Protocol

DNALONGBENCH Contact map prediction (Table 4)

DNALONGBENCH CMP: Contact map prediction.

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

5 recorded evaluations, 30 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

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All evaluations

5 evaluations · 30 results. Different protocols are not a single leaderboard.

Protocol: DNALONGBENCH Contact map prediction (Table 4) · Dataset: DNALONGBENCH Contact map prediction test set

Sorted by Stratum adjusted correlation coefficient (average over CMP conditions as printed) (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	Stratum adjusted correlation coefficient (average over CMP conditions as printed)	Stratum adjusted correlation coefficient (GM12878)	Stratum adjusted correlation coefficient (H1hESC)	Stratum adjusted correlation coefficient (HCT116)	Stratum adjusted correlation coefficient (HFF)	Stratum adjusted correlation coefficient (IMR90)
Akita (DNALONGBENCH)Evaluation	0.23 (best in column)	0.227 (best in column)	0.247 (best in column)	0.21 (best in column)	0.258 (best in column)	0.21 (best in column)
Caduceus-Ph (DNALONGBENCH)Evaluation	0.133	0.101	0.13	0.145	0.153	0.138
Caduceus-PS (DNALONGBENCH)Evaluation	0.127	0.097	0.123	0.139	0.142	0.132
HyenaDNA (DNALONGBENCH)Evaluation	0.115	0.099	0.122	0.118	0.139	0.097
CNN (DNALONGBENCH, CMP)Evaluation	0.015	0.01	0.024	0.001	0.025	0.013

All 30 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.133 Stratum adjusted correlation coefficient (average over CMP conditions as printed) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'Avg'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.101 Stratum adjusted correlation coefficient (GM12878) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'GM12878'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.13 Stratum adjusted correlation coefficient (H1hESC) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'H1hESC'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.145 Stratum adjusted correlation coefficient (HCT116) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'HCT116'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.153 Stratum adjusted correlation coefficient (HFF) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'HFF'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.138 Stratum adjusted correlation coefficient (IMR90) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'IMR90'
Configuration: Caduceus-PS (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.127 Stratum adjusted correlation coefficient (average over CMP conditions as printed) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-PS', column 'Avg'
Configuration: Caduceus-PS (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.097 Stratum adjusted correlation coefficient (GM12878) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-PS', column 'GM12878'
Configuration: Caduceus-PS (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.123 Stratum adjusted correlation coefficient (H1hESC) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-PS', column 'H1hESC'
Configuration: Caduceus-PS (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.139 Stratum adjusted correlation coefficient (HCT116) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-PS', column 'HCT116'
Configuration: Caduceus-PS (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.142 Stratum adjusted correlation coefficient (HFF) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-PS', column 'HFF'
Configuration: Caduceus-PS (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.132 Stratum adjusted correlation coefficient (IMR90) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-PS', column 'IMR90'
Configuration: CNN (DNALONGBENCH, CMP)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.015 Stratum adjusted correlation coefficient (average over CMP conditions as printed) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'CNN', column 'Avg'
Configuration: CNN (DNALONGBENCH, CMP)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.01 Stratum adjusted correlation coefficient (GM12878) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'CNN', column 'GM12878'
Configuration: CNN (DNALONGBENCH, CMP)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.024 Stratum adjusted correlation coefficient (H1hESC) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'CNN', column 'H1hESC'
Configuration: CNN (DNALONGBENCH, CMP)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.001 Stratum adjusted correlation coefficient (HCT116) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'CNN', column 'HCT116'
Configuration: CNN (DNALONGBENCH, CMP)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.025 Stratum adjusted correlation coefficient (HFF) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'CNN', column 'HFF'
Configuration: CNN (DNALONGBENCH, CMP)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.013 Stratum adjusted correlation coefficient (IMR90) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'CNN', column 'IMR90'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.23 Stratum adjusted correlation coefficient (average over CMP conditions as printed) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'Avg'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.227 Stratum adjusted correlation coefficient (GM12878) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'GM12878'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.247 Stratum adjusted correlation coefficient (H1hESC) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'H1hESC'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.21 Stratum adjusted correlation coefficient (HCT116) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'HCT116'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.258 Stratum adjusted correlation coefficient (HFF) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'HFF'
Configuration: Akita (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.21 Stratum adjusted correlation coefficient (IMR90) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Expert Model', column 'IMR90'
Configuration: HyenaDNA (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.115 Stratum adjusted correlation coefficient (average over CMP conditions as printed) 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 CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'HyenaDNA', column 'Avg'

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

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Author-reported evaluations: 1
External evaluations: 4

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Evidence table

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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-cmp

areas: dna-genomes
contexts: research
protocol: Contact map prediction; models trained or fine-tuned on the task training split and scored on the held-out test set; columns as printed in Table 4.
version: Nature Communications 2025
metric: stratum-adjusted-correlation-coefficient
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 4; Methods

Related records

part of: DNALONGBENCH
uses data: DNALONGBENCH Contact map prediction test set
assessment: Caduceus-Ph on DNALONGBENCH CMP
assessment: Caduceus-PS on DNALONGBENCH CMP
assessment: CNN on DNALONGBENCH CMP
assessment: Expert Model on DNALONGBENCH CMP
assessment: HyenaDNA on DNALONGBENCH CMP

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