Scikit Learn SVC decision_function and predict

I'm trying to understand the relationship between decision_function and predict, which are instance methods of SVC (http://scikit-learn.org/stable/modules/generated/sklearn.svm.SVC.html). So far I've gathered that decision function returns pairwise scores between classes. I was under the impression that predict chooses the class that maximizes its pairwise score, but I tested this out and got different results. Here's the code I was using to try and understand the relationship between the two. First I generated the pairwise score matrix, and then I printed out the class that has maximal pairwise score which was different than the class predicted by clf.predict.

        result = clf.decision_function(vector)[0]
        counter = 0
        num_classes = len(clf.classes_)
        pairwise_scores = np.zeros((num_classes, num_classes))
        for r in xrange(num_classes):
            for j in xrange(r + 1, num_classes):
                pairwise_scores[r][j] = result[counter]
                pairwise_scores[j][r] = -result[counter]
                counter += 1

        index = np.argmax(pairwise_scores)
        class = index_star / num_classes
        print class
        print clf.predict(vector)[0]

Does anyone know the relationship between these predict and decision_function?

I don't fully understand your code, but let's go trough the example of the documentation page you referenced:

import numpy as np
X = np.array([[-1, -1], [-2, -1], [1, 1], [2, 1]])
y = np.array([1, 1, 2, 2])
from sklearn.svm import SVC
clf = SVC()
clf.fit(X, y) 

Now let's apply both the decision function and predict to the samples:

clf.decision_function(X)
clf.predict(X)

The output we get is:

array([[-1.00052254],
       [-1.00006594],
       [ 1.00029424],
       [ 1.00029424]])
array([1, 1, 2, 2])

And that is easy to interpret: The desion function tells us on which side of the hyperplane generated by the classifier we are (and how far we are away from it). Based on that information, the estimator then label the examples with the corresponding label.

For those interested, I'll post a quick example of the predict function translated from C++ (here) to python:

# I've only implemented the linear and rbf kernels
def kernel(params, sv, X):
    if params.kernel == 'linear':
        return [np.dot(vi, X) for vi in sv]
    elif params.kernel == 'rbf':
        return [math.exp(-params.gamma * np.dot(vi - X, vi - X)) for vi in sv]

# This replicates clf.decision_function(X)
def decision_function(params, sv, nv, a, b, X):
    # calculate the kernels
    k = kernel(params, sv, X)

    # define the start and end index for support vectors for each class
    start = [sum(nv[:i]) for i in range(len(nv))]
    end = [start[i] + nv[i] for i in range(len(nv))]

    # calculate: sum(a_p * k(x_p, x)) between every 2 classes
    c = [ sum(a[ i ][p] * k[p] for p in range(start[j], end[j])) +
          sum(a[j-1][p] * k[p] for p in range(start[i], end[i]))
                for i in range(len(nv)) for j in range(i+1,len(nv))]

    # add the intercept
    return [sum(x) for x in zip(c, b)]

# This replicates clf.predict(X)
def predict(params, sv, nv, a, b, cs, X):
    ''' params = model parameters
        sv = support vectors
        nv = # of support vectors per class
        a  = dual coefficients
        b  = intercepts 
        cs = list of class names
        X  = feature to predict       
    '''
    decision = decision_function(params, sv, nv, a, b, X)
    votes = [(i if decision[p] > 0 else j) for p,(i,j) in enumerate((i,j) 
                                           for i in range(len(cs))
                                           for j in range(i+1,len(cs)))]

    return cs[max(set(votes), key=votes.count)]

There are a lot of input arguments for predict and decision_function, but note that these are all used internally in by the model when calling predict(X). In fact, all of the arguments are accessible to you inside the model after fitting:

# Create model
clf = svm.SVC(gamma=0.001, C=100.)

# Fit model using features, X, and labels, Y.
clf.fit(X, y)

# Get parameters from model
params = clf.get_params()
sv = clf.support_vectors
nv = clf.n_support_
a  = clf.dual_coef_
b  = clf._intercept_
cs = clf.classes_

# Use the functions to predict
print(predict(params, sv, nv, a, b, cs, X))

# Compare with the builtin predict
print(clf.predict(X))