Not What the Doctor Ordered: Surveying LLM-based De-identification and Quantifying Clinical Information Loss
Bibliographic record
Abstract
De-identification in the healthcare setting is an application of NLP where automated algorithms are used to remove personally identifying information of patients (and, sometimes, providers). With the recent rise of generative large language models (LLMs), there has been a corresponding rise in the number of papers that apply LLMs to de-identification. Although these approaches often report near-perfect results, significant challenges concerning reproducibility and utility of the research papers persist. This paper identifies three key limitations in the current literature: inconsistent reporting metrics hindering direct comparisons, the inadequacy of traditional classification metrics in capturing errors which LLMs may be more prone to (i.e., altering clinically relevant information), and lack of manual validation of automated metrics which aim to quantify these errors. To address these issues, we first present a survey of LLM-based de-identification research, highlighting the heterogeneity in reporting standards. Second, we evaluated a diverse set of models to quantify the extent of inappropriate removal of clinical information. Next, we conduct a manual validation of an existing evaluation metric to measure the removal of clinical information, employing clinical experts to assess their efficacy. We highlight poor performance and describe the inherent limitations of such metrics in identifying clinically significant changes. Lastly, we propose a novel methodology for the detection of clinically relevant information removal.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.162 | 0.558 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.012 | 0.010 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.006 | 0.007 |
| Open science | 0.003 | 0.004 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".