Impute‐then‐exclude versus exclude‐then‐impute: Lessons when imputing a variable used both in cohort creation and as an independent variable in the analysis model
Bibliographic record
Abstract
We examined the setting in which a variable that is subject to missingness is used both as an inclusion/exclusion criterion for creating the analytic sample and subsequently as the primary exposure in the analysis model that is of scientific interest. An example is cancer stage, where patients with stage IV cancer are often excluded from the analytic sample, and cancer stage (I to III) is an exposure variable in the analysis model. We considered two analytic strategies. The first strategy, referred to as "exclude-then-impute," excludes subjects for whom the observed value of the target variable is equal to the specified value and then uses multiple imputation to complete the data in the resultant sample. The second strategy, referred to as "impute-then-exclude," first uses multiple imputation to complete the data and then excludes subjects based on the observed or filled-in values in the completed samples. Monte Carlo simulations were used to compare five methods (one based on "exclude-then-impute" and four based on "impute-then-exclude") along with the use of a complete case analysis. We considered both missing completely at random and missing at random missing data mechanisms. We found that an impute-then-exclude strategy using substantive model compatible fully conditional specification tended to have superior performance across 72 different scenarios. We illustrated the application of these methods using empirical data on patients hospitalized with heart failure when heart failure subtype was used for cohort creation (excluding subjects with heart failure with preserved ejection fraction) and was also an exposure in the analysis model.
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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 | 0.380 | 0.634 |
| Meta-epidemiology (narrow) | 0.002 | 0.002 |
| Meta-epidemiology (broad) | 0.005 | 0.006 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.002 | 0.007 |
| Scholarly communication | 0.006 | 0.007 |
| Open science | 0.008 | 0.006 |
| Research integrity | 0.005 | 0.014 |
| Insufficient payload (model declined to judge) | 0.003 | 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; 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".