[SOLVED] Fitting SVC model on Khan Gene Data Set in Python

Issue

I have four .csv files containing the training data (data points and their classes) plus test data (data points and their classes) that has been stored into X_train, y_train, X_test and y_test variables respectively.

I need to train a CSV model and test it with the test data and as sklearn.svm.SVC gets numpy arrays as input I tried converting pandas data frames to numoy arrays as follows:

X_train_gene = pd.read_csv("Khan_xtrain.csv").drop('Unnamed: 0', axis=1).values.ravel()
y_train_gene = pd.read_csv("Khan_ytrain.csv").drop('Unnamed: 0', axis=1).values.ravel()
X_test_gene = pd.read_csv("Khan_xtest.csv").drop('Unnamed: 0', axis=1).values.ravel()
y_test_gene = pd.read_csv("Khan_ytest.csv").drop('Unnamed: 0', axis=1).values.ravel()

Then I tried the following lines of code to train my model:

from sklearn.svm import SVC
svm_gene = SVC(C=10, kernel='linear')
svm_gene.fit(X_train_gene, y_train_gene)

But I get a value error:

ValueError: Expected 2D array, got 1D array instead:
array=[ 0.7733437 -2.438405 -0.4825622 … -1.115962 -0.7837286 -1.339411 ].
Reshape your data either using array.reshape(-1, 1) if your data has a single feature or array.reshape(1, -1) if it contains a single sample.

The full error message can be viewed in the following image:

The Error Message

How can I fix this issue?

Solution

I fixed the issue by using the following lines of code:

X_train_gene = pd.read_csv("file_path/file.csv", header=None)
#deleting the first column which contains numbers
del X_train_gene[X_train_gene.columns[0]]
#deleting the first row which contains strings and predictors' names
X_train_gene = X_train_gene.iloc[1:]

y_train_gene = pd.read_csv("file_path/file.csv", header=None)
#deleting the first column which contains numbers
del y_train_gene[y_train_gene.columns[0]]
#deleting the first row which contains strings and predictors' names
y_train_gene = y_train_gene.iloc[1:]

X_test_gene = pd.read_csv("file_path/file.csv", header=None)
#deleting the first column which contains numbers
del X_test_gene[X_test_gene.columns[0]]
#deleting the first row which contains strings and predictors' names
X_test_gene = X_test_gene.iloc[1:]

y_test_gene = pd.read_csv("file_path/file.csv", header=None)
#deleting the first column which contains numbers
del y_test_gene[y_test_gene.columns[0]]
#deleting the first row which contains strings and predictors' names
y_test_gene = y_test_gene.iloc[1:]


#Converting the pandas data frames to numpy arrays as the SVC functions accepts numpy arrays as input.
X_train_gene = X_train_gene.values

y_train_gene = y_train_gene.values.ravel()

X_test_gene = X_test_gene.values

y_test_gene = y_test_gene.values.ravel()

Answered By – Naser.Sadeghi

Answer Checked By – Willingham (BugsFixing Volunteer)

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