| --- |
| license: apache-2.0 |
| base_model: zuzab/pico-extractor |
| library_name: transformers |
| pipeline_tag: token-classification |
| language: |
| - en |
| tags: |
| - mlx |
| - safetensors |
| - fp16 |
| - biomedical |
| - pico |
| - ner |
| - bert |
| --- |
| |
| # pico-extractor |
|
|
| BIO token classifier tagging PICO elements (Population, Intervention, Comparator, Outcome) in clinical-trial abstracts; used by Mineris for PICO span extraction. |
|
|
| This is a **format conversion** of [`zuzab/pico-extractor`](https://huggingface.co/zuzab/pico-extractor) |
| for Mineris' MLX inference stack (`mineris_inference`) — not a fine-tune. Weights are |
| the full upstream `BertForTokenClassification` (encoder + classification head) cast to fp16 and stored as `model.safetensors`; a |
| `tokenizer.json` is included so the model loads without `transformers` or `torch`. |
|
|
| ## Labels |
|
|
| | id | label | |
| |---|---| |
| | 0 | `O` | |
| | 1 | `B-P` | |
| | 2 | `B-I` | |
| | 3 | `B-C` | |
| | 4 | `B-O` | |
| | 5 | `I-P` | |
| | 6 | `I-I` | |
| | 7 | `I-C` | |
| | 8 | `I-O` | |
|
|
| ## Provenance |
|
|
| | | | |
| |---|---| |
| | Upstream repo | [`zuzab/pico-extractor`](https://huggingface.co/zuzab/pico-extractor) | |
| | Upstream commit | `ed4df86e482d9c53d953791a71c15caa5a687d96` | |
| | License | `apache-2.0` (declared by Mineris, the upstream owner) | |
| | Conversion notebook | `notebook/notebooks/converter/convert_pico_extractor.ipynb` (mineris repo) | |
| | Mineris commit | `9817fe7bbeb2a4b23fd683144a28a5843af94af9` | |
| | Version | `v1.0.0` | |
| | dtype | fp16 | |
| | Tensors / size | 199 / 215.3 MB | |
|
|
| ## Conversion parity (fp16 mirror vs fp32 upstream, PyTorch) |
|
|
| | Metric | Value | |
| |---|---| |
| | Texts | 18 | |
| | Tokenizer id mismatches (`tokenizer.json` via `tokenizers` vs upstream tokenizer) | 0 | |
| | Token argmax label agreement, per text — min / mean | 1.000000 / 1.000000 | |
| | Logits, non-padding tokens — max abs diff / median relative diff | 9.82e-03 / 5.09e-04 | |
| | Threshold (min token argmax label agreement) | 0.995 | |
|
|
| MLX-runtime parity is tracked separately in the mineris `notebook/notebooks/benchmark/` notebooks. |
|
|
| ## Versioning |
|
|
| Releases are semver git tags on this repo (`vMAJOR.MINOR.PATCH`); consumers pin a tag. MAJOR = |
| output-incompatible change, MINOR = compatible re-conversion, PATCH = card/metadata only. |
|
|
| ## CHANGELOG |
|
|
| - `v1.0.0` — initial conversion from `zuzab/pico-extractor@ed4df86`. |
|
|
