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Add the BGE/PaCMAP structure map and retain the MiniLM/PCA view - #966

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realmarcin wants to merge 13 commits into
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fix/pacmap-semantic-view
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realmarcin wants to merge 13 commits into
mainfrom
fix/pacmap-semantic-view

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@realmarcin

@realmarcin realmarcin commented Sep 15, 2026

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CellStructureMech gains the fleet BGE-large-en-v1.5 semantic text map with actual PaCMAP for all 333 structure records in the integrated snapshot. The pinned 384-dimensional MiniLM/PCA map and cosine-neighbor view remain available and explicitly labelled; all five incoming MiniLM data/site assets are preserved byte-for-byte.

The versioned biological-text adapter and locked runtime bind each bundle to exact current inputs, encoder, vectors and reducer provenance. Rendering refuses stale or corrupt bundles before publishing. Semantic curation or membership changes require a local cache-backed refresh and new projection; ordinary CI and rendering verify artifacts without neural inference or fitting coordinates.

This refresh addresses the CI-proven source advancement in #967 by integrating only 0011421afd0a2298a6d26e7d4f5f775a86085708. All 332 prior input rows remain identical, with one new record: ventral disc microtubule array (GO:0097593). The full cached build encoded one vector, reused 332, and fitted and verified the 333-point PaCMAP bundle. It uses the same frozen profile, runtime and environment already exercised by the accepted two-new-record/31-record canary; no new canary or MiniLM inference/projection was needed.

Validation at merge commit b2876b0bafa6de92f9e16466aec8181d40dde92f:

  • Full 333-record input/cache/vector/PaCMAP check passed. Both runtimes 7a149d1a (numerical generation) and 9ef77083 (installed validation/staging, CLAW Add nuclear pore central transport channel record #440) verify the exact published three files.
  • All 333 common and 333 MiniLM point routes resolve to real record pages. Maintained MiniLM check, candidate rendering and reproduction passed. The promoted 359-file site exactly matches the independently reviewed candidate; all five specialty assets and prior 307/323/326/330/332 common generations are retained.
  • The exact 22-path local merge preserves the captured source/history and specialty bytes. Current affected tests: 52 passed in 65.49s (0:01:05). README documentation, history, strict schema, generated-site and corpus-report checks also passed on this exact head (89.02 seconds for the six selected checks).
  • The prior 96dac5d9 full local QC passed 587 tests with 3 skips for its 330-record snapshot. That historical result remains distinct from the current affected checks; full native GitHub QC is still required on this draft head.
  • Required GitHub checks passed on b2876b0bafa6de92f9e16466aec8181d40dde92f: full QC, identifier-liveness, label-correspondence and vendored-sync.

This additive integration retains the deployed governance pin c8b8f89ecf29574d7e24f6c65cfd925aefbdd007. Canonical registration follows CultureBotAI/culturebotai-claw#432; the subsequent pin update must use its actual main-reachable canonical merge commit.

Closes #910. Closes #967. Coordinates with CultureBotAI/culturebotai-claw#426, CultureBotAI/culturebotai-claw#436 and CultureBotAI/culturebotai-claw#440. The retained MiniLM work from #907/#909 remains separate from the common BGE cache.

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Refresh the common map for three incoming vacuolar records before PR #966 admission Add provenance-checked PaCMAP and the shared semantic text view

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