outis 0.1.0__tar.gz

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outis-0.1.0/NOTICE

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+Outis
+Copyright 2026
+
+The default detector is fine-tuned from DeBERTa-v3-base, Copyright Microsoft
+Corporation, licensed under the MIT License.
+Source: https://huggingface.co/microsoft/deberta-v3-base
+
+Earlier detector checkpoints, and candidates that may still be trained, are
+fine-tuned from ModernBERT-base, Copyright Answer.AI, licensed under the Apache
+License, Version 2.0.
+Source: https://huggingface.co/answerdotai/ModernBERT-base
+
+The optional `generators` extra uses OpenAI Privacy Filter (`opf`), Copyright
+OpenAI, licensed under the Apache License, Version 2.0, pinned to commit
+f7f00ca7fb869683eb732c010299d901457f19c3, only to compute token offsets for
+legacy corpus statistics.
+Source: https://github.com/openai/privacy-filter
+
+PyTorch, Hugging Face Transformers, FastAPI, Uvicorn, tiktoken and other
+dependencies retain their respective licenses. No externally sourced clinical
+training dataset is included or downloaded.
+
+Project-authored synthetic corpus text and annotations are dedicated to the
+public domain under CC0 1.0 Universal:
+https://creativecommons.org/publicdomain/zero/1.0/

outis-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: outis
+Version: 0.1.0
+Summary: Local clinical PHI detection, redaction and consistent synthetic replacement
+Author: Eric Hauser
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/ewhauser/outis
+Project-URL: Documentation, https://github.com/ewhauser/outis/tree/main/docs
+Project-URL: Changelog, https://github.com/ewhauser/outis/blob/main/CHANGELOG.md
+Project-URL: Issues, https://github.com/ewhauser/outis/issues
+Keywords: de-identification,phi,clinical-nlp,ner,privacy,hipaa
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: NOTICE
+Requires-Dist: torch>=2.6
+Requires-Dist: transformers>=5.6
+Requires-Dist: safetensors>=0.5
+Requires-Dist: huggingface-hub>=0.35
+Requires-Dist: fastapi>=0.115
+Requires-Dist: uvicorn[standard]>=0.30
+Requires-Dist: pydantic>=2.10
+Requires-Dist: python-dateutil>=2.9
+Requires-Dist: tiktoken>=0.9
+Requires-Dist: numpy>=2.0
+Requires-Dist: regex>=2024.11
+Requires-Dist: defusedxml>=0.7
+Requires-Dist: sentencepiece>=0.2
+Requires-Dist: protobuf>=5
+Provides-Extra: pdf
+Requires-Dist: pypdf>=6.19.0; extra == "pdf"
+Requires-Dist: reportlab>=4; extra == "pdf"
+Dynamic: license-file
+
+# Outis
+
+[![CI](https://github.com/ewhauser/outis/actions/workflows/ci.yml/badge.svg)](https://github.com/ewhauser/outis/actions/workflows/ci.yml)
+[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](LICENSE)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue.svg)](pyproject.toml)
+
+Local PHI detection, typed redaction and patient-consistent synthetic
+replacement for English clinical text.
+
+Outis is Greek for "nobody": the name Odysseus gave the Cyclops.
+
+The detector is a fully fine-tuned
+[DeBERTa-v3-base](https://huggingface.co/microsoft/deberta-v3-base) token
+classifier with a constrained BIOES decoder. There is no rule layer: every
+detected span comes from the model. Everything runs on your machine; no text
+is sent to a hosted service. It ships as a Python library, a CLI and a FastAPI
+server.
+
+- **Model:** [ewhauser/outis-deberta-v3-base](https://huggingface.co/ewhauser/outis-deberta-v3-base) on Hugging Face
+- **Training data:** [ewhauser/outis-synthetic-phi](https://huggingface.co/datasets/ewhauser/outis-synthetic-phi), the synthetic
+  corpora the model was trained and selected on
+
+> [!IMPORTANT]
+> This is research software. It has **not** met all of its [evaluation targets](docs/evaluation.md), and it has been evaluated only on
+> synthetic and public benchmark text, never on real clinical records. It does
+> not by itself provide HIPAA Safe Harbor or Expert Determination
+> de-identification. See [Limitations](#limitations).
+
+## Features
+
+- **14 PHI types**: NAME, DATE, AGE, ADDRESS, LOCATION, FACILITY, PHONE, EMAIL,
+  URL, IP, MRN, SSN, ACCOUNT and ID.
+- **Redaction or replacement**: typed markers or masks, or fictional values that
+  stay consistent per patient. Dates shift by a stable per-patient offset that
+  preserves intervals.
+- **Model-only detection**: one fine-tuned encoder, decoded to exact original
+  character offsets.
+- **Configurable policies**: per-type actions, custom identifier rules, linked
+  messages, explicit restoration, and JSON, CSV, XML and plain-text file input.
+- **Local by design**: loopback-only by default, optional API key, no request
+  logging, `Cache-Control: no-store` on responses.
+
+## Quickstart
+
+Requires Python 3.11+ and [uv](https://docs.astral.sh/uv/).
+
+```sh
+git clone https://github.com/ewhauser/outis.git
+cd outis
+uv sync
+```
+
+The default model's configuration and tokenizer are in
+`models/deid-deberta-v3-base`. Download its 736 MB weight file from
+[Hugging Face](https://huggingface.co/ewhauser/outis-deberta-v3-base):
+
+```sh
+uv run hf download ewhauser/outis-deberta-v3-base hf/model.safetensors --local-dir models/deid-deberta-v3-base
+```
+
+Add the `pdf` extra (`uv sync --extra pdf`) for PDF file input.
+
+### Python
+
+Run it with `uv run python`.
+
+```python
+from outis import Deidentifier
+
+deid = Deidentifier(secret=b"application-secret-at-least-32-bytes")
+
+result = deid.deidentify("Mara Calder was seen on 2024-02-28.", mode="redact")
+print(result["text"])
+
+synthetic = deid.deidentify(
+    "Mara Calder was seen on 2024-02-28.",
+    mode="synthetic",
+    patient_id="internal-patient-42",
+)
+print(synthetic["text"])
+```
+
+Each result contains the transformed text and, for every entity, its type,
+original character offsets, replacement and score. It also lists any warnings
+and the model version.
+
+### HTTP API
+
+```sh
+uv run scripts/serve_local.py --port 8000
+```
+
+```sh
+curl http://127.0.0.1:8000/v1/deidentify \
+  -H 'Content-Type: application/json' \
+  -d '{"text":"Patient Mara Calder, DOB 1974-06-13. Creatinine 1.2 mg/dL.","mode":"redact"}'
+```
+
+Interactive docs are served at `http://127.0.0.1:8000/docs`, and the OpenAPI
+schema at `/openapi.json`. The local launcher creates and reuses a replacement
+secret in `.cache/local-api-secret`. For other deployments, see
+[deployment](docs/deployment.md).
+
+### CLI
+
+```sh
+uv run outis text --input note.txt --mode redact
+```
+
+## How it works
+
+```
+text ─▶ DeBERTa-v3-base token classifier (overlapping 512-token windows)
+          └─▶ constrained BIOES decoder ─▶ spans at original offsets ─▶ redact / replace
+```
+
+The default model was fine-tuned on about 116,000 synthetic notes from 46
+banks written by this project's generators and independent synthetic authors. No real
+clinical data was used for training. See the [model card](MODEL_CARD.md).
+
+## Results
+
+All results come from synthetic text. None of them measures accuracy on real
+clinical notes.
+
+### Public benchmarks
+
+Every model is scored the same way, under this project's annotation policy
+([details](docs/external-verification.md)). ↑ means higher is better, ↓ lower
+is better; the best result in each row is in bold.
+
+| Benchmark | Measure | Outis | [MedDeID](https://huggingface.co/stighellemans/meddeid-english-synth) | [GLiNER-PII](https://huggingface.co/nvidia/gliner-PII)\* |
+|---|---|---:|---:|---:|
+| [ASQ-PHI](https://doi.org/10.17632/csz5dzp7nx.1)<br>1,051 search queries | PHI characters masked ↑ | **99.94%** | 99.66% | 98.57% |
+|  | Non-PHI text removed ↓ | **0.18%** | 0.91% | 2.43% |
+|  | Notes fully masked ↑ | **99.52%** | 97.60% | 94.47% |
+| [MedDeID English](https://huggingface.co/datasets/stighellemans/meddeid-english-synthetic-benchmark)<br>300 notes | PHI characters masked ↑ | **99.27%** | 99.19% | 94.87% |
+|  | Non-PHI text removed ↓ | **0.01%** | 0.15% | 0.64% |
+|  | Notes fully masked ↑ | **95.00%** | 93.00% | 69.67% |
+| [Technetium-I](https://huggingface.co/datasets/temlm-foundation/Technetium-I)<br>5,000-note sample | PHI characters masked ↑ | 99.65% | 99.65% | not run |
+|  | Non-PHI text removed ↓ | **0.57%** | 1.14% | not run |
+|  | Notes fully masked ↑ | 84.60% | 84.60% | not run |
+
+\* `nvidia/gliner-PII` with one added zero-shot label for hospitals.
+
+We have looked at Outis's failures on ASQ-PHI and MedDeID English while
+developing it, so those two are not fully independent tests; Technetium-I has
+not been inspected. Per-identifier results are in the
+[full comparison](benchmarks/results/COMPARISON.md).
+
+### Held-out synthetic notes
+
+On 2,400 synthetic notes from an author whose writing was never used in
+training:
+
+| Measure | Result |
+|---|---:|
+| Direct identifiers masked (names, record numbers, phone numbers, emails, addresses and similar) | 99.64% |
+| Names masked (95% lower bound) | 99.79% (99.71%) |
+| Indirect identifiers masked (dates, ages over 89, places, facilities) | 98.97% |
+| Detected spans that are real PHI | 99.63% |
+| Exact type and boundary match (F1) | 97.34% |
+| Notes with every identifier masked* | 86.25% |
+
+\* Counts ages over 89, the ages HIPAA's Safe Harbor method lists as
+identifiers; ages of 89 and under stay in the output by default. The model
+detects every age, so setting the request policy's `ages` option to `all`
+removes younger ages too (see the [API guide](docs/api.md)). Counting every
+age, 81.90% of notes are fully masked.
+
+On these same notes MedDeID masked 86.08% of direct identifiers and GLiNER-PII
+79.09%. The notes follow this project's annotation conventions, which this
+model was trained on, so that gap overstates its advantage; the public
+benchmarks above are the fair comparison.
+
+A separate test of real place names (2,352 notes) masked 98.81% of city and
+care-site name characters, but tagged a bare state or country in 4% of notes
+that contained no PHI.
+
+How these numbers are computed is described in
+[evaluation methodology](docs/evaluation.md).
+
+## Limitations
+
+- **Not yet measured on real notes.** Held-out synthetic authors are the best
+  available evidence; real institutional notes may differ substantially.
+- **Synthetic evaluation only.** Training and internal test text comes from
+  this project's own generators. Real institutional formats, rare identifying
+  narratives and unseen identity styles are not measured.
+- **Scope.** English plain text only. OCR, scanned images, audio and
+  multilingual text are out of scope.
+- **Some options return PHI.** Restoration mappings, sensitive entity analysis
+  and per-type `keep` deliberately return original values. Treat those
+  responses as PHI.
+- **Scores are not calibrated.** Model scores are not safety probabilities.
+- **Replacement is not anonymity.** Fictional values can resemble real people,
+  and date shifting changes seasonal context. Surrogates do not guarantee
+  resistance to re-identification.
+
+Use human review and an appropriate privacy determination before releasing
+any output.
+
+## Documentation
+
+| Guide | Contents |
+|---|---|
+| [Evaluation methodology](docs/evaluation.md) | Targets, any-label masking and how models are compared |
+| [API guide](docs/api.md) | Endpoints, policies, masks, structured data, files, WebSockets |
+| [Synthetic replacement](docs/replacement.md) | Secrets, patient anchors, date shifting, identity linking |
+| [Deployment](docs/deployment.md) | Launcher, default model, batch limits, security controls |
+| [Model card](MODEL_CARD.md) | Architecture, training data, evaluation, risks |
+| [Training](docs/training.md) | Training candidates and generating corpora |
+| [External verification](docs/external-verification.md) | Public benchmark protocol and results |
+| [Annotation policy](docs/annotation-policy-v2.md) | Span conventions for every entity type |
+| [Places addendum](docs/annotation-policy-v2-places.md) | Real localities, care-site abbreviations and public references |
+
+## Contributing
+
+See [CONTRIBUTING.md](CONTRIBUTING.md). Report security issues privately, as
+described in [SECURITY.md](SECURITY.md). Never put real PHI in an issue, pull
+request or test fixture.
+
+## Citation
+
+If you use this project, please cite it using [CITATION.cff](CITATION.cff).
+
+## License
+
+Source code and the fine-tuned model are licensed under
+[Apache-2.0](LICENSE). Generated synthetic corpus text and annotations are
+dedicated to the public domain under CC0-1.0. The DeBERTa-v3-base base model
+is MIT-licensed; see [NOTICE](NOTICE).