Configuration

dna_gpt3b_m (GENEB leaderboard)

dna_gpt3b_m: frozen embeddings; leaderboard display name 'dna_gpt3b_m'.

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)
dna_gpt3b_m (GENEB leaderboard)Evaluation	GENEB leaderboard, 1-shot, MCC aggregates	0.173	0.174	0.0332	0.169	0.113	0.0323	0.0626	0.355	0.111	0.26	0.0852	0.136	-0.00608	0.131	0.159	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
dna_gpt3b_m (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	0.522	0.692	0.0911	0.311	0.225	0.0435	0.229	0.55	0.167	0.513	0.208	0.318	0.137	0.308	0.299	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
dna_gpt3b_m (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	0.538	0.86	0.367	0.485	0.477	0.31	0.512	0.743	0.457	0.693	0.571	0.59	0.436	0.541	0.541

All 45 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.522 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Chromatin Acc.'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.692 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Coding/NC'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0911 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.DNA Methyl.'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.311 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Enhancers'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.225 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Histone Mod.'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0435 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.lncRNA'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.308 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'macro_MCC'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.299 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'micro_MCC'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.229 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Mouse Enh.'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.55 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Promoters'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.167 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Regulatory'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.513 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Species Clf.'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.208 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Splice Sites'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.318 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.TF Binding'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.137 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Virus/Phage'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.173 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Chromatin Acc.'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.174 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Coding/NC'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0332 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.DNA Methyl.'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.169 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Enhancers'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.113 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Histone Mod.'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0323 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.lncRNA'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.131 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'macro_MCC'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.159 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'micro_MCC'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0626 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 dna_gpt3b_m 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 'dna_gpt3b_m', key 'cat_MCC.Mouse Enh.'
Configuration: dna_gpt3b_m (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.355 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 dna_gpt3b_m 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 'dna_gpt3b_m', 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-dna-gpt3b-m

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: dna_gpt3b_m
foundation model eligible: true
parameters: 3000000000 parameters as listed; frozen embeddings; leaderboard display name 'dna_gpt3b_m'
access reuse: Public checkpoint as named on the leaderboard
version: dna_gpt3b_m
source locator: leaderboard.json data.full row model 'dna_gpt3b_m'
provenance note: dna_gpt3b_m as evaluated on the GENEB leaderboard.

Related records

configuration of: DNAGPT
system: dna_gpt3b_m on GENEB (10-shot)
system: dna_gpt3b_m on GENEB (1-shot)
system: dna_gpt3b_m on GENEB (full training data)

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