Evaluation

deepgene 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)
deepgene (GENEB leaderboard)Evaluation	0.593	0.723	0.144	0.419	0.392	0.156	0.337	0.656	0.362	0.684	0.275	0.472	0.382	0.43	0.424

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: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.593 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 deepgene 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 'deepgene', key 'cat_MCC.Chromatin Acc.'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.723 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 deepgene 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 'deepgene', key 'cat_MCC.Coding/NC'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.144 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 deepgene 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 'deepgene', key 'cat_MCC.DNA Methyl.'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.419 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 deepgene 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 'deepgene', key 'cat_MCC.Enhancers'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.392 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 deepgene 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 'deepgene', key 'cat_MCC.Histone Mod.'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.156 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 deepgene 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 'deepgene', key 'cat_MCC.lncRNA'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.43 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 deepgene 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 'deepgene', key 'macro_MCC'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.424 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 deepgene 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 'deepgene', key 'micro_MCC'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.337 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 deepgene 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 'deepgene', key 'cat_MCC.Mouse Enh.'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.656 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 deepgene 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 'deepgene', key 'cat_MCC.Promoters'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.362 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 deepgene 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 'deepgene', key 'cat_MCC.Regulatory'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.684 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 deepgene 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 'deepgene', key 'cat_MCC.Species Clf.'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.275 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 deepgene 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 'deepgene', key 'cat_MCC.Splice Sites'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.472 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 deepgene 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 'deepgene', key 'cat_MCC.TF Binding'
Configuration: deepgene (GENEB leaderboard)	Protocol: GENEB leaderboard, full training data, MCC aggregates Dataset: GENEB 100 tasks	0.382 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 deepgene 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 'deepgene', key 'cat_MCC.Virus/Phage'

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

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Evaluation procedure

GENEB leaderboard, full training data, MCC aggregates

Configuration: deepgene (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

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

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

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

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.full, model 'deepgene' 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 'deepgene' 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 'deepgene' 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 'deepgene' 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 'deepgene' 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 'deepgene' 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 'deepgene' 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 'deepgene' 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 'deepgene' 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 'deepgene' 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

How to read the evidence

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-deepgene-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 'deepgene'
missing metadata: comparison.dataset version: reason: unreported
limitations: Leaderboard entry status: 'official' (official=True).

Related records

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

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