Evidence claim

scRegNet (Geneformer backbone): description

Description of scRegNet (Geneformer backbone)

Predicts gene-regulatory links by combining context-aware gene representations from the pretrained Geneformer single-cell foundation model with graph-based representations learned from known regulatory interactions.

Replace a placeholder description with a sourced functional description (issue #88). Historical releases retain the original value.

Evidence

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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.

14 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Claimed field description Context-only references	huggingface.co/ctheodoris/Geneformer README.md Original source ↗ Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5 Retrieved: 2026-09-16T19:46:20.640731+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `56d6e570b349cbedae9a54634421c94e7af8ea467ce0fdd79193372ae3cbdbd8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field description Context-only references	Prediction of Gene Regulatory Connections with Joint Single-Cell Foundation Models and Graph-Based Learning Original source ↗ Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC11838224.2 Retrieved: 2026-09-16T10:41:16.541287+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `65b3272d47bb9c4ee1e7a965169bef63add9dbeb31508d4076e5145b761af4ec` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Identity as reported in this paper. Unspecified versions are not assumed equivalent to other papers. Context-only references	huggingface.co/ctheodoris/Geneformer README.md Original source ↗ Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5 Retrieved: 2026-09-16T19:46:20.640731+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `56d6e570b349cbedae9a54634421c94e7af8ea467ce0fdd79193372ae3cbdbd8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value Identity as reported in this paper. Unspecified versions are not assumed equivalent to other papers. Context-only references	Prediction of Gene Regulatory Connections with Joint Single-Cell Foundation Models and Graph-Based Learning Original source ↗ Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC11838224.2 Retrieved: 2026-09-16T10:41:16.541287+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `65b3272d47bb9c4ee1e7a965169bef63add9dbeb31508d4076e5145b761af4ec` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Context-only references	huggingface.co/ctheodoris/Geneformer README.md Original source ↗ Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5 Retrieved: 2026-09-16T19:46:20.640731+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `56d6e570b349cbedae9a54634421c94e7af8ea467ce0fdd79193372ae3cbdbd8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Context-only references	Prediction of Gene Regulatory Connections with Joint Single-Cell Foundation Models and Graph-Based Learning Original source ↗ Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC11838224.2 Retrieved: 2026-09-16T10:41:16.541287+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `65b3272d47bb9c4ee1e7a965169bef63add9dbeb31508d4076e5145b761af4ec` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value Predicts gene-regulatory links by combining context-aware gene representations from the pretrained Geneformer single-cell foundation model with graph-based representations learned from known regulatory interactions. Context-only references	huggingface.co/ctheodoris/Geneformer README.md Original source ↗ Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5 Retrieved: 2026-09-16T19:46:20.640731+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `56d6e570b349cbedae9a54634421c94e7af8ea467ce0fdd79193372ae3cbdbd8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value Predicts gene-regulatory links by combining context-aware gene representations from the pretrained Geneformer single-cell foundation model with graph-based representations learned from known regulatory interactions. Context-only references	Prediction of Gene Regulatory Connections with Joint Single-Cell Foundation Models and Graph-Based Learning Original source ↗ Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC11838224.2 Retrieved: 2026-09-16T10:41:16.541287+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `65b3272d47bb9c4ee1e7a965169bef63add9dbeb31508d4076e5145b761af4ec` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Replace a placeholder description with a sourced functional description (issue #88). Historical releases retain the original value. Context-only references	huggingface.co/ctheodoris/Geneformer README.md Original source ↗ Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5 Retrieved: 2026-09-16T19:46:20.640731+00:00	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `56d6e570b349cbedae9a54634421c94e7af8ea467ce0fdd79193372ae3cbdbd8` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Replace a placeholder description with a sourced functional description (issue #88). Historical releases retain the original value. Context-only references	Prediction of Gene Regulatory Connections with Joint Single-Cell Foundation Models and Graph-Based Learning Original source ↗ Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC11838224.2 Retrieved: 2026-09-16T10:41:16.541287+00:00	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `65b3272d47bb9c4ee1e7a965169bef63add9dbeb31508d4076e5145b761af4ec` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

2 source records and release history

Prediction of Gene Regulatory Connections with Joint Single-Cell Foundation Models and Graph-Based Learning · Original source · PMC11838224.2
huggingface.co/ctheodoris/Geneformer README.md · Original source · 1f7fbae4e469a5f4f1af8c111a529cfe1b3829f5

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Technical metadata and extraction receipts

Stable ID: metadata-correction-c42e9111297b344e773f

areas: cells-tissues
field: description
previous value: Identity as reported in this paper. Unspecified versions are not assumed equivalent to other papers.
value: Predicts gene-regulatory links by combining context-aware gene representations from the pretrained Geneformer single-cell foundation model with graph-based representations learned from known regulatory interactions.
source locator: Reviewed profile (2026-09-16): summary at Conclusions and Discussions (paragraph 1); Results/Performance on benchmark datasets (paragraph 2); architecture fact at Method/Graph-based learning with GNNs (paragraph 1); Method/Gene representations from foundation models (paragraph 1); description text also read at Introduction (scRegNet framework description); Abstract/Results
review: method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Extractor: Claude integrator agent for issue #88. Reviewer: a separate Claude review agent, independent of the extractor; no human review claimed.; date: 2026-10-11; method note: Compared the store diff with origin/main, read each new description against its cited source passage and checked the licence of each new source record.; note: Approved. Checked all 11 scTab and MPRabc method descriptions against PMC11298532 and PMC13232518, and Lazypipe-nt, scaLR, CATHe2, DiffDock-NMDN, PC-mer and Hi-Enhancer against their papers; all match. The other pipeline descriptions are consistent with their pinned papers.; receipt: data/omics/qa-descriptions-20261011-c/review.json

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subject: scRegNet (Geneformer backbone)

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