Add grobid_custom_hybrid profile with SciELO-preprints reference segmenter - #680
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de-code wants to merge 12 commits into
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Add grobid_custom_hybrid profile with SciELO-preprints reference segmenter#680de-code wants to merge 12 commits into
de-code wants to merge 12 commits into
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…enter Introduces a new sequence-model profile that overlays the grobid 0.9.0 CRF/wapiti baseline with our own retrained DELFT models, starting with a CustomBidLSTM_CRF reference segmenter trained on SciELO preprints. Intended to grow as more custom models are retrained and swapped in.
ScienceBeam Parser EvaluationOverall (277 docs across 6 corpora)grobid 0.9.0-crf (default): 277 docs | sciencebeam-parser:main-03689765-20260805.0803 (grobid_crf): 277 docs | sciencebeam-parser:pr-680-00a07b58-20260805.1014 (grobid_custom_hybrid): 277 docs
biorxiv (43 docs)grobid 0.9.0-crf (default): 43 docs | sciencebeam-parser:main-03689765-20260805.0803 (grobid_crf): 43 docs | sciencebeam-parser:pr-680-00a07b58-20260805.1014 (grobid_custom_hybrid): 43 docs
ore (50 docs)grobid 0.9.0-crf (default): 50 docs | sciencebeam-parser:main-03689765-20260805.0803 (grobid_crf): 50 docs | sciencebeam-parser:pr-680-00a07b58-20260805.1014 (grobid_custom_hybrid): 50 docs
pkp (50 docs)grobid 0.9.0-crf (default): 50 docs | sciencebeam-parser:main-03689765-20260805.0803 (grobid_crf): 50 docs | sciencebeam-parser:pr-680-00a07b58-20260805.1014 (grobid_custom_hybrid): 50 docs
scielo_br (50 docs)grobid 0.9.0-crf (default): 50 docs | sciencebeam-parser:main-03689765-20260805.0803 (grobid_crf): 50 docs | sciencebeam-parser:pr-680-00a07b58-20260805.1014 (grobid_custom_hybrid): 50 docs
scielo_mx (34 docs)grobid 0.9.0-crf (default): 34 docs | sciencebeam-parser:main-03689765-20260805.0803 (grobid_crf): 34 docs | sciencebeam-parser:pr-680-00a07b58-20260805.1014 (grobid_custom_hybrid): 34 docs
scielo_preprints-jats (50 docs)grobid 0.9.0-crf (default): 50 docs | sciencebeam-parser:main-03689765-20260805.0803 (grobid_crf): 50 docs | sciencebeam-parser:pr-680-00a07b58-20260805.1014 (grobid_custom_hybrid): 50 docs
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…enter Introduces a new sequence-model profile that overlays the grobid 0.9.0 CRF/wapiti baseline with our own retrained DELFT models, starting with a CustomBidLSTM_CRF reference segmenter trained on SciELO preprints. Intended to grow as more custom models are retrained and swapped in. Also wires up the profile:grobid_custom_hybrid PR label in the benchmark workflow so it selects this profile.
Replaces the hardcoded per-profile contains() checks with a step that extracts any profile:<name> label directly, validated against a safe character set, so new profiles no longer require a benchmark.yml edit.
Authenticate CI to GCP via Workload Identity Federation so the grobid_custom_hybrid profile can pull the reference-segmenter model from gs://sciencebeam-v2-models while the trained model's release is not yet public.
TensorFlow's built-in gs:// filesystem support only recognizes plain service-account JSON keys, not the Workload Identity Federation external_account credential files google-github-actions/auth produces - those reference a credential source that can't be resolved from inside the sciencebeam-parser container, causing anonymous (unauthenticated) requests. Decode a service account key from the GCS_MODEL_READER_SA_KEY_B64 secret instead and mount it into the container.
Points the citation model at the new CustomBidLSTM_CRF model in the private sciencebeam-v2-models GCS bucket, replacing the grobid 0.9.0 wapiti model, while its release is not yet public.
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This doesn't look that good unfortunately |
Custom hybrid profiles are expected to grow beyond this one, so inherit from a base profile via a code-resolved `extends` key rather than a YAML anchor - it deep-merges instead of replacing whole model entries, gives clear errors for unknown/circular references, and keeps working if profiles ever get split across files.
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part of https://github.com/eLifePathways/ScienceBeam2.0/issues/113
Introduces a new sequence-model profile that overlays the grobid 0.9.0 CRF/wapiti baseline with our own retrained DELFT models, starting with a CustomBidLSTM_CRF reference segmenter trained on SciELO preprints. Intended to grow as more custom models are retrained and swapped in.