Extensive Error Analysis and a Learning-Based Evaluation of Medical Entity Recognition Systems to Approximate User Experience
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
When comparing entities extracted by a medical entity recognition system with gold standard annotations over a test set, two types of mismatches might occur, label mismatch or span mismatch. Here we focus on span mismatch and show that its severity can vary from a serious error to a fully acceptable entity extraction due to the subjectivity of span annotations. For a domain-specific BERT-based NER system, we showed that 25% of the errors have the same labels and overlapping span with gold standard entities. We collected expert judgement which shows more than 90% of these mismatches are accepted or partially accepted by the user. Using the training set of the NER system, we built a fast and lightweight entity classifier to approximate the user experience of such mismatches through accepting or rejecting them. The decisions made by this classifier are used to calculate a learning-based F-score which is shown to be a better approximation of a forgiving user's experience than the relaxed F-score. We demonstrated the results of applying the proposed evaluation metric for a variety of deep learning medical entity recognition models trained with two datasets.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 it