The effect of resampling techniques on the performances of machine learning clinical risk prediction models in the setting of severe class imbalance: development and internal validation in a retrospective cohort
Bibliographic record
Abstract
Purpose: The availability of population datasets and machine learning techniques heralded a new era of sophisticated prediction models involving a large number of routinely collected variables. However, severe class imbalance in clinical datasets is a major challenge. The aim of this study is to investigate the impact of commonly-used resampling techniques in combination with commonly-used machine learning algorithms in a clinical dataset, to determine whether combination(s) of these approaches improve upon the original multivariable logistic regression with no resampling. Methods: We previously developed and internally validated a multivariable logistic regression 30-day mortality prediction model in 30,619 patients using preoperative and intraoperative features.Using the same dataset, we systematically evaluated and compared model performances after application of resampling techniques [random under-sampling, near miss under-sampling, random oversampling, and synthetic minority oversampling (SMOTE)] in combination with machine learning algorithms (logistic regression, elastic net, decision trees, random forest, and extreme gradient boosting). Results: We found that in the setting of severe class imbalance, the impact of resampling techniques on model performance varied by the machine learning algorithm and the evaluation metric. Existing resampling techniques did not meaningfully improve area under receiving operating curve (AUROC). The area under the precision recall curve (AUPRC) was only increased by random under-sampling and SMOTE for decision trees, and oversampling and SMOTE for extreme gradient boosting. Importantly, some combinations of algorithm and resampling technique decreased AUROC and AUPRC compared to no resampling. Conclusion: Existing resampling techniques had a variable impact on models, depending on the algorithms and the evaluation metrics. Future research is needed to improve predictive performances in the setting of severe class imbalance.
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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 | 0.069 | 0.114 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| 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 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".