Evidence claim

scGPT + residual geometry: description

Description of scGPT + residual geometry

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.

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

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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	bowang-lab/scGPT README.md Original source ↗ 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) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: cebd6fae655b9c585a4807daa3ac31bb764f06b4 Retrieved: 2026-09-16T20:00:00.816587+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `b0503e8ca789f19f1fc2350c5aaf57b1b323bbae43b354655231b5f4a1586c83` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field description Context-only references	Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Original source ↗ 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) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record Retrieved: 2026-09-16T10:41:06Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `77546faec51cfb5c78b73c5943f940c4e0097d130b1ddde4ab8287b507b36df6` 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	bowang-lab/scGPT README.md Original source ↗ 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) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: cebd6fae655b9c585a4807daa3ac31bb764f06b4 Retrieved: 2026-09-16T20:00:00.816587+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `b0503e8ca789f19f1fc2350c5aaf57b1b323bbae43b354655231b5f4a1586c83` 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	Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Original source ↗ 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) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record Retrieved: 2026-09-16T10:41:06Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `77546faec51cfb5c78b73c5943f940c4e0097d130b1ddde4ab8287b507b36df6` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location 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) Context-only references	bowang-lab/scGPT README.md Original source ↗ 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) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: cebd6fae655b9c585a4807daa3ac31bb764f06b4 Retrieved: 2026-09-16T20:00:00.816587+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `b0503e8ca789f19f1fc2350c5aaf57b1b323bbae43b354655231b5f4a1586c83` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location 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) Context-only references	Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Original source ↗ 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) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record Retrieved: 2026-09-16T10:41:06Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `77546faec51cfb5c78b73c5943f940c4e0097d130b1ddde4ab8287b507b36df6` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value 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. Context-only references	bowang-lab/scGPT README.md Original source ↗ 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) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: cebd6fae655b9c585a4807daa3ac31bb764f06b4 Retrieved: 2026-09-16T20:00:00.816587+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `b0503e8ca789f19f1fc2350c5aaf57b1b323bbae43b354655231b5f4a1586c83` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value 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. Context-only references	Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Original source ↗ 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) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record Retrieved: 2026-09-16T10:41:06Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `77546faec51cfb5c78b73c5943f940c4e0097d130b1ddde4ab8287b507b36df6` 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	bowang-lab/scGPT README.md Original source ↗ 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) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: cebd6fae655b9c585a4807daa3ac31bb764f06b4 Retrieved: 2026-09-16T20:00:00.816587+00:00	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `b0503e8ca789f19f1fc2350c5aaf57b1b323bbae43b354655231b5f4a1586c83` 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	Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Original source ↗ 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) Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record Retrieved: 2026-09-16T10:41:06Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `77546faec51cfb5c78b73c5943f940c4e0097d130b1ddde4ab8287b507b36df6` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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

2 source records and release history

Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Original source · version of record
bowang-lab/scGPT README.md · Original source · cebd6fae655b9c585a4807daa3ac31bb764f06b4

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Technical metadata and extraction receipts

Stable ID: metadata-correction-1c5a72892c11a1e942b2

areas: cells-tissues
field: description
previous value: Identity as reported in this paper. Unspecified versions are not assumed equivalent to other papers.
value: 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.
source locator: 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)
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: scGPT + residual geometry

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