Benchmarking missing-values approaches for predictive models on health databases v2
Bibliographic record
Abstract
BACKGROUND As databases grow larger, it becomes harder to fully control their collection, and they frequently come with missing values: incomplete observations. These large databases are well suited to train machine-learning models, for instance for forecasting or to extract biomarkers in biomedical settings. Such predictive approaches can use discriminative --rather than generative-- modeling, and thus open the door to new missing-values strategies. Yet existing empirical evaluations of strategies to handle missing values have focused on inferential statistics. RESULTS Here we conduct a systematic benchmark of missing-values strategies in predictive models with a focus on large health databases: four electronic health record datasets, a population brain imaging one, a health survey and two intensive care ones. Using gradient-boosted trees, we compare native support for missing values with simple and state-of-the-art imputation prior to learning. We investigate prediction accuracy and computational time. For prediction after imputation, we find that adding an indicator to express which values have been imputed is important, suggesting that the data are missing not at random. Elaborate missing values imputation can improve prediction compared to simple strategies but requires longer computational time on large data. Learning trees that model missing values --with missing incorporated attribute-- leads to robust, fast, and well-performing predictive modeling. CONCLUSIONS Native support for missing values in supervised machine learning predicts better than state-of-the-art imputation with much less computational cost. When using imputation, it is important to add indicator columns expressing which values have been imputed.
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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 | 0.036 | 0.102 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.003 | 0.004 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.005 | 0.003 |
| Research integrity | 0.003 | 0.003 |
| Insufficient payload (model declined to judge) | 0.005 | 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; 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".