I am trying to replicate a quadratic SVM classifier from Matlab to Python, however I am having different results regarding the accuracy. In Matlab the accuracy is 0.8955 meanwhile in Python the accuracy is 0.82089. I believe a 7% difference is high enough to be something there that I am doing wrong. For instance my Python code is the following:

        # Standardize the input data
        mean = np.zeros(descriptors)
        std = np.zeros(descriptors)
        scaled_mean = np.zeros(descriptors)
        scaled_std = np.zeros(descriptors)

        for i in range (0,descriptors):
            mean[i] = x_train[i].mean()
            std[i] = x_train[i].std(ddof = 1)
            x_train[i] = (x_train[i] - mean[i])/std[i]
            scaled_mean[i] = x_train[i].mean()
            scaled_std[i] = x_train[i].std(ddof = 1)
        #If gamma = 'auto' it goes into an infinite loop, Matlab gamma therefore is used
        clf = svm.SVC(kernel = 'poly', degree = 2, gamma = 0.4955, cache_size = 1000)
        clf.fit(x_train, y_train)
        # save the model to disk 
        joblib.dump(clf, filename) 

As my training dataset consists of 3 features with 66 rows each I have done no validation in the classification learner app that Matlab provides, but I do have in mind that overfitting might be a problem in the future.

Aside from that I would like to point out that I have used previously the scaler that sklearn provides to standardize, but since it does not take into account the ddof parameter that Matlab does I have chosen to compute the standardization myself.

I leave the datasets that I have used here, but please note that in the the matlab train.mat file only the first 3 columns are used to train, and the last column contains the labels (0,1), the remaining ones are not used at all.


  • $\begingroup$ Have you tried to set the same randon seed in both programs? It might be that $\endgroup$ – Gabriel Blanco Feb 23 at 16:21
  • $\begingroup$ Thanks for the suggestion! However I have tried that and it seems it is not the root of the problem. $\endgroup$ – BizarroJr Feb 24 at 11:31
  • $\begingroup$ The problem was that I had not taken into account a parameter of the function called coef0. Upon testing I saw that if changed that value the results also changed. I then created a function to optimize that value and it was all nice and smooth. The thing is that Matlab somehow does the optimization of the value but svm library does not. $\endgroup$ – BizarroJr Apr 7 at 15:29

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