Benchmark

MPRabc K562 enhancer–gene evaluation

Source study/challenge grouping of the exact imported protocols. No claim that this intake implements or reproduces an executable benchmark.

6 evaluations · 10 results

Overview

Source study/challenge grouping of the exact imported protocols. No claim that this intake implements or reproduces an executable benchmark.

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

6 recorded evaluations, 10 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

6 evaluations · 10 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Activity-by-Contact (ABC) — K562 published comparison	Protocol: MPRabc K562 CRISPRi enhancer–gene evaluation Dataset: MPRabc K562 CRISPRi benchmark	0.612 (0.567–0.656) auprc fraction · higher Uncertainty: type: bootstrap_percentile_confidence_interval; level: 0.95; lower: 0.567; upper: 0.656; replicates: 10000 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source mprabc abc Not reported Aggregation: Not reported MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Results, Figure 2 comparison paragraph, Activity-by-Contact (ABC), auprc
Configuration: MPRabc — K562 published comparison	Protocol: MPRabc K562 CRISPRi enhancer–gene evaluation Dataset: MPRabc K562 CRISPRi benchmark	0.707 (0.663–0.746) auprc fraction · higher Uncertainty: type: bootstrap_percentile_confidence_interval; level: 0.95; lower: 0.663; upper: 0.746; replicates: 10000 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source mprabc full Not reported Aggregation: Not reported MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Table 3, MPRabc, auprc
Configuration: MPRabc — K562 published comparison	Protocol: MPRabc K562 CRISPRi enhancer–gene evaluation Dataset: MPRabc K562 CRISPRi benchmark	0.680 (0.637–0.724) precision-at-70-recall fraction · higher Uncertainty: type: bootstrap_percentile_confidence_interval; level: 0.95; lower: 0.637; upper: 0.724; replicates: 10000 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source mprabc full Not reported Aggregation: Not reported MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Table 3, MPRabc, precision-at-70-recall
Configuration: MPRabc megamap Hi-C — K562 published comparison	Protocol: MPRabc K562 CRISPRi enhancer–gene evaluation Dataset: MPRabc K562 CRISPRi benchmark	0.69 auprc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source mprabc megamap Not reported Aggregation: Not reported MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Results, Figure 2 comparison paragraph, MPRabc megamap Hi-C, auprc
Configuration: MPRabc (MPRALegNet only; no Sei) — K562 published comparison	Protocol: MPRabc K562 CRISPRi enhancer–gene evaluation Dataset: MPRabc K562 CRISPRi benchmark	0.686 (0.642–0.728) auprc fraction · higher Uncertainty: type: bootstrap_percentile_confidence_interval; level: 0.95; lower: 0.642; upper: 0.728; replicates: 10000 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source mprabc mpralegnet Not reported Aggregation: Not reported MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Table 3, MPRabc (MPRALegNet only; no Sei), auprc
Configuration: MPRabc (MPRALegNet only; no Sei) — K562 published comparison	Protocol: MPRabc K562 CRISPRi enhancer–gene evaluation Dataset: MPRabc K562 CRISPRi benchmark	0.655 (0.610–0.695) precision-at-70-recall fraction · higher Uncertainty: type: bootstrap_percentile_confidence_interval; level: 0.95; lower: 0.610; upper: 0.695; replicates: 10000 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source mprabc mpralegnet Not reported Aggregation: Not reported MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Table 3, MPRabc (MPRALegNet only; no Sei), precision-at-70-recall
Configuration: ENCODE-rE2G — K562 published comparison	Protocol: MPRabc K562 CRISPRi enhancer–gene evaluation Dataset: MPRabc K562 CRISPRi benchmark	0.634 (0.587–0.684) auprc fraction · higher Uncertainty: type: bootstrap_percentile_confidence_interval; level: 0.95; lower: 0.587; upper: 0.684; replicates: 10000 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source mprabc re2g Not reported Aggregation: Not reported MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Table 3, ENCODE-rE2G, auprc
Configuration: ENCODE-rE2G — K562 published comparison	Protocol: MPRabc K562 CRISPRi enhancer–gene evaluation Dataset: MPRabc K562 CRISPRi benchmark	0.543 (0.501–0.583) precision-at-70-recall fraction · higher Uncertainty: type: bootstrap_percentile_confidence_interval; level: 0.95; lower: 0.501; upper: 0.583; replicates: 10000 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source mprabc re2g Not reported Aggregation: Not reported MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Table 3, ENCODE-rE2G, precision-at-70-recall
Configuration: MPRabc (Sei only; no MPRALegNet) — K562 published comparison	Protocol: MPRabc K562 CRISPRi enhancer–gene evaluation Dataset: MPRabc K562 CRISPRi benchmark	0.707 (0.664–0.746) auprc fraction · higher Uncertainty: type: bootstrap_percentile_confidence_interval; level: 0.95; lower: 0.664; upper: 0.746; replicates: 10000 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source mprabc sei Not reported Aggregation: Not reported MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Table 3, MPRabc (Sei only; no MPRALegNet), auprc
Configuration: MPRabc (Sei only; no MPRALegNet) — K562 published comparison	Protocol: MPRabc K562 CRISPRi enhancer–gene evaluation Dataset: MPRabc K562 CRISPRi benchmark	0.678 (0.634–0.720) precision-at-70-recall fraction · higher Uncertainty: type: bootstrap_percentile_confidence_interval; level: 0.95; lower: 0.634; upper: 0.720; replicates: 10000 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source mprabc sei Not reported Aggregation: Not reported MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Table 3, MPRabc (Sei only; no MPRALegNet), precision-at-70-recall

Source checking is not independent reproduction. Release 2026-09-30-e37e3ab1284d.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Protocols

MPRabc K562 CRISPRi enhancer–gene evaluation

These source-backed links do not make different protocols or scores interchangeable.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

Baseline status by linked protocol

MPRabc K562 CRISPRi enhancer–gene evaluation · 0/2 roles measured

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-30-e37e3ab1284d. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

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MPRabc K562 CRISPRi enhancer–gene evaluation

Run instructions

No runnable recipe has been reviewed for this benchmark. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Evidence

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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.

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Claims, original sources and review scope · Release 2026-09-30-e37e3ab1284d
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Sources and history

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Release 2026-09-30-e37e3ab1284d · Record review: source checked

1 source records and release history

MPRA-informed modeling improves context-specific enhancer–gene regulatory interactions · Original source · PMC13232518 published article XML retrieved 2026-09-30

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Technical metadata and extraction receipts

Stable ID: ucc-research-benchmark-mprabc

entity level: suite
review: method: automated_source_review; actor: Codex research coverage worker; reviewed at: 2026-09-30T21:43:56Z; note: Primary-source table transcription and scope review; no independent reproduction or human scientific review.
source locator: Table 3; Benchmarking; Figure 2

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