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Add raw-only rc8 release with ONNX dynamic q8

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  1. .gitattributes +0 -30
  2. .gitignore +3 -0
  3. LICENSE +73 -0
  4. NOTICE +9 -0
  5. README.md +177 -0
  6. common.py +443 -0
  7. config.json +353 -0
  8. eval/benchmark_manual_suite_multilabel_base_irish_core_pii_v1.json +197 -0
  9. eval/benchmark_manual_suite_multilabel_base_irish_ppsn_phone_edge_v1.json +76 -0
  10. eval/benchmark_multilingual_ppsn_v1_all_openmed_mliteclinical_base_cpu.json +159 -0
  11. eval/benchmark_summary.json +90 -0
  12. eval/benchmark_summary.md +40 -0
  13. eval/rc8h_cal3_core_t050_cpu.json +108 -0
  14. eval/rc8h_cal3_edge_t050_cpu.json +36 -0
  15. eval/rc8h_cal3_finance_boundary_t050_cpu.json +76 -0
  16. eval/rc8h_cal3_finance_t050_cpu.json +76 -0
  17. eval/rc8h_cal3_gaweak_t050_cpu.json +28 -0
  18. eval/rc8h_cal3_multilingual_t050_cpu.json +28 -0
  19. eval/rc8h_cal3_q8_core_t050_cpu.json +108 -0
  20. eval/rc8h_cal3_q8_edge_t050_cpu.json +36 -0
  21. eval/rc8h_cal3_q8_finance_boundary_t050_cpu.json +76 -0
  22. eval/rc8h_cal3_q8_finance_t050_cpu.json +76 -0
  23. eval/rc8h_cal3_q8_gaweak_t050_cpu.json +28 -0
  24. eval/rc8h_cal3_q8_multilingual_t050_cpu.json +28 -0
  25. eval/rc8h_cal3_q8_user_t050_cpu.json +28 -0
  26. eval/rc8h_cal3_user_t050_cpu.json +28 -0
  27. inference_mask.py +104 -0
  28. inference_mask_onnx.py +90 -0
  29. model.py +75 -0
  30. model.safetensors +3 -0
  31. multitask_head_meta.json +43 -0
  32. multitask_model.py +91 -0
  33. onnx/model.onnx +3 -0
  34. onnx/model.preprocessed.onnx +3 -0
  35. onnx/model_quantized.onnx +3 -0
  36. onnx/onnx_export.json +12 -0
  37. onnx/quantization.json +26 -0
  38. pyproject.toml +17 -0
  39. qa_config.json +14 -0
  40. special_tokens_map.json +37 -0
  41. tokenizer.json +0 -0
  42. tokenizer_config.json +61 -0
  43. training_sources.json +73 -0
  44. vocab.txt +0 -0
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NOTICE ADDED
@@ -0,0 +1,9 @@
 
 
 
 
 
 
 
 
 
 
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+ This release is derived from OpenMed/OpenMed-PII-mLiteClinical-Base-135M-v1 (Apache-2.0).
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+
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+ Additional training data attribution:
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+ - temsa/OpenMed-Irish-CorePII-TrainMix-v1 (composite train mix)
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+ - temsa/OpenMed-Irish-PPSN-Eircode-Spec-v1 (synthetic dataset)
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+ - joelniklaus/mapa (CC-BY-4.0)
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+ - gretelai/synthetic_pii_finance_multilingual (Apache-2.0)
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+
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+ This repo distributes model artifacts and synthetic benchmark files. It does not redistribute third-party dataset rows from upstream datasets.
README.md ADDED
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+ ---
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+ language:
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+ - en
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+ - ga
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+ license: apache-2.0
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+ library_name: transformers
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+ pipeline_tag: token-classification
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+ tags:
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+ - pii
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+ - de-identification
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+ - token-classification
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+ - ireland
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+ - irish
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+ - gaelic
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+ - raw-only
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+ - ppsn
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+ - eircode
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+ - passport
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+ - phone-number
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+ - onnx
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+ - int8
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+ - dynamic-quantization
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+ base_model:
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+ - OpenMed/OpenMed-PII-mLiteClinical-Base-135M-v1
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+ datasets:
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+ - temsa/OpenMed-Irish-CorePII-TrainMix-v1
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+ - temsa/OpenMed-Irish-PPSN-Eircode-Spec-v1
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+ - joelniklaus/mapa
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+ - gretelai/synthetic_pii_finance_multilingual
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+ ---
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+
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+ # OpenMed-mLiteClinical-IrishCorePII-135M-v2-rc8
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+
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+ Raw-only Irish core PII release derived from `OpenMed/OpenMed-PII-mLiteClinical-Base-135M-v1`.
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+
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+ This repo does **not** require the scanner / validator layer used by `temsa/OpenMed-mLiteClinical-IrishCorePII-135M-v2-rc7`.
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+ Both the full checkpoint and the ONNX q8 artifact use the same learned score-only decoder over token-presence and typed boundary heads.
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+
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+ ## Coverage
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+
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+ - `PPSN`
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+ - `ACCOUNT_NUMBER`
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+ - `BANK_ROUTING_NUMBER`
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+ - `CREDIT_DEBIT_CARD`
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+ - `PASSPORT_NUMBER`
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+ - `POSTCODE`
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+ - `PHONE_NUMBER`
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+ - `EMAIL`
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+ - `FIRST_NAME`
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+ - `LAST_NAME`
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+ - `SWIFT_BIC`
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+
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+ ## Included Variants
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+
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+ - Full `transformers` checkpoint in the repo root
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+ - Unquantized ONNX export in `onnx/model.onnx`
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+ - Dynamic q8 ONNX artifact in `onnx/model_quantized.onnx`
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+ - `inference_mask.py` for the full checkpoint
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+ - `inference_mask_onnx.py` for the ONNX q8 artifact
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+ - `common.py`, `model.py`, and `multitask_model.py` implementing the raw-only decoder
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+ - benchmark files in `eval/`
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+
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+ Artifact sizes:
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+
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+ - Full checkpoint: `515 MB` (`model.safetensors`)
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+ - Dynamic q8 ONNX: `393 MB` (`onnx/model_quantized.onnx`)
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+
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+ ## What Changed From rc7
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+
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+ `rc7` achieves its public quality with a bundled scanner / validator inference stack.
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+
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+ `rc8` removes that layer completely:
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+
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+ - no regex-based candidate extraction
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+ - no checksum validator dependency at inference time
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+ - no separate scanner spec or generated scanner code
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+ - same compact `mLiteClinical` encoder family, but with a raw-only multi-head decoder
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+
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+ The tradeoff is explicit:
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+
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+ - `rc7` is still stronger on the broad manual Irish core suite
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+ - `rc8` is easier to embed, simpler to maintain, and its ONNX q8 path stays very close to the full checkpoint
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+
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+ ## Architecture
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+
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+ `rc8` keeps the DistilBERT-size encoder class of the 135M `mLiteClinical` base and adds:
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+
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+ - a token-presence head for each released label
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+ - a typed start-boundary head
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+ - a typed end-boundary head
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+ - a score-only decoder that uses model scores, token offsets, continuity priors, and minimum-length priors from config
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+
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+ There is no scanner or external validator in the release path.
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+
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+ Design references that informed this direction:
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+
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+ - Split-NER: https://aclanthology.org/2023.acl-short.36/
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+ - SpanNER: https://aclanthology.org/2021.acl-long.558/
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+ - Boundary Smoothing for Named Entity Recognition: https://aclanthology.org/2022.acl-long.490/
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+ - TinyBERT: https://aclanthology.org/2020.findings-emnlp.372/
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+
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+ ## How To Use It
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+
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+ Full checkpoint:
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+
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+ ```bash
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+ uv run python inference_mask.py \
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+ --model temsa/OpenMed-mLiteClinical-IrishCorePII-135M-v2-rc8 \
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+ --min-score 0.5 \
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+ --text "My PPSN is 1234567TW, my Eircode is D02 X285, and my phone is 087 123 4567." \
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+ --json
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+ ```
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+
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+ Dynamic q8 ONNX:
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+
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+ ```bash
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+ uv run python inference_mask_onnx.py \
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+ --model temsa/OpenMed-mLiteClinical-IrishCorePII-135M-v2-rc8 \
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+ --min-score 0.5 \
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+ --text "Please provide your passport NN5123456 and call me on 0851234567." \
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+ --json
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+ ```
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+
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+ ## Benchmarks
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+
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+ Main comparison:
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+
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+ | Model | Irish core F1 | Edge F1 | Finance F1 | Finance-boundary F1 | User PPSN F1 | GA weak PPSN F1 | Multilingual PPSN F1 | Core CPU ex/s | Multilingual CPU ex/s |
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+ |---|---:|---:|---:|---:|---:|---:|---:|---:|---:|
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+ | Base OpenMed | 0.3743 | 0.0556 | - | - | - | - | 0.0000 | 15.1811 | 37.4666 |
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+ | Previous public `rc7` full | 1.0000 | - | 1.0000 | 1.0000 | - | 1.0000 | - | 3.5394 | - |
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+ | Previous public `rc7` ONNX q8 | 0.9934 | - | 1.0000 | 1.0000 | - | 1.0000 | - | 12.1653 | - |
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+ | `rc8` full | 0.9737 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 0.9176 | 2.2965 | 6.3095 |
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+ | `rc8` ONNX q8 | 0.9737 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 0.9176 | 46.1420 | 99.7166 |
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+
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+ Irish core label breakdown:
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+
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+ | Label | `rc8` full | `rc8` ONNX q8 |
139
+ |---|---:|---:|
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+ | PPSN | 1.0000 | 1.0000 |
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+ | PHONE_NUMBER | 0.9565 | 0.9565 |
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+ | POSTCODE | 1.0000 | 1.0000 |
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+ | ACCOUNT_NUMBER | 0.8000 | 0.8000 |
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+ | PASSPORT_NUMBER | 1.0000 | 1.0000 |
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+ | EMAIL | 1.0000 | 1.0000 |
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+ | FIRST_NAME | 0.9744 | 0.9744 |
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+ | LAST_NAME | 0.9744 | 0.9744 |
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+
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+ ## Dynamic q8 Artifact
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+
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+ Artifact paths:
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+
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+ - unquantized: `onnx/model.onnx`
154
+ - preprocessed: `onnx/model.preprocessed.onnx`
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+ - quantized: `onnx/model_quantized.onnx`
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+
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+ Quantization recipe used here:
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+
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+ - ONNX pre-processing before quantization
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+ - ONNX Runtime dynamic int8
161
+ - `qint8`
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+ - `per_channel=true`
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+ - `op_types=MatMul,Gemm,Attention`
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+
165
+ For CPU deployment, the ONNX q8 artifact is the recommended default.
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+
167
+ ## Limits
168
+
169
+ - `rc8` is raw-only. It intentionally gives up the scanner/validator stack used by `rc7`, so its broad manual-suite ceiling is lower.
170
+ - The current remaining local misses are a bare 8-digit account-number case and one Gaelic phone-number case in the manual core suite.
171
+ - If you need the exact `rc8` behavior, use the bundled inference scripts or import `decode_token_presence_segments` from `common.py`.
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+
173
+ ## License And Attribution
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+
175
+ - Release license: Apache-2.0
176
+ - Base model: `OpenMed/OpenMed-PII-mLiteClinical-Base-135M-v1`
177
+ - See `NOTICE` and `training_sources.json` for attribution and training details.
common.py ADDED
@@ -0,0 +1,443 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ from __future__ import annotations
3
+
4
+ import json
5
+ import tempfile
6
+ from pathlib import Path
7
+ from typing import Any
8
+
9
+ import numpy as np
10
+ from huggingface_hub import HfApi, hf_hub_download
11
+ from transformers import AutoConfig, AutoTokenizer
12
+
13
+ TOKENIZER_FILES = [
14
+ "tokenizer_config.json",
15
+ "tokenizer.json",
16
+ "special_tokens_map.json",
17
+ "vocab.txt",
18
+ "vocab.json",
19
+ "merges.txt",
20
+ "added_tokens.json",
21
+ "sentencepiece.bpe.model",
22
+ "spiece.model",
23
+ ]
24
+ DEFAULT_LABEL_MAX_SPAN_TOKENS = {
25
+ # Token-piece limits, not word limits. These need to reflect how the
26
+ # underlying tokenizer actually fragments compact identifiers.
27
+ "PPSN": 9,
28
+ "POSTCODE": 7,
29
+ "PHONE_NUMBER": 10,
30
+ "PASSPORT_NUMBER": 8,
31
+ "BANK_ROUTING_NUMBER": 5,
32
+ "ACCOUNT_NUMBER": 19,
33
+ "CREDIT_DEBIT_CARD": 12,
34
+ "SWIFT_BIC": 8,
35
+ "EMAIL": 15,
36
+ "FIRST_NAME": 5,
37
+ "LAST_NAME": 8,
38
+ }
39
+ DEFAULT_LABEL_MIN_NONSPACE_CHARS = {
40
+ "PPSN": 8,
41
+ "POSTCODE": 6,
42
+ "PHONE_NUMBER": 7,
43
+ "PASSPORT_NUMBER": 7,
44
+ "BANK_ROUTING_NUMBER": 6,
45
+ "ACCOUNT_NUMBER": 6,
46
+ "CREDIT_DEBIT_CARD": 12,
47
+ "SWIFT_BIC": 8,
48
+ "EMAIL": 6,
49
+ "FIRST_NAME": 2,
50
+ "LAST_NAME": 2,
51
+ }
52
+ WHITESPACE_BRIDGE_LABELS = {
53
+ "PPSN",
54
+ "POSTCODE",
55
+ "PHONE_NUMBER",
56
+ "PASSPORT_NUMBER",
57
+ "BANK_ROUTING_NUMBER",
58
+ "ACCOUNT_NUMBER",
59
+ "CREDIT_DEBIT_CARD",
60
+ "SWIFT_BIC",
61
+ "EMAIL",
62
+ }
63
+ CONSERVATIVE_BOUNDARY_REFINEMENT_LABELS = {
64
+ "PPSN",
65
+ "POSTCODE",
66
+ "PHONE_NUMBER",
67
+ "PASSPORT_NUMBER",
68
+ "BANK_ROUTING_NUMBER",
69
+ "ACCOUNT_NUMBER",
70
+ "CREDIT_DEBIT_CARD",
71
+ "SWIFT_BIC",
72
+ "EMAIL",
73
+ }
74
+ OUTPUT_PRIORITY = {
75
+ "PPSN": 0,
76
+ "PASSPORT_NUMBER": 1,
77
+ "ACCOUNT_NUMBER": 2,
78
+ "BANK_ROUTING_NUMBER": 3,
79
+ "CREDIT_DEBIT_CARD": 4,
80
+ "PHONE_NUMBER": 5,
81
+ "SWIFT_BIC": 6,
82
+ "POSTCODE": 7,
83
+ "EMAIL": 8,
84
+ "FIRST_NAME": 9,
85
+ "LAST_NAME": 10,
86
+ }
87
+
88
+
89
+ def normalize_entity_name(label: str) -> str:
90
+ label = (label or "").strip()
91
+ if label.startswith("B-") or label.startswith("I-"):
92
+ label = label[2:]
93
+ return label.upper()
94
+
95
+
96
+ def _sanitize_tokenizer_dir(tokenizer_path: Path) -> str:
97
+ tokenizer_cfg_path = tokenizer_path / "tokenizer_config.json"
98
+ if not tokenizer_cfg_path.exists():
99
+ return str(tokenizer_path)
100
+ data = json.loads(tokenizer_cfg_path.read_text(encoding="utf-8"))
101
+ if "fix_mistral_regex" not in data:
102
+ return str(tokenizer_path)
103
+ tmpdir = Path(tempfile.mkdtemp(prefix="openmed_span_tokenizer_"))
104
+ keep = set(TOKENIZER_FILES)
105
+ for child in tokenizer_path.iterdir():
106
+ if child.is_file() and child.name in keep:
107
+ (tmpdir / child.name).write_bytes(child.read_bytes())
108
+ data.pop("fix_mistral_regex", None)
109
+ (tmpdir / "tokenizer_config.json").write_text(json.dumps(data, ensure_ascii=False, indent=2) + "\n", encoding="utf-8")
110
+ return str(tmpdir)
111
+
112
+
113
+ def safe_auto_tokenizer(tokenizer_ref: str):
114
+ tokenizer_path = Path(tokenizer_ref)
115
+ if tokenizer_path.exists():
116
+ tokenizer_ref = _sanitize_tokenizer_dir(tokenizer_path)
117
+ else:
118
+ api = HfApi()
119
+ files = set(api.list_repo_files(repo_id=tokenizer_ref, repo_type="model"))
120
+ tmpdir = Path(tempfile.mkdtemp(prefix="openmed_remote_span_tokenizer_"))
121
+ copied = False
122
+ for name in TOKENIZER_FILES:
123
+ if name not in files:
124
+ continue
125
+ src = hf_hub_download(repo_id=tokenizer_ref, filename=name, repo_type="model")
126
+ (tmpdir / Path(name).name).write_bytes(Path(src).read_bytes())
127
+ copied = True
128
+ if copied:
129
+ tokenizer_ref = _sanitize_tokenizer_dir(tmpdir)
130
+
131
+ try:
132
+ return AutoTokenizer.from_pretrained(tokenizer_ref, use_fast=True, fix_mistral_regex=True)
133
+ except Exception:
134
+ pass
135
+ try:
136
+ return AutoTokenizer.from_pretrained(tokenizer_ref, use_fast=True, fix_mistral_regex=False)
137
+ except TypeError:
138
+ pass
139
+ try:
140
+ return AutoTokenizer.from_pretrained(tokenizer_ref, use_fast=True)
141
+ except Exception:
142
+ return AutoTokenizer.from_pretrained(tokenizer_ref, use_fast=False)
143
+
144
+
145
+ def label_names_from_config(config) -> list[str]:
146
+ names = list(getattr(config, "span_label_names", []))
147
+ if not names:
148
+ raise ValueError("Missing span_label_names in config")
149
+ return [normalize_entity_name(name) for name in names]
150
+
151
+
152
+ def label_thresholds_from_config(config, default_threshold: float) -> dict[str, float]:
153
+ raw = getattr(config, "span_label_thresholds", None) or {}
154
+ out = {normalize_entity_name(key): float(value) for key, value in raw.items()}
155
+ for label in label_names_from_config(config):
156
+ out.setdefault(label, float(default_threshold))
157
+ return out
158
+
159
+
160
+ def token_label_thresholds_from_config(config, default_threshold: float) -> dict[str, float]:
161
+ raw = getattr(config, "token_label_thresholds", None) or {}
162
+ out = {normalize_entity_name(key): float(value) for key, value in raw.items()}
163
+ for label in label_names_from_config(config):
164
+ out.setdefault(label, float(default_threshold))
165
+ return out
166
+
167
+
168
+ def token_extend_thresholds_from_config(config, default_fraction: float = 0.6) -> dict[str, float]:
169
+ raw = getattr(config, "token_extend_thresholds", None) or {}
170
+ out = {normalize_entity_name(key): float(value) for key, value in raw.items()}
171
+ for label in label_names_from_config(config):
172
+ out.setdefault(label, max(0.0, min(1.0, float(token_label_thresholds_from_config(config, 0.5).get(label, 0.5)) * default_fraction)))
173
+ return out
174
+
175
+
176
+ def boundary_label_thresholds_from_config(config, default_threshold: float = 0.0) -> dict[str, float]:
177
+ raw = getattr(config, "boundary_label_thresholds", None) or {}
178
+ out = {normalize_entity_name(key): float(value) for key, value in raw.items()}
179
+ for label in label_names_from_config(config):
180
+ out.setdefault(label, float(default_threshold))
181
+ return out
182
+
183
+
184
+ def label_max_span_tokens_from_config(config) -> dict[str, int]:
185
+ raw = getattr(config, "span_label_max_span_tokens", None) or {}
186
+ out = {normalize_entity_name(key): int(value) for key, value in raw.items()}
187
+ for label, value in DEFAULT_LABEL_MAX_SPAN_TOKENS.items():
188
+ out.setdefault(label, value)
189
+ for label in label_names_from_config(config):
190
+ out.setdefault(label, 8)
191
+ return out
192
+
193
+
194
+ def label_min_nonspace_chars_from_config(config) -> dict[str, int]:
195
+ raw = getattr(config, "span_label_min_nonspace_chars", None) or {}
196
+ out = {normalize_entity_name(key): int(value) for key, value in raw.items()}
197
+ for label, value in DEFAULT_LABEL_MIN_NONSPACE_CHARS.items():
198
+ out.setdefault(label, value)
199
+ for label in label_names_from_config(config):
200
+ out.setdefault(label, 1)
201
+ return out
202
+
203
+
204
+ def overlaps(a: dict, b: dict) -> bool:
205
+ return not (a["end"] <= b["start"] or b["end"] <= a["start"])
206
+
207
+
208
+ def dedupe_spans(spans: list[dict]) -> list[dict]:
209
+ ordered = sorted(
210
+ spans,
211
+ key=lambda item: (-float(item.get("score", 0.0)), item["start"], item["end"], OUTPUT_PRIORITY.get(item["label"], 99)),
212
+ )
213
+ kept = []
214
+ for span in ordered:
215
+ if any(overlaps(span, other) for other in kept):
216
+ continue
217
+ kept.append(span)
218
+ kept.sort(key=lambda item: (item["start"], item["end"], OUTPUT_PRIORITY.get(item["label"], 99)))
219
+ return kept
220
+
221
+
222
+ def _valid_offset(offset: tuple[int, int]) -> bool:
223
+ return bool(offset) and offset[1] > offset[0]
224
+
225
+
226
+ def _has_skippable_bridge(text: str, left: tuple[int, int], right: tuple[int, int], label: str) -> bool:
227
+ bridge = text[int(left[1]) : int(right[0])]
228
+ if bridge == "":
229
+ return True
230
+ return label in WHITESPACE_BRIDGE_LABELS and bridge.isspace()
231
+
232
+
233
+ def _has_left_extension_bridge(text: str, left: tuple[int, int], right: tuple[int, int]) -> bool:
234
+ bridge = text[int(left[1]) : int(right[0])]
235
+ return bridge == ""
236
+
237
+
238
+ def _nonspace_length(text: str, start: int, end: int) -> int:
239
+ return sum(0 if ch.isspace() else 1 for ch in text[int(start) : int(end)])
240
+
241
+
242
+ def decode_span_logits(
243
+ text: str,
244
+ offsets: list[tuple[int, int]],
245
+ start_scores: np.ndarray,
246
+ end_scores: np.ndarray,
247
+ label_names: list[str],
248
+ default_threshold: float,
249
+ label_thresholds: dict[str, float] | None = None,
250
+ label_max_span_tokens: dict[str, int] | None = None,
251
+ ) -> list[dict]:
252
+ thresholds = {label: float(default_threshold) for label in label_names}
253
+ if label_thresholds:
254
+ thresholds.update({normalize_entity_name(key): float(value) for key, value in label_thresholds.items()})
255
+ max_tokens = dict(DEFAULT_LABEL_MAX_SPAN_TOKENS)
256
+ if label_max_span_tokens:
257
+ max_tokens.update({normalize_entity_name(key): int(value) for key, value in label_max_span_tokens.items()})
258
+
259
+ spans: list[dict] = []
260
+ for label_index, label in enumerate(label_names):
261
+ threshold = thresholds.get(label, float(default_threshold))
262
+ max_span = max_tokens.get(label, 8)
263
+ start_candidates = [idx for idx in range(len(offsets)) if _valid_offset(offsets[idx]) and float(start_scores[idx, label_index]) >= threshold]
264
+ for start_idx in start_candidates:
265
+ best = None
266
+ for end_idx in range(start_idx, min(len(offsets), start_idx + max_span)):
267
+ if not _valid_offset(offsets[end_idx]):
268
+ continue
269
+ end_score = float(end_scores[end_idx, label_index])
270
+ if end_score < threshold:
271
+ continue
272
+ score = min(float(start_scores[start_idx, label_index]), end_score)
273
+ if best is None or score > best["score"]:
274
+ best = {
275
+ "label": label,
276
+ "start": int(offsets[start_idx][0]),
277
+ "end": int(offsets[end_idx][1]),
278
+ "score": score,
279
+ }
280
+ if best is not None and best["start"] < best["end"]:
281
+ best["text"] = text[best["start"]:best["end"]]
282
+ spans.append(best)
283
+ return dedupe_spans(spans)
284
+
285
+
286
+ def decode_token_presence_segments(
287
+ text: str,
288
+ offsets: list[tuple[int, int]],
289
+ token_scores: np.ndarray,
290
+ label_names: list[str],
291
+ default_threshold: float,
292
+ label_thresholds: dict[str, float] | None = None,
293
+ label_extend_thresholds: dict[str, float] | None = None,
294
+ label_max_span_tokens: dict[str, int] | None = None,
295
+ label_min_nonspace_chars: dict[str, int] | None = None,
296
+ boundary_label_thresholds: dict[str, float] | None = None,
297
+ start_scores: np.ndarray | None = None,
298
+ end_scores: np.ndarray | None = None,
299
+ ) -> list[dict]:
300
+ thresholds = {label: float(default_threshold) for label in label_names}
301
+ if label_thresholds:
302
+ thresholds.update({normalize_entity_name(key): float(value) for key, value in label_thresholds.items()})
303
+ extend_thresholds = {label: max(0.0, min(1.0, thresholds[label] * 0.6)) for label in label_names}
304
+ if label_extend_thresholds:
305
+ extend_thresholds.update({normalize_entity_name(key): float(value) for key, value in label_extend_thresholds.items()})
306
+ max_tokens = dict(DEFAULT_LABEL_MAX_SPAN_TOKENS)
307
+ if label_max_span_tokens:
308
+ max_tokens.update({normalize_entity_name(key): int(value) for key, value in label_max_span_tokens.items()})
309
+ min_nonspace_chars = dict(DEFAULT_LABEL_MIN_NONSPACE_CHARS)
310
+ if label_min_nonspace_chars:
311
+ min_nonspace_chars.update({normalize_entity_name(key): int(value) for key, value in label_min_nonspace_chars.items()})
312
+ boundary_thresholds = {label: 0.0 for label in label_names}
313
+ if boundary_label_thresholds:
314
+ boundary_thresholds.update({normalize_entity_name(key): float(value) for key, value in boundary_label_thresholds.items()})
315
+
316
+ spans: list[dict] = []
317
+ valid = [_valid_offset(offset) for offset in offsets]
318
+ num_tokens = len(offsets)
319
+ for label_index, label in enumerate(label_names):
320
+ threshold = thresholds.get(label, float(default_threshold))
321
+ extend_threshold = min(threshold, extend_thresholds.get(label, threshold))
322
+ max_span = max_tokens.get(label, 8)
323
+ idx = 0
324
+ while idx < num_tokens:
325
+ if not valid[idx] or float(token_scores[idx, label_index]) < threshold:
326
+ idx += 1
327
+ continue
328
+ start_idx = idx
329
+ end_idx = idx
330
+ while end_idx + 1 < num_tokens and valid[end_idx + 1] and float(token_scores[end_idx + 1, label_index]) >= threshold and (end_idx + 1 - start_idx + 1) <= max_span:
331
+ end_idx += 1
332
+ while (
333
+ start_idx - 1 >= 0
334
+ and valid[start_idx - 1]
335
+ and _has_left_extension_bridge(text, offsets[start_idx - 1], offsets[start_idx])
336
+ and float(token_scores[start_idx - 1, label_index]) >= extend_threshold
337
+ and (end_idx - (start_idx - 1) + 1) <= max_span
338
+ ):
339
+ start_idx -= 1
340
+ while (
341
+ end_idx + 1 < num_tokens
342
+ and valid[end_idx + 1]
343
+ and _has_skippable_bridge(text, offsets[end_idx], offsets[end_idx + 1], label)
344
+ and float(token_scores[end_idx + 1, label_index]) >= extend_threshold
345
+ and ((end_idx + 1) - start_idx + 1) <= max_span
346
+ ):
347
+ end_idx += 1
348
+ presence_slice = token_scores[start_idx : end_idx + 1, label_index]
349
+ score = float(presence_slice.mean())
350
+ out_start_idx = start_idx
351
+ out_end_idx = end_idx
352
+ if start_scores is not None and end_scores is not None:
353
+ refine_window = min(3, end_idx - start_idx + 1)
354
+ start_window = start_scores[start_idx : start_idx + refine_window, label_index]
355
+ best_start_rel = int(np.argmax(start_window))
356
+ best_start_idx = start_idx + best_start_rel
357
+ end_window_start = max(best_start_idx, end_idx - refine_window + 1)
358
+ end_window = end_scores[end_window_start : end_idx + 1, label_index]
359
+ best_end_rel = int(np.argmax(end_window))
360
+ best_end_idx = end_window_start + best_end_rel
361
+ if (
362
+ float(start_scores[best_start_idx, label_index]) < boundary_thresholds.get(label, 0.0)
363
+ or float(end_scores[best_end_idx, label_index]) < boundary_thresholds.get(label, 0.0)
364
+ ):
365
+ idx = end_idx + 1
366
+ continue
367
+ out_start_idx = best_start_idx
368
+ out_end_idx = best_end_idx
369
+ if label in CONSERVATIVE_BOUNDARY_REFINEMENT_LABELS and (
370
+ best_start_idx != start_idx or best_end_idx != end_idx
371
+ ):
372
+ outer_boundary = min(float(start_scores[start_idx, label_index]), float(end_scores[end_idx, label_index]))
373
+ refined_boundary = min(
374
+ float(start_scores[best_start_idx, label_index]),
375
+ float(end_scores[best_end_idx, label_index]),
376
+ )
377
+ if refined_boundary < outer_boundary + 0.08:
378
+ out_start_idx = start_idx
379
+ out_end_idx = end_idx
380
+ score = (
381
+ 0.65 * score
382
+ + 0.175 * float(start_scores[out_start_idx, label_index])
383
+ + 0.175 * float(end_scores[out_end_idx, label_index])
384
+ )
385
+ min_chars = int(min_nonspace_chars.get(label, 1))
386
+ if _nonspace_length(text, offsets[out_start_idx][0], offsets[out_end_idx][1]) < min_chars:
387
+ idx = end_idx + 1
388
+ continue
389
+ spans.append(
390
+ {
391
+ "label": label,
392
+ "start": int(offsets[out_start_idx][0]),
393
+ "end": int(offsets[out_end_idx][1]),
394
+ "score": score,
395
+ "text": text[int(offsets[out_start_idx][0]) : int(offsets[out_end_idx][1])],
396
+ }
397
+ )
398
+ idx = end_idx + 1
399
+ return dedupe_spans(spans)
400
+
401
+
402
+ def load_onnx_session(model_ref: str, onnx_file: str = "model_quantized.onnx", onnx_subfolder: str = "onnx"):
403
+ import onnxruntime as ort
404
+
405
+ model_path = Path(model_ref)
406
+ if model_path.exists():
407
+ candidates = []
408
+ if onnx_subfolder:
409
+ candidates.append(model_path / onnx_subfolder / onnx_file)
410
+ candidates.append(model_path / onnx_file)
411
+ onnx_path = next((path for path in candidates if path.exists()), candidates[0])
412
+ config = AutoConfig.from_pretrained(model_ref)
413
+ tokenizer = safe_auto_tokenizer(model_ref)
414
+ else:
415
+ remote_name = f"{onnx_subfolder}/{onnx_file}" if onnx_subfolder else onnx_file
416
+ onnx_path = Path(hf_hub_download(repo_id=model_ref, filename=remote_name, repo_type="model"))
417
+ config = AutoConfig.from_pretrained(model_ref)
418
+ tokenizer = safe_auto_tokenizer(model_ref)
419
+ session = ort.InferenceSession(str(onnx_path), providers=["CPUExecutionProvider"])
420
+ return session, tokenizer, config
421
+
422
+
423
+ def run_onnx(session, encoded: dict[str, Any]) -> tuple[np.ndarray, np.ndarray]:
424
+ feed = {}
425
+ input_names = {item.name for item in session.get_inputs()}
426
+ for key, value in encoded.items():
427
+ if key == "offset_mapping":
428
+ continue
429
+ if key in input_names:
430
+ feed[key] = value
431
+ outputs = session.run(None, feed)
432
+ return outputs[0], outputs[1]
433
+
434
+
435
+ def run_onnx_all(session, encoded: dict[str, Any]) -> list[np.ndarray]:
436
+ feed = {}
437
+ input_names = {item.name for item in session.get_inputs()}
438
+ for key, value in encoded.items():
439
+ if key == "offset_mapping":
440
+ continue
441
+ if key in input_names:
442
+ feed[key] = value
443
+ return session.run(None, feed)
config.json ADDED
@@ -0,0 +1,353 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
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+ "activation": "gelu",
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+ "architectures": [
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+ "IrishCoreTokenSpanModel"
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+ ],
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+ "attention_dropout": 0.1,
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+ "boundary_loss_weight": 1.0,
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+ "dim": 768,
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+ "dropout": 0.1,
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+ "hidden_dim": 3072,
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+ "id2label": {
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+ "0": "O",
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+ "1": "B-account_number",
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+ "2": "B-age",
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+ "3": "B-api_key",
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+ "4": "B-bank_routing_number",
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+ "5": "B-biometric_identifier",
19
+ "6": "B-blood_type",
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+ "7": "B-certificate_license_number",
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+ "8": "B-city",
22
+ "9": "B-company_name",
23
+ "10": "B-coordinate",
24
+ "11": "B-country",
25
+ "12": "B-county",
26
+ "13": "B-credit_debit_card",
27
+ "14": "B-customer_id",
28
+ "15": "B-cvv",
29
+ "16": "B-date",
30
+ "17": "B-date_of_birth",
31
+ "18": "B-date_time",
32
+ "19": "B-device_identifier",
33
+ "20": "B-education_level",
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+ "21": "B-email",
35
+ "22": "B-employee_id",
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+ "23": "B-employment_status",
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+ "24": "B-fax_number",
38
+ "25": "B-first_name",
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+ "26": "B-gender",
40
+ "27": "B-health_plan_beneficiary_number",
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+ "28": "B-http_cookie",
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+ "29": "B-ipv4",
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+ "30": "B-ipv6",
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+ "31": "B-language",
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+ "32": "B-last_name",
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+ "33": "B-license_plate",
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+ "34": "B-mac_address",
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+ "35": "B-medical_record_number",
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+ "36": "B-occupation",
50
+ "37": "B-password",
51
+ "38": "B-phone_number",
52
+ "39": "B-pin",
53
+ "40": "B-political_view",
54
+ "41": "B-postcode",
55
+ "42": "B-race_ethnicity",
56
+ "43": "B-religious_belief",
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+ "44": "B-sexuality",
58
+ "45": "B-ssn",
59
+ "46": "B-state",
60
+ "47": "B-street_address",
61
+ "48": "B-swift_bic",
62
+ "49": "B-tax_id",
63
+ "50": "B-time",
64
+ "51": "B-unique_id",
65
+ "52": "B-url",
66
+ "53": "B-user_name",
67
+ "54": "B-vehicle_identifier",
68
+ "55": "I-account_number",
69
+ "56": "I-api_key",
70
+ "57": "I-biometric_identifier",
71
+ "58": "I-blood_type",
72
+ "59": "I-certificate_license_number",
73
+ "60": "I-city",
74
+ "61": "I-company_name",
75
+ "62": "I-coordinate",
76
+ "63": "I-country",
77
+ "64": "I-county",
78
+ "65": "I-credit_debit_card",
79
+ "66": "I-customer_id",
80
+ "67": "I-date",
81
+ "68": "I-date_of_birth",
82
+ "69": "I-date_time",
83
+ "70": "I-device_identifier",
84
+ "71": "I-education_level",
85
+ "72": "I-email",
86
+ "73": "I-employee_id",
87
+ "74": "I-employment_status",
88
+ "75": "I-fax_number",
89
+ "76": "I-first_name",
90
+ "77": "I-gender",
91
+ "78": "I-health_plan_beneficiary_number",
92
+ "79": "I-http_cookie",
93
+ "80": "I-ipv4",
94
+ "81": "I-ipv6",
95
+ "82": "I-language",
96
+ "83": "I-last_name",
97
+ "84": "I-license_plate",
98
+ "85": "I-mac_address",
99
+ "86": "I-medical_record_number",
100
+ "87": "I-occupation",
101
+ "88": "I-password",
102
+ "89": "I-phone_number",
103
+ "90": "I-pin",
104
+ "91": "I-political_view",
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+ "92": "I-postcode",
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+ "93": "I-race_ethnicity",
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+ "94": "I-religious_belief",
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+ "95": "I-sexuality",
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+ "96": "I-ssn",
110
+ "97": "I-state",
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+ "98": "I-street_address",
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+ "100": "I-tax_id",
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+ "101": "I-time",
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+ "102": "I-unique_id",
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+ "103": "I-url",
117
+ "104": "I-user_name",
118
+ "105": "I-vehicle_identifier",
119
+ "106": "B-PPSN",
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+ "107": "I-PPSN",
121
+ "108": "B-PASSPORT_NUMBER",
122
+ "109": "I-PASSPORT_NUMBER",
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+ "110": "I-bank_routing_number"
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+ },
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+ "B-biometric_identifier": 5,
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+ "B-blood_type": 6,
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+ "B-certificate_license_number": 7,
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+ "B-city": 8,
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+ "B-county": 12,
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+ "B-customer_id": 14,
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+ "B-education_level": 20,
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+ "B-political_view": 40,
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+ "B-postcode": 41,
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+ "B-race_ethnicity": 42,
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+ "O": 0
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+ "max_position_embeddings": 512,
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+ "model_type": "distilbert",
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+ "n_heads": 12,
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+ "n_layers": 6,
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+ "num_span_labels": 11,
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+ "output_past": true,
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+ "pad_token_id": 0,
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+ "qa_dropout": 0.1,
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+ "seq_classif_dropout": 0.2,
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+ "sinusoidal_pos_embds": false,
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+ "span_label_max_span_tokens": {
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+ "ACCOUNT_NUMBER": 19,
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+ "BANK_ROUTING_NUMBER": 6,
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+ "CREDIT_DEBIT_CARD": 13,
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+ "EMAIL": 16,
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+ "PHONE_NUMBER": 10,
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+ "POSTCODE": 8,
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+ "SWIFT_BIC": 8
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+ },
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+ "span_label_names": [
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+ "ACCOUNT_NUMBER",
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+ "BANK_ROUTING_NUMBER",
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+ "CREDIT_DEBIT_CARD",
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+ "EMAIL",
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+ "FIRST_NAME",
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+ "LAST_NAME",
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+ "PASSPORT_NUMBER",
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+ "PHONE_NUMBER",
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+ "POSTCODE",
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+ "PPSN",
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+ "SWIFT_BIC"
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+ ],
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+ "tie_weights_": true,
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+ "token_extend_thresholds": {
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+ },
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+ "name": "openmed_irish_core_token_span_v1",
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+ "default_min_score": 0.5,
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+ "full_and_onnx_share_decoder": true
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+ }
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+ }
eval/benchmark_manual_suite_multilabel_base_irish_core_pii_v1.json ADDED
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1
+ {
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eval/benchmark_manual_suite_multilabel_base_irish_ppsn_phone_edge_v1.json ADDED
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eval/benchmark_multilingual_ppsn_v1_all_openmed_mliteclinical_base_cpu.json ADDED
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eval/benchmark_summary.json ADDED
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+ {
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+ "repo_id": "temsa/OpenMed-mLiteClinical-IrishCorePII-135M-v2-rc8",
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+ "previous_public_release": "temsa/OpenMed-mLiteClinical-IrishCorePII-135M-v2-rc7",
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eval/benchmark_summary.md ADDED
@@ -0,0 +1,40 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # Benchmark Summary
2
+
3
+ ## Release
4
+
5
+ - Release: `OpenMed-mLiteClinical-IrishCorePII-135M-v2-rc8`
6
+ - Repo: `temsa/OpenMed-mLiteClinical-IrishCorePII-135M-v2-rc8`
7
+ - Raw-only: `true`
8
+ - Scanner free: `true`
9
+ - Validator free: `true`
10
+ - Default `min_score`: `0.5`
11
+
12
+ ## Main Comparison
13
+
14
+ | Model | Irish core F1 | Edge F1 | Finance F1 | Finance-boundary F1 | User PPSN F1 | GA weak PPSN F1 | Multilingual PPSN F1 | Core CPU ex/s | Multilingual CPU ex/s |
15
+ |---|---:|---:|---:|---:|---:|---:|---:|---:|---:|
16
+ | Base OpenMed | 0.3743 | 0.0556 | - | - | - | - | 0.0000 | 15.1811 | 37.4666 |
17
+ | Previous public `rc7` full | 1.0000 | - | 1.0000 | 1.0000 | - | 1.0000 | - | 3.5394 | - |
18
+ | Previous public `rc7` ONNX q8 | 0.9934 | - | 1.0000 | 1.0000 | - | 1.0000 | - | 12.1653 | - |
19
+ | `rc8` full | 0.9737 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 0.9176 | 2.2965 | 6.3095 |
20
+ | `rc8` ONNX q8 | 0.9737 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 1.0000 | 0.9176 | 46.1420 | 99.7166 |
21
+
22
+ ## Irish Core Breakdown
23
+
24
+ | Label | `rc8` full | `rc8` ONNX q8 |
25
+ |---|---:|---:|
26
+ | PPSN | 1.0000 | 1.0000 |
27
+ | PHONE_NUMBER | 0.9565 | 0.9565 |
28
+ | POSTCODE | 1.0000 | 1.0000 |
29
+ | ACCOUNT_NUMBER | 0.8000 | 0.8000 |
30
+ | PASSPORT_NUMBER | 1.0000 | 1.0000 |
31
+ | EMAIL | 1.0000 | 1.0000 |
32
+ | FIRST_NAME | 0.9744 | 0.9744 |
33
+ | LAST_NAME | 0.9744 | 0.9744 |
34
+
35
+ ## Reading The Numbers
36
+
37
+ - `rc8` is the first public raw-only release in this line: no scanner, no regex extraction, no checksum validator layer.
38
+ - `rc7` is still stronger on the broad manual Irish core suite because it uses a bundled scanner/validator inference stack.
39
+ - `rc8` is simpler to embed and its ONNX q8 artifact stays very close to the full checkpoint on the release-gating suites.
40
+ - For CPU use, the ONNX q8 artifact is the default recommendation.
eval/rc8h_cal3_core_t050_cpu.json ADDED
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+ {
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+ "model": "models/openmed-mliteclinical-irish-core-multitask-rc8h_cal3",
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+ "POSTCODE": {
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+ "PPSN": {
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+ "SWIFT_BIC": {
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+ }
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+ }
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+ }
eval/rc8h_cal3_edge_t050_cpu.json ADDED
@@ -0,0 +1,36 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
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+ "model": "models/openmed-mliteclinical-irish-core-multitask-rc8h_cal3",
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+ "input": "eval/irish_ppsn_phone_edge_v1.jsonl",
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+ "tp": 78,
24
+ "fp": 2,
25
+ "fn": 6
26
+ }
27
+ }
28
+ }
eval/rc8h_cal3_q8_user_t050_cpu.json ADDED
@@ -0,0 +1,28 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "model": "models/openmed-mliteclinical-irish-core-multitask-rc8h_cal3_onnx_q8",
3
+ "input": "eval/user_raw_regression_cases_v1.jsonl",
4
+ "loader_type": "token_span_onnx_q8",
5
+ "examples": 7,
6
+ "min_score": 0.5,
7
+ "iou_threshold": 0.5,
8
+ "elapsed_seconds": 0.17300033092033118,
9
+ "examples_per_second": 40.462350347893775,
10
+ "overall": {
11
+ "precision": 1.0,
12
+ "recall": 1.0,
13
+ "f1": 1.0,
14
+ "tp": 3,
15
+ "fp": 0,
16
+ "fn": 0
17
+ },
18
+ "by_label": {
19
+ "PPSN": {
20
+ "precision": 1.0,
21
+ "recall": 1.0,
22
+ "f1": 1.0,
23
+ "tp": 3,
24
+ "fp": 0,
25
+ "fn": 0
26
+ }
27
+ }
28
+ }
eval/rc8h_cal3_user_t050_cpu.json ADDED
@@ -0,0 +1,28 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "model": "models/openmed-mliteclinical-irish-core-multitask-rc8h_cal3",
3
+ "input": "eval/user_raw_regression_cases_v1.jsonl",
4
+ "loader_type": "token_span_pt",
5
+ "examples": 7,
6
+ "min_score": 0.5,
7
+ "iou_threshold": 0.5,
8
+ "elapsed_seconds": 11.713831512955949,
9
+ "examples_per_second": 0.5975841459097078,
10
+ "overall": {
11
+ "precision": 1.0,
12
+ "recall": 1.0,
13
+ "f1": 1.0,
14
+ "tp": 3,
15
+ "fp": 0,
16
+ "fn": 0
17
+ },
18
+ "by_label": {
19
+ "PPSN": {
20
+ "precision": 1.0,
21
+ "recall": 1.0,
22
+ "f1": 1.0,
23
+ "tp": 3,
24
+ "fp": 0,
25
+ "fn": 0
26
+ }
27
+ }
28
+ }
inference_mask.py ADDED
@@ -0,0 +1,104 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ from __future__ import annotations
3
+
4
+ import argparse
5
+ import json
6
+ import os
7
+
8
+ os.environ.setdefault("TRANSFORMERS_NO_TF", "1")
9
+ os.environ.setdefault("TRANSFORMERS_NO_FLAX", "1")
10
+ os.environ.setdefault("TRANSFORMERS_NO_TORCHVISION", "1")
11
+ os.environ["USE_TF"] = "0"
12
+ os.environ["USE_FLAX"] = "0"
13
+ os.environ["USE_TORCH"] = "1"
14
+
15
+ import torch
16
+ from transformers import AutoConfig
17
+
18
+ from common import (
19
+ boundary_label_thresholds_from_config,
20
+ decode_token_presence_segments,
21
+ label_max_span_tokens_from_config,
22
+ label_min_nonspace_chars_from_config,
23
+ label_names_from_config,
24
+ safe_auto_tokenizer,
25
+ token_extend_thresholds_from_config,
26
+ token_label_thresholds_from_config,
27
+ )
28
+ from multitask_model import IrishCoreTokenSpanModel
29
+
30
+
31
+ def mask_text(text: str, spans: list[dict]) -> str:
32
+ out = text
33
+ for span in sorted(spans, key=lambda item: (item["start"], item["end"]), reverse=True):
34
+ out = out[: span["start"]] + f"[{span['label']}]" + out[span["end"] :]
35
+ return out
36
+
37
+
38
+ def predict(text: str, model, tokenizer, min_score: float):
39
+ encoded = tokenizer(text, return_offsets_mapping=True, return_tensors="pt", truncation=True)
40
+ offsets = [tuple(item) for item in encoded.pop("offset_mapping")[0].tolist()]
41
+ device = next(model.parameters()).device
42
+ encoded = {key: value.to(device) for key, value in encoded.items()}
43
+ with torch.no_grad():
44
+ output = model(**encoded)
45
+ token_scores = torch.sigmoid(output.token_logits[0]).cpu().numpy()
46
+ start_scores = torch.sigmoid(output.start_logits[0]).cpu().numpy()
47
+ end_scores = torch.sigmoid(output.end_logits[0]).cpu().numpy()
48
+ label_names = label_names_from_config(model.config)
49
+ thresholds = token_label_thresholds_from_config(model.config, min_score)
50
+ extend_thresholds = token_extend_thresholds_from_config(model.config)
51
+ max_span_tokens = label_max_span_tokens_from_config(model.config)
52
+ min_nonspace_chars = label_min_nonspace_chars_from_config(model.config)
53
+ boundary_thresholds = boundary_label_thresholds_from_config(model.config)
54
+ return decode_token_presence_segments(
55
+ text,
56
+ offsets,
57
+ token_scores,
58
+ label_names,
59
+ min_score,
60
+ thresholds,
61
+ extend_thresholds,
62
+ max_span_tokens,
63
+ min_nonspace_chars,
64
+ boundary_thresholds,
65
+ start_scores=start_scores,
66
+ end_scores=end_scores,
67
+ )
68
+
69
+
70
+ def main() -> None:
71
+ parser = argparse.ArgumentParser()
72
+ parser.add_argument("--model", required=True)
73
+ parser.add_argument("--text", required=True)
74
+ parser.add_argument("--min-score", type=float, default=0.5)
75
+ parser.add_argument("--device", choices=["auto", "cpu", "cuda"], default="auto")
76
+ parser.add_argument("--json", action="store_true")
77
+ args = parser.parse_args()
78
+
79
+ tokenizer = safe_auto_tokenizer(args.model)
80
+ config = AutoConfig.from_pretrained(args.model)
81
+ model = IrishCoreTokenSpanModel.from_pretrained(args.model, config=config)
82
+ if args.device == "auto":
83
+ device = "cuda" if torch.cuda.is_available() else "cpu"
84
+ else:
85
+ device = args.device
86
+ model.to(device)
87
+ model.eval()
88
+
89
+ spans = predict(args.text, model, tokenizer, args.min_score)
90
+ result = {
91
+ "model": args.model,
92
+ "backend": "transformers_token_span",
93
+ "min_score": args.min_score,
94
+ "spans": spans,
95
+ "masked_text": mask_text(args.text, spans),
96
+ }
97
+ if args.json:
98
+ print(json.dumps(result, indent=2, ensure_ascii=False))
99
+ else:
100
+ print(result["masked_text"])
101
+
102
+
103
+ if __name__ == "__main__":
104
+ main()
inference_mask_onnx.py ADDED
@@ -0,0 +1,90 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ from __future__ import annotations
3
+
4
+ import argparse
5
+ import json
6
+ import os
7
+
8
+ os.environ.setdefault("TRANSFORMERS_NO_TF", "1")
9
+ os.environ.setdefault("TRANSFORMERS_NO_FLAX", "1")
10
+ os.environ.setdefault("TRANSFORMERS_NO_TORCHVISION", "1")
11
+ os.environ["USE_TF"] = "0"
12
+ os.environ["USE_FLAX"] = "0"
13
+ os.environ["USE_TORCH"] = "1"
14
+
15
+ import numpy as np
16
+
17
+ from common import (
18
+ boundary_label_thresholds_from_config,
19
+ decode_token_presence_segments,
20
+ label_max_span_tokens_from_config,
21
+ label_min_nonspace_chars_from_config,
22
+ label_names_from_config,
23
+ load_onnx_session,
24
+ run_onnx_all,
25
+ token_extend_thresholds_from_config,
26
+ token_label_thresholds_from_config,
27
+ )
28
+
29
+
30
+ def mask_text(text: str, spans: list[dict]) -> str:
31
+ out = text
32
+ for span in sorted(spans, key=lambda item: (item["start"], item["end"]), reverse=True):
33
+ out = out[: span["start"]] + f"[{span['label']}]" + out[span["end"] :]
34
+ return out
35
+
36
+
37
+ def predict(text: str, session, tokenizer, config, min_score: float):
38
+ encoded = tokenizer(text, return_offsets_mapping=True, return_tensors="np", truncation=True)
39
+ offsets = [tuple(item) for item in encoded["offset_mapping"][0].tolist()]
40
+ token_logits, start_logits, end_logits = run_onnx_all(session, encoded)
41
+ token_scores = 1.0 / (1.0 + np.exp(-token_logits[0]))
42
+ start_scores = 1.0 / (1.0 + np.exp(-start_logits[0]))
43
+ end_scores = 1.0 / (1.0 + np.exp(-end_logits[0]))
44
+ label_names = label_names_from_config(config)
45
+ thresholds = token_label_thresholds_from_config(config, min_score)
46
+ extend_thresholds = token_extend_thresholds_from_config(config)
47
+ max_span_tokens = label_max_span_tokens_from_config(config)
48
+ min_nonspace_chars = label_min_nonspace_chars_from_config(config)
49
+ boundary_thresholds = boundary_label_thresholds_from_config(config)
50
+ return decode_token_presence_segments(
51
+ text,
52
+ offsets,
53
+ token_scores,
54
+ label_names,
55
+ min_score,
56
+ thresholds,
57
+ extend_thresholds,
58
+ max_span_tokens,
59
+ min_nonspace_chars,
60
+ boundary_thresholds,
61
+ start_scores=start_scores,
62
+ end_scores=end_scores,
63
+ )
64
+
65
+
66
+ def main() -> None:
67
+ parser = argparse.ArgumentParser()
68
+ parser.add_argument("--model", required=True)
69
+ parser.add_argument("--text", required=True)
70
+ parser.add_argument("--min-score", type=float, default=0.5)
71
+ parser.add_argument("--json", action="store_true")
72
+ args = parser.parse_args()
73
+
74
+ session, tokenizer, config = load_onnx_session(args.model, onnx_file="model_quantized.onnx", onnx_subfolder="onnx")
75
+ spans = predict(args.text, session, tokenizer, config, args.min_score)
76
+ result = {
77
+ "model": args.model,
78
+ "backend": "onnx_token_span_q8",
79
+ "min_score": args.min_score,
80
+ "spans": spans,
81
+ "masked_text": mask_text(args.text, spans),
82
+ }
83
+ if args.json:
84
+ print(json.dumps(result, indent=2, ensure_ascii=False))
85
+ else:
86
+ print(result["masked_text"])
87
+
88
+
89
+ if __name__ == "__main__":
90
+ main()
model.py ADDED
@@ -0,0 +1,75 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ from __future__ import annotations
3
+
4
+ from dataclasses import dataclass
5
+ from typing import Optional
6
+
7
+ import torch
8
+ import torch.nn as nn
9
+ from transformers import AutoConfig, AutoModel, PreTrainedModel
10
+ from transformers.utils import ModelOutput
11
+
12
+
13
+ def hidden_size_from_config(config) -> int:
14
+ return int(getattr(config, "hidden_size", getattr(config, "dim")))
15
+
16
+
17
+ @dataclass
18
+ class MultilabelSpanOutput(ModelOutput):
19
+ loss: Optional[torch.Tensor] = None
20
+ start_logits: Optional[torch.Tensor] = None
21
+ end_logits: Optional[torch.Tensor] = None
22
+
23
+
24
+ class IrishCoreSpanHeadModel(PreTrainedModel):
25
+ config_class = AutoConfig
26
+ base_model_prefix = "encoder"
27
+
28
+ def __init__(self, config):
29
+ super().__init__(config)
30
+ num_span_labels = int(getattr(config, "num_span_labels"))
31
+ self.encoder = AutoModel.from_config(config)
32
+ hidden_size = hidden_size_from_config(config)
33
+ dropout = float(getattr(config, "seq_classif_dropout", getattr(config, "dropout", 0.1)))
34
+ self.dropout = nn.Dropout(dropout)
35
+ self.start_classifier = nn.Linear(hidden_size, num_span_labels)
36
+ self.end_classifier = nn.Linear(hidden_size, num_span_labels)
37
+ pos_weight = float(getattr(config, "span_positive_weight", 6.0))
38
+ self.register_buffer("loss_pos_weight", torch.full((num_span_labels,), pos_weight), persistent=False)
39
+ self.post_init()
40
+
41
+ def forward(
42
+ self,
43
+ input_ids=None,
44
+ attention_mask=None,
45
+ token_type_ids=None,
46
+ start_positions=None,
47
+ end_positions=None,
48
+ token_mask=None,
49
+ **kwargs,
50
+ ) -> MultilabelSpanOutput:
51
+ encoder_kwargs = {
52
+ "input_ids": input_ids,
53
+ "attention_mask": attention_mask,
54
+ **kwargs,
55
+ }
56
+ if token_type_ids is not None and getattr(self.config, "model_type", "") not in {"distilbert", "roberta"}:
57
+ encoder_kwargs["token_type_ids"] = token_type_ids
58
+ outputs = self.encoder(**encoder_kwargs)
59
+ hidden = self.dropout(outputs.last_hidden_state)
60
+ start_logits = self.start_classifier(hidden)
61
+ end_logits = self.end_classifier(hidden)
62
+
63
+ loss = None
64
+ if start_positions is not None and end_positions is not None:
65
+ if token_mask is None:
66
+ token_mask = attention_mask
67
+ mask = token_mask.float().unsqueeze(-1)
68
+ pos_weight = self.loss_pos_weight.to(start_logits.device)
69
+ bce = nn.BCEWithLogitsLoss(reduction="none", pos_weight=pos_weight)
70
+ start_loss = bce(start_logits, start_positions.float()) * mask
71
+ end_loss = bce(end_logits, end_positions.float()) * mask
72
+ denom = mask.sum().clamp_min(1.0) * start_logits.shape[-1]
73
+ loss = (start_loss.sum() + end_loss.sum()) / (2.0 * denom)
74
+
75
+ return MultilabelSpanOutput(loss=loss, start_logits=start_logits, end_logits=end_logits)
model.safetensors ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3c7908e59662702202602a82808406bc724e1b8fedb0c7771992914411ea0e32
3
+ size 539050284
multitask_head_meta.json ADDED
@@ -0,0 +1,43 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "base_model": "models/openmed-mliteclinical-irish-core-span-rc8f_gapunct_cal",
3
+ "init_span_model": "models/openmed-mliteclinical-irish-core-span-rc8f_gapunct_cal",
4
+ "init_token_model": "release/OpenMed-mLiteClinical-IrishCorePII-135M-v2-rc7",
5
+ "label_names": [
6
+ "ACCOUNT_NUMBER",
7
+ "BANK_ROUTING_NUMBER",
8
+ "CREDIT_DEBIT_CARD",
9
+ "EMAIL",
10
+ "FIRST_NAME",
11
+ "LAST_NAME",
12
+ "PASSPORT_NUMBER",
13
+ "PHONE_NUMBER",
14
+ "POSTCODE",
15
+ "PPSN",
16
+ "SWIFT_BIC"
17
+ ],
18
+ "max_length": 128,
19
+ "task": "Irish core PII token-presence plus start/end span extraction",
20
+ "freeze_layers": 2,
21
+ "span_positive_weight": 6.0,
22
+ "token_positive_weight": 4.0,
23
+ "token_presence_weight": 1.0,
24
+ "boundary_loss_weight": 1.0,
25
+ "boundary_smoothing": 0.15,
26
+ "fitted_label_max_span_tokens": {
27
+ "ACCOUNT_NUMBER": 19,
28
+ "BANK_ROUTING_NUMBER": 6,
29
+ "CREDIT_DEBIT_CARD": 13,
30
+ "EMAIL": 16,
31
+ "FIRST_NAME": 5,
32
+ "LAST_NAME": 8,
33
+ "PASSPORT_NUMBER": 9,
34
+ "PHONE_NUMBER": 10,
35
+ "POSTCODE": 8,
36
+ "PPSN": 9,
37
+ "SWIFT_BIC": 8
38
+ },
39
+ "train_examples": 30000,
40
+ "valid_examples": 3750,
41
+ "test_examples": 3750,
42
+ "data": "data/irish_core_multitask_rc8_mix_v1"
43
+ }
multitask_model.py ADDED
@@ -0,0 +1,91 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ #!/usr/bin/env python3
2
+ from __future__ import annotations
3
+
4
+ from dataclasses import dataclass
5
+ from typing import Optional
6
+
7
+ import torch
8
+ import torch.nn as nn
9
+ from transformers import AutoConfig, AutoModel, PreTrainedModel
10
+ from transformers.utils import ModelOutput
11
+
12
+ from model import hidden_size_from_config
13
+
14
+
15
+ @dataclass
16
+ class MultitaskSpanOutput(ModelOutput):
17
+ loss: Optional[torch.Tensor] = None
18
+ token_logits: Optional[torch.Tensor] = None
19
+ start_logits: Optional[torch.Tensor] = None
20
+ end_logits: Optional[torch.Tensor] = None
21
+
22
+
23
+ class IrishCoreTokenSpanModel(PreTrainedModel):
24
+ config_class = AutoConfig
25
+ base_model_prefix = "encoder"
26
+
27
+ def __init__(self, config):
28
+ super().__init__(config)
29
+ num_span_labels = int(getattr(config, "num_span_labels"))
30
+ self.encoder = AutoModel.from_config(config)
31
+ hidden_size = hidden_size_from_config(config)
32
+ dropout = float(getattr(config, "seq_classif_dropout", getattr(config, "dropout", 0.1)))
33
+ self.dropout = nn.Dropout(dropout)
34
+ self.token_classifier = nn.Linear(hidden_size, num_span_labels)
35
+ self.start_classifier = nn.Linear(hidden_size, num_span_labels)
36
+ self.end_classifier = nn.Linear(hidden_size, num_span_labels)
37
+ boundary_pos_weight = float(getattr(config, "span_positive_weight", 6.0))
38
+ presence_pos_weight = float(getattr(config, "token_positive_weight", 4.0))
39
+ self.register_buffer("boundary_pos_weight", torch.full((num_span_labels,), boundary_pos_weight), persistent=False)
40
+ self.register_buffer("presence_pos_weight", torch.full((num_span_labels,), presence_pos_weight), persistent=False)
41
+ self.post_init()
42
+
43
+ def forward(
44
+ self,
45
+ input_ids=None,
46
+ attention_mask=None,
47
+ token_type_ids=None,
48
+ token_labels=None,
49
+ start_positions=None,
50
+ end_positions=None,
51
+ token_mask=None,
52
+ **kwargs,
53
+ ) -> MultitaskSpanOutput:
54
+ encoder_kwargs = {
55
+ "input_ids": input_ids,
56
+ "attention_mask": attention_mask,
57
+ **kwargs,
58
+ }
59
+ if token_type_ids is not None and getattr(self.config, "model_type", "") not in {"distilbert", "roberta"}:
60
+ encoder_kwargs["token_type_ids"] = token_type_ids
61
+ outputs = self.encoder(**encoder_kwargs)
62
+ hidden = self.dropout(outputs.last_hidden_state)
63
+ token_logits = self.token_classifier(hidden)
64
+ start_logits = self.start_classifier(hidden)
65
+ end_logits = self.end_classifier(hidden)
66
+
67
+ loss = None
68
+ if token_labels is not None and start_positions is not None and end_positions is not None:
69
+ if token_mask is None:
70
+ token_mask = attention_mask
71
+ mask = token_mask.float().unsqueeze(-1)
72
+ boundary_pos_weight = self.boundary_pos_weight.to(token_logits.device)
73
+ presence_pos_weight = self.presence_pos_weight.to(token_logits.device)
74
+ bce_boundary = nn.BCEWithLogitsLoss(reduction="none", pos_weight=boundary_pos_weight)
75
+ bce_presence = nn.BCEWithLogitsLoss(reduction="none", pos_weight=presence_pos_weight)
76
+ token_loss = bce_presence(token_logits, token_labels.float()) * mask
77
+ start_loss = bce_boundary(start_logits, start_positions.float()) * mask
78
+ end_loss = bce_boundary(end_logits, end_positions.float()) * mask
79
+ denom = mask.sum().clamp_min(1.0) * token_logits.shape[-1]
80
+ token_loss = token_loss.sum() / denom
81
+ boundary_loss = (start_loss.sum() + end_loss.sum()) / (2.0 * denom)
82
+ token_weight = float(getattr(self.config, "token_presence_weight", 1.0))
83
+ boundary_weight = float(getattr(self.config, "boundary_loss_weight", 1.0))
84
+ loss = token_weight * token_loss + boundary_weight * boundary_loss
85
+
86
+ return MultitaskSpanOutput(
87
+ loss=loss,
88
+ token_logits=token_logits,
89
+ start_logits=start_logits,
90
+ end_logits=end_logits,
91
+ )
onnx/model.onnx ADDED
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+ version = "0.1.0"
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+ description = "Raw-only Irish core PII release for OpenMed mLiteClinical"
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+ requires-python = ">=3.10"
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+ {
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+ "full_example": "My PPSN is 1234567TW, my Eircode is D02 X285, and my phone is 087 123 4567.",
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+ "notes": [
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+ "No scanner or validator layer is required for release behavior.",
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+ "Use the bundled inference scripts or import common.decode_token_presence_segments.",
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+ "ONNX q8 is the recommended CPU path."
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+ ]
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+ }
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+ {
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+ "public_baseline_reference": "temsa/OpenMed-mLiteClinical-IrishCorePII-135M-v2-rc7",
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+ "coverage": [
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+ "ACCOUNT_NUMBER",
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+ "training_data": {
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+ "published": [
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+ "temsa/OpenMed-Irish-CorePII-TrainMix-v1",
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+ "temsa/OpenMed-Irish-PPSN-Eircode-Spec-v1",
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+ "joelniklaus/mapa",
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+ "gretelai/synthetic_pii_finance_multilingual"
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+ ],
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+ "title": "Split-NER",
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+ "url": "https://aclanthology.org/2023.acl-short.36/"
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+ "url": "https://aclanthology.org/2021.acl-long.558/"
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+ "title": "Boundary Smoothing for Named Entity Recognition",
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+ "url": "https://aclanthology.org/2022.acl-long.490/"
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+ "title": "TinyBERT",
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+ "url": "https://aclanthology.org/2020.findings-emnlp.372/"
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+ }
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