Lexically-Triggered Hidden Markov Models for Clinical Document Coding
Bibliographic record
Abstract
The automatic coding of clinical documents is an important task for today’s healthcare providers. Though it can be viewed as multi-label document classification, the coding problem has the interesting property that most code assignments can be supported by a single phrase found in the input document. We propose a Lexically-Triggered Hidden Markov Model (LT-HMM) that leverages these phrases to improve coding accuracy. The LT-HMM works in two stages: first, a lexical match is performed against a term dictionary to collect a set of candidate codes for a document. Next, a discriminative HMM selects the best subset of codes to assign to the document by tagging candidates as present or absent. By confirming codes proposed by a dictionary, the LT-HMM can share features across codes, enabling strong performance even on rare codes. In fact, we are able to recover codes that do not occur in the training set at all. Our approach achieves the best ever performance on the 2007 Medical NLP Challenge test set, with an F-measure of 89.84. 1
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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 | 0.002 | 0.011 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 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".