Protocol

GENEB leaderboard, full training data, MCC aggregates

GENEB probing of frozen embeddings, full training data regime.

Overview

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41 recorded evaluations, 615 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

41 evaluations · 615 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.562 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.Chromatin Acc.'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.792 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.Coding/NC'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.211 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.DNA Methyl.'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.446 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.Enhancers'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.475 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.Histone Mod.'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.336 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.lncRNA'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.497 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'macro_MCC'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.496 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'micro_MCC'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.418 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.Mouse Enh.'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.693 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.Promoters'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.433 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.Regulatory'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.697 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.Species Clf.'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.455 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.Splice Sites'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.462 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.TF Binding'
Configuration: agro-NT-1b (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.48 MCC (full training data; 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 agro-NT-1b on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'agro-nucleotide-transformer-1b', key 'cat_MCC.Virus/Phage'
Configuration: BioFM-265M (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.402 MCC (full training data; 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 BioFM-265M on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'BioFM-265M', key 'cat_MCC.Chromatin Acc.'
Configuration: BioFM-265M (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.783 MCC (full training data; 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 BioFM-265M on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'BioFM-265M', key 'cat_MCC.Coding/NC'
Configuration: BioFM-265M (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.275 MCC (full training data; 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 BioFM-265M on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'BioFM-265M', key 'cat_MCC.DNA Methyl.'
Configuration: BioFM-265M (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.275 MCC (full training data; 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 BioFM-265M on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'BioFM-265M', key 'cat_MCC.Enhancers'
Configuration: BioFM-265M (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.296 MCC (full training data; 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 BioFM-265M on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'BioFM-265M', key 'cat_MCC.Histone Mod.'
Configuration: BioFM-265M (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	-0.0184 MCC (full training data; 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 BioFM-265M on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'BioFM-265M', key 'cat_MCC.lncRNA'
Configuration: BioFM-265M (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.342 MCC (full training data; 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 BioFM-265M on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'BioFM-265M', key 'macro_MCC'
Configuration: BioFM-265M (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.336 MCC (full training data; 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 BioFM-265M on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'BioFM-265M', key 'micro_MCC'
Configuration: BioFM-265M (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.344 MCC (full training data; 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 BioFM-265M on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'BioFM-265M', key 'cat_MCC.Mouse Enh.'
Configuration: BioFM-265M (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.502 MCC (full training data; 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 BioFM-265M on GENEB (full training data) lit-genomics-20261011-geneb-protocol-full Aggregation: Not reported GENEB leaderboard (leaderboard.json, 13 task-type aggregates) · leaderboard.json data.full, model 'BioFM-265M', key 'cat_MCC.Promoters'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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External evaluations: 40
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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-protocol-full

areas: dna-genomes
contexts: research
protocol: Logistic-regression probe (max_iter=1000) on frozen embeddings, trained per task in the full training data regime; MCC aggregated as the micro average over all 100 tasks, the macro average (unweighted mean of the 13 category MCCs) and per category.
version: Leaderboard at commit 9642d481e40c
metric: matthews-correlation-coefficient
metric direction: higher
unit: unitless
limitations: Leaderboard aggregates; per-task values not extracted.
source locator: leaderboard.json data.full

Related records

part of: GENEB leaderboard
uses data: GENEB 100 tasks
assessment: agro-NT-1b on GENEB (full training data)
assessment: BioFM-265M on GENEB (full training data)
assessment: Caduceus-PH-1k-256 on GENEB (full training data)
assessment: Caduceus-PS-131k-256 on GENEB (full training data)
assessment: deepgene on GENEB (full training data)
assessment: dna_gpt0.1b_h on GENEB (full training data)
assessment: dna_gpt3b_m on GENEB (full training data)
assessment: DNABERT-S on GENEB (full training data)
assessment: dnabert2 on GENEB (full training data)
assessment: eccdnamamba_weights on GENEB (full training data)
assessment: enformer-official-rough on GENEB (full training data)
assessment: evo-1-131k on GENEB (full training data)
assessment: gena-lm-bert on GENEB (full training data)
assessment: gena-lm-bert-t2t-multi on GENEB (full training data)
assessment: gena-lm-bert-large-t2t on GENEB (full training data)
assessment: GENERator-eukaryote-1.2b on GENEB (full training data)
assessment: GENERator-eukaryote-3b on GENEB (full training data)
assessment: GenomeOcean-4B on GENEB (full training data)
assessment: GenomeOcean-500M on GENEB (full training data)
assessment: genomics-fm on GENEB (full training data)
assessment: gpt2_gene_multi_v2_ft on GENEB (full training data)
assessment: gpt2_gene_v1 on GENEB (full training data)
assessment: GROVER on GENEB (full training data)
assessment: hyenadna-large-1m on GENEB (full training data)
assessment: hyenadna-medium-160k on GENEB (full training data)
assessment: JanusDNA_72_w on GENEB (full training data)
assessment: JanusDNA_72_wo on GENEB (full training data)
assessment: LucaOne-default-step36M on GENEB (full training data)
assessment: METAGENE-1 on GENEB (full training data)
assessment: MutBERT on GENEB (full training data)
assessment: NT-2.5B-MS on GENEB (full training data)
assessment: NT-v2-100m-MS on GENEB (full training data)
assessment: NT-v2-250m-MS on GENEB (full training data)
assessment: NT-v2-50m-3mer-MS on GENEB (full training data)
assessment: NT-v2-50m-MS on GENEB (full training data)
assessment: Omni-DNA-1B on GENEB (full training data)
assessment: Omni-DNA-300M on GENEB (full training data)
assessment: OmniNA-220m on GENEB (full training data)
assessment: PlantCaduceus_l32 on GENEB (full training data)
assessment: space on GENEB (full training data)
assessment: SpliceBERT 1024nt on GENEB (full training data)

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