Papers › MASK: A flexible framework to facilitate de-identification of clinical texts
MASK: A flexible framework to facilitate de-identification of clinical texts
Nikola Milosevic, Gangamma Kalappa, Hesam Dadafarin, Mahmoud Azimaee, Goran Nenadic
Medical health records and clinical summaries contain a vast amount of important information in textual form that can help advancing research on treatments, drugs and public health. However, the majority of these information is not shared because they contain private information about patients, their families, or medical staff treating them. Regulations such as HIPPA in the US, PHIPPA in Canada and GDPR regulate the protection, processing and distribution of this information. In case this information is de-identified and personal information are replaced or redacted, they could be distributed to the research community. In this paper, we present MASK, a software package that is designed to perform the de-identification task. The software is able to perform named entity recognition using some of the state-of-the-art techniques and then mask or redact recognized entities. The user is able to select named entity recognition algorithm (currently implemented are two versions of CRF-based techniques and BiLSTM-based neural network with pre-trained GLoVe and ELMo embedding) and masking algorithm (e.g. shift dates, replace names/locations, totally redact entity).
Code
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Tasks
Results from the paper archive 2025-07-28
| Task | Dataset | Model | Metric | Value | Rank at snapshot | Leaderboard | Report |
|---|---|---|---|---|---|---|---|
| Named Entity Recognition (NER) | i2b2 De-identification Dataset | BiLSTM with ELMo | F1 | 0.97 | #1 of 1 | Archive leaderboard | report |
| Named Entity Recognition (NER) | i2b2 De-identification Dataset | BiLSTM with ELMo | Precision | 96 | #1 of 1 | Archive leaderboard | report |
Ranks are positions in the archive's leaderboards as they stood at the 2025-07-28 snapshot. Results published since then are not among these rows, so a rank here is not a current standing.
Methods
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