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OHDSI Best Practices for Patient Level Prediction
This document is under development. Changes can be proposed and discussed via the Patient-Level Prediction Workgroup meetings.
General principles
- Transparency: others should be able to reproduce your study in every detail using the information you provide. Make sure all analysis code is available as open source.
- Prespecify what you're going to predict and how. This will avoid fishing expeditions, p-value hacking.
- Code validation: it is important to add unit tests, code review, or double coding steps to validate the developed code base. We recommend to test the code on benchmark datasets.
Best practices
Data characterisation and cleaning: Before modelling it is important to characterize the cohorts, for example by looking at the prevalence of certain covariates. Tools are being developed in the community to facilitate this. A data cleaning step is recommended, e.g. remove outliers in lab values.
Dealing with missing values : A best practice still needs to established.
Feature construction and selection: Both feature construction and selection should be completely transparent using a standardised approach to be able repeat the modelling but also to enable application of the model on unseen data.
Inclusion and exclusion criteria should be made explicit. It is recommended to do sensitivity analyses on the choices made. Visualisation tools could help and this will be further explored in the WG.
Model development is done using a split-sample approach. The percentage used for training could depend on the number of cases, but as a rule of thumb 80/20 split is recommended. Hyper-parameter training should only be done on the training set.
Internal validation is done only once on the holdout set. The following performance measures should be calculated:
. Overall performance: Brier score (unscaled/scaled) . Discrimination: Area under the ROC curve (AUC) . Calibration: Intercept + Gradient of the line fit on the observed vs predicted probabilities
We recommend box plots of the predicted probabilities for the outcome vs non-outcome people, the ROC plot and a scatter plot of the observed vs predicted probabilities with the line fit to that data and the line x=y added.
