Add J+aB and APS methods

.gitignore

@@ -2,15 +2,19 @@
 __pycache__/
 *.py[cod]
 *$py.class
+.DS_Store
 
 # C extensions
 *.so
 
-# scikit-learn specific
+# documentation specific
 doc/_build/
+doc/examples_classification/
+doc/examples_regression/
 doc/auto_examples/
 doc/modules/generated/
 doc/datasets/generated/
+doc/generated/
 
 # Distribution / packaging
 
@@ -68,3 +72,7 @@ target/
 
 # VSCode
 .vscode
+
+# Images
+*.png
+*.jpeg

AUTHORS.rst

@@ -18,5 +18,6 @@ Contributors
 * Alizé Papp <[email protected]>
 * Abdou Akim Goumbala <[email protected]>
 * Adirtha Borgohain <[email protected]>
-
-To be continued ...
+* Thomas Morzadec <[email protected]>
+* Julien Roussel <[email protected]>
+To be continued ...

HISTORY.rst

@@ -2,7 +2,14 @@
 History
 =======
 
-0.3.0 (XXXX-XX-XX)
+0.3.1 (XXXX-XX-XX)
+------------------
+
+* Add Jackknife+-after-Bootstrap method and add mean and median as aggregation functions
+* Add "cumulative_score" method in MapieClassifier
+
+
+0.3.0 (2021-09-10)
 ------------------
 
 * Renaming estimators.py module to regression.py

Makefile

@@ -1,6 +1,5 @@
 .PHONY: tests doc build
-
-lint:
+lint:	
 	flake8 . --exclude=doc
 
 type-check:
@@ -10,7 +9,7 @@ tests:
 	pytest -vs --doctest-modules mapie
 
 coverage:
-	pytest -vs --doctest-modules --cov-branch --cov=mapie --pyargs mapie
+	pytest -vs --doctest-modules --cov-branch --cov=mapie --pyargs --cov-report term-missing mapie
 
 doc:
 	$(MAKE) clean -C doc

doc/tutorial_classification.rst

@@ -6,4 +6,171 @@
 Tutorial
 ========
 
-TO BE CONTINUED
+In this tutorial, we compare the prediction sets estimating by :class:`mapie.classification.MapieClassifier`.
+
+Throughout this tutorial, we will answer the following question:
+
+How does the number of classes in the prediction sets vary according to the significance level ?
+
+1. Conformal Prediction method using the softmax score of the true label
+========================================================================
+We will use MAPIE to estimate a prediction set of several classes such that the probability that the true label
+of a new test point is included in the prediction set is always higher than the target confidence level :
+:math:` P(Y \in C) \geq 1 - \alpha`.
+We start by using the softmax score output by the base classifier as the conformity score on a toy two-dimensional dataset.
+We estimate the prediction sets as follows :
+
+* First we generate a dataset with train, calibration and test, the model is fitted on the training set.
+* We set the conformal score :math:`S_i = \hat{f}(X_{i})_{y_i}` the softmax output of the true class for each sample in the calibration set.
+* Then we define :math:`\hat{q}` as being the :math:`(n + 1) (\alpha) / n` previous quantile of :math:`S_{1}, ..., S_{n}`
+(this is essentially the quantile :math:`\alpha`, but with a small sample correction). 
+* Finally, for a new test data point (where :math:`X_{n + 1}` is known but :math:`Y_{n + 1}` is not), create a prediction set
+:math:`C(X_{n+1}) = \{y: \hat{f}(X_{n+1})_{y} > \hat{q}\}` which includes all the classes with a sufficiently high softmax output.
+
+We use a two-dimensional dataset with three labels. The distribution of the data is a bivariate normal with diagonal covariance matrices for each label. 
+
+.. code-block:: python
+
+    import numpy as np
+    centers = [(0, 3.5), (-2, 0), (2, 0)]
+    covs = [np.eye(2), np.eye(2)*2, np.diag([5, 1])]
+    x_min, x_max, y_min, y_max, step = -6, 8, -6, 8, 0.1
+    n_samples = 500
+    n_classes = 3
+    np.random.seed(42)
+    X = np.vstack([
+        np.random.multivariate_normal(center, cov, n_samples)
+        for center, cov in zip(centers, covs)
+    ])
+    y = np.hstack([np.full(n_samples, i) for i in range(n_classes)])
+    X_train, X_cal, y_train, y_cal = train_test_split(X, y, test_size=0.3)
+
+    xx, yy = np.meshgrid(
+        np.arange(x_min, x_max, step), np.arange(x_min, x_max, step)
+    )
+    X_test = np.stack([xx.ravel(), yy.ravel()], axis=1)
+
+Let's see our training data
+
+.. code-block:: python
+
+   import matplotlib.pyplot as plt
+   colors = {0: "#1f77b4", 1: "#ff7f0e", 2:  "#2ca02c", 3: "#d62728"}
+   y_train_col = list(map(colors.get, y_train))
+   fig = plt.figure()
+   plt.scatter(
+       X_train[:, 0],
+       X_train[:, 1],
+       color=y_train_col,
+       marker='o',
+       s=10,
+       edgecolor='k'
+   )
+   plt.xlabel("X")
+   plt.ylabel("Y")
+   plt.show()
+
+.. image:: images/tuto_classification_1.jpeg
+    :align: center
+
+We fit our training data with a Gaussian Naive Base estimator. And then we apply :class:`mapie.classification.MapieClassifier` in the calibration data with the method ``score`` to the estimator indicating that it has already been fitted with `cv="prefit"`.
+We then estimate the prediction sets with differents alpha values with a
+``fit`` and ``predict`` process. 
+
+.. code-block:: python
+
+   from sklearn.naive_bayes import GaussianNB
+   from mapie.classification import MapieClassifier
+   from mapie.metrics import classification_coverage_score
+   clf = GaussianNB().fit(X_train, y_train)
+   y_pred = clf.predict(X_test)
+   y_pred_proba = clf.predict_proba(X_test)
+   y_pred_proba_max = np.max(y_pred_proba, axis=1)
+   mapie = MapieClassifier(estimator=clf, cv="prefit")
+   mapie.fit(X_cal, y_cal)
+   alpha = [0.2, 0.1, 0.05]
+   y_pred_mapie, y_ps_mapie = mapie.predict(X_test, alpha=alpha)
+
+
+* ``y_pred_mapie``: represents the prediction in the test set by the base estimator.
+* ``y_ps_mapie``: the prediction sets estimated by MAPIE.
+
+.. code-block:: python
+
+   def plot_scores(n, alphas, scores, quantiles):      
+    colors = {0:'#1f77b4', 1:'#ff7f0e', 2:'#2ca02c'}
+    fig = plt.figure()
+    plt.hist(scores, bins='auto')
+    i=0         
+    for quantile in quantiles:
+        plt.vlines(x = quantile, ymin=0, ymax=400, color = colors[i], linestyles = 'dashed',label=f'alpha = {alphas[i]}') 
+        i=i+1
+    plt.title("Distribution of scores")
+    plt.legend()
+    plt.xlabel("scores")
+    plt.ylabel("count")
+    plt.show()
+
+Let's see the distribution of the scores with the calculated quantiles.
+
+.. code-block:: python
+
+   scores = mapie.scores_
+   n = mapie.n_samples_val_
+   quantiles = mapie.quantiles_ 
+   plot_scores(n, alpha, scores, quantiles)
+
+.. image:: images/tuto_classification_2.jpeg
+    :align: center
+
+The estimated quantile depends on alpha and a high value of alpha can potentially lead to a high quantile which would
+not necessarily be reached by any class in uncertain areas, resulting in null regions.
+
+We will now compare the differences between the prediction sets of the different values ​​of alpha.
+
+.. code-block:: python
+
+   def plot_results(alphas, y_pred_mapie, y_ps_mapie):
+    tab10 = plt.cm.get_cmap('Purples', 4)
+    colors = {0: "#1f77b4", 1: "#ff7f0e", 2:  "#2ca02c", 3: "#d62728"}
+    y_pred_col = list(map(colors.get, y_pred_mapie))
+    fig, [[ax1, ax2], [ax3, ax4]] = plt.subplots(2, 2, figsize=(10, 10))
+    axs = {0: ax1, 1: ax2, 2:  ax3, 3: ax4}
+    axs[0].scatter(
+       X_test[:, 0],
+       X_test[:, 1],
+       color=y_pred_col,
+       marker='.',
+       s=10,
+       alpha=0.4
+    )
+    axs[0].set_title("Predicted labels")
+    for i, alpha in enumerate(alphas):
+       y_pi_sums = y_ps_mapie[:, :, i].sum(axis=1)
+       num_labels = axs[i+1].scatter(
+           X_test[:, 0],
+           X_test[:, 1],
+           c=y_pi_sums,
+           marker='.',
+           s=10,
+           alpha=1,
+           cmap=tab10,
+           vmin=0,
+           vmax=3
+       )
+       cbar = plt.colorbar(num_labels, ax=axs[i+1])
+       coverage= classification_coverage_score(y_pred_mapie,y_ps_mapie[:,:,i])
+       axs[i+1].set_title(f"Number of labels for alpha={alpha_}")
+    plt.show()
+
+.. code-block:: python
+
+   plot_results(alpha, y_pred_mapie, y_ps_mapie)
+
+.. image:: images/tuto_classification_3.jpeg
+    :align: center
+
+When the class coverage is not large enough, the prediction sets can be empty
+when the model is uncertain at the border between two class. The null region
+disappears for larger class coverages but ambiguous classification regions
+arise with several labels included in the prediction sets.