Processing of Electronic Medical Records for Health Services Research in an Academic Medical Center: Methods and Validation
Bibliographic record
Abstract
BACKGROUND: Electronic medical records (EMRs) contain a wealth of information that can support data-driven decision making in health care policy design and service planning. Although research using EMRs has become increasingly prevalent, challenges such as coding inconsistency, data validity, and lack of suitable measures in important domains still hinder the progress. OBJECTIVE: The objective of this study was to design a structured way to process records in administrative EMR systems for health services research and assess validity in selected areas. METHODS: On the basis of a local hospital EMR system in Singapore, we developed a structured framework for EMR data processing, including standardization and phenotyping of diagnosis codes, construction of cohort with multilevel views, and generation of variables and proxy measures to supplement primary data. Disease complexity was estimated by Charlson Comorbidity Index (CCI) and Polypharmacy Score (PPS), whereas socioeconomic status (SES) was estimated by housing type. Validity of modified diagnosis codes and derived measures were investigated. RESULTS: Visit-level (N=7,778,761) and patient-level records (n=549,109) were generated. The International Classification of Diseases, Tenth Revision, Australian Modification (ICD-10-AM) codes were standardized to the International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) with a mapping rate of 87.1%. In all, 97.4% of the ICD-9-CM codes were phenotyped successfully using Clinical Classification Software by Agency for Healthcare Research and Quality. Diagnosis codes that underwent modification (truncation or zero addition) in standardization and phenotyping procedures had the modification validated by physicians, with validity rates of more than 90%. Disease complexity measures (CCI and PPS) and SES were found to be valid and robust after a correlation analysis and a multivariate regression analysis. CCI and PPS were correlated with each other and positively correlated with health care utilization measures. Larger housing type was associated with lower government subsidies received, suggesting association with higher SES. Profile of constructed cohorts showed differences in disease prevalence, disease complexity, and health care utilization in those aged above 65 years and those aged 65 years or younger. CONCLUSIONS: The framework proposed in this study would be useful for other researchers working with EMR data for health services research. Further analyses would be needed to better understand differences observed in the cohorts.
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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 | 0.198 | 0.276 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.009 | 0.009 |
| Science and technology studies | 0.002 | 0.002 |
| Scholarly communication | 0.003 | 0.002 |
| Open science | 0.003 | 0.005 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.002 |
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; the direct Gemma label and the distilled Codex classifier agree on what is shown here.
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".