def fit(self, X, y):
#creating a manifold on training data
self.model = LocallyLinearEmbedding(
method=self.method,
n_neighbors=self.n_neighbors,
n_components=self.n_components,
reg=self.reg,
eigen_solver=self.eigen_solver,
random_state=self.random_state).fit(X, y)
#determining centroids for given points
self.centroids = KMeans(n_clusters=self.n_clusters,
random_state=self.random_state).fit(
self.model.transform(X))
labels = self.centroids.predict(self.model.transform(
X)) # Every point is assigned to a certain cluster.
#assigning each centroid to the correct cluster
confusion_m = confusion_matrix(y, labels)
m = Munkres()
cost_m = make_cost_matrix(confusion_m)
target_cluster = m.compute(
cost_m) # (target, cluster) assignment pairs.
#saving mapping for predictions
self.mapping = {
cluster: target
for target, cluster in dict(target_cluster).items()
}
def evaluate(self, individual, X, y, random_state):
X_new = self.reduce(individual, X)
if self.fitness_function in [
"kmeans", "silhouette", "adjusted_rand_score",
"calinski_harabasz"
]:
# Clustering of the reduced dataset.
centroids = KMeans(n_clusters=self.n_clusters,
random_state=self.random_state).fit(X_new)
labels = centroids.labels_ # Every point is assigned to a certain cluster.
if self.fitness_function == "silhouette":
if len(Counter(labels)) == 1:
return -1
else:
return silhouette_score(X_new, labels)
elif self.fitness_function == "adjusted_rand_score":
return adjusted_rand_score(y, labels)
elif self.fitness_function == "calinski_harabasz":
if len(Counter(labels)) == 1:
return -1
else:
return calinski_harabasz_score(X_new, labels)
elif self.fitness_function == "kmeans":
confusion_m = confusion_matrix(y, labels)
m = Munkres()
cost_m = make_cost_matrix(confusion_m)
target_cluster = m.compute(
cost_m) # (target, cluster) assignment pairs.
cluster_target = {
cluster: target
for target, cluster in dict(target_cluster).items()
}
y_pred = list(map(cluster_target.get, labels))
return balanced_accuracy_score(y, y_pred)
elif self.fitness_function == "nn":
n_neighbors = self.k
# n_neighbors + 1 because the class of the point itself is not taken into account.
neighbors = NearestNeighbors(n_neighbors=n_neighbors +
1).fit(X_new)
nearest_neighbors = neighbors.kneighbors(X_new,
return_distance=False)[:,
1:]
classes = y[nearest_neighbors]
y_pred = mode(classes, axis=1)[0].reshape(len(y), )
return balanced_accuracy_score(y, y_pred)
elif self.fitness_function == "angles":
angles = np.apply_along_axis(
lambda row: math.atan2(row[1], row[0]), axis=1, arr=X_new)
# Mapping from (-pi,pi) to (0, 2*pi)
angles = (2 * np.pi +
angles) * (angles < 0) + angles * (angles > 0)
y_pred = list(
map(
lambda angle: check_in_which_slice(angle, self.n_clusters,
self.slices), angles))
return balanced_accuracy_score(y, y_pred)
def fit(self, X, y, sample_weight=None, groups=None):
self.dataset = self.dataset.split("/")[-1]
self.n_clusters = len(Counter(y))
data = pd.DataFrame(X)
data['target'] = y
f = open(
self.path + "/" + self.dataset + "." + str(self.random_state) +
"-train", "w")
f.write("classLast," + str(data.shape[1] - 1) + "," +
str(self.n_components) + ',comma\n')
f.close()
data.to_csv(self.path + "/" + self.dataset + "." +
str(self.random_state) + "-train",
header=None,
index=None,
mode='a',
sep=',')
#two empty lines at the end, adding header
#java code returns many lines, the result ends in the last ones
z = subprocess.check_output([
'java', '-cp', 'GPMaL/gp-mal-eurogp-19-bin.jar',
'featureLearn.RunGPMaL', 'dataset=' + os.getcwd() + "/" +
self.dataset + '.' + str(self.random_state) + '-train',
'numtrees=2', 'preprocessing=none',
'logPrefix=' + self.dataset + '-train', 'treeDepth=8',
'featureMin=0', 'featureMax=1', 'normalisePostCreation=false',
'scalePostCreation=false', 'roundPostCreation=true',
'featureLearnParamFile=GPMaL/flNeighboursFG.params', 'doNNs=false',
'n_jobs=' + str(self.n_jobs),
'random_state=' + str(self.random_state)
]).decode("utf-8")
print(str(z))
z = z.split('\n')[-X.shape[0] - 3:-2]
#loading the data into pandas df
X_new = pd.read_csv(StringIO('\n'.join(z)), sep=',')
X_new.drop('class', axis=1, inplace=True)
# for f in range(0,X.shape[1]-1):
for f in range(0, X_new.shape[1] - self.n_components):
X_new.drop('F' + str(f), axis=1, inplace=True)
print(X_new)
self.centroids = KMeans(n_clusters=self.n_clusters,
random_state=self.random_state).fit(X_new)
labels = self.centroids.predict(X_new)
confusion_m = confusion_matrix(y, labels)
m = Munkres()
cost_m = make_cost_matrix(confusion_m)
target_cluster = m.compute(
cost_m) # (target, cluster) assignment pairs.
self.mapping = {
cluster: target
for target, cluster in dict(target_cluster).items()
}
return self
def fit(self,X,y):
self.X_train=X
#creating a manifold on training data
self.model = TSNE(n_iter=self.n_iter, n_components=self.n_components, perplexity=self.perplexity).fit_transform(X,y)
#determining centroids for given classes
self.centroids = KMeans(n_clusters=self.n_clusters, random_state=self.random_state).fit(self.model)
self.labels = self.centroids.predict(self.model) # Every point is assigned to a certain cluster.
#assigning each centroid to the correct cluster
confusion_m = confusion_matrix(y, self.labels)
m = Munkres()
cost_m = make_cost_matrix(confusion_m)
target_cluster = m.compute(cost_m) # (target, cluster) assignment pairs.
#saving mapping for predictions
self.mapping = {cluster : target for target, cluster in dict(target_cluster).items()}
def fit(self,X,y):
pset = create_pset(in_type=float, in_types_length=X.shape[1], out_type=float)
self.toolbox = create_toolbox(weights=self.weights,
pset=pset,
min_tree_height=self.min_tree_height,
max_tree_height=self.max_tree_height,
n_components=self.n_components)
self.toolbox.register("evaluate", self.evaluate, X=X, y=y, random_state=self.random_state)
population = self.toolbox.population(self.pop_size)
best_individuals = []
self.n_clusters=len(Counter(y))
self.slices = [(i*2*math.pi/self.n_clusters, (i+1)*2*math.pi/self.n_clusters) for i in range(self.n_clusters)]
self.rejected = 0
self.cx_count = 0
self.mut_count = 0
for g in range(self.n_iter):
population = self.toolbox.selectBest(population, self.pop_size)
best_individuals.append(self.toolbox.selectBest(population, 1)[0])
random.shuffle(population)
for parent1, parent2 in zip(population[::2], population[1::2]):
if random.random() < self.cxpb:
self.cx_count += 1
child1 = self.toolbox.clone(parent1)
child2 = self.toolbox.clone(parent2)
for i in range(self.n_components):
self.toolbox.mate(child1[i], child2[i])
reject = False
for i in range(self.n_components):
if get_height(child1[i]) > self.max_tree_height:
reject = True
self.rejected += 1
break
if not reject:
del child1.fitness.values
population.append(child1)
reject = False
for i in range(self.n_components):
if get_height(child2[i]) > self.max_tree_height:
reject = True
self.rejected += 1
break
if not reject:
del child2.fitness.values
population.append(child2)
for individual in population.copy():
if random.random() < self.mutpb:
self.mut_count += 1
mutant = self.toolbox.clone(individual)
for i in range(self.n_components):
self.toolbox.mutate(mutant[i])
reject = False
for i in range(self.n_components):
if get_height(mutant[i]) > self.max_tree_height:
reject = True
self.rejected += 1
break
if not reject:
del mutant.fitness.values
population.append(mutant)
invalid_ind = [ind for ind in population if not ind.fitness.valid]
fitnesses = list(map(self.toolbox.evaluate, invalid_ind))
for ind, fit in zip(invalid_ind, fitnesses):
ind.fitness.values = (fit,)
# population = self.toolbox.selectTournament(population, self.tourn_size)
best_individuals.append(self.toolbox.selectBest(population, 1)[0])
self.best_fitness = best_individuals[-1].fitness.values[0]
self.model=best_individuals[-1]
X_new = self.reduce(self.model, X)
self.centroids=KMeans(n_clusters=self.n_clusters, random_state=self.random_state).fit(X_new)
labels = self.centroids.predict(X_new)
confusion_m = confusion_matrix(y, labels)
m = Munkres()
cost_m = make_cost_matrix(confusion_m)
target_cluster = m.compute(cost_m) # (target, cluster) assignment pairs.
self.mapping = {cluster : target for target, cluster in dict(target_cluster).items()}
# Nearest neighbors.
self.neighbors = NearestNeighbors(n_neighbors=1).fit(X_new)
self.y_train = y