Configuration

dnabert2 (GENEB leaderboard)

Configuration of DNABERT-2: dnabert2-no-flashattention; frozen embeddings; leaderboard display name 'dnabert2'.

Overview

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Evaluations and results

3 evaluations · 45 results. Different protocols are not a single leaderboard.

Dataset: GENEB 100 tasks

Sorted by MCC (1-shot; category 'Chromatin Acc.') (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	MCC (1-shot; category 'Chromatin Acc.')	MCC (1-shot; category 'Coding/NC')	MCC (1-shot; category 'DNA Methyl.')	MCC (1-shot; category 'Enhancers')	MCC (1-shot; category 'Histone Mod.')	MCC (1-shot; category 'lncRNA')	MCC (1-shot; category 'Mouse Enh.')	MCC (1-shot; category 'Promoters')	MCC (1-shot; category 'Regulatory')	MCC (1-shot; category 'Species Clf.')	MCC (1-shot; category 'Splice Sites')	MCC (1-shot; category 'TF Binding')	MCC (1-shot; category 'Virus/Phage')	MCC (1-shot; macro average: unweighted mean of the 13 category MCCs)	MCC (1-shot; micro average: mean over all 100 tasks)	MCC (10-shot; category 'Chromatin Acc.')	MCC (10-shot; category 'Coding/NC')	MCC (10-shot; category 'DNA Methyl.')	MCC (10-shot; category 'Enhancers')	MCC (10-shot; category 'Histone Mod.')	MCC (10-shot; category 'lncRNA')	MCC (10-shot; category 'Mouse Enh.')	MCC (10-shot; category 'Promoters')	MCC (10-shot; category 'Regulatory')	MCC (10-shot; category 'Species Clf.')	MCC (10-shot; category 'Splice Sites')	MCC (10-shot; category 'TF Binding')	MCC (10-shot; category 'Virus/Phage')	MCC (10-shot; macro average: unweighted mean of the 13 category MCCs)	MCC (10-shot; micro average: mean over all 100 tasks)	MCC (full training data; category 'Chromatin Acc.')	MCC (full training data; category 'Coding/NC')	MCC (full training data; category 'DNA Methyl.')	MCC (full training data; category 'Enhancers')	MCC (full training data; category 'Histone Mod.')	MCC (full training data; category 'lncRNA')	MCC (full training data; category 'Mouse Enh.')	MCC (full training data; category 'Promoters')	MCC (full training data; category 'Regulatory')	MCC (full training data; category 'Species Clf.')	MCC (full training data; category 'Splice Sites')	MCC (full training data; category 'TF Binding')	MCC (full training data; category 'Virus/Phage')	MCC (full training data; macro average: unweighted mean of the 13 category MCCs)	MCC (full training data; micro average: mean over all 100 tasks)
dnabert2 (GENEB leaderboard)Evaluation	GENEB leaderboard, 1-shot, MCC aggregates	0.156	0.162	0.00287	0.134	0.112	0.0163	0.0188	0.24	0.0709	0.177	0.0789	0.0663	0.0421	0.0982	0.119	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
dnabert2 (GENEB leaderboard)Evaluation	GENEB leaderboard, 10-shot, MCC aggregates	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.32	0.582	0.0414	0.332	0.265	0.0627	0.0982	0.471	0.216	0.402	0.218	0.147	0.134	0.253	0.272	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
dnabert2 (GENEB leaderboard)Evaluation	GENEB leaderboard, full training data, MCC aggregates	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.57	0.82	0.18	0.483	0.469	0.265	0.527	0.708	0.435	0.625	0.491	0.574	0.492	0.511	0.506

All 45 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.32 MCC (10-shot; category 'Chromatin Acc.') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Chromatin Acc.'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.582 MCC (10-shot; category 'Coding/NC') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Coding/NC'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0414 MCC (10-shot; category 'DNA Methyl.') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.DNA Methyl.'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.332 MCC (10-shot; category 'Enhancers') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Enhancers'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.265 MCC (10-shot; category 'Histone Mod.') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Histone Mod.'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0627 MCC (10-shot; category 'lncRNA') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.lncRNA'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.253 MCC (10-shot; macro average: unweighted mean of the 13 category MCCs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'macro_MCC'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.272 MCC (10-shot; micro average: mean over all 100 tasks) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'micro_MCC'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0982 MCC (10-shot; category 'Mouse Enh.') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Mouse Enh.'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.471 MCC (10-shot; category 'Promoters') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Promoters'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.216 MCC (10-shot; category 'Regulatory') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Regulatory'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.402 MCC (10-shot; category 'Species Clf.') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Species Clf.'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.218 MCC (10-shot; category 'Splice Sites') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Splice Sites'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.147 MCC (10-shot; category 'TF Binding') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.TF Binding'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.134 MCC (10-shot; category 'Virus/Phage') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (10-shot) lit-genomics-20261011-geneb-protocol-10shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.10shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Virus/Phage'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.156 MCC (1-shot; category 'Chromatin Acc.') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (1-shot) lit-genomics-20261011-geneb-protocol-1shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.1shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Chromatin Acc.'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.162 MCC (1-shot; category 'Coding/NC') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (1-shot) lit-genomics-20261011-geneb-protocol-1shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.1shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Coding/NC'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.00287 MCC (1-shot; category 'DNA Methyl.') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (1-shot) lit-genomics-20261011-geneb-protocol-1shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.1shot, model 'dnabert2-no-flashattention', key 'cat_MCC.DNA Methyl.'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.134 MCC (1-shot; category 'Enhancers') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (1-shot) lit-genomics-20261011-geneb-protocol-1shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.1shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Enhancers'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.112 MCC (1-shot; category 'Histone Mod.') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (1-shot) lit-genomics-20261011-geneb-protocol-1shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.1shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Histone Mod.'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0163 MCC (1-shot; category 'lncRNA') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (1-shot) lit-genomics-20261011-geneb-protocol-1shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.1shot, model 'dnabert2-no-flashattention', key 'cat_MCC.lncRNA'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0982 MCC (1-shot; macro average: unweighted mean of the 13 category MCCs) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (1-shot) lit-genomics-20261011-geneb-protocol-1shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.1shot, model 'dnabert2-no-flashattention', key 'macro_MCC'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.119 MCC (1-shot; micro average: mean over all 100 tasks) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (1-shot) lit-genomics-20261011-geneb-protocol-1shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.1shot, model 'dnabert2-no-flashattention', key 'micro_MCC'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0188 MCC (1-shot; category 'Mouse Enh.') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (1-shot) lit-genomics-20261011-geneb-protocol-1shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.1shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Mouse Enh.'
Configuration: dnabert2 (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.24 MCC (1-shot; category 'Promoters') unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source dnabert2 on GENEB (1-shot) lit-genomics-20261011-geneb-protocol-1shot Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.1shot, model 'dnabert2-no-flashattention', key 'cat_MCC.Promoters'

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GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · Original source · Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22)

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-geneb-config-dnabert2-no-flashattention

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: dnabert2-no-flashattention
foundation model eligible: true
parameters: 117000000 parameters as listed; frozen embeddings; leaderboard display name 'dnabert2'
access reuse: Public checkpoint as named on the leaderboard
version: dnabert2-no-flashattention
source locator: leaderboard.json data.full row model 'dnabert2-no-flashattention'
provenance note: dnabert2-no-flashattention as evaluated on the GENEB leaderboard.

Related records

configuration of: DNABERT-2
system: dnabert2 on GENEB (10-shot)
system: dnabert2 on GENEB (1-shot)
system: dnabert2 on GENEB (full training data)

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