Merge pull request #130 from johannfaouzi/master

Add example with sklearn pipeline #128

examples/plot_feature_extraction_classification.py

@@ -0,0 +1,58 @@
+"""
+UMAP as a Feature Extraction Technique for Classification
+---------------------------------------------------------
+
+The following script shows how UMAP can be used as a feature extraction
+technique to improve the accuracy on a classification task. It also shows
+how UMAP can be integrated in standard scikit-learn pipelines.
+
+The first step is to create a dataset for a classification task, which is
+performed with the function ``sklearn.datasets.make_classification``. The
+dataset is then split into a training set and a test set using the
+``sklearn.model_selection.train_test_split`` function.
+
+Second, a linear SVM is fitted on the training set. To choose the best
+hyperparameters automatically, a gridsearch is performed on the training set.
+The performance of the model is then evaluated on the test set with the
+accuracy metric.
+
+ Third, the previous step is repeated with a slight modification: UMAP is
+ used as a feature extraction technique. This small change results in a
+ substantial improvement compared to the model where raw data is used.
+"""
+from sklearn.datasets import make_classification
+from sklearn.model_selection import train_test_split, GridSearchCV
+from sklearn.pipeline import Pipeline
+from sklearn.svm import LinearSVC
+from umap import UMAP
+
+
+# Make a toy dataset
+X, y = make_classification(n_samples=1000, n_features=300, n_informative=250,
+                           n_redundant=0, n_repeated=0, n_classes=2,
+                           random_state=1212)
+
+# Split the dataset into a training set and a test set
+X_train, X_test, y_train, y_test = train_test_split(
+    X, y, test_size=0.2, random_state=42)
+
+# Classification with a linear SVM
+svc = LinearSVC(dual=False, random_state=123)
+params_grid = {"C": [10**k for k in range(-3, 4)]}
+clf = GridSearchCV(svc, params_grid)
+clf.fit(X_train, y_train)
+print("Accuracy on the test set with raw data: {:.3f}".format(
+    clf.score(X_test, y_test)))
+
+# Transformation with UMAP followed by classification with a linear SVM
+umap = UMAP(random_state=456)
+pipeline = Pipeline([("umap", umap),
+                     ("svc", svc)])
+params_grid_pipeline = {"umap__n_neighbors": [5, 20],
+                        "umap__n_components": [15, 25, 50],
+                        "svc__C": [10**k for k in range(-3, 4)]}
+
+clf_pipeline = GridSearchCV(pipeline, params_grid_pipeline)
+clf_pipeline.fit(X_train, y_train)
+print("Accuracy on the test set with UMAP transformation: {:.3f}".format(
+    clf_pipeline.score(X_test, y_test)))