Result

0.556 auprc

gschwind2026-heldout-encode-re2g-auprc auprc

Tested 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)
Procedure: regulatory-variant-20261009-protocol-gschwind2026-heldout-weighted
Evaluation: ENCODE-rE2G on held-out CRISPR pairs, five cell types
Coverage: Not reported scored / Not reported eligible
Uncertainty: 95% CI 0.467852411496632 to 0.631223913857611
Evidence: Author-reported evaluation · source checkedAn 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'

A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.

Reproduction

Split: Held out from training
Adaptation: Not reported
Scoring implementation: yardstick 1.2.0 weighted precision-recall; boot 1.3-28.1

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance
Reported result 0.556151043664563 Individual claims	An encyclopedia of human enhancer-gene regulatory interactions Original source ↗ Supplementary Table 3 'Held-out benchmarks', row 3 (D3:F3); Dataset 'Held-out', Predictor 'ENCODE-rE2G', metric 'Weighted AUPRC' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Nature 657(8130):179, published online 2026-07-15; PMC13471189 full-text XML Retrieved: 2026-10-09T21:03:18Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 author reported Audit details Deterministic parse of the pinned XLSX cell XML (extract/extract_regulatory_variant.py) with header row, dataset, predictor and metric labels asserted; printed_value is the shortest round-trip decimal of the stored double, raw_xml_value keeps the stored text. Pending independent review. Independent review 2026-10-09: value, interval or standard error, and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `df07ed8c37a62732ba0ae26b74a6c8bcb9b48540fefd03c064115d9a87a3b642` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `81f7f2a3c4379adfca9db362a3aa2c2a8b4121bed0a54337a747f9afeee85904` Extraction artifact
Reported result 0.556151043664563 Individual claims	Gschwind et al. 2026, Supplementary Table 3 Original source ↗ Supplementary Table 3 'Held-out benchmarks', row 3 (D3:F3); Dataset 'Held-out', Predictor 'ENCODE-rE2G', metric 'Weighted AUPRC' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Supplementary_Table_3.xlsx in 41586_2026_10781_MOESM3_ESM.zip (folder 2023-11-20318B-s3) inside the Europe PMC supplementaryFiles zip Retrieved: 2026-10-09T21:04:46Z	source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-09 author reported Audit details Deterministic parse of the pinned XLSX cell XML (extract/extract_regulatory_variant.py) with header row, dataset, predictor and metric labels asserted; printed_value is the shortest round-trip decimal of the stored double, raw_xml_value keeps the stored text. Pending independent review. Independent review 2026-10-09: value, interval or standard error, and identity match the source. Field: `attributes.printed_value` Source artifact SHA-256: `81f7f2a3c4379adfca9db362a3aa2c2a8b4121bed0a54337a747f9afeee85904` Hash scope: SHA-256 of the xlsx member. MOESM3 zip SHA-256 88eb6c5239019cbec55281b545a3b6e450e2a83384d067ca94a0974968428332; outer supplementaryFiles zip SHA-256 78dc8641d9c6861568465c274b80329f7046bf7a0145c2546deb422f9a2c0930 (assembled per request). Inspected artifact Extraction artifact SHA-256: `81f7f2a3c4379adfca9db362a3aa2c2a8b4121bed0a54337a747f9afeee85904` Extraction artifact

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Sources and history

Release 2026-10-10-6e93f504adfc · 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-result-gschwind2026-heldout-encode-re2g-auprc

metric: auprc
metric direction: higher
unit: fraction
printed value: 0.556151043664563
numeric value: 0.556151043664563
source locator: Supplementary Table 3 'Held-out benchmarks', row 3 (D3:F3); Dataset 'Held-out', Predictor 'ENCODE-rE2G', metric 'Weighted AUPRC'
review: method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Re-downloaded the Europe PMC supplementary zip; the MOESM3 zip and the Supplementary_Table_3.xlsx member matched their SHA-256. Read the cells with a separate stdlib OOXML reader written for this review (the extractor's scripts were not run). Checked raw text, printed and numeric value (shortest round-trip decimal), the Lower and Upper CI cells, metric and qualifier from column C, predictor, dataset and the linked configuration and protocol.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: 81f7f2a3c4379adfca9db362a3aa2c2a8b4121bed0a54337a747f9afeee85904; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13471189/supplementaryFiles; note: Deterministic parse of the pinned XLSX cell XML (extract/extract_regulatory_variant.py) with header row, dataset, predictor and metric labels asserted; printed_value is the shortest round-trip decimal of the stored double, raw_xml_value keeps the stored text. Pending independent review. Independent review 2026-10-09: value, interval or standard error, and identity match the source.
uncertainty: type: confidence_interval; printed: 0.467852411496632 to 0.631223913857611 (Lower CI, Upper CI columns); lower: 0.467852411496632; upper: 0.631223913857611; level: 0.95; method: bootstrap; resamples: 10000; source column: Lower CI; Upper CI
metric qualifier: weighted by estimated probability of a direct cis-effect
raw xml value: 0.55615104366456303

Related records

evaluation: ENCODE-rE2G on held-out CRISPR pairs, five cell types

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