rewirebio.iobenchmarks
Dataset

Enformer eQTL causal-variant dataset, Genomics Long-Range Benchmark version (Hegde et al. 2025)

Variant-centred sequences from the Enformer eQTL causal-variant dataset as distributed in InstaDeepAI/genomics-long-range-benchmark.

Evaluation results

3 evaluations · 8 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: DNABERT-2 117M, one layer pruned, fine-tuned to convergence (Hegde et al. 2025)Protocol: Fine-tuning wall time to convergence on the Enformer eQTL dataset (Hegde et al. 2025 Methods)
Dataset: Enformer eQTL causal-variant dataset, Genomics Long-Range Benchmark version (Hegde et al. 2025)
around 1 Runtime (Fine-tuning to convergence, average per pruned model)
hour · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

DNABERT-2 pruned models, fine-tuning time to convergence (Hegde et al. 2025)

gfm-guide-20261014-protocol-hegde-eqtl-finetune-convergence-time

Aggregation: Not reported

Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction · Methods paragraph 3: 'taking around 1 h per pruned model on average'
Configuration: NT 500M human reference, fine-tuned 5 epochs, unpruned (Hegde et al. 2025)Protocol: Fine-tuning and evaluation wall time, 5 epochs on the Enformer eQTL dataset (Hegde et al. 2025 Table A1)
Dataset: Enformer eQTL causal-variant dataset, Genomics Long-Range Benchmark version (Hegde et al. 2025)
8.49 Runtime (Evaluation on the eQTL test split after 5-epoch fine-tuning)
minute · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NT 500M human reference, 5-epoch fine-tuning time (Hegde et al. 2025 Table A1)

gfm-guide-20261014-protocol-hegde-eqtl-finetune-5-epochs-time

Aggregation: Not reported

Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction · Table A1, row seed 41, column 'Evaluation Time (Minutes)'
Configuration: NT 500M human reference, fine-tuned 5 epochs, unpruned (Hegde et al. 2025)Protocol: Fine-tuning and evaluation wall time, 5 epochs on the Enformer eQTL dataset (Hegde et al. 2025 Table A1)
Dataset: Enformer eQTL causal-variant dataset, Genomics Long-Range Benchmark version (Hegde et al. 2025)
8.51 Runtime (Evaluation on the eQTL test split after 5-epoch fine-tuning)
minute · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NT 500M human reference, 5-epoch fine-tuning time (Hegde et al. 2025 Table A1)

gfm-guide-20261014-protocol-hegde-eqtl-finetune-5-epochs-time

Aggregation: Not reported

Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction · Table A1, row seed 42, column 'Evaluation Time (Minutes)'
Configuration: NT 500M human reference, fine-tuned 5 epochs, unpruned (Hegde et al. 2025)Protocol: Fine-tuning and evaluation wall time, 5 epochs on the Enformer eQTL dataset (Hegde et al. 2025 Table A1)
Dataset: Enformer eQTL causal-variant dataset, Genomics Long-Range Benchmark version (Hegde et al. 2025)
8.49 Runtime (Evaluation on the eQTL test split after 5-epoch fine-tuning)
minute · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NT 500M human reference, 5-epoch fine-tuning time (Hegde et al. 2025 Table A1)

gfm-guide-20261014-protocol-hegde-eqtl-finetune-5-epochs-time

Aggregation: Not reported

Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction · Table A1, row seed 43, column 'Evaluation Time (Minutes)'
Configuration: NT 500M human reference, fine-tuned 5 epochs, unpruned (Hegde et al. 2025)Protocol: Fine-tuning and evaluation wall time, 5 epochs on the Enformer eQTL dataset (Hegde et al. 2025 Table A1)
Dataset: Enformer eQTL causal-variant dataset, Genomics Long-Range Benchmark version (Hegde et al. 2025)
7.53 Runtime (Fine-tuning, 5 epochs, unpruned model)
hour · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NT 500M human reference, 5-epoch fine-tuning time (Hegde et al. 2025 Table A1)

gfm-guide-20261014-protocol-hegde-eqtl-finetune-5-epochs-time

Aggregation: Not reported

Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction · Table A1, row seed 41, column 'Training Time (Hours)'
Configuration: NT 500M human reference, fine-tuned 5 epochs, unpruned (Hegde et al. 2025)Protocol: Fine-tuning and evaluation wall time, 5 epochs on the Enformer eQTL dataset (Hegde et al. 2025 Table A1)
Dataset: Enformer eQTL causal-variant dataset, Genomics Long-Range Benchmark version (Hegde et al. 2025)
7.5 Runtime (Fine-tuning, 5 epochs, unpruned model)
hour · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NT 500M human reference, 5-epoch fine-tuning time (Hegde et al. 2025 Table A1)

gfm-guide-20261014-protocol-hegde-eqtl-finetune-5-epochs-time

Aggregation: Not reported

Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction · Table A1, row seed 42, column 'Training Time (Hours)'
Configuration: NT 500M human reference, fine-tuned 5 epochs, unpruned (Hegde et al. 2025)Protocol: Fine-tuning and evaluation wall time, 5 epochs on the Enformer eQTL dataset (Hegde et al. 2025 Table A1)
Dataset: Enformer eQTL causal-variant dataset, Genomics Long-Range Benchmark version (Hegde et al. 2025)
7.48 Runtime (Fine-tuning, 5 epochs, unpruned model)
hour · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NT 500M human reference, 5-epoch fine-tuning time (Hegde et al. 2025 Table A1)

gfm-guide-20261014-protocol-hegde-eqtl-finetune-5-epochs-time

Aggregation: Not reported

Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction · Table A1, row seed 43, column 'Training Time (Hours)'
Configuration: NT 500M human reference, fine-tuned to convergence (Hegde et al. 2025)Protocol: Fine-tuning wall time to convergence on the Enformer eQTL dataset (Hegde et al. 2025 Methods)
Dataset: Enformer eQTL causal-variant dataset, Genomics Long-Range Benchmark version (Hegde et al. 2025)
approximately 19 Runtime (Fine-tuning to convergence, unpruned model)
hour · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

NT 500M human reference, fine-tuning time to convergence (Hegde et al. 2025)

gfm-guide-20261014-protocol-hegde-eqtl-finetune-convergence-time

Aggregation: Not reported

Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction · Methods paragraph 3: 'training to convergence on 2 × NVIDIA TITAN Xp GPUs took approximately 19 h'

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

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

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

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

6 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statementOriginal source and locationReview and provenance
Accession
https://huggingface.co/datasets/InstaDeepAI/genomics-long-range-benchmark (accessed 29 September 2025)
Context-only references
Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction

Original source ↗

Table 1; Methods paragraph 2; Data Availability Statement

Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML
Retrieved: 2026-10-14T12:48:26Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.accession

Source artifact SHA-256: 9ea68b688637b40f0aeced7c905822f6b14c352a3a935c61c407945f3d66ef47

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Population
Train split 44,655 benign and 44,405 pathogenic; test split 4,306 benign and 4,556 pathogenic (Table 1)
Context-only references
Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction

Original source ↗

Table 1; Methods paragraph 2; Data Availability Statement

Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML
Retrieved: 2026-10-14T12:48:26Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.population

Source artifact SHA-256: 9ea68b688637b40f0aeced7c905822f6b14c352a3a935c61c407945f3d66ef47

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Source location
Table 1; Methods paragraph 2; Data Availability Statement
Context-only references
Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction

Original source ↗

Table 1; Methods paragraph 2; Data Availability Statement

Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML
Retrieved: 2026-10-14T12:48:26Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.source_locator

Source artifact SHA-256: 9ea68b688637b40f0aeced7c905822f6b14c352a3a935c61c407945f3d66ef47

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Split
Benchmark train and test splits
Context-only references
Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction

Original source ↗

Table 1; Methods paragraph 2; Data Availability Statement

Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML
Retrieved: 2026-10-14T12:48:26Z

not individually reviewed

No individual claim review recorded

Audit details

Field: attributes.split

Source artifact SHA-256: 9ea68b688637b40f0aeced7c905822f6b14c352a3a935c61c407945f3d66ef47

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Description
Variant-centred sequences from the Enformer eQTL causal-variant dataset as distributed in InstaDeepAI/genomics-long-range-benchmark.
Context-only references
Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction

Original source ↗

Table 1; Methods paragraph 2; Data Availability Statement

Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML
Retrieved: 2026-10-14T12:48:26Z

not individually reviewed

No individual claim review recorded

Audit details

Field: description

Source artifact SHA-256: 9ea68b688637b40f0aeced7c905822f6b14c352a3a935c61c407945f3d66ef47

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Name
Enformer eQTL causal-variant dataset, Genomics Long-Range Benchmark version (Hegde et al. 2025)
Context-only references
Reaping the Fruits of LLM Pruning: Towards Small Language Models for Efficient Non-Coding Variant Effect Prediction

Original source ↗

Table 1; Methods paragraph 2; Data Availability Statement

Version: Genes 16(11):1358, 2025; PMC12652071 full-text XML
Retrieved: 2026-10-14T12:48:26Z

not individually reviewed

No individual claim review recorded

Audit details

Field: name

Source artifact SHA-256: 9ea68b688637b40f0aeced7c905822f6b14c352a3a935c61c407945f3d66ef47

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Sources and history

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

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: gfm-guide-20261014-data-hegde-enformer-eqtl

areas
dna-genomes
contexts
research
accession
https://huggingface.co/datasets/InstaDeepAI/genomics-long-range-benchmark (accessed 29 September 2025)
population
Train split 44,655 benign and 44,405 pathogenic; test split 4,306 benign and 4,556 pathogenic (Table 1)
split
Benchmark train and test splits
source locator
Table 1; Methods paragraph 2; Data Availability Statement
missing metadata
version: reason: unreported; note: No dataset revision; Methods give 88,717 training and 8,846 evaluation sequences, which differ from the Table 1 totals (89,060 and 8,862)
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