scikit-learn return value of LogisticRegression.predict_proba
4.65761066e-03 + 9.95342389e-01 = 19.75851270e-01 + 2.41487300e-02 = 19.99983374e-01 + 1.66258341e-05 = 1The first column is the probability that the entry has the -1 label and the second column is the probability that the entry has the +1 label. Note that classes are ordered as they are in self.classes_.
If you would like to get the predicted probabilities for the positive label only, you can use logistic_model.predict_proba(data)[:,1]. This will yield you the [9.95342389e-01, 2.41487300e-02, 1.66258341e-05] result.