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"""Runs an automatically optimized sklearn.HDBSCAN clustering on dimensionality reduced space.
The HDBSCAN_scores_ @Property returns the cluster number of each sample (_labels) and the DBCV best score.
Returns:
_labels (pd.DataFrame): DataFrame with the cluster belonging number for each sample
_hdbscan_score (float): a float with the best DBCV score after optimization
- clustering = HDBSCAN((data)
- scores = clustering.HDBSCAN_scores_
def __init__(self, data):
"""Initiate the HDBSCAN calculation
Args:
data (pd.DataFrame): the Dimensionality reduced space, raw result of the UMAP.fit()
param_dist (dictionary): the HDBSCAN optimization parameters to test
_score (pd.DataFrame): is a dataframe with the DBCV value for each combination of param_dist. We search for the higher value to then compute an HDBSCAN with the best parameters.
"""
# Really fast
# self._param_dist = {'min_samples': [1],
# 'min_cluster_size':[5],
# 'metric' : ['euclidean','manhattan'],
# }
# Medium
self._param_dist = {'min_samples': [1,10],
'min_cluster_size':[5,50],
'metric' : ['euclidean','manhattan'],
}
# Complete
# self._param_dist = {'min_samples': [1,5,10,],
# 'min_cluster_size':[5,25,50,],
# 'metric' : ['euclidean','manhattan'],
# }
self._clusterable_embedding = data
# RandomizedSearchCV not working...
# def scoring(model, clusterable_embedding):
# label = HDBSCAN().fit_predict(clusterable_embedding)
# hdbscan_score = DBCV(clusterable_embedding, label, dist_function=euclidean)
# return hdbscan_score
# tunning = RandomizedSearchCV(estimator=HDBSCAN(), param_distributions=param_dist, scoring=scoring)
# tunning.fit(clusterable_embedding)
# return tunning
# compute optimization. Test each combination of parameters and store DBCV score into _score.
self._score = pd.DataFrame()
for i in self._param_dist.get('min_samples'):
for j in self._param_dist.get('min_cluster_size'):
self._ij_label = HDBSCAN(min_samples=i, min_cluster_size=j).fit_predict(self._clusterable_embedding)
self._ij_hdbscan_score = self.DBCV(self._clusterable_embedding, self._ij_label,)# dist_function=euclidean)
self._score.at[i,j] = self._ij_hdbscan_score
# get the best DBCV score
self._hdbscan_score = max(self._score.max())
# find the coordinates of the best clustering parameters and run HDBSCAN below
self._bparams = np.where(self._score == self._hdbscan_score)
# run HDBSCAN with best params
self._labels = HDBSCAN(min_samples=self._param_dist['min_samples'][self._bparams[0][0]], min_cluster_size=self._param_dist['min_cluster_size'][self._bparams[1][0]], metric=self._param_dist['metric'][self._bparams[1][0]]).fit_predict(self._clusterable_embedding)
def DBCV(self, X, labels, dist_function=euclidean):
"""
Implimentation of Density-Based Clustering Validation "DBCV"
Citation: Moulavi, Davoud, et al. "Density-based clustering validation."
Proceedings of the 2014 SIAM International Conference on Data Mining.
Society for Industrial and Applied Mathematics, 2014.
Density Based clustering validation
Args:
X (np.ndarray): ndarray with dimensions [n_samples, n_features]
data to check validity of clustering
labels (np.array): clustering assignments for data X
dist_dunction (func): function to determine distance between objects
func args must be [np.array, np.array] where each array is a point
Returns:
cluster_validity (float): score in range[-1, 1] indicating validity of clustering assignments
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"""
graph = self._mutual_reach_dist_graph(X, labels, dist_function)
mst = self._mutual_reach_dist_MST(graph)
cluster_validity = self._clustering_validity_index(mst, labels)
return cluster_validity
def _core_dist(self, point, neighbors, dist_function):
"""
Computes the core distance of a point.
Core distance is the inverse density of an object.
Args:
point (np.array): array of dimensions (n_features,)
point to compute core distance of
neighbors (np.ndarray): array of dimensions (n_neighbors, n_features):
array of all other points in object class
dist_dunction (func): function to determine distance between objects
func args must be [np.array, np.array] where each array is a point
Returns: core_dist (float)
inverse density of point
"""
n_features = np.shape(point)[0]
n_neighbors = np.shape(neighbors)[0]
distance_vector = cdist(point.reshape(1, -1), neighbors)
distance_vector = distance_vector[distance_vector != 0]
numerator = ((1/distance_vector)**n_features).sum()
core_dist = (numerator / (n_neighbors - 1)) ** (-1/n_features)
return core_dist
def _mutual_reachability_dist(self, point_i, point_j, neighbors_i,
neighbors_j, dist_function):
""".
Computes the mutual reachability distance between points
Args:
point_i (np.array): array of dimensions (n_features,)
point i to compare to point j
point_j (np.array): array of dimensions (n_features,)
point i to compare to point i
neighbors_i (np.ndarray): array of dims (n_neighbors, n_features):
array of all other points in object class of point i
neighbors_j (np.ndarray): array of dims (n_neighbors, n_features):
array of all other points in object class of point j
dist_function (func): function to determine distance between objects
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func args must be [np.array, np.array] where each array is a point
Returns: mutual_reachability (float)
mutual reachability between points i and j
"""
core_dist_i = self._core_dist(point_i, neighbors_i, dist_function)
core_dist_j = self._core_dist(point_j, neighbors_j, dist_function)
dist = dist_function(point_i, point_j)
mutual_reachability = np.max([core_dist_i, core_dist_j, dist])
return mutual_reachability
def _mutual_reach_dist_graph(self, X, labels, dist_function):
"""
Computes the mutual reach distance complete graph.
Graph of all pair-wise mutual reachability distances between points
Args:
X (np.ndarray): ndarray with dimensions [n_samples, n_features]
data to check validity of clustering
labels (np.array): clustering assignments for data X
dist_dunction (func): function to determine distance between objects
func args must be [np.array, np.array] where each array is a point
Returns: graph (np.ndarray)
array of dimensions (n_samples, n_samples)
Graph of all pair-wise mutual reachability distances between points.
"""
n_samples = np.shape(X)[0]
graph = []
counter = 0
for row in range(n_samples):
graph_row = []
for col in range(n_samples):
point_i = X[row]
point_j = X[col]
class_i = labels[row]
class_j = labels[col]
members_i = self._get_label_members(X, labels, class_i)
members_j = self._get_label_members(X, labels, class_j)
dist = self._mutual_reachability_dist(point_i, point_j,
members_i, members_j,
dist_function)
graph_row.append(dist)
counter += 1
graph.append(graph_row)
graph = np.array(graph)
return graph
def _mutual_reach_dist_MST(self, dist_tree):
"""
Computes minimum spanning tree of the mutual reach distance complete graph
Args:
dist_tree (np.ndarray): array of dimensions (n_samples, n_samples)
Graph of all pair-wise mutual reachability distances
between points.
Returns: minimum_spanning_tree (np.ndarray)
array of dimensions (n_samples, n_samples)
minimum spanning tree of all pair-wise mutual reachability
distances between points.
"""
mst = minimum_spanning_tree(dist_tree).toarray()
return mst + np.transpose(mst)
def _cluster_density_sparseness(self, MST, labels, cluster):
"""
Computes the cluster density sparseness, the minimum density
within a cluster
Args:
MST (np.ndarray): minimum spanning tree of all pair-wise
mutual reachability distances between points.
labels (np.array): clustering assignments for data X
cluster (int): cluster of interest
Returns: cluster_density_sparseness (float)
value corresponding to the minimum density within a cluster
"""
indices = np.where(labels == cluster)[0]
cluster_MST = MST[indices][:, indices]
cluster_density_sparseness = np.max(cluster_MST)
return cluster_density_sparseness
def _cluster_density_separation(self, MST, labels, cluster_i, cluster_j):
"""
Computes the density separation between two clusters, the maximum
density between clusters.
Args:
MST (np.ndarray): minimum spanning tree of all pair-wise
mutual reachability distances between points.
labels (np.array): clustering assignments for data X
cluster_i (int): cluster i of interest
cluster_j (int): cluster j of interest
Returns: density_separation (float):
value corresponding to the maximum density between clusters
"""
indices_i = np.where(labels == cluster_i)[0]
indices_j = np.where(labels == cluster_j)[0]
shortest_paths = csgraph.dijkstra(MST, indices=indices_i)
relevant_paths = shortest_paths[:, indices_j]
density_separation = np.min(relevant_paths)
return density_separation
def _cluster_validity_index(self, MST, labels, cluster):
"""
Computes the validity of a cluster (validity of assignmnets)
Args:
MST (np.ndarray): minimum spanning tree of all pair-wise
mutual reachability distances between points.
labels (np.array): clustering assignments for data X
cluster (int): cluster of interest
Returns: cluster_validity (float)
value corresponding to the validity of cluster assignments
"""
min_density_separation = np.inf
for cluster_j in np.unique(labels):
if cluster_j != cluster:
cluster_density_separation = self._cluster_density_separation(MST,
labels,
cluster,
cluster_j)
if cluster_density_separation < min_density_separation:
min_density_separation = cluster_density_separation
cluster_density_sparseness = self._cluster_density_sparseness(MST,
labels,
cluster)
numerator = min_density_separation - cluster_density_sparseness
denominator = np.max([min_density_separation, cluster_density_sparseness])
cluster_validity = numerator / denominator
return cluster_validity
def _clustering_validity_index(self, MST, labels):
"""
Computes the validity of all clustering assignments for a
clustering algorithm
Args:
MST (np.ndarray): minimum spanning tree of all pair-wise
mutual reachability distances between points.
labels (np.array): clustering assignments for data X
Returns: validity_index (float):
score in range[-1, 1] indicating validity of clustering assignments
"""
n_samples = len(labels)
validity_index = 0
for label in np.unique(labels):
fraction = np.sum(labels == label) / float(n_samples)
cluster_validity = self._cluster_validity_index(MST, labels, label)
validity_index += fraction * cluster_validity
return validity_index
def _get_label_members(self, X, labels, cluster):
"""
Helper function to get samples of a specified cluster.
Args:
X (np.ndarray): ndarray with dimensions [n_samples, n_features]
data to check validity of clustering
labels (np.array): clustering assignments for data X
cluster (int): cluster of interest
Returns: members (np.ndarray)
array of dimensions (n_samples, n_features) of samples of the
specified cluster.
"""
indices = np.where(labels == cluster)[0]
members = X[indices]
return members
@property
def HDBSCAN_scores_(self):
return self._labels, self._hdbscan_score