def visualize_results(save_plot=False):
"""
visualize the embeddings of multiple models in a scatter plot
"""
fig, axs = plt.subplots(6, 10)
fig.set_figheight(16)
fig.set_figwidth(16)
embedding = ut.load_numpy_file(ut.embedding_path +
"gae_first_embedding.npy")
visualise_single_embedding(embedding, "gae_first", 0, axs)
embedding = ut.load_numpy_file(ut.embedding_path +
"gae_concat_embedding.npy")
visualise_single_embedding(embedding, "gae_concat", 1, axs)
embedding = ut.load_numpy_file(ut.embedding_path +
"gae_mixed_embedding.npy")
visualise_single_embedding(embedding, "gae_mixed", 2, axs)
embedding = ut.load_numpy_file(ut.embedding_path +
"gae_l1_sum_embedding.npy")
visualise_single_embedding(embedding, "gae_l1_sum", 3, axs)
embedding = ut.load_numpy_file(ut.embedding_path +
"matrix_factorization_embedding.npy")
visualise_single_embedding(embedding, "MF", 4, axs)
for ax in axs.flat:
ax.label_outer()
plt.tight_layout()
if save_plot:
plt.savefig('embedding.png', dpi=200)
plt.show()
def cluster_embeddings(embedding_model_name):
"""
Cluster the embeddings of a model using K-means
:param embedding_model_name: the name of the model that generated the embeddings
"""
x = ut.load_numpy_file(ut.embedding_path + embedding_model_name +
"_embedding.npy")
y = ut.node_labels
clusters = KMeans(n_clusters=ut.number_classes).fit(x)
predicted = clusters.labels_
arindex = sk.adjusted_rand_score(y, predicted)
clustering_accuracy = score_clustering_accuracy(y, predicted)
nmi = sk.normalized_mutual_info_score(y, predicted)
add_score(embedding_model_name, 'kmeans-acc', clustering_accuracy)
add_score(embedding_model_name, 'kmeans-nmi', nmi)
add_score(embedding_model_name, 'kmeans-ari', arindex)
c, num_clust, predicted = FINCH(x, req_clust=7, verbose=False)
arindex = sk.adjusted_rand_score(y, predicted)
clustering_accuracy = score_clustering_accuracy(y, predicted)
nmi = sk.normalized_mutual_info_score(y, predicted)
add_score(embedding_model_name, 'finch-acc', clustering_accuracy)
add_score(embedding_model_name, 'finch-nmi', nmi)
add_score(embedding_model_name, 'finch-ari', arindex)
def visualize_Large(model_name, feature):
"""
visualize one large plot for a model and
color it according to certain feature labels
:param model_name:
:param feature:
"""
embedding = ut.load_numpy_file(ut.embedding_path + model_name +
"_embedding.npy")
tsne = TSNE(n_components=2, verbose=1, perplexity=40, n_iter=300)
tsne_results = tsne.fit_transform(embedding)
x = tsne_results[:, 0]
y = tsne_results[:, 1]
area = np.pi * 3
dot_colors = [
"blue", "red", "orange", "green", "yellow", "cyan", "purple", "black",
"pink"
]
label_types = [feature + "_lables"]
plot_secondary_index = 0
for label_type in label_types:
if label_type == "node_labels":
labels = ut.node_labels
else:
labels = ut.load_numpy_file(ut.topo_features_labels_path +
label_type + ".npy")
number_classes = len(set(labels))
xc = []
yc = []
for c in range(0, number_classes):
xc.append([])
yc.append([])
for i in range(0, len(ut.graph.nodes)):
if labels[i] == c:
xc[c].append(x[i])
yc[c].append(y[i])
plt.scatter(xc[c], yc[c], s=area, c=dot_colors[c], alpha=0.5)
plot_secondary_index += 1
plt.show()
def generate_features_labels(bins):
"""
this function divides all the features into classes (bins)
:param bins: The number of bins
"""
degree = ut.load_numpy_file(ut.topo_features_path + "degree.npy")
clustering = ut.load_numpy_file(ut.topo_features_path + "clustering.npy")
eigenvector_centrality = ut.load_numpy_file(ut.topo_features_path +
"eigenvector_centrality.npy")
betweenness_centrality = ut.load_numpy_file(ut.topo_features_path +
"betweenness_centrality.npy")
if not ut.is_directed:
triangles = ut.load_numpy_file(ut.topo_features_path + "triangles.npy")
bin_feature(degree, "degree", False, bins)
bin_feature(clustering, "clustering", False, bins)
bin_feature(eigenvector_centrality, "eigenvector_centrality", False, bins)
bin_feature(betweenness_centrality, "betweenness_centrality", False, bins)
if not ut.is_directed:
bin_feature(triangles, "triangles", False, bins)
def save_topo_features():
"""
concatenate topological features into one array
and save them to a file
"""
degree = np.array(list(dict(nx.degree(ut.graph)).values()))
clustering = np.array(list(nx.clustering(ut.graph).values()))
eigenvector_centrality = np.array(
list(nx.eigenvector_centrality_numpy(ut.graph).values()))
betweenness_centrality = np.array(
list(nx.betweenness_centrality(ut.graph).values()))
if not ut.is_directed:
triangles = np.array(list(nx.triangles(ut.graph).values()))
np.save(ut.topo_features_path + "degree.npy", degree)
np.save(ut.topo_features_path + "clustering.npy", clustering)
np.save(ut.topo_features_path + "eigenvector_centrality.npy",
eigenvector_centrality)
np.save(ut.topo_features_path + "betweenness_centrality.npy",
betweenness_centrality)
if not ut.is_directed:
np.save(ut.topo_features_path + "triangles.npy", triangles)
# concatenate the features (in case to be used as entry)
degree = np.reshape(degree, (-1, 1))
clustering = np.reshape(clustering, (-1, 1))
eigenvector_centrality = np.reshape(eigenvector_centrality, (-1, 1))
betweenness_centrality = np.reshape(betweenness_centrality, (-1, 1))
if not ut.is_directed:
triangles = np.reshape(triangles, (-1, 1))
topofeatures = np.concatenate([degree, clustering], axis=1)
topofeatures = np.concatenate([topofeatures, eigenvector_centrality],
axis=1)
topofeatures = np.concatenate([topofeatures, betweenness_centrality],
axis=1)
if not ut.is_directed:
topofeatures = np.concatenate([topofeatures, triangles], axis=1)
np.save(ut.topo_features_path + "topofeatures.npy", topofeatures)
topofeatures = ut.load_numpy_file(ut.topo_features_path +
"topofeatures.npy")
print("Toplogical Features Calculated:")
print(topofeatures)
print("-------------")
def calculate_similarity(embedding_model_name):
"""
calculate the similarity score of the clusters
-davies_bouldin_score
-calinski_harabasz
-silhouette_score
:param embedding_model_name:
:return:
"""
x = ut.load_numpy_file(ut.embedding_path + embedding_model_name +
"_embedding.npy")
y = ut.node_labels
davies_bouldin = sk.davies_bouldin_score(x, y)
calinski_harabasz = sk.calinski_harabasz_score(x, y)
silhouette_score = sk.silhouette_score(x, y)
add_score(embedding_model_name, 'davies_bouldin', davies_bouldin)
add_score(embedding_model_name, 'calinski_harabasz', calinski_harabasz)
add_score(embedding_model_name, 'silhouette_score', silhouette_score)
def classify_embeddings(embedding_model_name):
"""
classify the embeddings of each embedding model
:param embedding_model_name: the name of the embedding model
:return:
"""
# load embedding
x = ut.load_numpy_file(ut.embedding_path + embedding_model_name + "_embedding.npy")
# load classes
y = ut.node_labels
max_iter = 200
# logistic regression
lr = LogisticRegression(max_iter=max_iter)
scores = cross_validate(lr, x, y, scoring=["f1_macro", "f1_micro"])
add_score(embedding_model_name, 'lr_f1_macro', np.mean(scores['test_f1_macro']))
add_score(embedding_model_name, 'lr_f1_micro', np.mean(scores['test_f1_micro']))
# svm linear
svm = SVC(kernel='linear', C=1, max_iter=max_iter)
scores = cross_validate(svm, x, y, scoring=["f1_macro", "f1_micro"])
add_score(embedding_model_name, 'svm_ln_f1_macro', np.mean(scores['test_f1_macro']))
add_score(embedding_model_name, 'svm_ln_f1_micro', np.mean(scores['test_f1_micro']))
# svm rbf
svm = SVC(kernel='rbf', C=1, max_iter=max_iter)
scores = cross_validate(svm, x, y, scoring=["f1_macro", "f1_micro"])
add_score(embedding_model_name, 'svm_rbf_f1_macro', np.mean(scores['test_f1_macro']))
add_score(embedding_model_name, 'svm_rbf_f1_micro', np.mean(scores['test_f1_micro']))
# mlp
mlp = MLPClassifier(hidden_layer_sizes=2, activation='relu', solver='adam', max_iter=max_iter)
scores = cross_validate(mlp, x, y, scoring=["f1_macro", "f1_micro"])
add_score(embedding_model_name, 'mlp_f1_macro', np.mean(scores['test_f1_macro']))
add_score(embedding_model_name, 'mlp_f1_micro', np.mean(scores['test_f1_micro']))
def visualise_single_embedding(embedding, model_name, plot_index, axs):
"""
Visualize the embeddings of a model
:param embedding: the embedding matrix
:param plot_index: the index of the sub plot (column)
:param axs: axs object of the subplot
:return:
"""
# reduce dimensionality with TSNE to 2 dimension
tsne = TSNE(n_components=2, verbose=1, perplexity=40, n_iter=300)
tsne_results = tsne.fit_transform(embedding)
x = tsne_results[:, 0]
y = tsne_results[:, 1]
area = np.pi * 3
# dot_colors = list(mcolors.CSS4_COLORS)
# random.shuffle(dot_colors)
dot_colors = [
"blue", "red", "orange", "green", "yellow", "cyan", "purple", "black",
"pink"
]
label_types = [
"node_labels", "degree_lables", "betweenness_centrality_lables",
"clustering_lables", "eigenvector_centrality_lables",
"triangles_lables"
]
titles = [
model_name + " " + "label", model_name + " " + "degree",
model_name + " " + "betweenness", model_name + " " + "clustering",
model_name + " " + "eigenvector", model_name + " " + "triangles"
]
plot_secondary_index = 0
# loop through the label types and plot it
for label_type in label_types:
if label_type == "node_labels":
labels = ut.node_labels
else:
labels = ut.load_numpy_file(ut.topo_features_labels_path +
label_type + ".npy")
number_classes = len(set(labels))
xc = []
yc = []
for c in range(0, number_classes):
xc.append([])
yc.append([])
for i in range(0, len(ut.graph.nodes)):
if labels[i] == c:
xc[c].append(x[i])
yc[c].append(y[i])
axs[plot_secondary_index, plot_index].scatter(xc[c],
yc[c],
s=area,
c=dot_colors[c],
alpha=0.5)
axs[plot_secondary_index,
plot_index].set_title(titles[plot_secondary_index])
axs[plot_secondary_index, plot_index].axis('off')
plot_secondary_index += 1
def classify_features(embedding_model_name, feature_name):
"""
classify the topological features using the model embeddings
:param embedding_model_name: the model that generated the embeddings
:param feature_name: the topo feature that we are classifying
"""
x = ut.load_numpy_file(ut.embedding_path + embedding_model_name +
"_embedding.npy")
y = ut.load_numpy_file(ut.topo_features_labels_path + feature_name +
"_lables.npy")
max_iter = 200
# linear regression
r = LogisticRegression(max_iter=max_iter)
scores = cross_validate(r,
x,
y,
scoring=[
"neg_mean_squared_error",
"neg_mean_absolute_error",
])
add_score(embedding_model_name, feature_name, 'r_mse',
abs(np.mean(scores['test_neg_mean_squared_error'])))
add_score(embedding_model_name, feature_name, 'r_mae',
abs(np.mean(scores['test_neg_mean_absolute_error'])))
# logistic regression
lr = LogisticRegression(max_iter=max_iter)
scores = cross_validate(lr, x, y, scoring=["f1_macro", "f1_micro"])
add_score(embedding_model_name, feature_name, 'lr_f1_macro',
np.mean(scores['test_f1_macro']))
add_score(embedding_model_name, feature_name, 'lr_f1_micro',
np.mean(scores['test_f1_micro']))
# SVM linear
svm = SVC(kernel='linear', C=1, max_iter=max_iter)
scores = cross_validate(svm, x, y, scoring=["f1_macro", "f1_micro"])
add_score(embedding_model_name, feature_name, 'svm_ln_f1_macro',
np.mean(scores['test_f1_macro']))
add_score(embedding_model_name, feature_name, 'svm_ln_f1_micro',
np.mean(scores['test_f1_micro']))
# SVM Kernel RBF
svm = SVC(kernel='rbf', C=1, max_iter=max_iter)
scores = cross_validate(svm, x, y, scoring=["f1_macro", "f1_micro"])
add_score(embedding_model_name, feature_name, 'svm_rbf_f1_macro',
np.mean(scores['test_f1_macro']))
add_score(embedding_model_name, feature_name, 'svm_rbf_f1_micro',
np.mean(scores['test_f1_micro']))
# MPL 2 Layers
mlp = MLPClassifier(hidden_layer_sizes=2,
activation='relu',
solver='adam',
max_iter=max_iter)
scores = cross_validate(mlp, x, y, scoring=["f1_macro", "f1_micro"])
add_score(embedding_model_name, feature_name, 'mlp_f1_macro',
np.mean(scores['test_f1_macro']))
add_score(embedding_model_name, feature_name, 'mlp_f1_micro',
np.mean(scores['test_f1_micro']))
