Configuration

NT-v2-250m-MS (GENEB leaderboard)

NT-v2-250m-MS, a configuration of Nucleotide Transformer v2: frozen embeddings; leaderboard display name 'NT-v2-250m-MS'.

3 evaluations · 45 results

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

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)
NT-v2-250m-MS (GENEB leaderboard)Evaluation	GENEB leaderboard, 1-shot, MCC aggregates	0.176	0.284	0.0159	0.159	0.0829	0.00862	0.0248	0.222	0.0692	0.21	0.0478	0.0202	0.0062	0.102	0.106	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
NT-v2-250m-MS (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	0.386	0.534	0.0411	0.288	0.261	0.0528	0.121	0.482	0.178	0.52	0.0802	0.125	0.144	0.247	0.263	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
NT-v2-250m-MS (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	0.652	0.812	0.339	0.469	0.468	0.337	0.486	0.722	0.457	0.747	0.47	0.537	0.482	0.537	0.524

All 45 result rows with coverage, uncertainty and sources

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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: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.386 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Chromatin Acc.'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.534 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Coding/NC'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0411 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.DNA Methyl.'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.288 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Enhancers'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.261 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Histone Mod.'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0528 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.lncRNA'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.247 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'macro_MCC'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.263 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'micro_MCC'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.121 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Mouse Enh.'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.482 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Promoters'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.178 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Regulatory'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.52 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Species Clf.'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0802 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Splice Sites'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.125 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.TF Binding'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.144 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Virus/Phage'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.176 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Chromatin Acc.'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.284 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Coding/NC'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0159 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.DNA Methyl.'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.159 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Enhancers'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0829 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Histone Mod.'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.00862 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.lncRNA'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.102 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'macro_MCC'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.106 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'micro_MCC'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0248 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', key 'cat_MCC.Mouse Enh.'
Configuration: NT-v2-250m-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 1-shot, MCC aggregates Dataset: GENEB 100 tasks	0.222 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 NT-v2-250m-MS 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 'nucleotide-transformer-v2-250m-multi-species', 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-nucleotide-transformer-v2-250m-multi-species

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: nucleotide-transformer-v2-250m-multi-species
foundation model eligible: true
parameters: 250000000 parameters as listed; frozen embeddings; leaderboard display name 'NT-v2-250m-MS'
access reuse: Public checkpoint as named on the leaderboard
version: nucleotide-transformer-v2-250m-multi-species
source locator: leaderboard.json data.full row model 'nucleotide-transformer-v2-250m-multi-species'
provenance note: nucleotide-transformer-v2-250m-multi-species as evaluated on the GENEB leaderboard.

Related records

configuration of: Nucleotide Transformer v2
system: NT-v2-250m-MS on GENEB (10-shot)
system: NT-v2-250m-MS on GENEB (1-shot)
system: NT-v2-250m-MS on GENEB (full training data)

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