New translations knn.py (French)

lang/fr/gklearn/utils/knn.py

@@ -0,0 +1,141 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Mon May 11 11:03:01 2020
+
+@author: ljia
+"""
+import numpy as np
+from sklearn.model_selection import ShuffleSplit
+from sklearn.neighbors import KNeighborsClassifier
+from sklearn.metrics import accuracy_score
+from gklearn.utils.utils import get_graph_kernel_by_name
+# from gklearn.preimage.utils import get_same_item_indices
+
+def sum_squares(a, b):
+	"""
+	Return the sum of squares of the difference between a and b, aka MSE
+	"""
+	return np.sum([(a[i] - b[i])**2 for i in range(len(a))])
+
+
+def euclid_d(x, y):
+	"""
+	1D euclidean distance
+	"""
+	return np.sqrt((x-y)**2)
+
+
+def man_d(x, y):
+	"""
+	1D manhattan distance
+	"""
+	return np.abs((x-y))
+
+
+def knn_regression(D_app, D_test, y_app, y_test, n_neighbors, verbose=True, text=None):
+
+	from sklearn.neighbors import KNeighborsRegressor
+	knn = KNeighborsRegressor(n_neighbors=n_neighbors, metric='precomputed')
+	knn.fit(D_app, y_app)
+	y_pred = knn.predict(D_app)
+	y_pred_test = knn.predict(D_test.T)
+	perf_app = np.sqrt(sum_squares(y_pred, y_app)/len(y_app))
+	perf_test = np.sqrt(sum_squares(y_pred_test, y_test)/len(y_test))
+
+	if (verbose):
+		print("Learning error with {} train examples : {}".format(text, perf_app))
+		print("Test error with {} train examples : {}".format(text, perf_test))
+
+	return perf_app, perf_test
+
+
+def knn_classification(d_app, d_test, y_app, y_test, n_neighbors, verbose=True, text=None):
+	knn = KNeighborsClassifier(n_neighbors=n_neighbors, metric='precomputed')
+	knn.fit(d_app, y_app)
+	y_pred = knn.predict(d_app)
+	y_pred_test = knn.predict(d_test.T)
+	perf_app = accuracy_score(y_app, y_pred)
+	perf_test = accuracy_score(y_test, y_pred_test)
+
+	if (verbose):
+		print("Learning accuracy with {} costs : {}".format(text, perf_app))
+		print("Test accuracy with {} costs : {}".format(text, perf_test))
+		
+	return perf_app, perf_test
+	
+
+def knn_cv(dataset, kernel_options, trainset=None, n_neighbors=1, n_splits=50, test_size=0.9, verbose=True):
+	'''
+	Perform a knn classification cross-validation on given dataset.
+	'''
+# 	Gn = dataset.graphs
+	y_all = dataset.targets
+	
+	# compute kernel distances.
+	dis_mat = __compute_kernel_distances(dataset, kernel_options, trainset=trainset)
+		
+	
+	rs = ShuffleSplit(n_splits=n_splits, test_size=test_size, random_state=0)
+# 	train_indices = [[] for _ in range(n_splits)] 
+# 	test_indices = [[] for _ in range(n_splits)]
+# 	idx_targets = get_same_item_indices(y_all)
+# 	for key, item in idx_targets.items():
+# 		i = 0
+# 		for train_i, test_i in rs.split(item): # @todo: careful when parallel.
+# 			train_indices[i] += [item[idx] for idx in train_i]
+# 			test_indices[i] += [item[idx] for idx in test_i]
+# 			i += 1
+	
+	accuracies = []
+# 	for trial in range(len(train_indices)):
+# 		train_index = train_indices[trial]
+# 		test_index = test_indices[trial] 
+	for train_index, test_index in rs.split(y_all):
+# 		print(train_index, test_index)
+# 		G_app = [Gn[i] for i in train_index]
+# 		G_test = [Gn[i] for i in test_index]
+		y_app = [y_all[i] for i in train_index]
+		y_test = [y_all[i] for i in test_index]
+		
+		N = len(train_index)
+		
+		d_app = dis_mat.copy()
+		d_app = d_app[train_index,:]
+		d_app = d_app[:,train_index]
+		
+		d_test = np.zeros((N, len(test_index)))
+		
+		for i in range(N):
+			for j in range(len(test_index)):
+				d_test[i, j] = dis_mat[train_index[i], test_index[j]]
+				
+		accuracies.append(knn_classification(d_app, d_test, y_app, y_test, n_neighbors, verbose=verbose, text=''))
+		
+	results = {}
+	results['ave_perf_train'] = np.mean([i[0] for i in accuracies], axis=0)
+	results['std_perf_train'] = np.std([i[0] for i in accuracies], axis=0, ddof=1)
+	results['ave_perf_test'] = np.mean([i[1] for i in accuracies], axis=0)
+	results['std_perf_test'] = np.std([i[1] for i in accuracies], axis=0, ddof=1)
+
+	return results
+		
+		
+def __compute_kernel_distances(dataset, kernel_options, trainset=None):
+	graph_kernel = get_graph_kernel_by_name(kernel_options['name'], 
+				  node_labels=dataset.node_labels,
+				  edge_labels=dataset.edge_labels, 
+				  node_attrs=dataset.node_attrs,
+				  edge_attrs=dataset.edge_attrs,
+				  ds_infos=dataset.get_dataset_infos(keys=['directed']),
+				  kernel_options=kernel_options)
+	
+	gram_matrix, run_time = graph_kernel.compute(dataset.graphs, **kernel_options)
+
+	dis_mat, _, _, _ = graph_kernel.compute_distance_matrix()
+	
+	if trainset is not None:
+		gram_matrix_unnorm = graph_kernel.gram_matrix_unnorm
+		
+
+	return dis_mat