Configuration

GENIE3

Exact source-reported configuration or submission label. Family membership, checkpoint identity and aliases have not been inferred.

44 evaluations · 44 results

Overview

Exact source-reported configuration or submission label. Family membership, checkpoint identity and aliases have not been inferred.

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

Evaluations and results

44 evaluations · 44 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: GENIE3	Protocol: BEELINE 2020 Figure 5 · mHSC-E · Reference network: Non-specific ChIP-Seq; Gene selection: TFs+1000 Dataset subset: mHSC-E	4.65 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mHSC-E BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 9, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mDC · Reference network: Non-specific ChIP-Seq; Gene selection: TFs+1000 Dataset subset: mDC	3 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mDC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 13, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mHSC-E · Reference network: STRING; Gene selection: TFs+1000 Dataset subset: mHSC-E	6.99 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mHSC-E BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 4, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mHSC-E · Reference network: Cell-type specific ChIP-Seq; Gene selection: TFs+1000 Dataset subset: mHSC-E	1.02 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mHSC-E BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 14, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mESC · Reference network: Non-specific ChIP-Seq; Gene selection: TFs+500 Dataset subset: mESC	3.28 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mESC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 12, column 7
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mHSC-L · Reference network: Non-specific ChIP-Seq; Gene selection: TFs+1000 Dataset subset: mHSC-L	3.05 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mHSC-L BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 10, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mHSC-L · Reference network: STRING; Gene selection: TFs+1000 Dataset subset: mHSC-L	7.17 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mHSC-L BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 5, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · hESC · Reference network: Non-specific ChIP-Seq; Gene selection: TFs+500 Dataset subset: hESC	1.8 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · hESC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 22, column 7
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · hHep · Reference network: STRING; Gene selection: TFs+1000 Dataset subset: hHep	3.2 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · hHep BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 21, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mHSC-L · Reference network: Cell-type specific ChIP-Seq; Gene selection: TFs+1000 Dataset subset: mHSC-L	1.03 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mHSC-L BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 15, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · MHSC-GM · Reference network: STRING; Gene selection: TFs+1000 Dataset subset: MHSC-GM	8.45 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · MHSC-GM BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 6, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mHSC-E · Reference network: Cell-type specific ChIP-Seq; Gene selection: TFs+500 Dataset subset: mHSC-E	1.03 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mHSC-E BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 14, column 7
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mESC · Reference network: STRING; Gene selection: TFs+500 Dataset subset: mESC	3.16 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mESC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 7, column 7
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · hHep · Reference network: Cell-type specific ChIP-Seq; Gene selection: TFs+1000 Dataset subset: hHep	1.12 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · hHep BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 25, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · hESC · Reference network: Cell-type specific ChIP-Seq; Gene selection: TFs+500 Dataset subset: hESC	0.95 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · hESC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 24, column 7
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · MHSC-GM · Reference network: Cell-type specific ChIP-Seq; Gene selection: TFs+500 Dataset subset: MHSC-GM	1.05 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · MHSC-GM BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 16, column 7
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mESC · Reference network: log/gof; Gene selection: TFs+1000 Dataset subset: mESC	1.33 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mESC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 19, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · hESC · Reference network: STRING; Gene selection: TFs+1000 Dataset subset: hESC	3.66 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · hESC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 20, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mESC · Reference network: STRING; Gene selection: TFs+1000 Dataset subset: mESC	3.48 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mESC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 7, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · MHSC-GM · Reference network: STRING; Gene selection: TFs+500 Dataset subset: MHSC-GM	8.7 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · MHSC-GM BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 6, column 7
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mESC · Reference network: Cell-type specific ChIP-Seq; Gene selection: TFs+1000 Dataset subset: mESC	1.06 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mESC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 17, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mDC · Reference network: Cell-type specific ChIP-Seq; Gene selection: TFs+1000 Dataset subset: mDC	0.97 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mDC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 18, column 16
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mHSC-L · Reference network: Cell-type specific ChIP-Seq; Gene selection: TFs+500 Dataset subset: mHSC-L	1.05 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mHSC-L BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 15, column 7
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · hHep · Reference network: Non-specific ChIP-Seq; Gene selection: TFs+500 Dataset subset: hHep	2.01 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · hHep BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 23, column 7
Configuration: GENIE3	Protocol: BEELINE 2020 Figure 5 · mDC · Reference network: STRING; Gene selection: TFs+1000 Dataset subset: mDC	2.16 Early Precision Ratio ratio · higher Uncertainty: status: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENIE3 · BEELINE 2020 Figure 5 · mDC BEELINE 2020 Figure 5 Aggregation: unreported BEELINE: 10.1038/s41592-019-0690-6 source data published 2020 · Figure 5 source CSV row 8, column 16

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Evidence

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Release 2026-09-29-06401fd5b220 · 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-configuration-b78c9479151b421d2751

source locator: Figure 5 source CSV row 4, column 7
reported configuration: GENIE3
reference kind: not_a_reference
missing metadata: checkpoint revision: unreported; model family: unextracted

Related records

model: GENIE3 · BEELINE 2020 Figure 5 · mESC
model: GENIE3 · BEELINE 2020 Figure 5 · mDC
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-L
model: GENIE3 · BEELINE 2020 Figure 5 · mESC
model: GENIE3 · BEELINE 2020 Figure 5 · hHep
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-L
model: GENIE3 · BEELINE 2020 Figure 5 · mDC
model: GENIE3 · BEELINE 2020 Figure 5 · hESC
model: GENIE3 · BEELINE 2020 Figure 5 · hESC
model: GENIE3 · BEELINE 2020 Figure 5 · hESC
model: GENIE3 · BEELINE 2020 Figure 5 · hHep
model: GENIE3 · BEELINE 2020 Figure 5 · hESC
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-L
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-E
model: GENIE3 · BEELINE 2020 Figure 5 · mDC
model: GENIE3 · BEELINE 2020 Figure 5 · mESC
model: GENIE3 · BEELINE 2020 Figure 5 · hHep
model: GENIE3 · BEELINE 2020 Figure 5 · hESC
model: GENIE3 · BEELINE 2020 Figure 5 · MHSC-GM
model: GENIE3 · BEELINE 2020 Figure 5 · MHSC-GM
model: GENIE3 · BEELINE 2020 Figure 5 · MHSC-GM
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-L
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-E
model: GENIE3 · BEELINE 2020 Figure 5 · MHSC-GM
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-L
model: GENIE3 · BEELINE 2020 Figure 5 · MHSC-GM
model: GENIE3 · BEELINE 2020 Figure 5 · hESC
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-E
model: GENIE3 · BEELINE 2020 Figure 5 · hHep
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-E
model: GENIE3 · BEELINE 2020 Figure 5 · mESC
model: GENIE3 · BEELINE 2020 Figure 5 · MHSC-GM
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-E
model: GENIE3 · BEELINE 2020 Figure 5 · mESC
model: GENIE3 · BEELINE 2020 Figure 5 · mESC
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-E
model: GENIE3 · BEELINE 2020 Figure 5 · mDC
model: GENIE3 · BEELINE 2020 Figure 5 · hHep
model: GENIE3 · BEELINE 2020 Figure 5 · mDC
model: GENIE3 · BEELINE 2020 Figure 5 · mESC
model: GENIE3 · BEELINE 2020 Figure 5 · mESC
model: GENIE3 · BEELINE 2020 Figure 5 · hHep
model: GENIE3 · BEELINE 2020 Figure 5 · mHSC-L
model: GENIE3 · BEELINE 2020 Figure 5 · mDC

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