docs.md

DNAttend - ML framework for predicting patient non-attendance

Additional documentation and example visualisations

Note: This documentation is still a work progress and will be updated.

Table of contents

• Workflow
• Model Evaluation
  • Feature Importance
  • ROC Curve
  • Precision-Recall Curve
  • Calibration Curve
  • Evaluation Report

Worklow

DNAttend trains two models independently; a baseline logistic regression model and a CatBoost model. The CatBoost model is trained via a cross-validated randomised hyper-parameter search with over-fit detection. In addition, over-fit detection is performed using a holdout validation set to determine the optimal boosting iterations. Output probability of both models are calibrated via cross-validation. Finally, decision thresholds are tuned, using the training dataset, to optimise either the ROC or F1 score. This choice of threshold metric is determined by the tuneThresholdBy option of the configuration file (defult = f1).

Detailed overview of the DNAttend workflow

Model Evaluation

Feature Importance

featureImportances = test.getFeatureImportance(models['catboost']['model'])
fig = featureImportances.plot.barh()
fig.figure.savefig('featureImportances.png')

Feature Importances.

ROC Curve

fig, ax = test.plotROC(models, data)
fig.figure.savefig('ROCcurve.png')

Receiver Operating Characteristic curve for both CatBoost and Logistic Model.

Precision-Recall Curve

fig, ax = test.plotPrecisionRecall(models, data)
fig.figure.savefig('PRcurve.png', dpi=300)

Precision-Recall curve for both CatBoost and Logistic Model.

Calibration Curve

fig, ax = test.plotCalibrationCurve(models, data, strategy='quantile')
fig.figure.savefig('CalibrationCurve.png')

Calibration curve for both CatBoost and Logistic Model.

Evaluation Report

The evaluate() function computes a comprehensive set of performance metrics using the test data.

report = test.evaluate(models['catboost']['model'], data)

print(report)
{
    'Attend': {
        'precision': 0.7976354138025845,
        'recall':    0.7815193965517241,
        'f1-score':  0.7894951694108042,
        'support':   3712
    },
    'DNA': {
        'precision': 0.7901138716356108,
        'recall':    0.8057534969648984,
        'f1-score':  0.7978570495230629,
        'support':   3789
    },
    'accuracy':      0.7937608318890814,
    'macro avg': {
        'precision': 0.7938746427190977,
        'recall':    0.7936364467583112,
        'f1-score':  0.7936761094669336,
        'support':   7501
    },
    'weighted avg': {
        'precision': 0.7938360372833652,
        'recall':    0.7937608318890814,
        'f1-score':  0.7937190280623637,
        'support':   7501
    }
}