def cluster(
vector_names,
vectors,
reduced_vectors,
normalized_vectors,
vectorizer,
strategy="automatic",
cluster_method="kmeans",
n_clusters=2,
epsilon=0.5,
min_samples=5,
metric="euclidean",
):
"""
Clustering options:
Manual:
The user supplies all required information to do the clustering. This includes the clustering algorithm and
hyper parameters
Assisted:
The user assists the algorithm by suggesting that some samples should or should not be clustered together
Automatic:
The multiple clustering strategies and parameters are used in an attempt to get the best clusters
"""
if strategy == "manual":
if cluster_method == "kmeans":
return cluster_with_kmeans(normalized_vectors,
n_clusters=n_clusters)
elif cluster_method == "dbscan":
return cluster_with_dbscan(normalized_vectors,
epsilon=epsilon,
min_samples=min_samples,
metric=metric)
elif cluster_method == "agglomerative":
return cluster_with_agglomerative(normalized_vectors,
n_clusters=n_clusters,
metric=metric)
else:
# Unknown clustering method
raise NotImplementedError()
elif strategy == "assisted":
"""
To display a information about a vector to a user, you can use the following:
display_vector_index_details(vector_index, vectors, vector_names, vectorizer)
"""
# todo Try with normalized vectors
return cluster_interactive(reduced_vectors, vectorizer, vectors,
vector_names)
elif strategy == "viz":
clusteringnmap.interactive_state._vector_names = vector_names
clusteringnmap.interactive_state._vectors = vectors
clusteringnmap.interactive_state._vectorizer = vectorizer
clusteringnmap.interactive_state._reduced_vectors = reduced_vectors
clusteringnmap.interactive_state._normalized_vectors = normalized_vectors
clusteringnmap.interactive_state._labels = [0] * vectors.shape[0]
print "Go to http://localhost:5006/Interactive_Clustering_bokeh"
print "Press CTRL-C to exit web interface"
parser = argparse.ArgumentParser(Serve.args)
s = Serve(parser)
s.invoke(
parser.parse_args(
["clusteringnmap/Interactive_Clustering_bokeh.py"]))
return clusteringnmap.interactive_state._labels
elif strategy == "automatic":
results = []
smallest_cluster_count = vectors.shape[0]
for cluster_method in [
"kmeans",
"dbscan",
"agglomerative",
]:
if cluster_method == "kmeans":
logging.debug("Starting prospective KMeans clusterings")
move_to_next_method = False
for n_clusters in xrange(2, smallest_cluster_count):
logging.debug("Trying {0}".format(
"kmeans(n_clusters={0})".format(n_clusters)))
labels = cluster_with_kmeans(reduced_vectors,
n_clusters=n_clusters)
overall_score, per_cluster_score = validate_clusters(
vectors, labels)
mean_distance = get_average_distance_per_cluster(
vectors, labels)[0]
tsp, msp, msn = get_common_feature_stats(
vectors, labels, vectorizer)
# If any cluster has 0 shared features, we just ignore the result
if msp <= tsp:
logging.debug("Not all clusters are informative")
continue
if len(set(labels)) > smallest_cluster_count:
move_to_next_method = True
break
if len(set(labels)) < smallest_cluster_count:
smallest_cluster_count = len(set(labels))
logging.debug(
repr((overall_score, min(per_cluster_score.values()),
mean_distance, labels, len(set(labels)), tsp,
msp, msn,
"kmeans(n_clusters={0})".format(n_clusters))))
results.append(
(overall_score, min(per_cluster_score.values()),
mean_distance, labels, len(set(labels)), tsp, msp,
msn, "kmeans(n_clusters={0})".format(n_clusters)))
if move_to_next_method:
continue
if cluster_method == "agglomerative":
logging.debug("Starting prospective Agglomerative clusterings")
move_to_next_method = False
for n_clusters in xrange(2, smallest_cluster_count):
logging.debug("Trying {0}".format(
"agglomerative(n_clusters={0})".format(n_clusters)))
labels = cluster_with_agglomerative(reduced_vectors,
n_clusters=n_clusters,
metric=metric)
overall_score, per_cluster_score = validate_clusters(
vectors, labels)
mean_distance = get_average_distance_per_cluster(
vectors, labels)[0]
tsp, msp, msn = get_common_feature_stats(
vectors, labels, vectorizer)
# If any cluster has 0 shared features, we just ignore the result
if msp <= tsp:
logging.debug("Not all clusters are informative")
continue
if len(set(labels)) > smallest_cluster_count:
move_to_next_method = True
break
if len(set(labels)) < smallest_cluster_count:
smallest_cluster_count = len(set(labels))
logging.debug(
repr(
(overall_score, min(per_cluster_score.values()),
mean_distance, labels, len(set(labels)), tsp, msp,
msn,
"agglomerative(n_clusters={0})".format(n_clusters)
)))
results.append(
(overall_score, min(per_cluster_score.values()),
mean_distance, labels, len(set(labels)), tsp, msp,
msn,
"agglomerative(n_clusters={0})".format(n_clusters)))
if move_to_next_method:
continue
if cluster_method == "dbscan":
logging.debug("Starting prospective DBSCAN clusterings")
distance_matrix = precompute_distances(vectors, metric=metric)
min_distance = sorted(set(list(distance_matrix.flatten())))[1]
max_distance = sorted(set(list(distance_matrix.flatten())))[-1]
num_steps = 25.0
step_size = float(max_distance -
min_distance) / float(num_steps)
epsilon = min_distance
while True:
logging.debug("Trying {0}".format(
"dbscan(epsilon={0})".format(epsilon)))
labels = cluster_with_dbscan(reduced_vectors,
epsilon=epsilon,
min_samples=1,
distances=distance_matrix)
if len(set(labels)) == 1 and list(set(labels))[0] == 0:
break
overall_score, per_cluster_score = validate_clusters(
vectors, labels)
mean_distance = get_average_distance_per_cluster(
vectors, labels)[0]
tsp, msp, msn = get_common_feature_stats(
vectors, labels, vectorizer)
# If any cluster has 0 shared features, we just ignore the result
if msp <= tsp:
logging.debug("Not all clusters are informative")
epsilon += step_size
continue
logging.debug(
repr(
(overall_score, min(per_cluster_score.values()),
mean_distance, labels, len(set(labels)), tsp, msp,
msn, "dbscan(epsilon={0})".format(epsilon))))
results.append(
(overall_score, min(per_cluster_score.values()),
mean_distance, labels, len(set(labels)), tsp, msp,
msn, "dbscan(epsilon={0})".format(epsilon)))
epsilon += step_size
# Pick best result
"""
We want to maximize the silhouette score while minimizing the number of labels
"""
sorted_results = sort_items_by_multiple_keys(
results,
{
#0: True, # AVG Silhouette
#1: True, # Min Silhouette
#2: False, # Average distance
4: False, # Number of clusters
#6: True, # Min common features per cluster
},
{
#0: 1,
#1: 1,
#2: 1,
4: 1,
#6: 1
})
logging.debug(sorted_results)
best_result = results[sorted_results[0][0]]
logging.debug(best_result)
best_method = best_result[-1]
best_silhouette = best_result[0]
best_labels = best_result[3]
logging.info(
"Best clustering method: {0} (adjusted silhouette == {1})".format(
best_method, best_silhouette))
return best_labels
else:
# Unknown strategy
raise NotImplementedError()
def cluster(
vector_names,
vectors,
reduced_vectors,
normalized_vectors,
vectorizer,
strategy="automatic",
cluster_method="kmeans",
n_clusters=2,
epsilon=0.5,
min_samples=5,
metric="euclidean",
):
"""
Clustering options:
Manual:
The user supplies all required information to do the clustering. This includes the clustering algorithm and
hyper parameters
Assisted:
The user assists the algorithm by suggesting that some samples should or should not be clustered together
Automatic:
The multiple clustering strategies and parameters are used in an attempt to get the best clusters
"""
if strategy == "manual":
if cluster_method == "kmeans":
return cluster_with_kmeans(normalized_vectors, n_clusters=n_clusters)
elif cluster_method == "dbscan":
return cluster_with_dbscan(normalized_vectors, epsilon=epsilon, min_samples=min_samples, metric=metric)
elif cluster_method == "agglomerative":
return cluster_with_agglomerative(normalized_vectors, n_clusters=n_clusters, metric=metric)
else:
# Unknown clustering method
raise NotImplementedError()
elif strategy == "assisted":
"""
To display a information about a vector to a user, you can use the following:
display_vector_index_details(vector_index, vectors, vector_names, vectorizer)
"""
# todo Try with normalized vectors
return cluster_interactive(reduced_vectors, vectorizer, vectors, vector_names)
elif strategy == "viz":
clusteringnmap.interactive_state._vector_names = vector_names
clusteringnmap.interactive_state._vectors = vectors
clusteringnmap.interactive_state._vectorizer = vectorizer
clusteringnmap.interactive_state._reduced_vectors = reduced_vectors
clusteringnmap.interactive_state._normalized_vectors = normalized_vectors
clusteringnmap.interactive_state._labels = [0] * vectors.shape[0]
print "Go to http://localhost:5006/Interactive_Clustering_bokeh"
print "Press CTRL-C to exit web interface"
parser = argparse.ArgumentParser(Serve.args)
s = Serve(parser)
s.invoke(parser.parse_args(["clusteringnmap/Interactive_Clustering_bokeh.py"]))
return clusteringnmap.interactive_state._labels
elif strategy == "automatic":
results = []
smallest_cluster_count = vectors.shape[0]
for cluster_method in [
"kmeans",
"dbscan",
"agglomerative",
]:
if cluster_method == "kmeans":
logging.debug("Starting prospective KMeans clusterings")
move_to_next_method = False
for n_clusters in xrange(2, smallest_cluster_count):
logging.debug("Trying {0}".format("kmeans(n_clusters={0})".format(n_clusters)))
labels = cluster_with_kmeans(reduced_vectors, n_clusters=n_clusters)
overall_score, per_cluster_score = validate_clusters(vectors, labels)
mean_distance = get_average_distance_per_cluster(vectors, labels)[0]
tsp, msp, msn = get_common_feature_stats(vectors, labels, vectorizer)
# If any cluster has 0 shared features, we just ignore the result
if msp <= tsp:
logging.debug("Not all clusters are informative")
continue
if len(set(labels)) > smallest_cluster_count:
move_to_next_method = True
break
if len(set(labels)) < smallest_cluster_count:
smallest_cluster_count = len(set(labels))
logging.debug(repr((
overall_score,
min(per_cluster_score.values()),
mean_distance,
labels,
len(set(labels)),
tsp,
msp,
msn,
"kmeans(n_clusters={0})".format(n_clusters)
)))
results.append(
(
overall_score,
min(per_cluster_score.values()),
mean_distance,
labels,
len(set(labels)),
tsp,
msp,
msn,
"kmeans(n_clusters={0})".format(n_clusters)
)
)
if move_to_next_method:
continue
if cluster_method == "agglomerative":
logging.debug("Starting prospective Agglomerative clusterings")
move_to_next_method = False
for n_clusters in xrange(2, smallest_cluster_count):
logging.debug("Trying {0}".format("agglomerative(n_clusters={0})".format(n_clusters)))
labels = cluster_with_agglomerative(reduced_vectors, n_clusters=n_clusters, metric=metric)
overall_score, per_cluster_score = validate_clusters(vectors, labels)
mean_distance = get_average_distance_per_cluster(vectors, labels)[0]
tsp, msp, msn = get_common_feature_stats(vectors, labels, vectorizer)
# If any cluster has 0 shared features, we just ignore the result
if msp <= tsp:
logging.debug("Not all clusters are informative")
continue
if len(set(labels)) > smallest_cluster_count:
move_to_next_method = True
break
if len(set(labels)) < smallest_cluster_count:
smallest_cluster_count = len(set(labels))
logging.debug(repr((
overall_score,
min(per_cluster_score.values()),
mean_distance,
labels,
len(set(labels)),
tsp,
msp,
msn,
"agglomerative(n_clusters={0})".format(n_clusters)
)))
results.append(
(
overall_score,
min(per_cluster_score.values()),
mean_distance,
labels,
len(set(labels)),
tsp,
msp,
msn,
"agglomerative(n_clusters={0})".format(n_clusters)
)
)
if move_to_next_method:
continue
if cluster_method == "dbscan":
logging.debug("Starting prospective DBSCAN clusterings")
distance_matrix = precompute_distances(vectors, metric=metric)
min_distance = sorted(set(list(distance_matrix.flatten())))[1]
max_distance = sorted(set(list(distance_matrix.flatten())))[-1]
num_steps = 25.0
step_size = float(max_distance - min_distance) / float(num_steps)
epsilon = min_distance
while True:
logging.debug("Trying {0}".format("dbscan(epsilon={0})".format(epsilon)))
labels = cluster_with_dbscan(reduced_vectors, epsilon=epsilon, min_samples=1, distances=distance_matrix)
if len(set(labels)) == 1 and list(set(labels))[0] == 0:
break
overall_score, per_cluster_score = validate_clusters(vectors, labels)
mean_distance = get_average_distance_per_cluster(vectors, labels)[0]
tsp, msp, msn = get_common_feature_stats(vectors, labels, vectorizer)
# If any cluster has 0 shared features, we just ignore the result
if msp <= tsp:
logging.debug("Not all clusters are informative")
epsilon += step_size
continue
logging.debug(repr((
overall_score,
min(per_cluster_score.values()),
mean_distance,
labels,
len(set(labels)),
tsp,
msp,
msn,
"dbscan(epsilon={0})".format(epsilon)
)))
results.append(
(
overall_score,
min(per_cluster_score.values()),
mean_distance,
labels,
len(set(labels)),
tsp,
msp,
msn,
"dbscan(epsilon={0})".format(epsilon)
)
)
epsilon += step_size
# Pick best result
"""
We want to maximize the silhouette score while minimizing the number of labels
"""
sorted_results = sort_items_by_multiple_keys(
results,
{
#0: True, # AVG Silhouette
#1: True, # Min Silhouette
#2: False, # Average distance
4: False, # Number of clusters
#6: True, # Min common features per cluster
},
{
#0: 1,
#1: 1,
#2: 1,
4: 1,
#6: 1
}
)
logging.debug(sorted_results)
best_result = results[sorted_results[0][0]]
logging.debug(best_result)
best_method = best_result[-1]
best_silhouette = best_result[0]
best_labels = best_result[3]
logging.info("Best clustering method: {0} (adjusted silhouette == {1})".format(best_method, best_silhouette))
return best_labels
else:
# Unknown strategy
raise NotImplementedError()
# Analysis relevant to the person reading results
universal_positive_features, universal_negative_features, shared_features = get_common_features_from_cluster(
vectors, labels, vectorizer)
# Reduce results and relevant information to per cluster data
cluster_details = {}
for cluster_id in per_cluster_score.keys():
cluster_details[cluster_id] = {
"silhouette":
per_cluster_score[cluster_id],
"shared_positive_features":
shared_features[cluster_id]['positive'],
#"shared_negative_features": shared_features[cluster_id]['negative'],
"ips": [
vector_names[x] for x in xrange(len(vector_names))
if labels[x] == cluster_id
]
}
print_cluster_details(cluster_details, shared_features)
if args.plot:
create_plot(reduced_vectors, labels, vector_names)
# Write DOT diagram out to cluster.dot, designed for input into Gephi (https://gephi.org/)
with open("cluster.dot", "w") as f:
f.write(
generate_dot_graph_for_gephi(
precompute_distances(vectors, metric=args.metric),
vector_names, labels))
# Cluster the vectors
logging.info("Clustering")
labels = cluster(vector_names, vectors, reduced_vectors, normalized_vectors, vectorizer, args.strategy, args.method, args.n_clusters, args.epsilon, args.min_samples, args.metric)
logging.info("Clustering Complete")
# Test cluster validity
overall_score, per_cluster_score = validate_clusters(vectors, labels)
# Analysis relevant to the person reading results
universal_positive_features, universal_negative_features, shared_features = get_common_features_from_cluster(vectors, labels, vectorizer)
# Reduce results and relevant information to per cluster data
cluster_details = {}
for cluster_id in per_cluster_score.keys():
cluster_details[cluster_id] = {
"silhouette": per_cluster_score[cluster_id],
"shared_positive_features": shared_features[cluster_id]['positive'],
#"shared_negative_features": shared_features[cluster_id]['negative'],
"ips": [vector_names[x] for x in xrange(len(vector_names)) if labels[x] == cluster_id]
}
print_cluster_details(cluster_details, shared_features)
if args.plot:
create_plot(reduced_vectors, labels, vector_names)
# Write DOT diagram out to cluster.dot, designed for input into Gephi (https://gephi.org/)
with open("cluster.dot", "w") as f:
f.write(generate_dot_graph_for_gephi(precompute_distances(vectors, metric=args.metric), vector_names, labels))
