I am doing text classification based on TF-IDF Vector Space Model.I have only no more than 3000 samples.For the fair evaluation, I'm evaluating the classifier using 5-fold cross-validation.But what confuses me is that whether it is necessary to rebuild the TF-IDF Vector Space Model in each fold cross-validation. Namely, would I need to rebuild the vocabulary and recalculate the IDF value in vocabulary in each fold cross-validation?
Currently I'm doing TF-IDF tranforming based on scikit-learn toolkit, and training my classifier using SVM. My method is as follows: firstly,I'm dividing the sample in hand by the ratio of 3:1, 75 percent of them are applied to fit the parameter of the TF-IDF Vector Space Model.Herein, the parameter is the size of vocabulary and the terms that contained in it, also the IDF value of each term in vocabulary.Then I'm transforming the remainder in this TF-IDF SVM and using these vectors to make 5-fold cross-validation (Notably, I don't use the previous 75 percent samples for transforming).
My code is as follows:
# train, test split, the train data is just for TfidfVectorizer() fit
x_train, x_test, y_train, y_test = train_test_split(data_x, data_y, train_size=0.75, random_state=0)
tfidf = TfidfVectorizer()
tfidf.fit(x_train)
# vectorizer test data for 5-fold cross-validation
x_test = tfidf.transform(x_test)
scoring = ['accuracy']
clf = SVC(kernel='linear')
scores = cross_validate(clf, x_test, y_test, scoring=scoring, cv=5, return_train_score=False)
print(scores)
My confusion is that whether my method doing TF-IDF transforming and making 5-fold cross-validation is correct, or whether it's necessary to rebuild the TF-IDF Vector Model Space using train data and then transform into TF-IDF vectors with both train and test data? Just as follows:
skf = StratifiedKFold(n_splits=5, shuffle=True, random_state=0)
for train_index, test_index in skf.split(data_x, data_y):
x_train, x_test = data_x[train_index], data_x[test_index]
y_train, y_test = data_y[train_index], data_y[test_index]
tfidf = TfidfVectorizer()
x_train = tfidf.fit_transform(x_train)
x_test = tfidf.transform(x_test)
clf = SVC(kernel='linear')
clf.fit(x_train, y_train)
y_pred = clf.predict(x_test)
score = accuracy_score(y_test, y_pred)
print(score)
The StratifiedKFold approach, which you had adopted to build the TfidfVectorizer() is the right way, by doing so you are making sure that features are generated only based out of the training dataset.
If you think about building the TfidfVectorizer() on the whole dataset, then its situation of leaking the test dataset to the model even though we are not explicitly feeding the test dataset. The parameters such as size of vocabulary, IDF value of each term in vocabulary would greatly differ when test documents are included.
The simpler way could be using pipeline and cross_validate.
Use this!
from sklearn.pipeline import make_pipeline
clf = make_pipeline(TfidfVectorizer(), svm.SVC(kernel='linear'))
scores = cross_validate(clf, data_x, data_y, scoring=['accuracy'], cv=5, return_train_score=False)
print(scores)
Note: It is not useful to do cross_validate on the test data alone. we have to do on the [train + validation] dataset.
Related
#split dataset in features and target variable
feature_cols = ['RIAGENDR_0', 'RIDAGEYR', 'RIDRETH3_2', 'RIDRETH3_3', 'RIDRETH3_4', 'RIDRETH3_6', 'RIDRETH3_7', 'INDFMPIR', 'DMDMARTZ_1.0', 'DMDMARTZ_2.0', 'DMDMARTZ_3.0', 'DMDMARTZ_4.0', 'DMDMARTZ_6.0', 'DMDEDUC2', 'RFXT010', 'BMXWT', 'BMXBMI', 'URXUMA', 'LBDHDD', 'LBXFER', 'LBXGH', 'LBXBPB', 'LBXBCD', 'LBXBSE', 'LBXBMN', 'URXUBA', 'URXUCD', 'URXUCO', 'URXUCS', 'URXUMO', 'URXUMN', 'URXUPB', 'URXUSB', 'URXUSN', 'URXUTL', 'URXUTU']
X = data[feature_cols] # Features
scale = StandardScaler()
X = scale.fit_transform(X)
y = data['depre_score'] # Target variable
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.3, random_state=1) # 70% training and 30% test
clf = DecisionTreeClassifier()
clf = clf.fit(X_train,y_train)
y_pred = clf.predict(X_test)
print(y_test)
print(y_pred)
confusion = metrics.confusion_matrix(y_test, y_pred)
print(confusion)
print("Accuracy:",metrics.accuracy_score(y_test, y_pred))
recall_sensitivity = metrics.recall_score(y_test, y_pred, pos_label=1)
recall_specificity = metrics.recall_score(y_test, y_pred, pos_label=0)
print(recall_sensitivity, recall_specificity)
Why do you think you are doing something wrong? Perhaps your data are such that you can achieve a perfect classification... e.g., see this mushroom classification.
Having said that, it is also possible that there is some leakage in your data as specified by #gtomer. That means an exact point that is present in training set is available in your test set. You can do K-fold test on your data and see how it follows up with the accuracy. And secondly, use different classifiers too (it is better to use Random Forests compared to Decision Trees)
I would like to use scikit learn to predict with X a variable y. I would like to train a classifier on a training dataset using cross validation and then to apply this classifier to an unseen test dataset (as in https://www.nature.com/articles/s41586-022-04492-9)
from sklearn import datasets
from sklearn.model_selection import cross_validate
from sklearn.model_selection import train_test_split
from sklearn.svm import SVC
# Import dataset
X, y = datasets.load_iris(return_X_y=True)
# Create binary variable y
y[y == 0] = 1
# Divide in train and test set
x_train, x_test, y_train, y_test = train_test_split(X, y,test_size=75, random_state=4, stratify=y)
# Cross validation on the train data
cv_model = cross_validate(model, x_train, y_train, cv=5)
Now I would like to use this cross validated model and to apply it to the unseen test set. I am unable to find how.
It would be something like
result = cv_model.score(x_test, y_test)
Except this does not work
You cannot do that; you need to fit the model before using it to predict new data. cross_validate is just a convenience function to get the scores; as clearly mentioned in the documentation, it returns just that, i.e. scores, and not a (fitted) model:
Evaluate metric(s) by cross-validation and also record fit/score times.
[...]
Returns: scores : dict of float arrays of shape (n_splits,)
Array of scores of the estimator for each run of the cross validation.
A dict of arrays containing the score/time arrays for each scorer is returned.
When I do something like:
scoring = ["accuracy", "balanced_accuracy", "f1", "precision", "recall", "roc_auc"]
scores = cross_validate(SVC(), my_x, my_y, scoring = scoring , cv=5, verbose=3, return_train_score=True, return_estimator=True)
how can I get a confusion matrix of a single validation run, e.g. the first one or ideally the best one?
I don't need a plot or something beautiful, only the numbers. If I could see at least the split, then I could recalculate it.
If you want to use cross-validation to perform something quite specific during each iteration, maybe it is best to use a CV splitter like StratifiedKFold :
from sklearn.metrics import accuracy_score, confusion_matrix
from sklearn.model_selection import StratifiedKFold
from sklearn.svm import SVC
svm = SVC()
kf = StratifiedKFold(n_splits=5)
scores = []
results = []
for train_index, test_index in kf.split(X, y):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
svm.fit(X_train, y_train)
y_pred = svm.predict(y_test)
scores.append(accuracy_score(y_test, y_pred)) # use other scoring as prefered
results.append(confusion_matrix(y_test, y_pred))
This will compute the confusion matrix for each of the five iterations and store them in results. If you want to get the confusion matrix of the best validation round, you can additionally compute the scoring metric in the loop as well (see the scores list) and retrieve the corresponding confusion matrix.
Is there any way that I can track my model's performance in terms of it's classified labels, during the training phase? Any classifier from sklearn would work as an example.
To be more specific, I want to get something like a list of Confusion Matrices here:
clf = LinearSVC(random_state=42).fit(X_train, y_train)
# ... here ...
y_pred = clf.predict(X_test)
My objective here is to see how well the model is learning (during training). This is similar to analyzing the training loss, that is a common practice in DNN's, and libraries such as pyTorch, Keras, and Tensorflow have such capability already implemented.
I thought a quick browsing of the web would give me what I want, but apparently not. I still believe this should be fairly simple though.
Some ML practitioners like to work with three folds of data: training, validation and testing sets. The latter should not be seen in any training at all, but the middle could. For example, cross-validation uses K different folds of validation sets "during the training phase" to get a less biased performance estimation when training with different parts of the data.
But you can do this on a single validation fold for the purpose of what you asked.
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)
X_train2, X_valid, y_train2, y_valid = train_test_split(X_train, y_train, test_size=0.2)
# Fit a classifier with train data only
clf = LinearSVC(random_state=42).fit(X_train2, y_train2)
y_valid_pred = clf.predict(X_valid)
confusionm_valid = confusion_matrix(y_valid, y_valid_pred) # ... here ...
# Refit with all your training data
clf = LinearSVC(random_state=42).fit(X_train, y_train)
y_pred = clf.predict(X_valid)
I am using sklearn for SVM training. I am using the cross-validation to evaluate the estimator and avoid the overfitting model.
I split the data into two parts. Train data and test data. Here is the code:
import numpy as np
from sklearn import cross_validation
from sklearn import datasets
from sklearn import svm
X_train, X_test, y_train, y_test = cross_validation.train_test_split(
iris.data, iris.target, test_size=0.4, random_state=0
)
clf = svm.SVC(kernel='linear', C=1)
scores = cross_validation.cross_val_score(clf, X_train, y_train, cv=5)
print scores
Now I need to evaluate the estimator clf on X_test.
clf.score(X_test, y_test)
here, I get an error saying that the model is not fitted using fit(), but normally, in cross_val_score function the model is fitted? What is the problem?
cross_val_score is basically a convenience wrapper for the sklearn cross-validation iterators. You give it a classifier and your whole (training + validation) dataset and it automatically performs one or more rounds of cross-validation by splitting your data into random training/validation sets, fitting the training set, and computing the score on the validation set. See the documentation here for an example and more explanation.
The reason why clf.score(X_test, y_test) raises an exception is because cross_val_score performs the fitting on a copy of the estimator rather than the original (see the use of clone(estimator) in the source code here). Because of this, clf remains unchanged outside of the function call, and is therefore not properly initialized when you call clf.fit.