My input data is a (23948,) pandas.Series of strings containing newspaper headlines. My target are 20 labels of the headline (e.g. 'crime', 'politics') each binarily encoded with [0, 1]. The labels are not exclusive, a headline could be about crime and politics at the same time. I would like to compare three algorithms for this problem. I use the following pipeline to predict the labels:

pipeline = Pipeline([
    ('vect', CountVectorizer(tokenizer=tokenize)),
    ('tfidf', TfidfTransformer()),
    ('clf', MultiOutputClassifier(RandomForestClassifier()))

parameters = [
    {"clf": [RandomForestClassifier()],
     "clf__n_estimators": [10, 100, 250],
    {"clf": [LinearSVC()],
     "clf__C": [1.0, 10.0, 100.0, 1000.0],
    {"clf": [GaussianNB()]}

rkf = RepeatedKFold(

cv = GridSearchCV(

The pipeline works fine for the random forest, but breaks at the LinearSVC() with the following error:

ValueError: bad input shape (20972, 20)

If I remove the LinearSVC(), it stops at:

A sparse matrix was passed, but dense data is required. Use X.toarray() to convert to a dense numpy array.

There is a list "Support multilabel:" in the sci-kit learn documentation on multilabel classification (https://scikit-learn.org/stable/modules/multiclass.html) and only the random forest is included. However, the documentation states that "Multioutput classification support can be added to any classifier with MultiOutputClassifier."

I am bit confused, do LinearSVC() and GaussianNB() support multilabel classification when wrapped in MultiOutputClassifier()? If not, is there a workaround?


When you run your grid search, the clf step of the pipeline is replaced by each of RandomForestClassifier, LinearSVC, GaussianNB; you never actually use the MultiOutputClassifier.

You should be able to just wrap the two offending classifiers with a MultiOutputClassifier. You'll need to prefix your hyperparameters with estimator__ to get through the MOC into the underlying classifier: clf__estimator__C.

  • $\begingroup$ Thanks, this works. After reading this post stackoverflow.com/questions/42819460/… I am wondering whether OneVsRestClassifier() does actually make more sense. Is the only difference that in MultiOutputClassifier the variables do not need to be binary but may feature multiple classes? $\endgroup$ – 00schneider Aug 29 '19 at 15:46
  • $\begingroup$ @00schneider, "The labels are not exclusive" suggests that one-vs-rest is not appropriate for you, yes? $\endgroup$ – Ben Reiniger Aug 29 '19 at 16:19
  • $\begingroup$ Hm, I guess I am making a follow up post... $\endgroup$ – 00schneider Aug 30 '19 at 8:47

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