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feat!: switch the QC embedding stage to the Babel-fine-tuned SapBERT - #214
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Stage 4 of the QC cascade now scores residual pairs with RenaissanceComputing/SapBERT-PubMedBERT-BabelSynonyms-v2025-01-23, RENCI's fine-tune of cambridgeltl/SapBERT-from-PubMedBERT-fulltext on synonym pairs sampled from NCATS Translator Babel identifier cliques (release 2025-01-23), instead of the base checkpoint. Drop-in for sentence-transformers: same PubMedBERT architecture, 768-dim embeddings. The model cache moves from .tablassert/sapbert/ to .tablassert/sapbert-babel/ so installs holding the base checkpoint re-download rather than silently serving it as the new model; stale .tablassert/sapbert/ directories can be deleted. The 0.5 pass threshold is unchanged and remains un-tuned for the new score distribution. docs/api/qc.md tracks the new checkpoint, provenance, and cache location; tests/test_cover_qc.py pins the new HF repo id.
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SkyeAv
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Oct 14, 2026
Cut 20.0.0 and bump the package version in pyproject.toml, CITATION.cff, and uv.lock. Major: two breaking changes and one feature ship since 19.7.0. The experimental agent pipeline, the GEPA prompt-optimization surface, and the distillation dataset export/weigh surface are removed, including the `tablassert agent` / `distill-export` / `distill-weigh` commands, the `--optimize` flag family, the `[agent]`/`[optimize]`/`[distill]` extras, and the agent-only error codes (#215). The QC embedding stage now runs RenaissanceComputing's Babel-fine-tuned SapBERT checkpoint with its own `.tablassert/sapbert-babel/` cache dir (#214). `build-kg` gains the opt-in `--linkouts`/`-lo` flag for EdgeLinkouts edge deep links (#216). Changelog: - Versioned the 20.0.0 section with Breaking Changes and Added entries, PR links, and a migration note for the removed surfaces. Docs: CHANGELOG.md, CITATION.cff, and pyproject.toml only; the merged PRs carried their own docs updates. Testing: - make check -> exit 0 (ruff check, ruff format --check, pyright, cargo fmt, cargo test, clippy -D warnings) - uv run pytest -> 1209 passed, 1 skipped in 21.28s - uv lock --check -> resolved, in sync - docs guards -> 192 passed
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Swaps the QC cascade's Stage 4 checkpoint from
cambridgeltl/SapBERT-from-PubMedBERT-fulltexttoRenaissanceComputing/SapBERT-PubMedBERT-BabelSynonyms-v2025-01-23, RENCI's fine-tune of that same base model on synonym pairs sampled from NCATS Translator Babel identifier cliques (release 2025-01-23). The fine-tuning signal matches the stage's audit task (whether two names denote the same concept) on exactly the equivalence data Translator normalizes against.Model swap
get_sapbert()insrc/tablassert/qc.pynow downloadsRenaissanceComputing/SapBERT-PubMedBERT-BabelSynonyms-v2025-01-23; drop-in forsentence-transformers(same PubMedBERT architecture, 768-dim embeddings, documented drop-in replacement on the model card).qc.MODELmoves.tablassert/sapbert/->.tablassert/sapbert-babel/, matching the BioBERT-to-SapBERT swap precedent, so installs holding the base checkpoint re-download instead of silently serving it as the new model. Stale.tablassert/sapbert/directories can be deleted.qc.SIMILARITY_THRESHOLDstays at0.5, carried over and un-tuned, same caveat as the previous swap; reject rates may shift with the new score distribution.tests/test_cover_qc.pypins the new repo id inHF_REPO.Docs
docs/api/qc.md: new model name, fine-tune provenance, and cache location with the staleness note.Testing
make check: exit 0 (ruff, ruff format, pyright, pytest1726 passed, 52 skipped, cargo test, clippy).Deferred
qc.SIMILARITY_THRESHOLDagainst real reject logs; already flagged in the code comment.