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EpiMap (Gschwind et al. 2026)

EpiMap (Gschwind et al. 2026) as evaluated in the cited comparison.

Overview

EpiMap (Gschwind et al. 2026) as evaluated in the cited comparison.

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Evaluations and results

2 evaluations · 6 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: EpiMap (Gschwind et al. 2026)	Protocol: Held-out CRISPR enhancer-gene benchmark, weighted metrics, five cell types (Gschwind et al. 2026 Supplementary Table 3) Dataset: Held-out CRISPR enhancer-gene pairs in five cell types (Gschwind et al. 2026)	0.268 auprc fraction · higher Uncertainty: 95% CI 0.202767496369732 to 0.342972872868445 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EpiMap on held-out CRISPR pairs, five cell types regulatory-variant-20261009-protocol-gschwind2026-heldout-weighted Aggregation: Not reported An encyclopedia of human enhancer-gene regulatory interactions; Gschwind et al. 2026, Supplementary Table 3 · Supplementary Table 3 'Held-out benchmarks', row 5 (D5:F5); Dataset 'Held-out', Predictor 'EpiMap', metric 'Weighted AUPRC'
Configuration: EpiMap (Gschwind et al. 2026)	Protocol: Held-out CRISPR enhancer-gene benchmark, weighted metrics, five cell types (Gschwind et al. 2026 Supplementary Table 3) Dataset: Held-out CRISPR enhancer-gene pairs in five cell types (Gschwind et al. 2026)	0.292 precision fraction · higher Uncertainty: 95% CI 0.244244656893669 to 0.342593944957384 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EpiMap on held-out CRISPR pairs, five cell types regulatory-variant-20261009-protocol-gschwind2026-heldout-weighted Aggregation: Not reported An encyclopedia of human enhancer-gene regulatory interactions; Gschwind et al. 2026, Supplementary Table 3 · Supplementary Table 3 'Held-out benchmarks', row 11 (D11:F11); Dataset 'Held-out', Predictor 'EpiMap', metric 'Weighted precision at threshold'
Configuration: EpiMap (Gschwind et al. 2026)	Protocol: Held-out CRISPR enhancer-gene benchmark, weighted metrics, five cell types (Gschwind et al. 2026 Supplementary Table 3) Dataset: Held-out CRISPR enhancer-gene pairs in five cell types (Gschwind et al. 2026)	0.545 recall fraction · higher Uncertainty: 95% CI 0.471122984227133 to 0.616597040982763 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EpiMap on held-out CRISPR pairs, five cell types regulatory-variant-20261009-protocol-gschwind2026-heldout-weighted Aggregation: Not reported An encyclopedia of human enhancer-gene regulatory interactions; Gschwind et al. 2026, Supplementary Table 3 · Supplementary Table 3 'Held-out benchmarks', row 17 (D17:F17); Dataset 'Held-out', Predictor 'EpiMap', metric 'Weighted recall at threshold'
Configuration: EpiMap (Gschwind et al. 2026)	Protocol: Combined K562 CRISPR training pairs, weighted metrics (Gschwind et al. 2026 Supplementary Table 3) Dataset: MPRabc K562 CRISPRi benchmark	0.311 auprc fraction · higher Uncertainty: 95% CI 0.261110315175289 to 0.361017256946356 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EpiMap on combined K562 CRISPR training pairs regulatory-variant-20261009-protocol-gschwind2026-k562-training-weighted Aggregation: Not reported An encyclopedia of human enhancer-gene regulatory interactions; Gschwind et al. 2026, Supplementary Table 3 · Supplementary Table 3 'Held-out benchmarks', row 23 (D23:F23); Dataset 'Combined K562 (training)', Predictor 'EpiMap', metric 'Weighted AUPRC'
Configuration: EpiMap (Gschwind et al. 2026)	Protocol: Combined K562 CRISPR training pairs, weighted metrics (Gschwind et al. 2026 Supplementary Table 3) Dataset: MPRabc K562 CRISPRi benchmark	0.187 precision fraction · higher Uncertainty: 95% CI 0.166855358972052 to 0.2065905167216 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EpiMap on combined K562 CRISPR training pairs regulatory-variant-20261009-protocol-gschwind2026-k562-training-weighted Aggregation: Not reported An encyclopedia of human enhancer-gene regulatory interactions; Gschwind et al. 2026, Supplementary Table 3 · Supplementary Table 3 'Held-out benchmarks', row 29 (D29:F29); Dataset 'Combined K562 (training)', Predictor 'EpiMap', metric 'Weighted precision at threshold'
Configuration: EpiMap (Gschwind et al. 2026)	Protocol: Combined K562 CRISPR training pairs, weighted metrics (Gschwind et al. 2026 Supplementary Table 3) Dataset: MPRabc K562 CRISPRi benchmark	0.714 recall fraction · higher Uncertainty: 95% CI 0.669049563420841 to 0.757391291403457 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EpiMap on combined K562 CRISPR training pairs regulatory-variant-20261009-protocol-gschwind2026-k562-training-weighted Aggregation: Not reported An encyclopedia of human enhancer-gene regulatory interactions; Gschwind et al. 2026, Supplementary Table 3 · Supplementary Table 3 'Held-out benchmarks', row 35 (D35:F35); Dataset 'Combined K562 (training)', Predictor 'EpiMap', metric 'Weighted recall at threshold'

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Sources and history

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2 source records and release history

An encyclopedia of human enhancer-gene regulatory interactions · Original source · Nature 657(8130):179, published online 2026-07-15; PMC13471189 full-text XML
Gschwind et al. 2026, Supplementary Table 3 · Original source · Supplementary_Table_3.xlsx in 41586_2026_10781_MOESM3_ESM.zip (folder 2023-11-20318B-s3) inside the Europe PMC supplementaryFiles zip

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Technical metadata and extraction receipts

Stable ID: regulatory-variant-20261009-config-gschwind2026-epimap

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: EpiMap (Gschwind et al. 2026)
foundation model eligible: false
missing metadata: version: reason: unreported; note: Predictor version not printed in Supplementary Table 3; parameters are in Supplementary Table 1 (not read)
source locator: Supplementary Table 3 'Held-out benchmarks', predictor 'EpiMap'

Related records

configuration of: EpiMap enhancer-gene links
subject: developer_overlap: regulatory-variant-20261009-config-gschwind2026-epimap
system: EpiMap on held-out CRISPR pairs, five cell types
system: EpiMap on combined K562 CRISPR training pairs

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