Evaluation

gena-lm-bert-large-t2t on GENEB (full training data)

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, full training data, MCC aggregates · Dataset: GENEB 100 tasks

Sorted by MCC (full training data; 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 (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)
gena-lm-bert-large-t2t (GENEB leaderboard)Evaluation	0.645	0.866	0.207	0.488	0.468	0.267	0.615	0.745	0.426	0.693	0.55	0.638	0.569	0.552	0.533

All 15 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: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.645 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.Chromatin Acc.'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.866 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.Coding/NC'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.207 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.DNA Methyl.'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.488 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.Enhancers'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.468 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.Histone Mod.'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.267 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.lncRNA'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.552 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'macro_MCC'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.533 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'micro_MCC'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.615 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.Mouse Enh.'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.745 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.Promoters'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.426 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.Regulatory'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.693 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.Species Clf.'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.55 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.Splice Sites'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.638 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.TF Binding'
Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.569 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 gena-lm-bert-large-t2t 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 'gena-lm-bert-large-t2t', key 'cat_MCC.Virus/Phage'

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Evaluation procedure

GENEB leaderboard, full training data, MCC aggregates

Configuration: gena-lm-bert-large-t2t (GENEB leaderboard)
Protocol: GENEB leaderboard, full training data, 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-full
dataset version: Not reported
split: full training data
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: full training data

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

Reproduction

Split: full training data
Adaptation: Logistic-regression probe on frozen embeddings
Scoring implementation: MCC

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Evidence

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Evidence table

Inspect claims, sources and review details

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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.full, model 'gena-lm-bert-large-t2t' 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.full, model 'gena-lm-bert-large-t2t' 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 full training data Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.full, model 'gena-lm-bert-large-t2t' 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.full, model 'gena-lm-bert-large-t2t' 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.full, model 'gena-lm-bert-large-t2t' 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.full, model 'gena-lm-bert-large-t2t' 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.full, model 'gena-lm-bert-large-t2t' 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-full Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.full, model 'gena-lm-bert-large-t2t' 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 full training data Context-only references	GENEB leaderboard (leaderboard.json, 13 task-type aggregates) Original source ↗ leaderboard.json data.full, model 'gena-lm-bert-large-t2t' 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.full, model 'gena-lm-bert-large-t2t' 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)

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-geneb-eval-gena-lm-bert-large-t2t-full

areas: dna-genomes
contexts: research
origin: independent_paper
protocol: lit-genomics-20261011-geneb-protocol-full
version: Primary source as retrieved 2026-10-11
comparison: protocol id: lit-genomics-20261011-geneb-protocol-full; dataset version: Not reported; split: full training data; 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: full training data
source locator: leaderboard.json data.full, model 'gena-lm-bert-large-t2t'
missing metadata: comparison.dataset version: reason: unreported
limitations: Leaderboard entry status: 'official' (official=True).

Related records

system: gena-lm-bert-large-t2t (GENEB leaderboard)
assessment: GENEB leaderboard, full training data, MCC aggregates
data: GENEB 100 tasks
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.Chromatin Acc.
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.Coding/NC
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.DNA Methyl.
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.Enhancers
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.Histone Mod.
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.lncRNA
evaluation: gena-lm-bert-large-t2t GENEB full macro_MCC
evaluation: gena-lm-bert-large-t2t GENEB full micro_MCC
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.Mouse Enh.
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.Promoters
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.Regulatory
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.Species Clf.
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.Splice Sites
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.TF Binding
evaluation: gena-lm-bert-large-t2t GENEB full cat_MCC.Virus/Phage

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