Lexicon Development for COVID-19-related Concepts Using Open-source Word Embedding Sources: An Intrinsic and Extrinsic Evaluation
Bibliographic record
Abstract
BACKGROUND: Scientists are developing new computational methods and prediction models to better clinically understand COVID-19 prevalence, treatment efficacy, and patient outcomes. These efforts could be improved by leveraging documented COVID-19-related symptoms, findings, and disorders from clinical text sources in an electronic health record. Word embeddings can identify terms related to these clinical concepts from both the biomedical and nonbiomedical domains, and are being shared with the open-source community at large. However, it's unclear how useful openly available word embeddings are for developing lexicons for COVID-19-related concepts. OBJECTIVE: Given an initial lexicon of COVID-19-related terms, this study aims to characterize the returned terms by similarity across various open-source word embeddings and determine common semantic and syntactic patterns between the COVID-19 queried terms and returned terms specific to the word embedding source. METHODS: We compared seven openly available word embedding sources. Using a series of COVID-19-related terms for associated symptoms, findings, and disorders, we conducted an interannotator agreement study to determine how accurately the most similar returned terms could be classified according to semantic types by three annotators. We conducted a qualitative study of COVID-19 queried terms and their returned terms to detect informative patterns for constructing lexicons. We demonstrated the utility of applying such learned synonyms to discharge summaries by reporting the proportion of patients identified by concept among three patient cohorts: pneumonia (n=6410), acute respiratory distress syndrome (n=8647), and COVID-19 (n=2397). RESULTS: We observed high pairwise interannotator agreement (Cohen kappa) for symptoms (0.86-0.99), findings (0.93-0.99), and disorders (0.93-0.99). Word embedding sources generated based on characters tend to return more synonyms (mean count of 7.2 synonyms) compared to token-based embedding sources (mean counts range from 2.0 to 3.4). Word embedding sources queried using a qualifier term (eg, dry cough or muscle pain) more often returned qualifiers of the similar semantic type (eg, "dry" returns consistency qualifiers like "wet" and "runny") compared to a single term (eg, cough or pain) queries. A higher proportion of patients had documented fever (0.61-0.84), cough (0.41-0.55), shortness of breath (0.40-0.59), and hypoxia (0.51-0.56) retrieved than other clinical features. Terms for dry cough returned a higher proportion of patients with COVID-19 (0.07) than the pneumonia (0.05) and acute respiratory distress syndrome (0.03) populations. CONCLUSIONS: Word embeddings are valuable technology for learning related terms, including synonyms. When leveraging openly available word embedding sources, choices made for the construction of the word embeddings can significantly influence the words learned.
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How this classification was reachedexpand
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 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| 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 itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, 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".