Protocol

BEELINE 2020 Figure 2 · TF · {}

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 · TF · {}: 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 · TF

SINCERITIES · Configuration · Author-reported evaluation1.543158751
SCRIBE · Configuration · Author-reported evaluation1.385790893
SINGE · Configuration · Author-reported evaluation1.305317998
PPCOR · Configuration · Author-reported evaluation1.750816384
PIDC · Configuration · Author-reported evaluation1.91128518
GENIE3 · Configuration · Author-reported evaluation1.766796532
LEAP · Configuration · Author-reported evaluation1.738950975
GRNBOOST2 · Configuration · Author-reported evaluation1.617434265
GRISLI · Configuration · Author-reported evaluation1.198924083
GRNVBEM · Configuration · Author-reported evaluation1.270301649
SCNS · Configuration · Author-reported evaluation1.226074981
SCODE · Configuration · Author-reported evaluation1.304743806

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 7 through Figure 2 source CSV row 14, column 7

Values, uncertainty and evidence

AUPRC Ratio: original source values
Tested entity	Printed value	Uncertainty	Evidence
SINCERITIES · Configuration	1.543158751 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 7
SCRIBE · Configuration	1.385790893 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 7
SINGE · Configuration	1.305317998 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 7
PPCOR · Configuration	1.750816384 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 7
PIDC · Configuration	1.91128518 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 7
GENIE3 · Configuration	1.766796532 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 7
LEAP · Configuration	1.738950975 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 7
GRNBOOST2 · Configuration	1.617434265 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 7
GRISLI · Configuration	1.198924083 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 7
GRNVBEM · Configuration	1.270301649 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 7
SCNS · Configuration	1.226074981 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 7
SCODE · Configuration	1.304743806 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 7

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
PPCOR · BEELINE 2020 Figure 2 · TF Configuration: PPCORProtocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.718181818 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 13 Source checking is not independent reproduction.
1.750816384 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 7 Source checking is not independent reproduction.
PIDC · BEELINE 2020 Figure 2 · TF Configuration: PIDCProtocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.636363636 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 13 Source checking is not independent reproduction.
1.91128518 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 7 Source checking is not independent reproduction.
SCODE · BEELINE 2020 Figure 2 · TF Configuration: SCODEProtocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
1.304743806 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 7 Source checking is not independent reproduction.
0.545454545 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 13 Source checking is not independent reproduction.
GRNBOOST2 · BEELINE 2020 Figure 2 · TF Configuration: GRNBOOST2Protocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
1.617434265 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 7 Source checking is not independent reproduction.
0.7 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 13 Source checking is not independent reproduction.
SCNS · BEELINE 2020 Figure 2 · TF Configuration: SCNSProtocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.416666667 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 13 Source checking is not independent reproduction.
1.226074981 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 7 Source checking is not independent reproduction.
SCRIBE · BEELINE 2020 Figure 2 · TF Configuration: SCRIBEProtocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
1.385790893 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 7 Source checking is not independent reproduction.
0.307692308 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 13 Source checking is not independent reproduction.
GENIE3 · BEELINE 2020 Figure 2 · TF Configuration: GENIE3Protocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
1.766796532 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 7 Source checking is not independent reproduction.
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 8, column 13 Source checking is not independent reproduction.
SINGE · BEELINE 2020 Figure 2 · TF Configuration: SINGEProtocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
1.305317998 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 7 Source checking is not independent reproduction.
0.307692308 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 13 Source checking is not independent reproduction.
SINCERITIES · BEELINE 2020 Figure 2 · TF Configuration: SINCERITIESProtocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.307692308 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 13 Source checking is not independent reproduction.
1.543158751 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 7 Source checking is not independent reproduction.
GRISLI · BEELINE 2020 Figure 2 · TF Configuration: GRISLIProtocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.416666667 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 13 Source checking is not independent reproduction.
1.198924083 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 7 Source checking is not independent reproduction.
LEAP · BEELINE 2020 Figure 2 · TF Configuration: LEAPProtocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF 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 9, column 13 Source checking is not independent reproduction.
1.738950975 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 7 Source checking is not independent reproduction.
GRNVBEM · BEELINE 2020 Figure 2 · TF Configuration: GRNVBEMProtocol: BEELINE 2020 Figure 2 · TF · {}Dataset subset: TF BEELINE 2020 Figure 2 Author-reported evaluation · Evaluation metadata: discovered
0.53452381 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 13 Source checking is not independent reproduction.
1.270301649 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 7 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 7 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-bcd8db0965dd367f6c2b 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

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Technical metadata and extraction receipts

Stable ID: acquired-protocol-19f8c76e99a986094a6f

source locator: Figure 2 source CSV row 3, column 7
procedure: BEELINE 2020 Figure 2
comparison panels: id: acquired-figure-f096282362ff8aa692f8; title: BEELINE 2020 Figure 2 · TF · {}: AUPRC Ratio; protocol id: acquired-protocol-19f8c76e99a986094a6f; dataset id: acquired-dataset-52841d9a4fb051470230; metric: AUPRC Ratio; unit: ratio; direction: higher; result ids: acquired-result-d544b872cce5da4d2932; acquired-result-766a921559aed48e3dd7; acquired-result-7a1f3984719b0bdb9cff; acquired-result-f7913e727614878aceee; acquired-result-f587e6f2cb073b7f245b; acquired-result-781f18688726dcb16fd8; acquired-result-e793839bc8bc7098c0fc; acquired-result-3e9424399e8f5214f11a; acquired-result-db3ec8b413a9b70d6953; acquired-result-fd3e75015f9bcc3c92bb; acquired-result-f55e18907ffc0d5ac6bb; acquired-result-357907fc41c2b48e246d; source ids: acquired-source-0f6c059ffdc338b70a5c; source locator: Figure 2 source CSV row 3, column 7 through Figure 2 source CSV row 14, column 7; 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-46a2d4b1c70840fa3b86; title: BEELINE 2020 Figure 2 · TF · {}: Stability Across Datasets; protocol id: acquired-protocol-19f8c76e99a986094a6f; dataset id: acquired-dataset-52841d9a4fb051470230; metric: Stability Across Datasets; unit: fraction; direction: higher; result ids: acquired-result-81a92f5f3e58562dd7b4; acquired-result-975e798d30000e898a2d; acquired-result-cfb02903ef14139acb45; acquired-result-202d9ad07d7a6cdff2b7; acquired-result-31df73774ba80a302f26; acquired-result-cab69e5d11b11091fb12; acquired-result-d4112f9fec581c198fee; acquired-result-7f5d8fee44669d26a406; acquired-result-cf39d9075b5baf962cc2; acquired-result-e2ec943d4dff35b99efa; acquired-result-6e1eef16af9044da7f00; acquired-result-40676275b6b4c6f62637; source ids: acquired-source-0f6c059ffdc338b70a5c; source locator: Figure 2 source CSV row 3, column 13 through Figure 2 source CSV row 14, column 13; 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: LEAP · BEELINE 2020 Figure 2 · TF
benchmark: GRNVBEM · BEELINE 2020 Figure 2 · TF
benchmark: PIDC · BEELINE 2020 Figure 2 · TF
benchmark: SINCERITIES · BEELINE 2020 Figure 2 · TF
benchmark: GRNBOOST2 · BEELINE 2020 Figure 2 · TF
benchmark: SCRIBE · BEELINE 2020 Figure 2 · TF
benchmark: SCODE · BEELINE 2020 Figure 2 · TF
benchmark: PPCOR · BEELINE 2020 Figure 2 · TF
benchmark: GRISLI · BEELINE 2020 Figure 2 · TF
benchmark: GENIE3 · BEELINE 2020 Figure 2 · TF
benchmark: SCNS · BEELINE 2020 Figure 2 · TF
benchmark: SINGE · BEELINE 2020 Figure 2 · TF
subject: BEELINE 2020 Figure 2: benchmark membership

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