Protocol

BEELINE 2020 Figure 2 · BFC · {}

Source-specific evaluation. Input conditions: {}. No equivalence to other releases, protocols or model families is inferred.

12 evaluations · 24 metric rows

Published comparisons

Each figure keeps its source, protocol, dataset and metric together. Results from different protocols are shown separately, without a pooled ranking.

Comparison and metric

BEELINE 2020 Figure 2 · BFC · {}: AUPRC Ratio

AUPRC Ratio (ratio) · Higher values are better for this metric.

Complete selected source table is retained across source-order panels. These point estimates do not establish statistical significance or a universal ranking.

Evaluation protocol · BFC

SINCERITIES · Configuration · Author-reported evaluation3.505301111
SCRIBE · Configuration · Author-reported evaluation2.71619574
SINGE · Configuration · Author-reported evaluation2.047176068
PPCOR · Configuration · Author-reported evaluation2.573910046
PIDC · Configuration · Author-reported evaluation2.181970548
GENIE3 · Configuration · Author-reported evaluation2.040091735
LEAP · Configuration · Author-reported evaluation2.041717081
GRNBOOST2 · Configuration · Author-reported evaluation2.236588969
GRISLI · Configuration · Author-reported evaluation2.296901484
GRNVBEM · Configuration · Author-reported evaluation2.160471895
SCNS · Configuration · Author-reported evaluation1.29608017
SCODE · Configuration · Author-reported evaluation1.045003187

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 3, column 6 through Figure 2 source CSV row 14, column 6

Values, uncertainty and evidence

AUPRC Ratio: original source values
Tested entity	Printed value	Uncertainty	Evidence
SINCERITIES · Configuration	3.505301111 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 3, column 6
SCRIBE · Configuration	2.71619574 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 4, column 6
SINGE · Configuration	2.047176068 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 5, column 6
PPCOR · Configuration	2.573910046 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 6, column 6
PIDC · Configuration	2.181970548 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 7, column 6
GENIE3 · Configuration	2.040091735 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 8, column 6
LEAP · Configuration	2.041717081 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 9, column 6
GRNBOOST2 · Configuration	2.236588969 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 10, column 6
GRISLI · Configuration	2.296901484 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 11, column 6
GRNVBEM · Configuration	2.160471895 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 12, column 6
SCNS · Configuration	1.29608017 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 13, column 6
SCODE · Configuration	1.045003187 ratio	status: unreported	Author-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 14, column 6

Scope and limitations

Source-specific evaluation. Input conditions: {}. No equivalence to other releases, protocols or model families is inferred.
Across-dataset stability is median pairwise top-k edge-set Jaccard index (paper Online Methods), not Spearman correlation. Not an independent experimental run.
Missing source cells and quarantined conflicts are recorded in acquisition and audit tables. Per-result scoring denominators may be unreported.

Source transcription and grouping reviewed by automated source review on 2026-09-19. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-19-eb6149e5d766 · 12 evaluations · 24 metric rows. Different protocols are not a single leaderboard. Charts retain each source table’s protocol and dataset.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
SCNS · BEELINE 2020 Figure 2 · BFC Configuration: SCNSProtocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.789473684 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 13, column 12 Source checking is not independent reproduction.
1.29608017 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 13, column 6 Source checking is not independent reproduction.
SCODE · BEELINE 2020 Figure 2 · BFC Configuration: SCODEProtocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
1.045003187 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 14, column 6 Source checking is not independent reproduction.
0.428571429 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 14, column 12 Source checking is not independent reproduction.
GRNBOOST2 · BEELINE 2020 Figure 2 · BFC Configuration: GRNBOOST2Protocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.666666667 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 10, column 12 Source checking is not independent reproduction.
2.236588969 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 10, column 6 Source checking is not independent reproduction.
SCRIBE · BEELINE 2020 Figure 2 · BFC Configuration: SCRIBEProtocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.25 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 4, column 12 Source checking is not independent reproduction.
2.71619574 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 4, column 6 Source checking is not independent reproduction.
GRNVBEM · BEELINE 2020 Figure 2 · BFC Configuration: GRNVBEMProtocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
2.160471895 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 12, column 6 Source checking is not independent reproduction.
0.461309524 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 12, column 12 Source checking is not independent reproduction.
SINGE · BEELINE 2020 Figure 2 · BFC Configuration: SINGEProtocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
2.047176068 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 5, column 6 Source checking is not independent reproduction.
0.25 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 5, column 12 Source checking is not independent reproduction.
PPCOR · BEELINE 2020 Figure 2 · BFC Configuration: PPCORProtocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
2.573910046 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 6, column 6 Source checking is not independent reproduction.
0.777777778 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 6, column 12 Source checking is not independent reproduction.
PIDC · BEELINE 2020 Figure 2 · BFC Configuration: PIDCProtocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
2.181970548 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 7, column 6 Source checking is not independent reproduction.
0.777777778 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 7, column 12 Source checking is not independent reproduction.
LEAP · BEELINE 2020 Figure 2 · BFC Configuration: LEAPProtocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.875 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 9, column 12 Source checking is not independent reproduction.
2.041717081 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 9, column 6 Source checking is not independent reproduction.
SINCERITIES · BEELINE 2020 Figure 2 · BFC Configuration: SINCERITIESProtocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
3.505301111 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 3, column 6 Source checking is not independent reproduction.
0.363636364 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 3, column 12 Source checking is not independent reproduction.
GRISLI · BEELINE 2020 Figure 2 · BFC Configuration: GRISLIProtocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
2.296901484 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 11, column 6 Source checking is not independent reproduction.
0.363636364 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 11, column 12 Source checking is not independent reproduction.
GENIE3 · BEELINE 2020 Figure 2 · BFC Configuration: GENIE3Protocol: BEELINE 2020 Figure 2 · BFC · {}Dataset subset: BFC BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.875 Stability Across Datasets Unit: fraction · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 8, column 12 Source checking is not independent reproduction.
2.040091735 AUPRC Ratio Unit: ratio · Direction: higher Aggregation: Median across source-described simulation datasets	Uncertainty: status: unreported Scored: Not reported · Eligible: Not reported	source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 2 source CSV row 8, column 6 Source checking is not independent reproduction.

Overview

Source-specific evaluation. Input conditions: {}. No equivalence to other releases, protocols or model families is inferred.

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

Evaluation design

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

Benchmarks

BEELINE

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

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Run instructions

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

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 2026-09-19-eb6149e5d766
Property and statement	Original source and location	Review and provenance
Relationship: part of discovery-benchmark-beeline Individual claims	BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 Original source ↗ Figure 2 source CSV row 3, column 6 Version: 10.1038/s41592-019-0690-6 source data published 2020 Retrieved: 2026-09-19	source checked ai assisted source review · 2026-09-19 Audit details Field: `links:part_of:discovery-benchmark-beeline` Claim: acquired-membership-3c846ae60d006c90f703 Source artifact SHA-256: `21df5e45c94decf352af1861340e2ac4052c477a9c173b643dcfcd146fffe506` Hash scope: Exact downloaded bytes, before optional gzip storage Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

Release 2026-09-19-eb6149e5d766 · Record review: discovered

1 source records and release history

BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Original source · 10.1038/s41592-019-0690-6 source data published 2020

Download this release

Technical metadata and extraction receipts

Stable ID: acquired-protocol-562a238b609a61077d81

source locator: Figure 2 source CSV row 3, column 6
procedure: BEELINE 2020 Figure 2
comparison panels: id: acquired-figure-809d4b699617a54afcae; title: BEELINE 2020 Figure 2 · BFC · {}: AUPRC Ratio; protocol id: acquired-protocol-562a238b609a61077d81; dataset id: acquired-dataset-03bede40fb43bb3fe678; metric: AUPRC Ratio; unit: ratio; direction: higher; result ids: acquired-result-a3505c3d5dde69831256; acquired-result-b603917eea83bc05c4ef; acquired-result-50c2a1627cacdb645c97; acquired-result-51e569bcc28676c02d15; acquired-result-8b3af40048db9aa15e9a; acquired-result-d76ac532632644606823; acquired-result-c2d6a26b7e4f5c7d6c4e; acquired-result-ffbd9f18c83667f4a101; acquired-result-a76862c654436e096b16; acquired-result-2942d0d08d5febcef1ae; acquired-result-8d2531e01889b9adeb7d; acquired-result-1538239885749a6c1ee1; source ids: acquired-source-0f6c059ffdc338b70a5c; source locator: Figure 2 source CSV row 3, column 6 through Figure 2 source CSV row 14, column 6; context: Complete selected source table is retained across source-order panels. These point estimates do not establish statistical significance or a universal ranking.; caveats: Source-specific evaluation. Input conditions: {}. No equivalence to other releases, protocols or model families is inferred.; Across-dataset stability is median pairwise top-k edge-set Jaccard index (paper Online Methods), not Spearman correlation. Not an independent experimental run.; Missing source cells and quarantined conflicts are recorded in acquisition and audit tables. Per-result scoring denominators may be unreported.; review: method: automated_source_review; date: 2026-09-19; id: acquired-figure-f15516627d2e2bcfae1e; title: BEELINE 2020 Figure 2 · BFC · {}: Stability Across Datasets; protocol id: acquired-protocol-562a238b609a61077d81; dataset id: acquired-dataset-03bede40fb43bb3fe678; metric: Stability Across Datasets; unit: fraction; direction: higher; result ids: acquired-result-bae39edabd1f52d2ae05; acquired-result-1ed9a2ca476182b0febe; acquired-result-d97cce85e07fb6174ea0; acquired-result-febaab96b6c227530147; acquired-result-9afeb46beb7a67db0852; acquired-result-c6eb2cbf84d6bed063ef; acquired-result-9220d19d10245d9937d1; acquired-result-1cae0aeeef290ab03e68; acquired-result-c38c823e03e2c933aa28; acquired-result-697b1abf8313e9230ebd; acquired-result-10c9639a85a59478e170; acquired-result-94b29dbec947666b45a5; source ids: acquired-source-0f6c059ffdc338b70a5c; source locator: Figure 2 source CSV row 3, column 12 through Figure 2 source CSV row 14, column 12; context: Complete selected source table is retained across source-order panels. These point estimates do not establish statistical significance or a universal ranking.; caveats: Source-specific evaluation. Input conditions: {}. No equivalence to other releases, protocols or model families is inferred.; Across-dataset stability is median pairwise top-k edge-set Jaccard index (paper Online Methods), not Spearman correlation. Not an independent experimental run.; Missing source cells and quarantined conflicts are recorded in acquisition and audit tables. Per-result scoring denominators may be unreported.; review: method: automated_source_review; date: 2026-09-19
scope limitations: Across-dataset stability is median pairwise top-k edge-set Jaccard index (paper Online Methods), not Spearman correlation. Not an independent experimental run.

Related records

part of: BEELINE
benchmark: SCODE · BEELINE 2020 Figure 2 · BFC
benchmark: PIDC · BEELINE 2020 Figure 2 · BFC
benchmark: GENIE3 · BEELINE 2020 Figure 2 · BFC
benchmark: GRISLI · BEELINE 2020 Figure 2 · BFC
benchmark: LEAP · BEELINE 2020 Figure 2 · BFC
benchmark: GRNVBEM · BEELINE 2020 Figure 2 · BFC
benchmark: SINGE · BEELINE 2020 Figure 2 · BFC
benchmark: GRNBOOST2 · BEELINE 2020 Figure 2 · BFC
benchmark: SCRIBE · BEELINE 2020 Figure 2 · BFC
benchmark: SINCERITIES · BEELINE 2020 Figure 2 · BFC
benchmark: SCNS · BEELINE 2020 Figure 2 · BFC
benchmark: PPCOR · BEELINE 2020 Figure 2 · BFC
subject: BEELINE 2020 Figure 2: benchmark membership

Suggest a correction