Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues
2026 · version of record · Peer-reviewed
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Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
| Model or configuration | Metric | Value | Dataset | Evaluation |
|---|---|---|---|---|
| scGPT + residual geometry | AUROC | 0.677 unitless | immune tissue | scGPT + residual geometry: gene-regulatory signal prediction |
Claims
Statements this source supports, each with where in the source it was checked.
- Reported AUROC for scGPT + residual geometry: Printed value 0.677 (Table 4, Immune row, scGPT > +geom AUROC column)
- scGPT + residual geometry: description: Description Adds geometric features of the scGPT residual stream, including centred cosine similarity between gene vectors and PCA projections, to an expression baseline for predicting transcription-factor-target links. (Reviewed profile (2026-09-16): summary at Results/Residual-stream geometry carries regulatory signal beyond expression confounds (paragraph 1); Background (paragraph 7); architecture fact at Methods/Geometric feature extraction (paragraph 2); Results/Residual-stream geometry carries regulatory signal beyond expression confounds (paragraph 1); description text also read at Abstract/Results; Results (per-feature comparison table))
- scGPT + residual geometry: uses model scGPT: Uses model scGPT (Methods residual stream feature extraction and nested classifier procedure; Tables 6, 9 and 10)
Models, benchmarks and other records
Pipelines (1)
Tasks (1)
Datasets (1)
Evaluations (1)
Evidence
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Evidence table
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Artifact retrieved at 2026-09-16T10:41:06Z Source metadata | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact SHA-256 77546faec51cfb5c78b73c5943f940c4e0097d130b1ddde4ab8287b507b36df6 Source metadata | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13418759/fullTextXML Source metadata | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.1186/s12859-026-06538-5 Source metadata | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Missing metadata: licence: reason unextracted Source metadata | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status peer_reviewed Source metadata | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-09-15T23:37:05Z Source metadata | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Scope decision included Source metadata | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Url https://pmc.ncbi.nlm.nih.gov/articles/PMC13418759/ Source metadata | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Version version of record Source metadata | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: discovered
Primary paper retained with its original identifier. Metadata inherited from the literature collection; individual result checks are separate.
Technical metadata and extraction receipts
Stable ID: single-cell-residual-geometry-2026
- areas
- cells-tissues
- url
- https://pmc.ncbi.nlm.nih.gov/articles/PMC13418759/
- version
- version of record
- retrieved at
- 2026-09-15T23:37:05Z
- doi
- 10.1186/s12859-026-06538-5
- publication status
- peer_reviewed
- year
- 2026
- artifact sha256
- 77546faec51cfb5c78b73c5943f940c4e0097d130b1ddde4ab8287b507b36df6
- artifact url
- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC13418759/fullTextXML
- artifact retrieved at
- 2026-09-16T10:41:06Z
- scope decision
- included
- missing metadata
- licence: reason: unextracted