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ENCODE-rE2G (Gschwind et al. 2026)

ENCODE-rE2G (Gschwind et al. 2026) as evaluated in the cited comparison.

Overview

ENCODE-rE2G (Gschwind et al. 2026) as evaluated in the cited comparison.

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

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: ENCODE-rE2G (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)	0.556 auprc fraction · higher Uncertainty: 95% CI 0.467852411496632 to 0.631223913857611 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ENCODE-rE2G 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 3 (D3:F3); Dataset 'Held-out', Predictor 'ENCODE-rE2G', metric 'Weighted AUPRC'
Configuration: ENCODE-rE2G (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)	0.544 precision fraction · higher Uncertainty: 95% CI 0.473562214144615 to 0.614971149178317 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ENCODE-rE2G 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 9 (D9:F9); Dataset 'Held-out', Predictor 'ENCODE-rE2G', metric 'Weighted precision at threshold'
Configuration: ENCODE-rE2G (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)	0.599 recall fraction · higher Uncertainty: 95% CI 0.526506289907121 to 0.670411257697732 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ENCODE-rE2G 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 15 (D15:F15); Dataset 'Held-out', Predictor 'ENCODE-rE2G', metric 'Weighted recall at threshold'
Configuration: ENCODE-rE2G (Gschwind et al. 2026)	Protocol: Combined K562 CRISPR training pairs, weighted metrics (Gschwind et al. 2026 Supplementary Table 3) Dataset: MPRabc K562 CRISPRi benchmark	0.666 auprc fraction · higher Uncertainty: 95% CI 0.614835111980482 to 0.711557617708767 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ENCODE-rE2G 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 21 (D21:F21); Dataset 'Combined K562 (training)', Predictor 'ENCODE-rE2G', metric 'Weighted AUPRC'
Configuration: ENCODE-rE2G (Gschwind et al. 2026)	Protocol: Combined K562 CRISPR training pairs, weighted metrics (Gschwind et al. 2026 Supplementary Table 3) Dataset: MPRabc K562 CRISPRi benchmark	0.548 precision fraction · higher Uncertainty: 95% CI 0.502957160758294 to 0.58983971918054 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ENCODE-rE2G 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 27 (D27:F27); Dataset 'Combined K562 (training)', Predictor 'ENCODE-rE2G', metric 'Weighted precision at threshold'
Configuration: ENCODE-rE2G (Gschwind et al. 2026)	Protocol: Combined K562 CRISPR training pairs, weighted metrics (Gschwind et al. 2026 Supplementary Table 3) Dataset: MPRabc K562 CRISPRi benchmark	0.73 recall fraction · higher Uncertainty: 95% CI 0.68634462 to 0.77396333 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ENCODE-rE2G 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 33 (D33:F33); Dataset 'Combined K562 (training)', Predictor 'ENCODE-rE2G', metric 'Weighted recall at threshold'

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Sources and history

Release 2026-10-10-7fcc3e48a123 · Record review: source checked

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-encode-re2g

areas: dna-genomes
contexts: research
method types: supervised_machine_learning
reported name: ENCODE-rE2G (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)
parameters: DNase-only ENCODE-rE2G logistic regression model
source locator: Supplementary Table 3 'Held-out benchmarks', predictor 'ENCODE-rE2G'

Related records

configuration of: ENCODE-rE2G
system: ENCODE-rE2G on held-out CRISPR pairs, five cell types
system: ENCODE-rE2G on combined K562 CRISPR training pairs

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