I was training a model using XGBoost Classifier on a heavy imbalanced database with 232:1 of binary class. Because my training data contains 750k rows and 320 features (after doing many feature engineering, feature correlation filtering, and low variance filtering), I prefer to use scale_pos_weight to dealing with imbalanced rather than oversampling data. After parameter tuning using Bayesian optimization to optimize PR AUC with 5 fold cross-validation, I got the best cross-validation score as below: PR AUC = 4.87%, ROC AUC = 78.5%, Precision = 1.49%, and Recall = 80.4% and when I tried to implement the result to a testing dataset the result is below:

accuracy: 0.562
roc_auc: 0.776293
pr_auc: 0.032544
log_loss: 0.706263
F1: 0.713779
Confusion Matrix:    
[[9946 7804]
 [  18   84]]
          precision     recall  f1-score   support

       0       1.00      0.56      0.72     17750
       1       0.01      0.82      0.02       102

    accuracy                           0.56     17852
   macro avg       0.50      0.69      0.37     17852
weighted avg       0.99      0.56      0.71     17852

My parameter range to be optimize (consume 2-3 days with 100 iteration) is:

{'learning_rate':(0.001,0.2),'min_split_loss':(0,20),'max_depth':(3,10),'min_child_weight':(0,50),'max_delta_step':(0,10),'subsample':(0.5,1),'colsample_bytree':(0.5,1),'colsample_bynode':(0.5,1),'colsample_bylevel':(0.5,1),'reg_lambda':(1e-5,100),'reg_alpha':(0,1), 'objective':'binary:logistic','booster':'gbtree','scale_pos_weight':232,'n_estimators':200}

According to business request, we have more consideration to high recall (to save those in positive class), however, I am frustrated by too low precision result (this is the impact to the cost to save positive class). Is there any solution to increase the precision at least to be 10% without hurting the Recall?

  • 1
    $\begingroup$ It's very probable that your features are not good predictors of the target. $\endgroup$ Apr 9, 2021 at 3:36
  • $\begingroup$ but we can reach 78% of roc_auc acore with that so hard to day not goot at all. $\endgroup$
    – zonna
    Sep 26, 2022 at 1:10

2 Answers 2


Given that both the f1-score and PR AUC are very low even for the prevalence of ~0.45%, it can not be deduced if the limitations are imposed by the nature of the data or the model (features plus the algorithm used).

In order to build a better understanding and to resolve the issue, I would suggest to break the problem into two parts:

  1. Build a model that works for the selected features. For this purpose, you may try creating a slightly balanced dataset 80-20? both for training and testing. Once you are satisfied with the performance of your approach, move to 2 below
  2. Use your original imbalanced dataset and see if the situation is any better. If not, it is now clearer that the issue is with the imbalanced nature of the data, and you should try all standard techniques for dealing with imbalanced classes. I hope this helps you, because otherwise only options at hand are synthesizing or collecting more data for the minority class.

It is important to understand that your precision and recall are associated with a binary decision threshold. Basically, the outputs of the model are converted to a binary decision using this threshold. There are usually default threshold selection process implemented in standard libraries, but they don't really work for imbalanced cases. One option is to use predict_proba and select a threshold yourself by varying the threshold value in a loop. That way you will have different options for balancing precision and recall. Given your low AUPR it is not garanteed you will have any good choice.


Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.