Fitting method in scickit'slearn Pipeline class - machine-learning

Let's say i have this python code:
from imblearn.pipeline import Pipeline
from sklearn.feature_selection import VarianceThreshold
from sklearn.preprocessing import StandardScaler
from imblearn.over_sampling import RandomOverSampler
from sklearn.decomposition import PCA
selector = VarianceThreshold()
scaler = StandardScaler()
ros = RandomOverSampler()
pca = PCA()
clf = neighbors.KNeighborsClassifier(n_jobs=-1)
pipe = Pipeline(steps=[('selector', selector), ('scaler', scaler), ('sampler', ros), ('pca', pca), ('kNN', clf)])
pipe.fit(X_train,y_train)
preds = pipe.predict(X_test)
What this does is import 4 transformers and an estimator from scickit learn.Then it fit's these in the data and lastly it predicts.If i understand correctly fit method applies the 4 transformers to the data and the predict method makes the final estimation(in our case using kNN).My question is this:For scaler as well as pca the alterations that are done in the train data must be also applied in the test data.But in fit's parameters we don't give test and as a result the test data won't be altered.How does that make sense?Is there something i am missing?

The model only learns the parameters from the training data and assumes that the test data will have similar patterns and transforms it accordingly. You cannot have a test data that is completely different from training data and expect good predictions, hence the same PCA and scaler models are also used on test dataset. If you fit a scaler on a smaller test dataset, the results might come out completely different than what the model is originally trained on.

Related

How to transform new data when ML model is loaded from pickle?

i have KNN model pickled with StandartScaler.
X_train = sc.fit_transform(X_train)
X_test = sc.transform(X_test)
when im trying to load model and pass new values via StandartScaler().transform() it give me an error:
sklearn.exceptions.NotFittedError: This StandardScaler instance is not
fitted yet. Call 'fit' with appropriate arguments before using this estimator.
im trying to load values from dictionary
dic = {'a':1, 'b':32323, 'c':12}
sc = StandartScaler()
load = pickle.load(open('KNN.mod'), 'rb'))
load.predict(sc.transform([[dic['a'], dic['b'], dic['c']]]))
as far i understand from error i have to fit new data to sc. but if do so it gives me wrong predictions. im not sure my im overfiting or smth, do random forest and decision tree works fine with that data without sc. logistic regresion semi ok
You need to train and pickle the entire machine learning pipeline at the same time. This can be done with the Pipeline tool from sklearn. In your case it will look like:
from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import Pipeline
from sklearn.neighbors import NearestNeighbors
pipeline = Pipeline([('scaler', StandardScaler()), ('knn', NearestNeighbors())])
pipe.fit(X_train, y_train)
# save the ml pipeline
pickle.dump(pipeline, open('KNN_pipeline.pkl'), 'wb'))
# load the ml pipeline and do prediction
pipeline = pickle.load(open('KNN_pipeline.pkl'), 'rb'))
pipeline.predict(X_test)

Implementation of Cross-validation

I am confused since many individuals have their own approach to apply the cross-validation. For instance, some apply it on the whole dataset and some apply it on the training set.
My question is whether the below code is appropriate to implement cross-validation and make predictions from such model while having Cross-validation being applied?
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.model_selection import KFold
model= GradientBoostingClassifier(n_estimators= 10,max_depth = 10, random_state = 0)#sepcifying the model
cv = KFold(n_splits=5, shuffle=True)
from sklearn.model_selection import cross_val_predict
from sklearn.model_selection import cross_val_score
#X -the whole dataset
#y - the whole dataset but target attributes only
y_pred = cross_val_predict(model, X, y, cv=cv)
scores = cross_val_score(model, X, y, cv=cv)
You need to have a test set to evaluate performance on completely unseen data even for cross validation. Performance tuning should not be done on this test set to avoid data leakage.
Split data into two segments train and test. There are various CV methods such as K-Fold, Stratified K-Fold etc. Visualization and further reading material here,
https://scikit-learn.org/stable/auto_examples/model_selection/plot_cv_indices.html
https://scikit-learn.org/stable/auto_examples/model_selection/plot_nested_cross_validation_iris.html
In K-Fold CV training data is split into K sets. Then for each fold, K-1 of the fold is trained and the remaining one is used for performance evaluation.
The image and further detail about cross validation, train/validation/test split etc. can be found here.
https://scikit-learn.org/stable/modules/cross_validation.html
Visualization of K-Fold cross validation for 3 classes,

How to build voting classifier in sklearn when the individual classifiers are being fit with different datasets?

I'm building a classifier using highly unbalanced data. The strategy I'm interesting in testing is ensembling a model using 3 different resampled datasets. In other words, each dataset will have all the samples from the rare class, but only n samples of the abundant class (technique #4 mentioned in this article).
I want to fit 3 different VotingClassifiers on each resampled dataset, and then combine the results of the individual models using another VotingClassifier (or similar). I know that building a single voting classifier looks like this:
# First Model
rnd_clf_1 = RandomForestClassifier()
xgb_clf_1 = XGBClassifier()
voting_clf_1 = VotingClassifier(
estimators = [
('rf', rnd_clf_1),
('xgb', xgb_clf_1),
],
voting='soft'
)
# And I can fit it with the first dataset this way:
voting_clf_1.fit(X_train_1, y_train_1)
But how to stack the three of them if they are fitted on different datasets? For example, if I had three fitted models (see code below), I could build a function that calls the .predict_proba() method on each of the models and then "manually" averages the individual probabilities.
But... is there a better way?
# Fitting the individual models... but how to combine the predictions?
voting_clf_1.fit(X_train_1, y_train_1)
voting_clf_2.fit(X_train_2, y_train_2)
voting_clf_3.fit(X_train_3, y_train_3)
Thanks!
Usually the #4 method shown in the article is implemented with same type of classifier. It looks like you want to try VotingClassifier on each sample dataset.
There is an implementation of this methodology already in imblearn.ensemble.BalancedBaggingClassifier, which is an extension from Sklearn Bagging approach.
You can feed the estimator as VotingClassifier and number of estimators as the number of times, which you want carry out the dataset sampling. Use sampling_strategy param to mention proportion of downsampling which you want on Majority class.
Working Example:
from collections import Counter
from sklearn.datasets import make_classification
from sklearn.model_selection import train_test_split
from sklearn.metrics import confusion_matrix
from sklearn.ensemble import RandomForestClassifier
import xgboost as xgb
from sklearn.ensemble import RandomForestClassifier, VotingClassifier
from imblearn.ensemble import BalancedBaggingClassifier # doctest: +NORMALIZE_WHITESPACE
X, y = make_classification(n_classes=2, class_sep=2,
weights=[0.1, 0.9], n_informative=3, n_redundant=1, flip_y=0,
n_features=20, n_clusters_per_class=1, n_samples=1000, random_state=10)
print('Original dataset shape %s' % Counter(y))
X_train, X_test, y_train, y_test = train_test_split(X, y,
random_state=0)
rnd_clf_1 = RandomForestClassifier()
xgb_clf_1 = xgb.XGBClassifier()
voting_clf_1 = VotingClassifier(
estimators = [
('rf', rnd_clf_1),
('xgb', xgb_clf_1),
],
voting='soft'
)
bbc = BalancedBaggingClassifier(base_estimator=voting_clf_1, random_state=42)
bbc.fit(X_train, y_train) # doctest: +ELLIPSIS
y_pred = bbc.predict(X_test)
print(confusion_matrix(y_test, y_pred))
See here. May be you can reuse _predict_proba() and _collect_probas() functions after fitting your estimators manually.

Build a Random Forest regressor with Cross Validation from scratch

I know this is a very classical question which might be answered many times in this forum, however I could not find any clear answer which explains this clearly from scratch.
Firstly, imgine that my dataset called my_data has 4 variables such as
my_data = variable1, variable2, variable3, target_variable
So, let's come to my problem. I'll explain all my steps and ask your help for where I've been stuck:
# STEP1 : split my_data into [predictors] and [targets]
predictors = my_data[[
'variable1',
'variable2',
'variable3'
]]
targets = my_data.target_variable
# STEP2 : import the required libraries
from sklearn import cross_validation
from sklearn.ensemble import RandomForestRegressor
#STEP3 : define a simple Random Forest model attirbutes
model = RandomForestClassifier(n_estimators=100)
#STEP4 : Simple K-Fold cross validation. 3 folds.
cv = cross_validation.KFold(len(my_data), n_folds=3, random_state=30)
# STEP 5
At this step, I want to fit my model based on the training dataset, and then
use that model on test dataset and predict test targets. I also want to calculate the required statistics such as MSE, r2 etc. for understanding the performance of my model.
I'd appreciate if someone helps me woth some basic codelines for Step5.
First off, you are using the deprecated package cross-validation of scikit library. New package is named model_selection. So I am using that in this answer.
Second, you are importing RandomForestRegressor, but defining RandomForestClassifier in the code. I am taking RandomForestRegressor here, because the metrics you want (MSE, R2 etc) are only defined for regression problems, not classification.
There are multiple ways to do what you want. I assume that since you are trying to use the KFold cross-validation here, you want to use the left-out data of each fold as test fold. To accomplish this, we can do:
predictors = my_data[[
'variable1',
'variable2',
'variable3'
]]
targets = my_data.target_variable
from sklearn import model_selection
from sklearn.ensemble import RandomForestRegressor
from sklearn import metrics
model = RandomForestRegressor(n_estimators=100)
cv = model_selection.KFold(n_splits=3)
for train_index, test_index in kf.split(predictors):
print("TRAIN:", train_index, "TEST:", test_index)
X_train, X_test = predictors[train_index], predictors[test_index]
y_train, y_test = targets[train_index], targets[test_index]
# For training, fit() is used
model.fit(X_train, y_train)
# Default metric is R2 for regression, which can be accessed by score()
model.score(X_test, y_test)
# For other metrics, we need the predictions of the model
y_pred = model.predict(X_test)
metrics.mean_squared_error(y_test, y_pred)
metrics.r2_score(y_test, y_pred)
For all this, documentation is your best friend. And scikit-learn documentation are one of the best I have ever seen. Following links may help you know more about them:
http://scikit-learn.org/stable/modules/cross_validation.html#cross-validation-evaluating-estimator-performance
http://scikit-learn.org/stable/modules/model_evaluation.html#regression-metrics
http://scikit-learn.org/stable/user_guide.html
Also in the for loop it should be:
model = RandomForestRegressor(n_estimators=100)
for train_index, test_index in cv.split(X):

scikit learn: How to include others features after performed fit and transform of TFIDFVectorizer?

Just a brief idea of my situation:
I have 4 columns of input: id, text, category, label.
I used TFIDFVectorizer on the text which gives me a list of instances with word tokens of TFIDF score.
Now I'd like to include the category (no need to pass TFIDF) as another feature in the data outputed by the vectorizer.
Also note that prior to the vectorization, the data have passed train_test_split.
How could I achieve this?
Initial code:
#initialization
import pandas as pd
path = 'data\data.csv'
rappler= pd.read_csv(path)
X = rappler.text
y = rappler.label
#rappler.category - contains category for each instance
#split train test data
from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=1)
#feature extraction
from sklearn.feature_extraction.text import CountVectorizer
vect = CountVectorizer()
X_train_dtm = vect.fit_transform(X_train)
#after or even prior to perform fit_transform, how can I properly add category as a feature?
X_test_dtm = vect.transform(X_test)
#actual classfication
from sklearn.naive_bayes import MultinomialNB
nb = MultinomialNB()
nb.fit(X_train_dtm, y_train)
y_pred_class = nb.predict(X_test_dtm)
#display result
from sklearn import metrics
print(metrics.accuracy_score(y_test,y_pred_class))
I would suggest doing your train test split after feature extraction.
Once you have the TF-IDF feature lists just add the other feature for each sample.
You will have to encode the category feature, a good choice would be sklearn's LabelEncoder. Then you should have two sets of numpy arrays that can be joined.
Here is a toy example:
X_tfidf = np.array([[0.1, 0.4, 0.2], [0.5, 0.4, 0.6]])
X_category = np.array([[1], [2]])
X = np.concatenate((X_tfidf, X_category), axis=1)
At this point you would continue as you were, starting with the train test split.
You should use FeatureUnions - as explained in the documentation
FeatureUnions combines several transformer objects into a new
transformer that combines their output. A FeatureUnion takes a list of
transformer objects. During fitting, each of these is fit to the data
independently. For transforming data, the transformers are applied in
parallel, and the sample vectors they output are concatenated
end-to-end into larger vectors.
Another good example on how to use FeatureUnions can be found here: http://scikit-learn.org/stable/auto_examples/hetero_feature_union.html
Just concatenating different matrices like #AlexG suggests is probably an easier option but FeatureUnions is the scikit-learn way to do these things.

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