rewire.it
Protocol

BEELINE 2020 Figure 4 · VSC · {}

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

12 evaluations · 36 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.

BEELINE 2020 Figure 4 · VSC · {}: 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 · VSC

  1. PIDC · Configuration · Author-reported evaluation2.723414782
  2. GENIE3 · Configuration · Author-reported evaluation2.756376658
  3. GRNBOOST2 · Configuration · Author-reported evaluation2.681333463
  4. PPCOR · Configuration · Author-reported evaluation2.142671976
  5. SCODE · Configuration · Author-reported evaluation1.340561819
  6. GRISLI · Configuration · Author-reported evaluation1.22323479
  7. SINGE · Configuration · Author-reported evaluation1.538039889
  8. SCNS · Configuration · Author-reported evaluation1.662311252
  9. LEAP · Configuration · Author-reported evaluation0.985424483
  10. SINCERITIES · Configuration · Author-reported evaluation1.040102538
  11. GRNVBEM · Configuration · Author-reported evaluation0.682233423
  12. SCRIBE · Configuration · Author-reported evaluation0.872725845

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 4 source CSV row 3, column 3 through Figure 4 source CSV row 14, column 3
Values, uncertainty and evidence
AUPRC Ratio: original source values
Tested entityPrinted valueUncertaintyEvidence
PIDC · Configuration2.723414782 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 3, column 3
GENIE3 · Configuration2.756376658 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 4, column 3
GRNBOOST2 · Configuration2.681333463 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 5, column 3
PPCOR · Configuration2.142671976 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 6, column 3
SCODE · Configuration1.340561819 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 7, column 3
GRISLI · Configuration1.22323479 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 8, column 3
SINGE · Configuration1.538039889 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 9, column 3
SCNS · Configuration1.662311252 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 10, column 3
LEAP · Configuration0.985424483 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 11, column 3
SINCERITIES · Configuration1.040102538 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 12, column 3
GRNVBEM · Configuration0.682233423 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 13, column 3
SCRIBE · Configuration0.872725845 ratiostatus: unreportedAuthor-reported evaluation · source checkedBEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 4 source CSV row 14, column 3
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 · 36 metric rows. Different protocols are not a single leaderboard. Charts retain each source table’s protocol and dataset.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
PPCOR · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

2.142671976 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 4 source CSV row 6, column 3

Source checking is not independent reproduction.

1.75 EPR Inhibition

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 4 source CSV row 6, column 15

Source checking is not independent reproduction.

1.75 Early Precision 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 4 source CSV row 6, column 7

Source checking is not independent reproduction.

SCRIBE · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

0.872725845 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 4 source CSV row 14, column 3

Source checking is not independent reproduction.

0.995555556 EPR Inhibition

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 4 source CSV row 14, column 15

Source checking is not independent reproduction.

0.995555556 Early Precision 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 4 source CSV row 14, column 7

Source checking is not independent reproduction.

PIDC · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

2.723414782 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 4 source CSV row 3, column 3

Source checking is not independent reproduction.

1.866666667 Early Precision 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 4 source CSV row 3, column 7

Source checking is not independent reproduction.

LEAP · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

0.622222222 Early Precision 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 4 source CSV row 11, column 7

Source checking is not independent reproduction.

0.622222222 EPR Inhibition

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 4 source CSV row 11, column 15

Source checking is not independent reproduction.

0.985424483 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 4 source CSV row 11, column 3

Source checking is not independent reproduction.

SINGE · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

1.515294118 Early Precision 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 4 source CSV row 9, column 7

Source checking is not independent reproduction.

1.538039889 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 4 source CSV row 9, column 3

Source checking is not independent reproduction.

SCODE · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

1.244444444 EPR Inhibition

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 4 source CSV row 7, column 15

Source checking is not independent reproduction.

1.340561819 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 4 source CSV row 7, column 3

Source checking is not independent reproduction.

1.244444444 Early Precision 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 4 source CSV row 7, column 7

Source checking is not independent reproduction.

SCNS · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

1.602631579 EPR Inhibition

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 4 source CSV row 10, column 15

Source checking is not independent reproduction.

1.662311252 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 4 source CSV row 10, column 3

Source checking is not independent reproduction.

1.602631579 Early Precision 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 4 source CSV row 10, column 7

Source checking is not independent reproduction.

SINCERITIES · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

0.995555556 Early Precision 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 4 source CSV row 12, column 7

Source checking is not independent reproduction.

GRNBOOST2 · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

2.737777778 Early Precision 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 4 source CSV row 5, column 7

Source checking is not independent reproduction.

2.681333463 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 4 source CSV row 5, column 3

Source checking is not independent reproduction.

GRNVBEM · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

0.510144928 Early Precision 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 4 source CSV row 13, column 7

Source checking is not independent reproduction.

GRISLI · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

1.132352941 Early Precision 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 4 source CSV row 8, column 7

Source checking is not independent reproduction.

GENIE3 · BEELINE 2020 Figure 4 · VSC

BEELINE 2020 Figure 4

Author-reported evaluation · Evaluation metadata: discovered

2.756376658 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 4 source CSV row 4, column 3

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

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 statementOriginal source and locationReview and provenance
Relationship: part of

discovery-benchmark-beeline

Individual claims
BEELINE: 10.1038/s41592-019-0690-6 source data published 2020

Original source ↗

Figure 4 source CSV row 3, column 3

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-9672535af65f380ccb6d

Source artifact SHA-256: 3582523c27176f7573e62fc3fa11843076568b9ce522e556cd2a6973029c90cb

Hash scope: Exact downloaded bytes, before optional gzip storage

Inspected artifact

Sources and history

View linked audit checks and correction history

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

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: acquired-protocol-37b5599b7d976211e8c1

source locator
Figure 4 source CSV row 3, column 3
procedure
BEELINE 2020 Figure 4
comparison panels
id: acquired-figure-4c911179177b3f930ca7; title: BEELINE 2020 Figure 4 · VSC · {}: AUPRC Ratio; protocol id: acquired-protocol-37b5599b7d976211e8c1; dataset id: acquired-dataset-caf90389169ff966e573; metric: AUPRC Ratio; unit: ratio; direction: higher; result ids: acquired-result-106d808f878c9a389099; acquired-result-8a2ac5807029b84a841a; acquired-result-a0cdbbe216e099f97e41; acquired-result-003e3111e0ee184b0278; acquired-result-6045b8dbada97fdf8a49; acquired-result-fe34ae3b788355446354; acquired-result-a072d97fd39d92a5c1b6; acquired-result-8f6f4df3a724b3592c15; acquired-result-6e98f9cc01c62f6931dd; acquired-result-b71fb3d8c25f528e8edf; acquired-result-d4b9b92f718dfffc0491; acquired-result-05cbb9e70d2faefb9a0f; source ids: acquired-source-3156602fda847ae943b4; source locator: Figure 4 source CSV row 3, column 3 through Figure 4 source CSV row 14, column 3; 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-5f67927a90b42c4a0655; title: BEELINE 2020 Figure 4 · VSC · {}: Early Precision Ratio; protocol id: acquired-protocol-37b5599b7d976211e8c1; dataset id: acquired-dataset-caf90389169ff966e573; metric: Early Precision Ratio; unit: ratio; direction: higher; result ids: acquired-result-96ee3a58840801bf3cce; acquired-result-b2bee0a5c3514b0d3a93; acquired-result-4d0caa4e6c6070389642; acquired-result-4267fe4e96025c2a3d49; acquired-result-726a6303bf1c25985f4e; acquired-result-5998eb1494319836be37; acquired-result-128e30179771ad658852; acquired-result-aee122fcb28c463df792; acquired-result-11298d60753d3ec42174; acquired-result-3a13b312668b38debfd0; acquired-result-4e4feb75e1595ff0fd18; acquired-result-77856c03a93e0d20d602; source ids: acquired-source-3156602fda847ae943b4; source locator: Figure 4 source CSV row 3, column 7 through Figure 4 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-fec9a408a698601daadf; title: BEELINE 2020 Figure 4 · VSC · {}: EPR Inhibition; protocol id: acquired-protocol-37b5599b7d976211e8c1; dataset id: acquired-dataset-caf90389169ff966e573; metric: EPR Inhibition; unit: ratio; direction: higher; result ids: acquired-result-e2aa1b477a35c39c370f; acquired-result-cc41411347bc1d8c0086; acquired-result-f5826c83df631798edc4; acquired-result-1752dfe79b27306ac1b4; acquired-result-38bff4df6e8222f70643; acquired-result-da5673f6370cb42be9bc; acquired-result-cd31b2b20f50bb7e8379; acquired-result-391300a132f1bf32cfbc; acquired-result-3b5947dbac5d391940a0; acquired-result-c6448a0a1dff87cb611f; acquired-result-d592010a91936b13a63a; acquired-result-1d63b0fa40c840610ae8; source ids: acquired-source-3156602fda847ae943b4; source locator: Figure 4 source CSV row 3, column 15 through Figure 4 source CSV row 14, column 15; 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.
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