Evaluation

NT-v2-50m-3mer-MS on GENEB (10-shot)

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 15 results. Different protocols are not a single leaderboard.

Protocol: GENEB leaderboard, 10-shot, MCC aggregates · Dataset: GENEB 100 tasks

Sorted by MCC (10-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	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)
NT-v2-50m-3mer-MS (GENEB leaderboard)Evaluation	0.481	0.587	0.0804	0.3	0.253	0.0526	0.171	0.545	0.161	0.564	0.129	0.242	0.147	0.286	0.293

All 15 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-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.481 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.Chromatin Acc.'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.587 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.Coding/NC'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0804 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.DNA Methyl.'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.3 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.Enhancers'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.253 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.Histone Mod.'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.0526 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.lncRNA'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.286 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'macro_MCC'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.293 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'micro_MCC'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.171 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.Mouse Enh.'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.545 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.Promoters'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.161 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.Regulatory'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.564 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.Species Clf.'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.129 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.Splice Sites'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.242 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.TF Binding'
Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)	Protocol: GENEB leaderboard, 10-shot, MCC aggregates Dataset: GENEB 100 tasks	0.147 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-v2-50m-3mer-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-v2-50m-3mer-multi-species', key 'cat_MCC.Virus/Phage'

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

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

GENEB leaderboard, 10-shot, MCC aggregates

Configuration: NT-v2-50m-3mer-MS (GENEB leaderboard)
Protocol: GENEB leaderboard, 10-shot, MCC aggregates
Dataset: GENEB 100 tasks

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: lit-genomics-20261011-geneb-protocol-10shot
dataset version: Not reported
split: 10-shot
population: 100 tasks
inputs: DNA sequence; frozen embeddings
adaptation: Logistic-regression probe on frozen embeddings
metric implementation: MCC
aggregation: micro, macro and per-category averages
budget: 10-shot

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: 10-shot
Adaptation: Logistic-regression probe on frozen embeddings
Scoring implementation: MCC

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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation Logistic-regression probe on frozen embeddings Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species' Version: Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22) Retrieved: 2026-10-11T01:42:40Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `7c8a9d985e7c2df24514f309bf6102e4f81d9da1b9afbb74856d87e78e01f738` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation micro, macro and per-category averages Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species' Version: Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22) Retrieved: 2026-10-11T01:42:40Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `7c8a9d985e7c2df24514f309bf6102e4f81d9da1b9afbb74856d87e78e01f738` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget 10-shot Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species' Version: Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22) Retrieved: 2026-10-11T01:42:40Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `7c8a9d985e7c2df24514f309bf6102e4f81d9da1b9afbb74856d87e78e01f738` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version Not reported Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species' Version: Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22) Retrieved: 2026-10-11T01:42:40Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `7c8a9d985e7c2df24514f309bf6102e4f81d9da1b9afbb74856d87e78e01f738` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs DNA sequence; frozen embeddings Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species' Version: Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22) Retrieved: 2026-10-11T01:42:40Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `7c8a9d985e7c2df24514f309bf6102e4f81d9da1b9afbb74856d87e78e01f738` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: metric implementation MCC Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species' Version: Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22) Retrieved: 2026-10-11T01:42:40Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `7c8a9d985e7c2df24514f309bf6102e4f81d9da1b9afbb74856d87e78e01f738` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: population 100 tasks Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species' Version: Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22) Retrieved: 2026-10-11T01:42:40Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `7c8a9d985e7c2df24514f309bf6102e4f81d9da1b9afbb74856d87e78e01f738` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: protocol id lit-genomics-20261011-geneb-protocol-10shot Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species' Version: Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22) Retrieved: 2026-10-11T01:42:40Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `7c8a9d985e7c2df24514f309bf6102e4f81d9da1b9afbb74856d87e78e01f738` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: split 10-shot Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species' Version: Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22) Retrieved: 2026-10-11T01:42:40Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `7c8a9d985e7c2df24514f309bf6102e4f81d9da1b9afbb74856d87e78e01f738` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 1 values Leaderboard entry status: 'official' (official=True). Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species' Version: Git commit 9642d481e40c0af23995dcd162b779613f789f97 (repository pushed 2026-08-22) Retrieved: 2026-10-11T01:42:40Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.limitations` Source artifact SHA-256: `7c8a9d985e7c2df24514f309bf6102e4f81d9da1b9afbb74856d87e78e01f738` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

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

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-geneb-eval-nucleotide-transformer-v2-50m-3mer-multi-species-10shot

areas: dna-genomes
contexts: research
origin: independent_paper
protocol: lit-genomics-20261011-geneb-protocol-10shot
version: Primary source as retrieved 2026-10-11
comparison: protocol id: lit-genomics-20261011-geneb-protocol-10shot; dataset version: Not reported; split: 10-shot; population: 100 tasks; inputs: DNA sequence; frozen embeddings; adaptation: Logistic-regression probe on frozen embeddings; metric implementation: MCC; aggregation: micro, macro and per-category averages; budget: 10-shot
source locator: leaderboard.json data.10shot, model 'nucleotide-transformer-v2-50m-3mer-multi-species'
missing metadata: comparison.dataset version: reason: unreported
limitations: Leaderboard entry status: 'official' (official=True).

Related records

system: NT-v2-50m-3mer-MS (GENEB leaderboard)
assessment: GENEB leaderboard, 10-shot, MCC aggregates
data: GENEB 100 tasks
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.Chromatin Acc.
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.Coding/NC
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.DNA Methyl.
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.Enhancers
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.Histone Mod.
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.lncRNA
evaluation: NT-v2-50m-3mer-MS GENEB 10shot macro_MCC
evaluation: NT-v2-50m-3mer-MS GENEB 10shot micro_MCC
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.Mouse Enh.
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.Promoters
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.Regulatory
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.Species Clf.
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.Splice Sites
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.TF Binding
evaluation: NT-v2-50m-3mer-MS GENEB 10shot cat_MCC.Virus/Phage

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