def fit(self, X_train, Y_train=None, I_train=None):
"""Fits data in the classifier.
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.
"""
logger.info('Clustering with classifier ...')
start = time.time()
# Creating a subgraph
self.subgraph = KNNSubgraph(X_train, Y_train, I_train)
# 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
end = time.time()
train_time = end - start
logger.info('Classifier has been clustered with.')
logger.info('Number of clusters: %d.', self.subgraph.n_clusters)
logger.info('Clustering time: %s seconds.', train_time)
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 predict(self, X_test, I_test=None):
"""Predicts new data using the pre-trained classifier.
Args:
X_test (np.array): Array of features.
I_test (np.array): Array of indexes.
Returns:
A list of predictions for each record of the data.
"""
logger.info('Predicting data ...')
start = time.time()
# Creating a prediction subgraph
pred_subgraph = KNNSubgraph(X_test, I=I_test)
# 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 i in range(pred_subgraph.n_nodes):
# Defines the current cost
cost = c.FLOAT_MAX * -1
# Filling array of distances with maximum value
distances.fill(c.FLOAT_MAX)
for j in range(self.subgraph.n_nodes):
if j != i:
if self.pre_computed_distance:
distances[best_k] = self.pre_distances[
pred_subgraph.nodes[i].idx][
self.subgraph.nodes[j].idx]
else:
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 k in range(best_k):
density += np.exp(-distances[k] / self.subgraph.constant)
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 k in range(best_k):
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 temp_cost > cost:
cost = temp_cost
# Propagates the predicted label from the neighbour
pred_subgraph.nodes[
i].predicted_label = self.subgraph.nodes[
neighbour].predicted_label
# 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
class KNNSupervisedOPF(OPF):
"""A KNNSupervisedOPF which implements the supervised version of OPF classifier with a KNN subgraph.
References:
J. P. Papa and A. X. Falcão. A Learning Algorithm for the Optimum-Path Forest Classifier.
Graph-Based Representations in Pattern Recognition (2009).
"""
def __init__(self,
max_k=1,
distance='log_squared_euclidean',
pre_computed_distance=None):
"""Initialization method.
Args:
max_k (int): Maximum `k` value for cutting the subgraph.
distance (str): An indicator of the distance metric to be used.
pre_computed_distance (str): A pre-computed distance file for feeding into OPF.
"""
logger.info('Overriding class: OPF -> KNNSupervisedOPF.')
super(KNNSupervisedOPF, self).__init__(distance, pre_computed_distance)
# Defining the maximum `k` value for cutting the subgraph
self.max_k = max_k
logger.info('Class overrided.')
@property
def max_k(self):
"""int: Maximum `k` value for cutting the subgraph.
"""
return self._max_k
@max_k.setter
def max_k(self, max_k):
if not isinstance(max_k, int):
raise e.TypeError('`max_k` should be an integer')
if max_k < 1:
raise e.ValueError('`max_k` should be >= 1')
self._max_k = max_k
def _clustering(self, force_prototype=False):
"""Clusters the subgraph.
Args:
force_prototype (bool): Whether clustering should for each class to have at least one prototype.
"""
for i in range(self.subgraph.n_nodes):
# For every adjacent node of `i`
for j in self.subgraph.nodes[i].adjacency:
# Making sure that variable is an integer
j = int(j)
# Checks if node `i` density is equals as node `j` density
if self.subgraph.nodes[i].density == self.subgraph.nodes[
j].density:
# Marks the insertion flag as True
insert = True
# For every adjacent node of `j`
for l in self.subgraph.nodes[j].adjacency:
# Making sure that variable is an integer
l = int(l)
# Checks if it is the same node as `i`
if i == l:
insert = False
if insert:
self.subgraph.nodes[j].adjacency.insert(0, i)
# Creating a maximum heap
h = Heap(size=self.subgraph.n_nodes, policy='max')
for i in range(self.subgraph.n_nodes):
# Updates the node's cost on the heap
h.cost[i] = self.subgraph.nodes[i].cost
# Defines node's `i` predecessor as NIL
self.subgraph.nodes[i].pred = c.NIL
# And its root as its same identifier
self.subgraph.nodes[i].root = i
# Inserts the node in the heap
h.insert(i)
while not h.is_empty():
p = h.remove()
# Appends its index to the ordered list
self.subgraph.idx_nodes.append(p)
if self.subgraph.nodes[p].pred == c.NIL:
# Updates its cost on the heap
h.cost[p] = self.subgraph.nodes[p].density
# Defines its predicted label as the node's true label
self.subgraph.nodes[p].predicted_label = self.subgraph.nodes[
p].label
# Apply current node's cost as the heap's cost
self.subgraph.nodes[p].cost = h.cost[p]
# For every possible adjacent node
for q in self.subgraph.nodes[p].adjacency:
# Making sure that variable is an integer
q = int(q)
if h.color[q] != c.BLACK:
current_cost = np.minimum(h.cost[p],
self.subgraph.nodes[q].density)
# If prototypes should be forced to belong to a class
if force_prototype:
if self.subgraph.nodes[p].label != self.subgraph.nodes[
q].label:
current_cost = -c.FLOAT_MAX
# If current cost is bigger than heap's cost
if current_cost > h.cost[q]:
# Apply `q` predecessor as `p`
self.subgraph.nodes[q].pred = p
# Gathers the same root's identifier
self.subgraph.nodes[q].root = self.subgraph.nodes[
p].root
# And its cluster label
self.subgraph.nodes[
q].predicted_label = self.subgraph.nodes[
p].predicted_label
# Updates node `q` on the heap with the current cost
h.update(q, current_cost)
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 fit(self, X_train, Y_train, X_val, Y_val, I_train=None, I_val=None):
"""Fits data in the classifier.
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.
I_train (np.array): Array of training indexes.
I_val (np.array): Array of validation indexes.
"""
logger.info('Fitting classifier ...')
start = time.time()
# Performing the learning process in order to find the best `k` value
self._learn(X_train, Y_train, I_train, X_val, Y_val, I_val)
# Creating arcs with the best `k` value
self.subgraph.create_arcs(self.subgraph.best_k, self.distance_fn,
self.pre_computed_distance,
self.pre_distances)
# Calculating p.d.f. with the best `k` value
self.subgraph.calculate_pdf(self.subgraph.best_k, self.distance_fn,
self.pre_computed_distance,
self.pre_distances)
# Clustering subgraph forcing each class to have at least one prototype
self._clustering(force_prototype=True)
self.subgraph.destroy_arcs()
# The subgraph has been properly trained
self.subgraph.trained = True
end = time.time()
train_time = end - start
logger.info('Classifier has been fitted with k = %d.',
self.subgraph.best_k)
logger.info('Training time: %s seconds.', train_time)
def predict(self, X_test, I_test=None):
"""Predicts new data using the pre-trained classifier.
Args:
X_test (np.array): Array of features.
I_test (np.array): Array of indexes.
Returns:
A list of predictions for each record of the data.
"""
logger.info('Predicting data ...')
start = time.time()
# Creating a prediction subgraph
pred_subgraph = KNNSubgraph(X_test, I=I_test)
# 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 i in range(pred_subgraph.n_nodes):
# Defines the current cost
cost = c.FLOAT_MAX * -1
# Filling array of distances with maximum value
distances.fill(c.FLOAT_MAX)
for j in range(self.subgraph.n_nodes):
if j != i:
if self.pre_computed_distance:
distances[best_k] = self.pre_distances[
pred_subgraph.nodes[i].idx][
self.subgraph.nodes[j].idx]
else:
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 k in range(best_k):
density += np.exp(-distances[k] / self.subgraph.constant)
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 k in range(best_k):
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 temp_cost > cost:
cost = temp_cost
# Propagates the predicted label from the neighbour
pred_subgraph.nodes[
i].predicted_label = self.subgraph.nodes[
neighbour].predicted_label
# 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, 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
import opfython.stream.loader as l import opfython.stream.parser as p from opfython.subgraphs import KNNSubgraph # Defining an input file input_file = 'data/boat.txt' # Loading a .txt file to a dataframe txt = l.load_txt(input_file) # Parsing a pre-loaded dataframe X, Y = p.parse_loader(txt) # Creating a knn-subgraph structure g = KNNSubgraph(X, Y) # KNNSubgraph can also be directly created from a file g = KNNSubgraph(from_file=input_file)
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 _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