Configuration

ABC (DNALONGBENCH)

ABC: Expert model for ETGP: Activity-by-Contact model using DNase-seq, H3K27ac ChIP-seq and Hi-C inputs, not sequence only.

1 evaluation · 2 results

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Evaluations and results

1 evaluation · 2 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	0.926

All 2 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: 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'

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

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Evidence

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Evidence table

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2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statement	Original source and location	Review and provenance
Facets: method types 1 values conventional_pipeline Individual claims	DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks Original source ↗ DNALongBench Results: the expert model is ABC, "which incorporates DNase-seq, H3K27ac ChIP-seq data, and a Hi-C matrix"; MPRAbc Introduction: ABC is "a mathematical framework" combining activity and contact Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature Communications 16, published 2025-11-18; PMC12627797 full-text XML Retrieved: 2026-10-11T01:34:19Z	conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit details Correct the method type from supervised_machine_learning to conventional_pipeline (use-case baseline review 2026-10-12, table 2). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. DNALongBench does not say ABC has no training step; the locator was corrected to what the source prints, with MPRAbc for the form of the ABC score. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: `"[\"conventional_pipeline\"]"`. Claim record status: source_checked. Field: `facets.method_types` Claim: metadata-correction-tags-20261012-f8695fd337149b7221c4 Source artifact SHA-256: `0d7db21f2a843dda3ba703c53cd0abad12c9c795cfbcf4fd1bdc6c4a863fe41b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `0d7db21f2a843dda3ba703c53cd0abad12c9c795cfbcf4fd1bdc6c4a863fe41b` Extraction artifact
Facets: method types 1 values conventional_pipeline Individual claims	MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions Original source ↗ DNALongBench Results: the expert model is ABC, "which incorporates DNase-seq, H3K27ac ChIP-seq data, and a Hi-C matrix"; MPRAbc Introduction: ABC is "a mathematical framework" combining activity and contact Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC13232518 published article XML retrieved 2026-09-30 Retrieved: 2026-09-30T21:23:27Z	conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit details Correct the method type from supervised_machine_learning to conventional_pipeline (use-case baseline review 2026-10-12, table 2). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. DNALongBench does not say ABC has no training step; the locator was corrected to what the source prints, with MPRAbc for the form of the ABC score. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: `"[\"conventional_pipeline\"]"`. Claim record status: source_checked. Field: `facets.method_types` Claim: metadata-correction-tags-20261012-f8695fd337149b7221c4 Source artifact SHA-256: `7717b5605e01c9346bd04e9510f4d99dff8a05c7af0feb956a82184b4dd7ce46` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `0d7db21f2a843dda3ba703c53cd0abad12c9c795cfbcf4fd1bdc6c4a863fe41b` Extraction artifact

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Sources and history

Release 2026-10-23-5347695500ed · Record review: source checked

1 source record and release history

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-config-abc

areas: dna-genomes
contexts: research
method types: conventional_pipeline
reported name: Expert Model (ABC)
foundation model eligible: false
parameters: Expert model for ETGP: Activity-by-Contact model using DNase-seq, H3K27ac ChIP-seq and Hi-C inputs, not sequence only
access reuse: Not stated in the main text
source locator: Methods 'Expert model', 'CNN' and 'DNA Foundation Model'
missing metadata: version: reason: unreported; note: Checkpoint or release not printed beyond the model name
provenance note: ABC as evaluated in DNALONGBENCH.

Related records

configuration of: Activity-by-Contact (ABC)
system: Expert Model on DNALONGBENCH ETGP
subject: ABC (DNALONGBENCH): facets.method_types

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