436
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Regulatory')	0.125
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Species Clf.')	0.207
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Splice Sites')	0.0657
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'TF Binding')	0.0386
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 10-shot, MCC aggregates	MCC (10-shot; category 'Virus/Phage')	0.0941
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Chromatin Acc.')	0.14
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Coding/NC')	0.293
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'DNA Methyl.')	0.0208
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Enhancers')	0.165
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Histone Mod.')	0.108
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'lncRNA')	0.00964
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; macro average: unweighted mean of the 13 category MCCs)	0.102
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; micro average: mean over all 100 tasks)	0.126
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Mouse Enh.')	0.0568
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Promoters')	0.279
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Regulatory')	0.0788
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Species Clf.')	0.103
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Splice Sites')	0.0643
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'TF Binding')	0.0084
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, 1-shot, MCC aggregates	MCC (1-shot; category 'Virus/Phage')	-0.00343
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Chromatin Acc.')	0.284
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Coding/NC')	0.719
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'DNA Methyl.')	0.0732
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Enhancers')	0.37
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Histone Mod.')	0.397
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'lncRNA')	0.119
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; macro average: unweighted mean of the 13 category MCCs)	0.298
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; micro average: mean over all 100 tasks)	0.342
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Mouse Enh.')	0.287
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Promoters')	0.537
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Regulatory')	0.269
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Species Clf.')	0.285
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Splice Sites')	0.16
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'TF Binding')	0.173
GENEB leaderboard (leaderboard.json, 13 task-type aggregates)	evo-1-131k (GENEB leaderboard)	GENEB leaderboard, full training data, MCC aggregates	MCC (full training data; category 'Virus/Phage')	0.205

In the other studies (12)
Study	Tool	Protocol or benchmark	Metric	Value
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	DNABERT-2 (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (mean over assays)	AUROC (PLL-D; mean over assays)	0.543±0.031
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	DNABERT-2 (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (median over assays)	AUROC (PLL-D; median over assays)	0.542
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	DNABERT-2 (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (mean over assays)	MCC (PLL-D; mean over assays)	0.069±0.052
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	DNABERT-2 (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (median over assays)	MCC (PLL-D; median over assays)	0.061
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	DNABERT-2 (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (mean over assays)	Absolute spearman correlation (PLL-D; mean over assays)	0.085±0.056
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	DNABERT-2 (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (median over assays)	Absolute spearman correlation (PLL-D; median over assays)	0.086
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	EVO1.5 (8k_base) (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (mean over assays)	AUROC (PLL-D; mean over assays)	0.588±0.056
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	EVO1.5 (8k_base) (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, AUC (median over assays)	AUROC (PLL-D; median over assays)	0.586
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	EVO1.5 (8k_base) (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (mean over assays)	MCC (PLL-D; mean over assays)	0.132±0.088
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	EVO1.5 (8k_base) (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, MCC (median over assays)	MCC (PLL-D; median over assays)	0.13
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	EVO1.5 (8k_base) (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (mean over assays)	Absolute spearman correlation (PLL-D; mean over assays)	0.179±0.114
Zero-shot benchmarking of RNA language models: Supplementary Information; Zero-shot benchmarking of RNA language models in structural, functional, and evolutionary learning	EVO1.5 (8k_base) (zero-shot, Wang et al. 2026)	Wang et al. 2026 zero-shot fitness, RNAGym ncRNA DMS assays (31 assays), PLL-D, SR (median over assays)	Absolute spearman correlation (PLL-D; median over assays)	0.178

Follow-up

Current state: Not yet reviewed.

No one has reviewed this finding yet.

How to help resolve this

If you know why these studies disagree, for example a different population, metric or preprocessing step, or you have a corrected value, tell us through the contribution form. A reviewer checks every submission against its source before anything changes, and the step is added to the follow-up above.

Finding discrepancy-e54c0fa997e1fd8d · All contested results · How findings are made and followed up