feat(Metalearner): Added k-Nearest Neighbors - Contributes to #129

aucmedi/ensemble/metalearner/__init__.py

@@ -54,6 +54,7 @@
 from aucmedi.ensemble.metalearner.best_model import Best_Model
 from aucmedi.ensemble.metalearner.averaging_mean_weighted import Averaging_WeightedMean
 from aucmedi.ensemble.metalearner.random_forest import Random_Forest
+from aucmedi.ensemble.metalearner.k_neighbors import KNearestNeighbors
 
 #-----------------------------------------------------#
 #           Access Functions to Metalearners          #
@@ -66,5 +67,6 @@
                     "best_model": Best_Model,
                     "weighted_mean": Averaging_WeightedMean,
                     "random_forest": Random_Forest,
+                    "k_neighbors": KNearestNeighbors,
 }
 """ Dictionary of implemented Metalearners. """

aucmedi/ensemble/metalearner/k_neighbors.py

@@ -0,0 +1,85 @@
+#==============================================================================#
+#  Author:       Dominik Müller                                                #
+#  Copyright:    2022 IT-Infrastructure for Translational Medical Research,    #
+#                University of Augsburg                                        #
+#                                                                              #
+#  This program is free software: you can redistribute it and/or modify        #
+#  it under the terms of the GNU General Public License as published by        #
+#  the Free Software Foundation, either version 3 of the License, or           #
+#  (at your option) any later version.                                         #
+#                                                                              #
+#  This program is distributed in the hope that it will be useful,             #
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of              #
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the               #
+#  GNU General Public License for more details.                                #
+#                                                                              #
+#  You should have received a copy of the GNU General Public License           #
+#  along with this program.  If not, see <http://www.gnu.org/licenses/>.       #
+#==============================================================================#
+#-----------------------------------------------------#
+#                   Library imports                   #
+#-----------------------------------------------------#
+# External libraries
+import pickle
+from sklearn.neighbors import KNeighborsClassifier
+import numpy as np
+# Internal libraries/scripts
+from aucmedi.ensemble.metalearner.ml_base import Metalearner_Base
+
+#-----------------------------------------------------#
+#           Metalearner: k-Nearest Neighbors          #
+#-----------------------------------------------------#
+class KNearestNeighbors(Metalearner_Base):
+    """ A k-Nearest Neighbors based Metalearner.
+
+    This class should be passed to a Ensemble function like Stacking for combining predictions.
+
+    !!! info
+        Can be utilized for binary, multi-class and multi-label tasks.
+
+    ???+ abstract "Reference - Implementation"
+        https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html
+
+        Scikit-learn: Machine Learning in Python, Pedregosa et al., JMLR 12, pp. 2825-2830, 2011.
+        https://jmlr.csail.mit.edu/papers/v12/pedregosa11a.html
+    """
+    #---------------------------------------------#
+    #                Initialization               #
+    #---------------------------------------------#
+    def __init__(self):
+        self.model = KNeighborsClassifier()
+
+    #---------------------------------------------#
+    #                  Training                   #
+    #---------------------------------------------#
+    def train(self, x, y):
+        # Train model
+        self.model = self.model.fit(x, y)
+
+    #---------------------------------------------#
+    #                  Prediction                 #
+    #---------------------------------------------#
+    def predict(self, data):
+        # Compute prediction probabilities via fitted model
+        pred = self.model.predict_proba(data)
+        # Postprocess decision tree predictions
+        pred = np.asarray(pred)
+        pred = np.swapaxes(pred[:,:,1], 0, 1)
+        # Return results as NumPy array
+        return pred
+
+    #---------------------------------------------#
+    #              Dump Model to Disk             #
+    #---------------------------------------------#
+    def dump(self, path):
+        # Dump model to disk via pickle
+        with open(path, "wb") as pickle_writer:
+            pickle.dump(self.model, pickle_writer)
+
+    #---------------------------------------------#
+    #             Load Model from Disk            #
+    #---------------------------------------------#
+    def load(self, path):
+        # Load model from disk via pickle
+        with open(path, "rb") as pickle_reader:
+            self.model = pickle.load(pickle_reader)

tests/test_metalearner.py

@@ -293,3 +293,34 @@ def test_Random_Forest_usage(self):
         preds = ml.predict(data=self.pred_data)
         # Check
         self.assertTrue(np.array_equal(preds.shape, (25,4)))
+
+    #-------------------------------------------------#
+    #               k-Nearest Neighbors               #
+    #-------------------------------------------------#
+    def test_KNearestNeighbors_create(self):
+        # Initializations
+        ml = KNearestNeighbors()
+        self.assertTrue("k_neighbors" in metalearner_dict)
+        ml = metalearner_dict["k_neighbors"]()
+        # Storage
+        model_path = os.path.join(self.tmp_data.name, "ml_model.pickle")
+        self.assertFalse(os.path.exists(model_path))
+        ml.dump(model_path)
+        self.assertTrue(os.path.exists(model_path))
+        # Loading
+        ml.model = None
+        self.assertTrue(ml.model is None)
+        ml.load(model_path)
+        self.assertFalse(ml.model is None)
+        # Cleanup
+        os.remove(model_path)
+
+    def test_KNearestNeighbors_usage(self):
+        # Initializations
+        ml = KNearestNeighbors()
+        # Training
+        ml.train(x=self.pred_data, y=self.labels_ohe)
+        # Inference
+        preds = ml.predict(data=self.pred_data)
+        # Check
+        self.assertTrue(np.array_equal(preds.shape, (25,4)))