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EPIraction (Gschwind et al. 2026)

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

Overview

EPIraction (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: EPIraction (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)	0.383 auprc fraction · higher Uncertainty: 95% CI 0.302549537433103 to 0.455764606497437 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EPIraction 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 4 (D4:F4); Dataset 'Held-out', Predictor 'EPIraction', metric 'Weighted AUPRC'
Configuration: EPIraction (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)	0.347 precision fraction · higher Uncertainty: 95% CI 0.292942536891562 to 0.401809875530837 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EPIraction 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 10 (D10:F10); Dataset 'Held-out', Predictor 'EPIraction', metric 'Weighted precision at threshold'
Configuration: EPIraction (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)	0.596 recall fraction · higher Uncertainty: 95% CI 0.525947724997951 to 0.666054834012973 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EPIraction 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 16 (D16:F16); Dataset 'Held-out', Predictor 'EPIraction', metric 'Weighted recall at threshold'
Configuration: EPIraction (Gschwind et al. 2026)	Protocol: Combined K562 CRISPR training pairs, weighted metrics (Gschwind et al. 2026 Supplementary Table 3) Dataset: MPRabc K562 CRISPRi benchmark	0.446 auprc fraction · higher Uncertainty: 95% CI 0.39383868 to 0.500921087804116 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EPIraction 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 22 (D22:F22); Dataset 'Combined K562 (training)', Predictor 'EPIraction', metric 'Weighted AUPRC'
Configuration: EPIraction (Gschwind et al. 2026)	Protocol: Combined K562 CRISPR training pairs, weighted metrics (Gschwind et al. 2026 Supplementary Table 3) Dataset: MPRabc K562 CRISPRi benchmark	0.381 precision fraction · higher Uncertainty: 95% CI 0.345706679909842 to 0.414719708782195 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EPIraction 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 28 (D28:F28); Dataset 'Combined K562 (training)', Predictor 'EPIraction', metric 'Weighted precision at threshold'
Configuration: EPIraction (Gschwind et al. 2026)	Protocol: Combined K562 CRISPR training pairs, weighted metrics (Gschwind et al. 2026 Supplementary Table 3) Dataset: MPRabc K562 CRISPRi benchmark	0.749 recall fraction · higher Uncertainty: 95% CI 0.705437423576133 to 0.791130313360929 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source EPIraction 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 34 (D34:F34); Dataset 'Combined K562 (training)', Predictor 'EPIraction', 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-epiraction

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: EPIraction (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 'EPIraction'

Related records

configuration of: EPIraction
subject: developer_overlap: regulatory-variant-20261009-config-gschwind2026-epiraction
system: EPIraction on held-out CRISPR pairs, five cell types
system: EPIraction on combined K562 CRISPR training pairs

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