Vaccine safety surveillance using routinely collected healthcare data – An empirical evaluation of epidemiological designs
Bibliographic record
Abstract
Abstract Background Routinely collected healthcare data such as administrative claims and electronic health records (EHR) can complement clinical trials and spontaneous reports when ensuring the safety of vaccines, but uncertainty remains about what epidemiological design to use. Methods Using 3 claims and 1 EHR database, we evaluate several variants of the case-control, comparative cohort, historical comparator, and self-controlled designs against historical vaccinations with real negative control outcomes (outcomes with no evidence to suggest that they could be caused by the vaccines) and simulated positive controls. Results Most methods show large type 1 error, often identifying false positive signals. The cohort method appears either positively or negatively biased, depending on the choice of comparator index date. Empirical calibration using effect-size estimates for negative control outcomes can restore type 1 error to close to nominal, often at the cost of increasing type 2 error. After calibration, the self-controlled case series (SCCS) design shows the shortest time to detection for small true effect sizes, while the historical comparator performs well for strong effects. Conclusions When applying any method for vaccine safety surveillance we recommend considering the potential for systematic error, especially due to confounding, which for many designs appears to be substantial. Adjusting for age and sex alone is likely not sufficient to address the differences between vaccinated and unvaccinated, and for the cohort method the choice of index date plays an important role in the comparability of the groups Inclusion of negative control outcomes allows both quantification of the systematic error and, if so desired, subsequent empirical calibration to restore type 1 error to its nominal value. In order to detect weaker signals, one may have to accept a higher type 1 error. Highlights Most methods used in vaccine safety surveillance show large type 1 error, which could lead to many false safety signals. Empirical calibration using effect-size estimates for negative control outcomes can restore type 1 error to close to nominal, often at the cost of marginal increases in type 2 error. After calibration, the self-controlled case series (SCCS) design shows the shortest time to detection for small true effect sizes, while the historical comparator appears best for large true effect sizes. Implementing negative control outcomes in a safety surveillance system is recommended to identify vulnerability to systematic error.
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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 | 0.438 | 0.698 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.009 |
| Bibliometrics | 0.003 | 0.002 |
| Science and technology studies | 0.001 | 0.006 |
| Scholarly communication | 0.003 | 0.005 |
| Open science | 0.004 | 0.004 |
| Research integrity | 0.004 | 0.003 |
| Insufficient payload (model declined to judge) | 0.004 | 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; 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".