Protocol

DNALONGBENCH Enhancer-target gene prediction (Table 3)

DNALONGBENCH ETGP: Enhancer-target gene prediction.

Overview

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5 recorded evaluations, 10 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

5 evaluations · 10 results. Different protocols are not a single leaderboard.

Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) · Dataset: DNALONGBENCH Enhancer-target gene prediction test set

Sorted by AUPRC (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	AUPRC	AUROC
ABC (DNALONGBENCH)Evaluation	0.407 (best in column)	0.926 (best in column)
Caduceus-Ph (DNALONGBENCH)Evaluation	0.38	0.826
Caduceus-PS (DNALONGBENCH)Evaluation	0.376	0.821
CNN (DNALONGBENCH, ETGP)Evaluation	0.31	0.797
HyenaDNA (DNALONGBENCH)Evaluation	0.249	0.828

All 10 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: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.38 AUPRC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ph on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'Caduceus-Ph', column 'AUPRC'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.826 AUROC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ph on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'Caduceus-Ph', column 'AUROC'
Configuration: Caduceus-PS (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.376 AUPRC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-PS on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'Caduceus-PS', column 'AUPRC'
Configuration: Caduceus-PS (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.821 AUROC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-PS on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'Caduceus-PS', column 'AUROC'
Configuration: CNN (DNALONGBENCH, ETGP)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.31 AUPRC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'CNN', column 'AUPRC'
Configuration: CNN (DNALONGBENCH, ETGP)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.797 AUROC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'CNN', column 'AUROC'
Configuration: ABC (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.407 AUPRC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Expert Model on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'Expert Model', column 'AUPRC'
Configuration: ABC (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.926 AUROC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Expert Model on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'Expert Model', column 'AUROC'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.249 AUPRC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'HyenaDNA', column 'AUPRC'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.828 AUROC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source HyenaDNA on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'HyenaDNA', column 'AUROC'

Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.

Methods and evaluation design

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Author-reported evaluations: 1
External evaluations: 4

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Sources and history

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DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Original source · Nature Communications 16, published 2025-11-18; PMC12627797 full-text XML

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-dnalongbench-protocol-etgp

areas: dna-genomes
contexts: research
protocol: Enhancer-target gene prediction; models trained or fine-tuned on the task training split and scored on the held-out test set; columns as printed in Table 3.
version: Nature Communications 2025
metric: auroc
metric direction: higher
unit: unitless
limitations: Single run per cell; no uncertainty printed.; Expert models differ by task and may use non-sequence inputs (ABC uses DNase-seq, H3K27ac and Hi-C).
source locator: Table 3; Methods

Related records

part of: DNALONGBENCH
uses data: DNALONGBENCH Enhancer-target gene prediction test set
assessment: Caduceus-Ph on DNALONGBENCH ETGP
assessment: Caduceus-PS on DNALONGBENCH ETGP
assessment: CNN on DNALONGBENCH ETGP
assessment: Expert Model on DNALONGBENCH ETGP
assessment: HyenaDNA on DNALONGBENCH ETGP

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