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My assumption is that my training set includes the test set, but I don't know how to change this.

from sklearn.model_selection import train_test_split
import sklearn.metrics as metrics

# dataframe to store model performances
scores=pd.DataFrame([],columns=['model', 'recall', 'f1', 'accuracy'])
from sklearn.tree import DecisionTreeClassifier

cv_scores_ac=[]
cv_scores_f1=[]    
cv_scores_re=[]            
for cv in range(1, 6):
    print ("Decision Tree - Iteration %i" % cv)
    X_train, X_test, y_train, y_test = train_test_split(X, y, stratify=y, random_state=cv)

    tree=DecisionTreeClassifier(min_samples_split=20)
    tree.fit(X_train, y_train)
    y_pred=tree.predict(X_test)
    cv_scores_ac.append(metrics.accuracy_score(y_test, y_pred))
    cv_scores_f1.append(metrics.f1_score(y_test, y_pred))
    cv_scores_re.append(metrics.recall_score(y_test, y_pred))
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  • $\begingroup$ How much is the length of X and Y? $\endgroup$ – BlackCurrant May 20 at 16:36
  • $\begingroup$ My data set has 12 columns (incl. the target column), and 100,000 lines. does that answer it ? :) $\endgroup$ – Sofia M May 20 at 16:49
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    $\begingroup$ Why don't you test your hypothesis that the test data is included in the training data? $\endgroup$ – Guillermo Mosse May 20 at 16:56
  • $\begingroup$ I meant check the length of X.Train, Y.Train, X.Test, Y.test. you probably ain't using the same data if you are calling.FIT on x_train,y_train.How are you splitting X and Y? Also check the confusion matrix, is only the accuracy high? what about precision , recall? Also, see if its over fitting? $\endgroup$ – BlackCurrant May 20 at 16:57
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The most probably is data leakage, in this situation, you have the same values in train and test data(or linearly dependent). So please check out the input values.

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Machine Learning is one of the few things where 99% is excellent and 100% is terrible.

Well, I cannot prove this because I don't have your data, but probably:

  • the test data is included in the training data.

To check this possibility, here's a hint:

print(X_test[X_test.isin(X_train)])

will print all the rows in X_test that appear in X_train. Can you think what to do with that information? :)

Or

  • you forgot to remove the target variable y from X.

To check this possibility, simply type:

print(X_train.columns)

and check whether one of the columns matches the name of the target variable.

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  • $\begingroup$ I think the same, one of those - but how do I do this ? can you help with the piece of the code I have to change? $\endgroup$ – Sofia M May 20 at 17:10
  • $\begingroup$ sure, one moment $\endgroup$ – Guillermo Mosse May 20 at 17:11
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    $\begingroup$ Solved! :) Thank you !!! $\endgroup$ – Sofia M May 20 at 20:48
  • $\begingroup$ If you think this solved your problem, please don't forget to press the green checkmark button at the left of my answer :-). Also, was the problem the first list item? I suspect that. $\endgroup$ – Guillermo Mosse May 20 at 21:06

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