| 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 checkedMethods, coverage and sourceDNABERT-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' |
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| 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 checkedMethods, coverage and sourceNT 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)' |
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| 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 checkedMethods, coverage and sourceNT 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)' |
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| 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 checkedMethods, coverage and sourceNT 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)' |
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| 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 checkedMethods, coverage and sourceNT 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)' |
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| 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 checkedMethods, coverage and sourceNT 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)' |
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| 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 checkedMethods, coverage and sourceNT 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)' |
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| 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 checkedMethods, coverage and sourceNT 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' |
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