Result

0.76 auprc

ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4): Supervised enhancer–gene linking, auprc

Tested pipeline: ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4)
Protocol: Supervised enhancer–gene linking (AlphaGenome paper)
Dataset subset: Supervised enhancer–gene linking: evaluated data subset
Procedure: Add the K562 RNA-seq input×gradient score to ENCODE-rE2G extended, rerun its full logistic-regression training pipeline and evaluate out-of-fold predictions.
Evaluation: ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4): Supervised enhancer–gene linking
Coverage: scored: unreported; eligible: unreported
Uncertainty: Not reported
Evidence: Author-reported evaluation · source checkedAlphaGenome Nature 2026 supplementary comparison tables · 'Suppl Table 4 Variant performan'!L18

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

Reproduction

Split: ENCODE-rE2G out-of-fold prediction/training pipeline; reuse the authors’ cross-validated comparison scores and rerun the feature-augmented pipeline. Exact fold assignments are not enumerated in this methods paragraph.
Adaptation: ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4)
Scoring implementation: Not reported

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.

Access requirements and official instructions: Supervised enhancer–gene linking (AlphaGenome paper)

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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Reported result 0.76 Individual claims	AlphaGenome Nature 2026 supplementary comparison tables Original source ↗ 'Suppl Table 4 Variant performan'!L18 Version: Nature version of record, 28 January 2026 Retrieved: 2026-09-17T06:31:06.887921+00:00	source checked OOXML extraction and separate automated primary-source review · 2026-09-17 author reported Audit details Checked against a second extraction. Fixed-format display and exact stored decimals preserved separately. No experiment rerun. Field: `attributes.printed_value` Source artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Hash scope: SHA-256 of exact retrieved original artifact bytes Format: xlsx Inspected artifact Extraction artifact SHA-256: `833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154` Extraction artifact

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: source checked

3 source records and release history

AlphaGenome Nature 2026 supplementary comparison tables · Original source · Nature version of record, 28 January 2026
AlphaGenome Nature 2026 supplementary methods · Original source · Supplement to Nature version of record, 28 January 2026; content hash pinned
alphagenome: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied

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Technical metadata and extraction receipts

Stable ID: alphagenome-2026-result-21401786b8288da1

areas: dna-genomes
printed value: 0.76
printed value basis: Canonical stored-number transcription of a General-format cell; visible spreadsheet precision depends on column width.
numeric value: 0.76
raw xml value: 0.76
workbook number format: General
metric: auprc
metric direction: higher
unit: dimensionless
aggregation: auPRC over labelled element–gene pairs, with separate distance-to-TSS strata in the paper.
uncertainty: Not reported
scored count: Not reported
eligible count: Not reported
source cells: 'Suppl Table 4 Variant performan'!L18
source locator: 'Suppl Table 4 Variant performan'!L18
review: method: OOXML extraction and separate automated primary-source review; date: 2026-09-17; artifact sha256: 833cb78b6ae6fe39415cfff296ac00c48d800326139f13eb307531a1cc133154; retrieval url: https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41586-025-10014-0/MediaObjects/41586_2025_10014_MOESM3_ESM.xlsx; note: Checked against a second extraction. Fixed-format display and exact stored decimals preserved separately. No experiment rerun.
missing metadata: uncertainty: unreported; scored count: unextracted; eligible count: unextracted; seeds: unreported
source warnings: None recorded

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evaluation: ENCODE e2g extended: ENCODE-rE2G extended logistic regression (paper Table 4): Supervised enhancer–gene linking

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