def build_graph_from_matrix(self,
x,
is_directed=True,
remove_self_loops=False,
normalized_edge=True,
outward_prob_check=False):
# The x matrix is exactly the relationship map between them.
logger.info("Building graph.")
self.edges = x #For memmap compatibility
if not issparse(self.edges):
logger.info("Transforming into scipy sparse matrix")
self.edges = csr_matrix(self.edges)
# Iterate through matrix to get directed node -> node relationship
logger.info("Build relation matrix (self.edges)")
row_idxs, col_idxs = csr_matrix.nonzero(self.edges)
assert len(row_idxs) == len(col_idxs)
for i in range(len(row_idxs)):
self.nodes[row_idxs[i]].append(col_idxs[i])
self.make_consistent()
if remove_self_loops:
self.remove_self_loops()
if not is_directed:
self.make_bidirection()
if normalized_edge:
self.normalize_edges()
self.check_valid(outward_prob_check=outward_prob_check)
def _apply_cfidf(csr_matrix):
num_docs, num_concepts = csr_matrix.shape
_, nz_concept_idx = csr_matrix.nonzero()
cf = np.bincount(nz_concept_idx, minlength=num_concepts)
icf = np.log(num_docs / cf)
icf[np.isinf(icf)] = 0
return safe_sparse_dot(csr_matrix, scipy.sparse.diags(icf))
def csr_to_symmetric(csr_matrix):
"""
This is suuuuupper slow
:param csr_matrix:
:return:
"""
rows, cols = csr_matrix.nonzero()
csr_matrix[cols, rows] = csr_matrix[rows, cols]
return csr_matrix
def save_sparse_file(csr_matrix,filename):
data = csr_matrix.data
rows, cols = csr_matrix.nonzero()
f = open(filename,'w')
for i in range(len(data)):
f.write(str(rows[i]+1)+' ')
f.write(str(cols[i]+1)+' ')
f.write(str(data[i])+'\n')
f.close()
def tpe(pc_xyz_noise, pc_weight_unit, pc_weight_sym):
pc_smooth_plane = np.zeros_like(pc_xyz_noise)
pc_smooth_patch = np.zeros_like(pc_xyz_noise)
pc_avg_plane = pc_weight_unit @ pc_xyz_noise
num_data = pc_xyz_noise.shape[0]
normal_vec = np.zeros((num_data, 3))
inter = np.zeros((num_data, 1))
for ii in range(num_data):
pc_neigh_plane_ii = pc_xyz_noise[csr_matrix.nonzero(pc_weight_unit[ii])[-1]].T
pc_neigh_patch_ii = pc_xyz_noise[csr_matrix.nonzero(pc_weight_sym[ii])[-1]].T
pc_neigh_mat_ii_tr = np.zeros_like(pc_neigh_plane_ii)[None, :, :]
pc_neigh_mat_ii_tr[0, :, :] = pc_neigh_plane_ii
pc_neigh_mat_ii = np.transpose(pc_neigh_mat_ii_tr, [1, 0, 2])
pc_avg_ii = pc_avg_plane[ii][:, None]
weight_ii = pc_weight_unit[ii] # sum to 1
weight_ii = np.asarray(weight_ii[:, csr_matrix.nonzero(pc_weight_unit[ii])[-1]].todense())
weight_mat_ii = np.tile(weight_ii, (3, 3, 1))
M_ii = np.sum(pc_neigh_mat_ii * pc_neigh_mat_ii_tr * weight_mat_ii, axis=-1) - pc_avg_ii @ pc_avg_ii.T # k: # of xyz(3), m:1, n: # of nonzero
D,V = np.linalg.eig(M_ii) # D: eigenvalue V: eigenvector
D_sort = np.sort(D)[::-1]
index = np.argsort(D)[::-1]
V_sort = V[:,index]
n_ii = V_sort[:, -1] # min eigenvector (normal vector)
c_ii = pc_avg_ii.T @ n_ii # intercept
normal_vec[ii , :] = n_ii
inter[ii , :] = c_ii
pc_neigh_plane_proj_ii = pc_xyz_noise[ii , :].T - (n_ii @ pc_xyz_noise[ii , :] - c_ii) * n_ii
pc_neigh_patch_proj_ii = pc_neigh_patch_ii - n_ii[:, None] * np.tile((n_ii @ pc_neigh_patch_ii - np.tile(c_ii, (1 , pc_neigh_patch_ii.shape[-1]))), (3 , 1))
weight_patch = np.asarray(pc_weight_sym[ii, csr_matrix.nonzero(pc_weight_sym[ii])[-1]].todense())
pc_smooth_plane[ii] = pc_neigh_plane_proj_ii.T
pc_smooth_patch[csr_matrix.nonzero(pc_weight_sym[ii])[-1], : ] = pc_smooth_patch[csr_matrix.nonzero(pc_weight_sym[ii])[-1], : ] + (weight_patch * pc_neigh_patch_proj_ii).T
pc_smooth_patch = pc_smooth_patch/(np.sum(pc_weight_sym, axis=1))
pc_xyz_denoise_wmp = np.array(pc_smooth_plane * 0.6 + pc_smooth_patch * 0.4)
return pc_xyz_denoise_wmp, normal_vec, inter
def csr_to_graph(csr_matrix):
graph = dict()
fathers, sons = csr_matrix.nonzero()
for father, son in zip(fathers, sons):
if father not in graph:
graph[father] = set([son])
else:
graph[father].add(son)
# Add the reverse edges as well
for son, father in zip(fathers, sons):
if father not in graph:
graph[father] = set([son])
else:
graph[father].add(son)
return graph
def shrink_corpus(corpus, length):
TfIdf_info = TfIdf(corpus)
scores = TfIdf_info['scores']
column_to_vocab = TfIdf_info['column_to_vocab']
new_corpus = []
for i in tqdm.tqdm(range(0, len(corpus))):
# obtain nonzero columns:
row = scores.getrow(i) # use getrow since scores is csr matrix
indices = csr_matrix.nonzero(row)[1]
# obtain the Tfidf-score of each word-index
entries = [scores[i, j] for j in indices]
# sort those scores and keep only the top ones
top_entries = np.argsort(entries)[-length:]
# get the corresponding column-index for each score
top_word_indices = [indices[j] for j in top_entries]
# get the corresponding word for each column index:
top_words = [column_to_vocab[j] for j in top_word_indices]
# shrink the commentt
shrunken_comment = [word for word in corpus[i] if word in top_words]
new_corpus.append(shrunken_comment)
return new_corpus
def wmp(pc_xyz_noise, pc_weight_unit, normal_vec, inter, lmd=2/3, eta=0.05):
num_data = pc_xyz_noise.shape[0]
pc_xyz_denoise = copy.deepcopy(pc_xyz_noise)
for ii in range(num_data):
pc_neigh_ii = csr_matrix.nonzero(pc_weight_unit[ii])[-1]
mu = 0
t = np.zeros(3)
num_neigh = len(pc_neigh_ii)
eta = np.log10(num_neigh)/num_neigh # might be changed
sum_prod = 0
for jj in pc_neigh_ii:
proj = pc_xyz_denoise[ii] - (normal_vec[ii] @ pc_xyz_denoise[ii] - inter[ii]) # argmin_t||p-t||_2^2
# t_prev = t
t = 1 / (lmd*pc_weight_unit[ii, jj]+eta) * (lmd*pc_weight_unit[ii, jj] * pc_xyz_denoise[ii]
+ eta * (proj - mu/eta))
# print((lmd*pc_weight_unit[ii, jj]+eta))
# print(lmd*pc_weight_unit[ii, jj] * pc_xyz_noise[ii])
# print(eta * (proj - mu/eta))
mu += 2 * eta * (t - proj)
sum_prod += pc_weight_unit[ii, jj] * t
pc_xyz_denoise[ii] = 1 / (1+lmd) * (pc_xyz_noise[ii] + lmd * sum_prod)
return pc_xyz_denoise
def get_node_neighbor_dict(adj, N):
node_neighbors_dict = {}
for i in range(N):
node = adj[i]
node_neighbors_dict[i] = csr_matrix.nonzero(node)[1]
return node_neighbors_dict
def BGCN_model_trial(trials_per_partition, data_partition_seed, trial_index,
log_dir):
def train_gcn_one_epoch(support_graph, epoch):
# Prepare feed dict for training set
t = time.time()
feed_dict_train = construct_feed_dict(features, support_graph, y_train,
train_mask, placeholders)
feed_dict_train.update({placeholders['dropout']: FLAGS.dropout})
# Training step
outs = sess.run([model.opt_op, model.loss, model.accuracy],
feed_dict=feed_dict_train)
# Validation set
cost_val, acc_val, duration = evaluate(features, support_original,
y_val, val_mask, placeholders)
# Test set using the sampled graph
test_cost, test_acc, test_duration = evaluate(features, support_graph,
y_test, test_mask,
placeholders)
# Test set using the original graph
test_cost_original_graph, test_acc_original_graph, _ = evaluate(
features, support_original, y_test, test_mask, placeholders)
#get the softmax using the sample graphs
feed_dict_val = construct_feed_dict(features, support_graph, y_test,
test_mask, placeholders)
feed_dict_val.update({placeholders['dropout']: 0})
soft_labels_sample_graphs = sess.run(tf.nn.softmax(model.outputs),
feed_dict=feed_dict_val)
#get the softmax of using the original graph
feed_dict_OG = construct_feed_dict(features, support_original, y_test,
test_mask, placeholders)
feed_dict_OG.update({placeholders['dropout']: 0})
soft_labels_OG_graph = sess.run(tf.nn.softmax(model.outputs),
feed_dict=feed_dict_OG)
# evaluate cross-entropy loss
cross_entropy_loss_avg_soft_labels = log_loss(
labels_value[test_set_index],
soft_labels_sample_graphs[test_set_index])
# Print results
if epoch % 10 == 9:
print(
"==================================================================="
)
print("Epoch:", '%04d' % (epoch + 1), "train_loss=",
"{:.5f}".format(outs[1]), "train_acc=",
"{:.5f}".format(outs[2]), "time=",
"{:.5f}".format(time.time() - t))
print("val_loss=", "{:.5f}".format(cost_val), "val_acc=",
"{:.5f}".format(acc_val))
return cost_val, soft_labels_OG_graph, soft_labels_sample_graphs
# data_partition_seed is used for data partition and generate a seed list for the neural network initial seed
np.random.seed(data_partition_seed)
trials_per_partition = trials_per_partition
seed_list = np.random.randint(1, 1e6, trials_per_partition)
for seed in seed_list:
np.random.seed(data_partition_seed) #decide the data partition seed
# ===========================load data========================================
timestamp = str(datetime.now())[0:10]
log_file_name = 'trial_index_' + str(trial_index) + '_data_partition_seed_' + str(data_partition_seed) \
+ '_seed_' + str(seed) + '_' + timestamp + '.txt'
if FLAGS.save_log:
sys.stdout = open(log_dir + log_file_name, 'w')
if not FLAGS.random_data_partition:
adj, features, y_train, y_val, y_test, train_mask, val_mask, test_mask, labels, order = \
data_partition_fixed(dataset_name=FLAGS.dataset, label_n_per_class=FLAGS.label_per_class_n)
else:
adj, features, y_train, y_val, y_test, train_mask, val_mask, test_mask, labels, order = \
data_partition_random(dataset_name=FLAGS.dataset, label_n_per_class=FLAGS.label_per_class_n)
np.random.seed(seed) # decide the seed for graph inference
random.seed(seed)
tf.set_random_seed(
seed) # decide the random seed for neural network initial weights
print("The index number for this trial is {}".format(trial_index))
print("The data partition seed for this trial is {}".format(
data_partition_seed))
print("The seed number for this trial is {}".format(seed))
N = len(y_train)
node_neighbors_dict = {}
for i in range(N):
node = adj[i]
node_neighbors_dict[i] = csr_matrix.nonzero(node)[1]
labels_value = labels.argmax(axis=1) #get the label value
test_set_index = np.where(test_mask == True)[0]
# ===========================================GCNN model set up========================================
features = preprocess_features(features)
if FLAGS.model == 'gcn':
support_original = [preprocess_adj(adj)]
num_supports = 1
model_func = GCN
elif FLAGS.model == 'gcn_cheby':
support_original = chebyshev_polynomials(adj, FLAGS.max_degree)
num_supports = 1 + FLAGS.max_degree
model_func = GCN
else:
raise ValueError('Invalid argument for model: ' + str(FLAGS.model))
# Define placeholders
placeholders = {
'support':
[tf.sparse_placeholder(tf.float32) for _ in range(num_supports)],
'features':
tf.sparse_placeholder(tf.float32,
shape=tf.constant(features[2],
dtype=tf.int64)),
'labels':
tf.placeholder(tf.float32, shape=(None, y_train.shape[1])),
'labels_mask':
tf.placeholder(tf.int32),
'dropout':
tf.placeholder_with_default(0., shape=()),
'num_features_nonzero':
tf.placeholder(tf.int32) # helper variable for sparse dropout
}
order = labels_value.argsort()
model = model_func(placeholders,
input_dim=features[2][1],
logging=True)
upper_tri_index = np.triu_indices(N, k=1)
# =======================================GCNN model initialization==============================================
# Initialize session
sess = tf.Session()
# Define model evaluation function
def evaluate(features, support, labels, mask, placeholders):
t_test = time.time()
feed_dict_val = construct_feed_dict(features, support, labels,
mask, placeholders)
outs_val = sess.run([model.loss, model.accuracy],
feed_dict=feed_dict_val)
return outs_val[0], outs_val[1], (time.time() - t_test)
# Init variables
sess.run(tf.global_variables_initializer())
cost_val_list = []
soft_max_sum_OG_graph = 0 # store the softmax output of the GCNN from different weight samples (from original graph)
soft_max_sum_sample_graph = 0 # store the softmax output of the GCNN from different weight samples (from sample graphs)
print(
"===============================Start training the GCNN Model========================"
)
for epoch in range(FLAGS.epochs):
if FLAGS.graph_generation_mode == 'Copying':
# =======================================GCNN pre train process=====================================
if epoch < FLAGS.pretrain_n:
cost_val, soft_labels_OG_graph, soft_labels_sample_graphs = train_gcn_one_epoch(
support_original, epoch)
cost_val_list.append(cost_val)
obtained_labels = soft_labels_OG_graph.argmax(axis=1)
if epoch == FLAGS.pretrain_n:
sampled_graph = sample_graph_copying(seed,
node_neighbors_dict,
obtained_labels,
order,
set_seed=True)
inferred_graph = csr_matrix(sampled_graph)
# pk.dump(MAP_graph, open(os.path.join(log_dir, MAP_graph), 'wb'))
if FLAGS.model == 'gcn_cheby':
support = chebyshev_polynomials(
inferred_graph, FLAGS.max_degree)
else:
support = [preprocess_adj(inferred_graph)]
cost_val, soft_labels_OG_graph, soft_labels_sample_graphs = train_gcn_one_epoch(
support, epoch)
cost_val_list.append(cost_val)
if epoch > FLAGS.pretrain_n:
sampled_graph = sample_graph_copying(seed,
node_neighbors_dict,
obtained_labels,
order,
set_seed=False)
inferred_graph = csr_matrix(sampled_graph)
# pk.dump(MAP_graph, open(os.path.join(log_dir, MAP_graph), 'wb'))
if FLAGS.model == 'gcn_cheby':
support = chebyshev_polynomials(
inferred_graph, FLAGS.max_degree)
else:
support = [preprocess_adj(inferred_graph)]
cost_val, soft_labels_OG_graph, soft_labels_sample_graphs = train_gcn_one_epoch(
support, epoch)
# ===========save the softmax output from different weight samples=================
if epoch > FLAGS.epoch_to_start_collect_weights and epoch % FLAGS.weight_sample_interval == 0:
soft_max_sum_OG_graph += soft_labels_OG_graph
hard_label_OG_graph = soft_max_sum_OG_graph.argmax(
axis=1)
acc_OG_graph = accuracy_score(
labels_value[test_set_index],
hard_label_OG_graph[test_set_index])
soft_max_sum_sample_graph += soft_labels_sample_graphs
hard_label_sample_graph = soft_max_sum_sample_graph.argmax(
axis=1)
acc_sample_graph = accuracy_score(
labels_value[test_set_index],
hard_label_sample_graph[test_set_index])
obtained_labels = hard_label_sample_graph
if epoch % 10 == 9:
print(
"============= weight sampling results at iteration {}=========="
.format(epoch + 1))
print(
"The accuracy from avg weight sampling using the original graph is {}"
.format(acc_OG_graph))
print(
"The accuracy from avg weight sampling using the sample graph is {}"
.format(acc_sample_graph))
cost_val_list.append(cost_val)
elif FLAGS.graph_generation_mode == 'None':
cost_val, soft_labels_OG_graph, soft_labels_sample_graphs = train_gcn_one_epoch(
support_original, epoch)
cost_val_list.append(cost_val)
if epoch > FLAGS.epoch_to_start_collect_weights and epoch % FLAGS.weight_sample_interval == 0:
soft_max_sum_OG_graph += soft_labels_OG_graph
hard_label_OG_graph = soft_max_sum_OG_graph.argmax(axis=1)
acc_OG_graph = accuracy_score(
labels_value[test_set_index],
hard_label_OG_graph[test_set_index])
if epoch % 10 == 9:
print(
"========= weight sampling results at iteration {}========"
.format(epoch + 1))
print(
"The accuracy from avg weight sampling using the original graph is {}"
.format(acc_OG_graph))
else:
raise ValueError('Invalid argument for model: ' +
str(FLAGS.graph_generation_mode))
print("Optimization Finished!")
print(
"===============================Start evaluate the final model performance ============================="
)
if FLAGS.graph_generation_mode != 'None':
softmax_log_file_name = 'BCGN_softmax_trial_index_' + str(
trial_index) + '_data_partition_seed_' + str(
data_partition_seed) + '_seed_' + str(
seed) + '_' + timestamp + '.pk'
pk.dump(soft_max_sum_OG_graph,
open(os.path.join(log_dir, softmax_log_file_name), 'wb'))
# Test set using the sampled graph
test_cost, test_acc, test_duration = evaluate(
features, support, y_test, test_mask, placeholders)
# Test set using the original graph
test_cost_original_graph, test_acc_original_graph, _ = evaluate(
features, support_original, y_test, test_mask, placeholders)
print("Model: Bayesian GCNN")
print(
"============1) final result using the weight at the last iteration (OG graph)========="
)
print("The accuracy from original graph is {}".format(
test_acc_original_graph))
print(
"============1) final result using the weight at the last iteration (Sample graph)========="
)
print("The accuracy from original graph is {}".format(test_acc))
print(
"============2) final result for weight samping and graph sampling========="
)
print(
"The accuracy from avg weight sampling using the original graph is {}"
.format(acc_OG_graph))
print(
"The accuracy from avg weight sampling using the sample graph is {}"
.format(acc_sample_graph))
else:
softmax_log_file_name = 'Vanilla_softmax_trial_index_' + str(
trial_index) + '_data_partition_seed_' + str(
data_partition_seed) + '_seed_' + str(
seed) + '_' + timestamp + '.pk'
pk.dump(soft_max_sum_OG_graph,
open(os.path.join(log_dir, softmax_log_file_name), 'wb'))
test_cost_original_graph, test_acc_original_graph, _ = evaluate(
features, support_original, y_test, test_mask, placeholders)
print("Model: Vanilla GCNN")
print(
"============1) final result using the weight at the last iteration========="
)
print("The accuracy from original graph is {}".format(
test_acc_original_graph))
print("============2) final result for weight samping===========")
print(
"The accuracy from avg weight sampling using the original graph is {}"
.format(acc_OG_graph))
sess.close()
tf.reset_default_graph()
return 0