def test_build_error():
new_exception = exception.BuildError('error')
try:
raise new_exception
except exception.BuildError:
pass
def fit(self, X_train, Y_train=None):
"""Fits data in the classifier.
Args:
X_train (np.array): Array of training features.
Y_train (np.array): Array of training labels.
"""
logger.info('Clustering with classifier ...')
# Initializing the timer
start = time.time()
# Creating a subgraph
self.subgraph = KNNSubgraph(X_train, Y_train)
# Checks if it is supposed to use pre-computed distances
if self.pre_computed_distance:
# Checks if its size is the same as the subgraph's amount of nodes
if self.pre_distances.shape[
0] != self.subgraph.n_nodes or self.pre_distances.shape[
1] != self.subgraph.n_nodes:
# If not, raises an error
raise e.BuildError(
'Pre-computed distance matrix should have the size of `n_nodes x n_nodes`'
)
# Performing the best minimum cut on the subgraph
self._best_minimum_cut(self.min_k, self.max_k)
# Clustering the data with best `k` value
self._clustering(self.subgraph.best_k)
# The subgraph has been properly trained
self.subgraph.trained = True
# Ending timer
end = time.time()
# Calculating training task time
train_time = end - start
logger.info('Classifier has been clustered with.')
logger.info(f'Number of clusters: {self.subgraph.n_clusters}.')
logger.info(f'Clustering time: {train_time} seconds.')
def _learn(self, X_train, Y_train, I_train, X_val, Y_val, I_val):
"""Learns the best `k` value over the validation set.
Args:
X_train (np.array): Array of training features.
Y_train (np.array): Array of training labels.
I_train (np.array): Array of training indexes.
X_val (np.array): Array of validation features.
Y_val (np.array): Array of validation labels.
I_val (np.array): Array of validation indexes.
"""
logger.info('Learning best `k` value ...')
# Creating a subgraph
self.subgraph = KNNSubgraph(X_train, Y_train, I_train)
if self.pre_computed_distance:
if self.pre_distances.shape[
0] != self.subgraph.n_nodes or self.pre_distances.shape[
1] != self.subgraph.n_nodes:
raise e.BuildError(
'Pre-computed distance matrix should have the size of `n_nodes x n_nodes`'
)
# Defining initial maximum accuracy as 0
max_acc = 0.0
for k in range(1, self.max_k + 1):
# Gathers current `k` as subgraph's best `k`
self.subgraph.best_k = k
# Calculate the arcs using the current `k` value
self.subgraph.create_arcs(k, self.distance_fn,
self.pre_computed_distance,
self.pre_distances)
# Calculate the p.d.f. using the current `k` value
self.subgraph.calculate_pdf(k, self.distance_fn,
self.pre_computed_distance,
self.pre_distances)
# Clusters the subgraph
self._clustering()
# Calculate the predictions over the validation set
preds = self.predict(X_val, I_val)
# Calculating the accuracy
acc = g.opf_accuracy(Y_val, preds)
if acc > max_acc:
max_acc = acc
best_k = k
logger.info('Accuracy over k = %d: %s', k, acc)
self.subgraph.destroy_arcs()
self.subgraph.best_k = best_k
def predict(self, X_val, I_val=None):
"""Predicts new data using the pre-trained classifier.
Args:
X_val (np.array): Array of validation features.
I_val (np.array): Array of validation indexes.
Returns:
A list of predictions for each record of the data.
"""
# Checks if there is a knn-subgraph
if not self.subgraph:
# If not, raises an BuildError
raise e.BuildError('KNNSubgraph has not been properly created')
# Checks if knn-subgraph has been properly trained
if not self.subgraph.trained:
# If not, raises an BuildError
raise e.BuildError('Classifier has not been properly clustered')
logger.info('Predicting data ...')
# Initializing the timer
start = time.time()
# Creating a prediction subgraph
pred_subgraph = KNNSubgraph(X_val, I=I_val)
# Gathering the best `k` value
best_k = self.subgraph.best_k
# Creating an array of distances
distances = np.zeros(best_k + 1)
# Creating an array of nearest neighbours indexes
neighbours_idx = np.zeros(best_k + 1)
# For every possible prediction node
for i in range(pred_subgraph.n_nodes):
# Defines the current cost
cost = -c.FLOAT_MAX
# Filling array of distances with maximum value
distances.fill(c.FLOAT_MAX)
# For every possible trained node
for j in range(self.subgraph.n_nodes):
# If they are different nodes
if j != i:
# If it is supposed to use a pre-computed distance
if self.pre_computed_distance:
# Gathers the distance from the matrix
distances[best_k] = self.pre_distances[
pred_subgraph.nodes[i].idx][
self.subgraph.nodes[j].idx]
# If it is supposed to calculate the distance
else:
# Calculates the distance between nodes `i` and `j`
distances[best_k] = self.distance_fn(
pred_subgraph.nodes[i].features,
self.subgraph.nodes[j].features)
# Apply node `j` as a neighbour
neighbours_idx[best_k] = j
# Gathers current `k`
cur_k = best_k
# While current `k` is bigger than 0 and the `k` distance is smaller than `k-1` distance
while cur_k > 0 and distances[cur_k] < distances[cur_k -
1]:
# Swaps the distance from `k` and `k-1`
distances[cur_k], distances[cur_k - 1] = distances[
cur_k - 1], distances[cur_k]
# Swaps the neighbours indexex from `k` and `k-1`
neighbours_idx[cur_k], neighbours_idx[
cur_k -
1] = neighbours_idx[cur_k -
1], neighbours_idx[cur_k]
# Decrements `k`
cur_k -= 1
# Defining the density as 0
density = 0.0
# For every possible k
for k in range(best_k):
# Accumulates the density
density += np.exp(-distances[k] / self.subgraph.constant)
# Gather its mean value
density /= best_k
# Scale the density between minimum and maximum values
density = ((c.MAX_DENSITY - 1) *
(density - self.subgraph.min_density) /
(self.subgraph.max_density - self.subgraph.min_density +
c.EPSILON)) + 1
# For every possible k
for k in range(best_k):
# If distance is different than maximum possible value
if distances[k] != c.FLOAT_MAX:
# Gathers the node's neighbour
neighbour = int(neighbours_idx[k])
# Calculate the temporary cost
temp_cost = np.minimum(self.subgraph.nodes[neighbour].cost,
density)
# If temporary cost is bigger than current cost
if temp_cost > cost:
# Replaces the current cost
cost = temp_cost
# Propagates the predicted label from the neighbour
pred_subgraph.nodes[
i].predicted_label = self.subgraph.nodes[
neighbour].predicted_label
# Propagates the cluster label from the neighbour
pred_subgraph.nodes[
i].cluster_label = self.subgraph.nodes[
neighbour].cluster_label
# Creating the list of predictions
preds = [pred.predicted_label for pred in pred_subgraph.nodes]
# Creating the list of clusters
clusters = [pred.cluster_label for pred in pred_subgraph.nodes]
# Ending timer
end = time.time()
# Calculating prediction task time
predict_time = end - start
logger.info('Data has been predicted.')
logger.info('Prediction time: %s seconds.', predict_time)
return preds, clusters
def predict(self, X_val, I_val=None):
"""Predicts new data using the pre-trained classifier.
Args:
X_val (np.array): Array of validation or test features.
I_val (np.array): Array of validation or test indexes.
Returns:
A list of predictions for each record of the data.
"""
if not self.subgraph:
raise e.BuildError('Subgraph has not been properly created')
if not self.subgraph.trained:
raise e.BuildError('Classifier has not been properly fitted')
logger.info('Predicting data ...')
start = time.time()
# Creating a prediction subgraph
pred_subgraph = Subgraph(X_val, I=I_val)
for i in range(pred_subgraph.n_nodes):
# Initializing the conqueror node
conqueror = -1
# Initializes the `j` counter
j = 0
# Gathers the first node from the ordered list
k = self.subgraph.idx_nodes[j]
if self.pre_computed_distance:
weight = self.pre_distances[self.subgraph.nodes[k].idx][pred_subgraph.nodes[i].idx]
else:
weight = self.distance_fn(self.subgraph.nodes[k].features, pred_subgraph.nodes[i].features)
# The minimum cost will be the maximum between the `k` node cost and its weight (arc)
min_cost = np.maximum(self.subgraph.nodes[k].cost, weight)
# The current label will be `k` node's predicted label
current_label = self.subgraph.nodes[k].predicted_label
# While `j` is a possible node and the minimum cost is bigger than the current node's cost
while j < (self.subgraph.n_nodes - 1) and min_cost > self.subgraph.nodes[self.subgraph.idx_nodes[j+1]].cost:
# Gathers the next node from the ordered list
l = self.subgraph.idx_nodes[j+1]
if self.pre_computed_distance:
weight = self.pre_distances[self.subgraph.nodes[l].idx][pred_subgraph.nodes[i].idx]
else:
weight = self.distance_fn(self.subgraph.nodes[l].features, pred_subgraph.nodes[i].features)
# The temporary minimum cost will be the maximum between the `l` node cost and its weight (arc)
temp_min_cost = np.maximum(self.subgraph.nodes[l].cost, weight)
# If temporary minimum cost is smaller than the minimum cost
if temp_min_cost < min_cost:
# Replaces the minimum cost
min_cost = temp_min_cost
# Gathers the identifier of `l` node
conqueror = l
# Updates the current label as `l` node's predicted label
current_label = self.subgraph.nodes[l].predicted_label
# Increments the `j` counter
j += 1
# Makes `k` and `l` equals
k = l
# Node's `i` predicted label is the same as current label
pred_subgraph.nodes[i].predicted_label = current_label
# Checks if any node has been conquered
if conqueror > -1:
# Marks the conqueror node and its path
self.subgraph.mark_nodes(conqueror)
# Creating the list of predictions
preds = [pred.predicted_label for pred in pred_subgraph.nodes]
end = time.time()
predict_time = end - start
logger.info('Data has been predicted.')
logger.info('Prediction time: %s seconds.', predict_time)
return preds
def _learn(self, X_train, Y_train, X_val, Y_val):
"""Learns the best `k` value over the validation set.
Args:
X_train (np.array): Array of training features.
Y_train (np.array): Array of training labels.
X_val (np.array): Array of validation features.
Y_val (np.array): Array of validation labels.
"""
logger.info('Learning best `k` value ...')
# Creating a subgraph
self.subgraph = KNNSubgraph(X_train, Y_train)
# Checks if it is supposed to use pre-computed distances
if self.pre_computed_distance:
# Checks if its size is the same as the subgraph's amount of nodes
if self.pre_distances.shape[
0] != self.subgraph.n_nodes or self.pre_distances.shape[
1] != self.subgraph.n_nodes:
# If not, raises an error
raise e.BuildError(
'Pre-computed distance matrix should have the size of `n_nodes x n_nodes`'
)
# Defining initial maximum accuracy as 0
max_acc = 0.0
# For every possible `k` value
for k in range(1, self.max_k + 1):
# Gathers current `k` as subgraph's best `k`
self.subgraph.best_k = k
# Calculate the arcs using the current `k` value
self.subgraph.create_arcs(k, self.distance_fn,
self.pre_computed_distance,
self.pre_distances)
# Calculate the p.d.f. using the current `k` value
self.subgraph.calculate_pdf(k, self.distance_fn,
self.pre_computed_distance,
self.pre_distances)
# Clusters the subgraph
self._clustering()
# Calculate the predictions over the validation set
preds = self.predict(X_val)
# Calculating the accuracy
acc = g.opf_accuracy(Y_val, preds)
# If accuracy is better than maximum accuracy
if acc > max_acc:
# Replaces the maximum accuracy value
max_acc = acc
# Defines current `k` as the best `k` value
best_k = k
logger.info(f'Accuracy over k = {k}: {acc}')
# Destroy the arcs
self.subgraph.destroy_arcs()
# Applying the best k to the subgraph's property
self.subgraph.best_k = best_k
def fit(self, X_train, Y_train, X_unlabeled):
"""Fits data in the semi-supervised classifier.
Args:
X_train (np.array): Array of training features.
Y_train (np.array): Array of training labels.
X_unlabeled (np.array): Array of unlabeled features.
"""
logger.info('Fitting semi-supervised classifier ...')
# Initializing the timer
start = time.time()
# Creating a subgraph
self.subgraph = Subgraph(X_train, Y_train)
# Finding prototypes
self._find_prototypes()
# Gather current number of nodes
current_n_nodes = self.subgraph.n_nodes
# Iterate over every possible unlabeled sample
for i, feature in enumerate(X_unlabeled):
# Creates a Node structure
node = Node(current_n_nodes + i, 1, feature)
# Appends the node to the list
self.subgraph.nodes.append(node)
# Checks if it is supposed to use pre-computed distances
if self.pre_computed_distance:
# Checks if its size is the same as the subgraph's amount of nodes
if self.pre_distances.shape[
0] != self.subgraph.n_nodes or self.pre_distances.shape[
1] != self.subgraph.n_nodes:
# If not, raises an error
raise e.BuildError(
'Pre-computed distance matrix should have the size of `n_nodes x n_nodes`'
)
# Creating a minimum heap
h = Heap(size=self.subgraph.n_nodes)
# For each possible node
for i in range(self.subgraph.n_nodes):
# Checks if node is a prototype
if self.subgraph.nodes[i].status == c.PROTOTYPE:
# If yes, it does not have predecessor nodes
self.subgraph.nodes[i].pred = c.NIL
# Its predicted label is the same as its true label
self.subgraph.nodes[i].predicted_label = self.subgraph.nodes[
i].label
# Its cost equals to zero
h.cost[i] = 0
# Inserts the node into the heap
h.insert(i)
# If node is not a prototype
else:
# Its cost equals to maximum possible value
h.cost[i] = c.FLOAT_MAX
# While the heap is not empty
while not h.is_empty():
# Removes a node
p = h.remove()
# Appends its index to the ordered list
self.subgraph.idx_nodes.append(p)
# Gathers its cost
self.subgraph.nodes[p].cost = h.cost[p]
# For every possible node
for q in range(self.subgraph.n_nodes):
# If we are dealing with different nodes
if p != q:
# If `p` node cost is smaller than `q` node cost
if h.cost[p] < h.cost[q]:
# Checks if we are using a pre-computed distance
if self.pre_computed_distance:
# Gathers the distance from the distance's matrix
weight = self.pre_distances[self.subgraph.nodes[
p].idx][self.subgraph.nodes[q].idx]
# If the distance is supposed to be calculated
else:
# Calls the corresponding distance function
weight = self.distance_fn(
self.subgraph.nodes[p].features,
self.subgraph.nodes[q].features)
# The current cost will be the maximum cost between the node's and its weight (arc)
current_cost = np.maximum(h.cost[p], weight)
# If current cost is smaller than `q` node's cost
if current_cost < h.cost[q]:
# `q` node has `p` as its predecessor
self.subgraph.nodes[q].pred = p
# And its predicted label is the same as `p`
self.subgraph.nodes[
q].predicted_label = self.subgraph.nodes[
p].predicted_label
# As we may have unlabeled nodes, make sure that `q` label equals to `q` predicted label
self.subgraph.nodes[q].label = self.subgraph.nodes[
q].predicted_label
# Updates the heap `q` node and the current cost
h.update(q, current_cost)
# The subgraph has been properly trained
self.subgraph.trained = True
# Ending timer
end = time.time()
# Calculating training task time
train_time = end - start
logger.info('Semi-supervised classifier has been fitted.')
logger.info(f'Training time: {train_time} seconds.')
def predict(self, X_val, I_val=None):
"""Predicts new data using the pre-trained classifier.
Args:
X_val (np.array): Array of validation features.
I_val (np.array): Array of validation indexes.
Returns:
A list of predictions for each record of the data.
"""
# Checks if there is a knn-subgraph
if not self.subgraph:
# If not, raises an BuildError
raise e.BuildError('ANNSubgraph has not been properly created')
# Checks if knn-subgraph has been properly trained
if not self.subgraph.trained:
# If not, raises an BuildError
raise e.BuildError('Classifier has not been properly clustered')
logger.info('Predicting data ...')
# Initializing the timer
start = time.time()
# Creating a prediction subgraph
pred_subgraph = ANNSubgraph(X_val, I=I_val)
# Gathering the best `k` value
best_k = self.subgraph.best_k
# Creating an array of distances
# distances = np.zeros(best_k + 1)
# Creating an array of nearest neighbours indexes
# neighbours_idx = np.zeros(best_k + 1)
# For every possible prediction node
for i in range(pred_subgraph.n_nodes):
# For every possible trained node
neighbors_idx, distances = self.ann_search.query(
pred_subgraph.nodes[i].features, best_k)
density = np.sum(
np.exp(-np.array(distances) / self.subgraph.constant))
# Gather its mean value
density /= best_k
# Scale the density between minimum and maximum values
density = ((c.MAX_DENSITY - 1) *
(density - self.subgraph.min_density) /
(self.subgraph.max_density - self.subgraph.min_density +
c.EPSILON)) + 1
neighbor_costs = [
self.subgraph.nodes[neighbor].cost
for neighbor in neighbors_idx
]
# Calculate the temporary cost
temp_cost = np.minimum(neighbor_costs, [density])
# Select the maximum cost among node's neighbors
k = np.argmax(temp_cost)
# Gathers the node's neighbor
neighbor = int(neighbors_idx[k])
# Propagates the predicted label from the neighbour
pred_subgraph.nodes[i].predicted_label = self.subgraph.nodes[
neighbor].predicted_label
# Propagates the cluster label from the neighbour
pred_subgraph.nodes[i].cluster_label = self.subgraph.nodes[
neighbor].cluster_label
del neighbor_costs
del neighbor
# Creating the list of predictions
preds = [pred.predicted_label for pred in pred_subgraph.nodes]
# Creating the list of clusters
clusters = [pred.cluster_label for pred in pred_subgraph.nodes]
# Ending timer
end = time.time()
# Calculating prediction task time
self.pred_time = end - start
logger.info('Data has been predicted.')
logger.info(f'Prediction time: {self.pred_time : .4f} seconds.')
return preds, clusters