Method

GENIE3

GENIE3 infers candidate gene-regulatory links from expression measurements using ensembles of trees.

Sources (3)

aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint

0 evaluations · 0 metric rows

How it worksGENIE3 workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources (3)

At a glance

Model type

Tree-ensemble gene-regulatory-network inference

Sources (3)

Inputs

Gene-expression matrix and the selected candidate-regulator set.

Sources (3)

Outputs

Ranked candidate regulator-to-target links.

Sources (3)

Source reviewed · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.

No evaluations linked in this release.

How it works

GENIE3 infers candidate gene-regulatory links from expression measurements using ensembles of trees. Tree-ensemble regression decomposes network inference into prediction of each target gene from candidate regulators. The documented inputs are gene-expression matrix and the selected candidate-regulator set. The output consists of ranked candidate regulator-to-target links.

Sources (3)

Versions and reproducibility

GENIE3 implementation and Bioconductor package; preserve the configured tree method and settings. Genes and observations in the input matrix; no token context.

Sources (3)

Strengths and limitations

Strengths supported by sources

A conventional machine-learning comparator whose target-wise regression and regulator importance are explicit.
Sources (3)
aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint

Limitations and conditions

Predictive association in expression data does not by itself establish causal regulation. This GENIE3 algorithm is unrelated to Genie 3 protein design.
Sources (3)
aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint

Profile review details

Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.

Stable record: discovery-model-genie3

Specifications

Inputs, training, access and other details

Explanatory profile: source reviewed · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Tree-ensemble gene-regulatory-network inference Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Architecture	Tree-ensemble regression decomposes network inference into prediction of each target gene from candidate regulators. Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Inputs	Gene-expression matrix and the selected candidate-regulator set. Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Outputs	Ranked candidate regulator-to-target links. Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Parameters	Fitted tree ensembles; count depends on genes, candidate regulators and tree settings. Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Known versions	GENIE3 implementation and Bioconductor package; preserve the configured tree method and settings. Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Training data	Fitted to the supplied gene-expression dataset, not a universal pretrained corpus. Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Training cutoff	Inapplicable to neural pretraining; reference-database and input-data dates must be recorded for each run. · Not applicable Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Context limits	Genes and observations in the input matrix; no token context. Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Weights licence	No universal pretrained checkpoint; each fitted network is dataset-specific. Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Access	Official project documentation and implementation: https://github.com/aertslab/GENIE3 Sources (3) aertslab/GENIE3: README.md; aertslab/GENIE3: DESCRIPTION; aertslab/GRNBoost: README.md · README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint
Code licence	GPL-2.0-or-later, as declared in the R package DESCRIPTION. Sources aertslab/GENIE3: DESCRIPTION · DESCRIPTION: License
Assumptions	Not extracted or verified for this record.

Applicable tests and references

Applicability is distinct from a completed evaluation.

BEELINE · Proposed association

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.

58 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	aertslab/GRNBoost: README.md Original source ↗ README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 26c836b3dcbb85852d3c6f4b8340e8655434da02 Retrieved: 2026-09-16T19:46:18.179520+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `f2befd99acf59576a22b8a44abd2345e8ed7304cf470609f27d311e08ed3f066` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	aertslab/GENIE3: DESCRIPTION Original source ↗ README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 54bc15636322e8773357de6e0b6683c6bc802825 Retrieved: 2026-09-16T19:46:18.166390+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `4a2d48a4198b2ea6cbe5fa7749e9aa7286b318ebe19021bd1be52f29435e3196` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	aertslab/GENIE3: README.md Original source ↗ README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 54bc15636322e8773357de6e0b6683c6bc802825 Retrieved: 2026-09-16T19:46:18.166390+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `045aa63715acf615327d45ff42a897e77fa6d4b88084d2ad4e2ea836eb5fb48a` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Expression matrix","Target-wise tree ensembles","Regulator importance","Candidate network links"] Individual claims	aertslab/GRNBoost: README.md Original source ↗ README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 26c836b3dcbb85852d3c6f4b8340e8655434da02 Retrieved: 2026-09-16T19:46:18.179520+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `f2befd99acf59576a22b8a44abd2345e8ed7304cf470609f27d311e08ed3f066` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Expression matrix","Target-wise tree ensembles","Regulator importance","Candidate network links"] Individual claims	aertslab/GENIE3: DESCRIPTION Original source ↗ README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 54bc15636322e8773357de6e0b6683c6bc802825 Retrieved: 2026-09-16T19:46:18.166390+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `4a2d48a4198b2ea6cbe5fa7749e9aa7286b318ebe19021bd1be52f29435e3196` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps ["Expression matrix","Target-wise tree ensembles","Regulator importance","Candidate network links"] Individual claims	aertslab/GENIE3: README.md Original source ↗ README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 54bc15636322e8773357de6e0b6683c6bc802825 Retrieved: 2026-09-16T19:46:18.166390+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `045aa63715acf615327d45ff42a897e77fa6d4b88084d2ad4e2ea836eb5fb48a` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title GENIE3 workflow Individual claims	aertslab/GRNBoost: README.md Original source ↗ README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 26c836b3dcbb85852d3c6f4b8340e8655434da02 Retrieved: 2026-09-16T19:46:18.179520+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `f2befd99acf59576a22b8a44abd2345e8ed7304cf470609f27d311e08ed3f066` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title GENIE3 workflow Individual claims	aertslab/GENIE3: DESCRIPTION Original source ↗ README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 54bc15636322e8773357de6e0b6683c6bc802825 Retrieved: 2026-09-16T19:46:18.166390+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `4a2d48a4198b2ea6cbe5fa7749e9aa7286b318ebe19021bd1be52f29435e3196` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title GENIE3 workflow Individual claims	aertslab/GENIE3: README.md Original source ↗ README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 54bc15636322e8773357de6e0b6683c6bc802825 Retrieved: 2026-09-16T19:46:18.166390+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `045aa63715acf615327d45ff42a897e77fa6d4b88084d2ad4e2ea836eb5fb48a` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Tree-ensemble gene-regulatory-network inference Individual claims	aertslab/GRNBoost: README.md Original source ↗ README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 26c836b3dcbb85852d3c6f4b8340e8655434da02 Retrieved: 2026-09-16T19:46:18.179520+00:00	source checked automated source review · 2026-09-16 Audit details Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `f2befd99acf59576a22b8a44abd2345e8ed7304cf470609f27d311e08ed3f066` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Sources and history

Release 2026-09-17-d277315f7d76 · Record review: discovered

4 source records and release history

aertslab/GENIE3 official source · Original source · 54bc15636322e8773357de6e0b6683c6bc802825
aertslab/GENIE3: README.md · Original source · 54bc15636322e8773357de6e0b6683c6bc802825
aertslab/GENIE3: DESCRIPTION · Original source · 54bc15636322e8773357de6e0b6683c6bc802825
aertslab/GRNBoost: README.md · Original source · 26c836b3dcbb85852d3c6f4b8340e8655434da02

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Technical metadata and extraction receipts

Stable ID: discovery-model-genie3

areas: biological-networks
access: official_source_linked
benchmark applicability: candidate; not evidence of a reported evaluation
candidate benchmark ids: discovery-benchmark-beeline
entity level: method
reported name: GENIE3
version: Not reported
historical missing metadata: checkpoint: unextracted; code licence: unextracted; parameters: unextracted; training cutoff: unextracted; training data: unextracted; version: unextracted; weights licence: unextracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: The cited architecture/procedure describes an algorithm, representation recipe or software toolkit, rather than a single released learned biological model. Fitted models, selected reference databases and concrete runs remain separate configurations.; source ids: evidence-official-f078ec10fa45b5d77ad7; evidence-official-ad7f5c1eb802d9895413; evidence-official-099d109417c7fae96e96; source locator: README.md: GENIE3 definition; GRNBoost README Introduction describes the GENIE3 target-wise regression blueprint; ambiguities: This procedure fits statistical learners for a supplied expression matrix; that does not make the general inference algorithm a single pretrained model checkpoint.

Related records

applicable to: BEELINE
model: Tree-ensemble regulatory inference

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