prorris/greek-deid-benchmark

Greek Clinical De-identification Benchmark

500 fully synthetic Greek hospital discharge notes (300 cardiac surgery, 100 cardiology, 100 nephrology) for evaluating clinical-text de-identification, scored on both sides:

• 7,937 must-redact identifier instances — dual full independent review (F1 = 0.998), arbitrated; annotations/gold_standard.json, character spans over text.
• 6,747 must-survive clinical probes — drug names, diagnoses, laboratory values, Greek section headers, procedures, measurements, abbreviations and eponyms that a system must leave intact; in each record's phi list (expect: "survive") and collected in annotations/must_survive.json. A probe is a category and a value, with no offsets: it is kept if the value still stands verbatim in the system's output.

Everything here is synthetic. No real patient data was used at any stage. Hospitals, towns and street names are real public facts; every person, identifier, telephone number and clinical history is invented. Invented values were made realistic and were not checked against any registry, so a number or a name may coincide with a real one; any such match is unintended and carries no information. To have a value changed, see the repository below.

This is an evaluation set: there is one split, test, and it is not meant for training.

Record of reference

This is a mirror. The record of reference — with the rendered PDFs, the complete scoring implementation, the evaluated system's outputs for two independent runs and every scored decision — is the Zenodo deposit and its GitHub repository:

• Zenodo: https://doi.org/10.5281/zenodo.22824895
• GitHub: https://github.com/prorris/greek-deid-benchmark
• Project website: https://clinicalminer.com/publications

Please cite the Zenodo record (see CITATION.cff there).

Surrogate pools of the evaluated engine

surrogates/morpheus_1.0_surrogate_pools.json lists the pools of artificial replacement values (names, towns, street and hospital-name parts) that the evaluated engine, Morpheus 1.0, drew from when it produced the published outputs. Values only — see surrogates/README.md. Every value is artificial and refers to no one.

Fields

id · text (the note) · phi (list of {category, expect, value}; expect is "redact" — the generation-time pre-annotation, superseded by annotations/gold_standard.json — or "survive").

Licence

Data: CC BY 4.0.