def reconstruct(sess, config):
batch_size = config["batch_size"]
model = importlib.import_module(config["model.py"])
dataset_filename = config["dataset"]
if "dataset_test" in config:
dataset_filename = config["dataset_test"]
all_data, info = load_data(config, filename=dataset_filename)
graph_index_list = []
for i in range(all_data.num):
graph_index_list.append([i, i])
info.graph_index_list = graph_index_list
info.pos_weight = get_pos_weight(all_data)
info.norm = get_norm(all_data)
print("pos_weight=", info.pos_weight)
print("norm=", info.pos_weight)
model = CoreModel(sess,
config,
info,
construct_feed_callback=construct_feed)
model.build(importlib.import_module(config["model.py"]), is_train=False)
vars_to_train = tf.trainable_variables()
for v in vars_to_train:
print(v)
# initialize session
saver = tf.train.Saver()
#sess.run(tf.global_variables_initializer())
print("[load]", config["load_model"])
saver.restore(sess, config["load_model"])
start_t = time.time()
cost, acc, pred_data = model.pred_and_eval(all_data)
recons_data = pred_data
"""
recons_data=[]
for i in range(3):
print(i)
cost,acc,pred_data=model.pred_and_eval(all_data)
recons_data.append(pred_data)
"""
if "reconstruction_test" in config:
filename = config["reconstruction_test"]
os.makedirs(os.path.dirname(filename), exist_ok=True)
print("[SAVE]", filename)
joblib.dump(recons_data, filename)
def infer(sess,graph,config):
batch_size=config["batch_size"]
model = importlib.import_module(config["model.py"])
dataset_filename=config["dataset"]
if "dataset_test" in config:
dataset_filename=config["dataset_test"]
all_data,info=load_data(config,filename=dataset_filename)
model = CoreModel(sess,config,info)
model.build(importlib.import_module(config["model.py"]),is_train=False)
# Initialize session
saver = tf.train.Saver()
#sess.run(tf.global_variables_initializer())
print("[LOAD]",config["load_model"])
saver.restore(sess,config["load_model"])
# Validation
start_t = time.time()
test_cost,test_metrics,prediction_data=model.pred_and_eval(all_data)
infer_time = time.time() - start_t
print("final cost =",test_cost)
print("accuracy =",test_metrics["accuracy"])
print("infer time:{0}".format(infer_time) + "[sec]")
if config["save_info_test"] is not None:
result={}
result["test_cost"]=test_cost
result["test_accuracy"]=test_metrics
result["infer_time"]=infer_time
save_path=config["save_info_test"]
print("[SAVE] ",save_path)
fp=open(save_path,"w")
json.dump(result,fp, indent=4, cls=NumPyArangeEncoder)
if config["prediction_data"] is None:
print("[ERROR] prediction_data is required")
quit()
obj = {}
obj["prediction_data"] = prediction_data
obj["labels" ] = all_data.labels
os.makedirs(os.path.dirname(config["prediction_data"]), exist_ok=True)
joblib.dump(obj,config["prediction_data"])
def train(sess,graph,config):
batch_size=config["batch_size"]
learning_rate=config["learning_rate"]
if config["validation_dataset"] is None:
_, train_data,valid_data,info = load_and_split_data(config,filename=config["dataset"],valid_data_rate=config["validation_data_rate"])
else:
print("[INFO] training")
train_data, info = load_data(config, filename=config["dataset"])
print("[INFO] validation")
valid_data, valid_info = load_data(config, filename=config["validation_dataset"])
info["graph_node_num"] = max(info["graph_node_num"], valid_info["graph_node_num"])
info["graph_num"] = info["graph_num"] + valid_info["graph_num"]
model = CoreModel(sess,config,info)
model.build(importlib.import_module(config["model.py"]))
if config["profile"]:
vars_to_train = tf.trainable_variables()
print(vars_to_train)
writer = tf.summary.FileWriter('logs', sess.graph)
# Training
start_t = time.time()
model.fit(train_data,valid_data)
train_time = time.time() - start_t
print("traing time:{0}".format(train_time) + "[sec]")
if valid_data.num>0:
# Validation
start_t = time.time()
validation_cost,validation_metrics,prediction_data=model.pred_and_eval(valid_data)
infer_time = time.time() - start_t
print("final cost =",validation_cost)
print("accuracy =",validation_metrics["accuracy"])
print("validation time:{0}".format(infer_time) + "[sec]")
# Saving
if config["save_info_valid"] is not None:
result={}
result["validation_cost"]=validation_cost
result["validation_accuracy"]=validation_metrics
result["train_time"]=train_time
result["infer_time"]=infer_time
save_path=config["save_info_valid"]
print("[SAVE] ",save_path)
fp=open(save_path,"w")
json.dump(result,fp, indent=4, cls=NumPyArangeEncoder)
if config["export_model"]:
try:
print("[SAVE]",config["export_model"])
graph_def = graph_util.convert_variables_to_constants(sess, graph.as_graph_def(), ['output'])
tf.train.write_graph(graph_def, '.', config["export_model"], as_text=False)
except:
print('[ERROR] output has been not found')
if config["save_result_valid"] is not None:
filename=config["save_result_valid"]
save_prediction(filename,prediction_data)
if config["make_plot"]:
plot_cost(config,valid_data,model)
plot_auc(config,valid_data.labels,np.array(prediction_data))
def reconstruct(sess, config):
dataset_filename = config["dataset"]
if "dataset_test" in config:
dataset_filename = config["dataset_test"]
all_data, info = load_data(config, filename=dataset_filename)
graph_index_list = []
for i in range(all_data.num):
graph_index_list.append([i, i])
info.graph_index_list = graph_index_list
info.pos_weight = get_pos_weight(all_data)
info.norm = get_norm(all_data)
print(f"pos_weight={info.pos_weight}")
print(f"norm={info.norm}")
model = CoreModel(sess,
config,
info,
construct_feed_callback=construct_feed)
load_model_py(model, config["model.py"], is_train=False)
vars_to_train = tf.trainable_variables()
for v in vars_to_train:
print(v)
# initialize session
restore_ckpt(sess, config["load_model"])
start_t = time.time()
cost, acc, pred_data = model.pred_and_eval(all_data)
recons_data = pred_data
"""
recons_data=[]
for i in range(3):
print(i)
cost,acc,pred_data=model.pred_and_eval(all_data)
recons_data.append(pred_data)
"""
if "reconstruction_test" in config:
filename = config["reconstruction_test"]
os.makedirs(os.path.dirname(filename), exist_ok=True)
print(f"[SAVE] {filename}")
joblib.dump(recons_data, filename)
def generate(sess, config):
batch_size = config["batch_size"]
dataset_filename = config["dataset"]
if "dataset_test" in config:
dataset_filename = config["dataset_test"]
all_data, info = load_data(config, filename=dataset_filename)
graph_index_list = []
for i in range(all_data.num):
graph_index_list.append([i, i])
info.graph_index_list = graph_index_list
info.pos_weight = get_pos_weight(all_data)
info.norm = get_norm(all_data)
print("pos_weight=", info.pos_weight)
print("norm=", info.pos_weight)
model = CoreModel(sess,
config,
info,
construct_feed_callback=construct_feed)
load_model_py(model, config["model.py"], is_train=False)
# initialize session
saver = tf.train.Saver()
#sess.run(tf.global_variables_initializer())
restore_ckpt(sess, config["load_model"])
start_t = time.time()
generated_data = None
#for i in range(3):
#print(i)
cost, acc, pred_data = model.pred_and_eval(all_data)
generated_data = pred_data
if "generation_test" in config:
filename = config["generation_test"]
dirname = os.path.dirname(filename)
if dirname != "": os.makedirs(dirname, exist_ok=True)
print("[SAVE]", filename)
joblib.dump(generated_data, filename)
def _train(layers):
config = _get_config()
_, train_data, valid_data, info = load_and_split_data(
config,
filename=config["dataset"],
valid_data_rate=config["validation_data_rate"])
metric_name = "accuracy"
with tf.Session() as sess:
model = CoreModel(sess, config, info)
model.build(GCN(layers), True, False, None)
model.fit(train_data, valid_data)
_, valid_metrics, _ = model.pred_and_eval(valid_data)
return valid_metrics[metric_name]
def load_model(model_name, config, class_num=None):
""" Load trained model of Tensorflow or Keras
Args:
model_name (str):
config (dict):
class_num (int):
Returns:
Loaded model instance
"""
model = None
if config['descriptor'] == 'ECFP':
if model_name == 'expansion':
model = models.load_model(config['expansion_model'])
elif model_name == 'rollout':
model = models.load_model(config['rollout_model'])
if config['descriptor'] == 'GCN':
graph = tf.Graph()
sess = tf.Session(graph=graph)
with graph.as_default():
from utils import MoleculeUtils
# dummy setting
mol = Chem.MolFromSmiles('C1=CC=CC=C1')
input_data = None
trained_model_path = None
if model_name == 'expansion':
gcn_config = get_config(config['gcn_expansion_config'])
input_data = MoleculeUtils.generate_gcn_descriptor(
mol, config['max_atom_num'], class_num)
trained_model_path = config['expansion_model']
elif model_name == 'rollout':
gcn_config = get_config(config['gcn_rollout_config'])
input_data = MoleculeUtils.generate_gcn_descriptor(
mol, config['max_atom_num'], class_num)
trained_model_path = config['rollout_model']
_, info = build_data(gcn_config, input_data, verbose=False)
model = CoreModel(sess, gcn_config, info)
load_model_py(model, gcn_config["model.py"], is_train=False)
# Initialize session
saver = tf.train.Saver()
saver.restore(sess, trained_model_path)
return model
def visualize(sess, config, args):
from kgcn.visualization import cal_feature_IG, cal_feature_IG_for_kg
# input a molecule at a time
batch_size = 1
dataset_filename = config["dataset"]
if "dataset_test" in config:
dataset_filename = config["dataset_test"]
all_data, info = load_data(config,
filename=dataset_filename,
prohibit_shuffle=True)
model = CoreModel(sess, config, info)
load_model_py(model,
config["model.py"],
is_train=False,
feed_embedded_layer=True,
batch_size=batch_size)
placeholders = model.placeholders
restore_ckpt(sess, config['load_model'])
# calculate integrated gradients
if config['visualize_type'] == 'graph':
cal_feature_IG(sess,
all_data,
placeholders,
info,
config,
model.prediction,
args.ig_modal_target,
args.ig_label_target,
logger=tf.logging,
model=model.nn,
args=args)
else:
cal_feature_IG_for_kg(sess,
all_data,
placeholders,
info,
config,
model.prediction,
logger=tf.logging,
model=model.nn,
args=args)
def infer(sess, graph, config):
dataset_filename = config["dataset"]
if "dataset_test" in config:
dataset_filename = config["dataset_test"]
if "test_label_list" in config:
config["label_list"] = config["test_label_list"]
all_data, info = load_data(config,
filename=dataset_filename,
prohibit_shuffle=True)
model = CoreModel(sess, config, info)
load_model_py(model, config["model.py"], is_train=False)
metric_name = ("mse" if config["task"] == "regression" else "gmfe"
if config["task"] == "regression_gmfe" else "accuracy")
# Initialize session
restore_ckpt(sess, config["load_model"])
# Validation
start_t = time.time()
test_cost, test_metrics, prediction_data = model.pred_and_eval(all_data)
infer_time = time.time() - start_t
print(f"final cost = {test_cost}\n"
f"{metric_name} = {test_metrics[metric_name]}\n"
f"infer time: {infer_time}[sec]\n")
if config["save_info_test"] is not None:
result = {}
result["test_cost"] = test_cost
result["test_accuracy"] = test_metrics
result["infer_time"] = infer_time
if config["task"] != "link_prediction":
result["test_metrics"] = compute_metrics(config, info,
prediction_data,
all_data.labels)
save_path = config["save_info_test"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print(f"[SAVE] {save_path}")
with open(save_path, "w") as fp:
json.dump(result, fp, indent=4, cls=NumPyArangeEncoder)
if config["save_result_test"] is not None:
filename = config["save_result_test"]
save_prediction(filename, prediction_data)
if config["make_plot"]:
if config["task"] == "regression":
pred_score = np.array(prediction_data)
plot_r2(config, all_data.labels, pred_score)
elif config["task"] == "regression_gmfe":
pred_score = np.array(prediction_data)
plot_r2(config, all_data.labels, pred_score)
elif config["task"] == "link_prediction":
pass
else:
plot_auc(config, all_data.labels, np.array(prediction_data))
if "save_edge_result_test" in config and config[
"save_edge_result_test"] is not None:
#output_left_pred = model.left_pred(all_data)
#print(output_left_pred.shape)
##
output_data = model.output(all_data)
pred_score = np.array(prediction_data)
true_label = np.array(all_data.label_list)
score_list = []
print(true_label.shape)
for pair in true_label[0]:
if len(prediction_data[0].shape) == 2:
i1, _, j1, i2, _, j2 = pair
s1 = pred_score[0, i1, j1]
s2 = pred_score[0, i2, j2]
elif len(prediction_data[0].shape) == 3:
i1, r1, j1, i2, r2, j2 = pair
s1 = pred_score[0, r1, i1, j1]
s2 = pred_score[0, r2, i2, j2]
score_list.append([s1, s2])
fold = {}
fold["output"] = output_data[0]
fold["score"] = np.array(score_list)
save_path = config["save_edge_result_test"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print(f"[SAVE] {save_path}")
_, ext = os.path.splitext(save_path)
if ext == ".json":
with open(save_path, "w") as fp:
json.dump(fold, fp, indent=4, cls=NumPyArangeEncoder)
else:
joblib.dump(fold, save_path, compress=True)
if config["prediction_data"] is not None:
obj = {}
obj["prediction_data"] = prediction_data
obj["labels"] = all_data.labels
os.makedirs(os.path.dirname(config["prediction_data"]), exist_ok=True)
joblib.dump(obj, config["prediction_data"], compress=True)
def train(sess, graph, config):
from sklearn.metrics import roc_curve, auc, accuracy_score, precision_recall_fscore_support
batch_size = config["batch_size"]
learning_rate = config["learning_rate"]
if config["validation_dataset"] is None:
_, train_data, valid_data, info = load_and_split_data(
config,
filename=config["dataset"],
valid_data_rate=config["validation_data_rate"])
else:
print("[INFO] training")
train_data, info = load_data(config, filename=config["dataset"])
print("[INFO] validation")
valid_data, valid_info = load_data(
config, filename=config["validation_dataset"])
info["graph_node_num"] = max(info["graph_node_num"],
valid_info["graph_node_num"])
info["graph_num"] = info["graph_num"] + valid_info["graph_num"]
model = CoreModel(sess, config, info)
load_model_py(model, config["model.py"])
if config["profile"]:
vars_to_train = tf.trainable_variables()
print(vars_to_train)
writer = tf.summary.FileWriter('logs', sess.graph)
# Training
start_t = time.time()
model.fit(train_data, valid_data)
train_time = time.time() - start_t
print("traing time:{0}".format(train_time) + "[sec]")
if valid_data.num > 0:
# Validation
start_t = time.time()
validation_cost, validation_metrics, prediction_data = model.pred_and_eval(
valid_data)
infer_time = time.time() - start_t
print("final cost =", validation_cost)
print("accuracy =", validation_metrics["accuracy"])
print("validation time:{0}".format(infer_time) + "[sec]")
# Saving
if config["save_info_valid"] is not None:
result = {}
result["validation_cost"] = validation_cost
result["validation_accuracy"] = validation_metrics
result["train_time"] = train_time
result["infer_time"] = infer_time
##
pred_score = np.array(prediction_data)
if len(pred_score.shape) == 3: # multi-label-multi-task
# #data x # task x #class
# => this program supports only 2 labels
pred_score = pred_score[:, :, 1]
true_label = np.array(valid_data.labels)
# #data x # task x #class
if len(pred_score.shape) == 1:
pred_score = pred_score[:, np.newaxis]
if len(true_label.shape) == 1:
true_label = true_label[:, np.newaxis]
v = []
for i in range(info.label_dim):
el = {}
if config["task"] == "regression":
el["r2"] = sklearn.metrics.r2_score(
true_label[:, i], pred_score[:, i])
el["mse"] = sklearn.metrics.mean_squared_error(
true_label[:, i], pred_score[:, i])
elif config["task"] == "regression_gmfe":
el["gmfe"] = np.exp(
np.mean(np.log(true_label[:, i] / pred_score[:, i])))
else:
pred = np.zeros(pred_score.shape)
pred[pred_score > 0.5] = 1
fpr, tpr, _ = roc_curve(true_label[:, i],
pred_score[:, i],
pos_label=1)
roc_auc = auc(fpr, tpr)
acc = accuracy_score(true_label[:, i], pred[:, i])
scores = precision_recall_fscore_support(true_label[:, i],
pred[:, i],
average='binary')
el["auc"] = roc_auc
el["acc"] = acc
el["pre"] = scores[0]
el["rec"] = scores[1]
el["f"] = scores[2]
el["sup"] = scores[3]
v.append(el)
result["valid_metrics"] = el
##
save_path = config["save_info_valid"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print("[SAVE] ", save_path)
fp = open(save_path, "w")
json.dump(result, fp, indent=4, cls=NumPyArangeEncoder)
if config["export_model"]:
try:
print("[SAVE]", config["export_model"])
graph_def = graph_util.convert_variables_to_constants(
sess, graph.as_graph_def(), ['output'])
tf.train.write_graph(graph_def,
'.',
config["export_model"],
as_text=False)
except:
print('[ERROR] output has been not found')
if config["save_result_valid"] is not None:
filename = config["save_result_valid"]
save_prediction(filename, prediction_data)
if config["make_plot"]:
plot_cost(config, valid_data, model)
plot_auc(config, valid_data.labels, np.array(prediction_data))
def train(sess, graph, config):
if config["validation_dataset"] is None:
_, train_data, valid_data, info = load_and_split_data(
config,
filename=config["dataset"],
valid_data_rate=config["validation_data_rate"])
else:
print("[INFO] training")
train_data, info = load_data(config, filename=config["dataset"])
print("[INFO] validation")
valid_data, valid_info = load_data(
config, filename=config["validation_dataset"])
info["graph_node_num"] = max(info["graph_node_num"],
valid_info["graph_node_num"])
info["graph_num"] = info["graph_num"] + valid_info["graph_num"]
model = CoreModel(sess, config, info)
load_model_py(model, config["model.py"])
metric_name = ("mse" if config["task"] == "regression" else "gmfe"
if config["task"] == "regression_gmfe" else "accuracy")
if config["profile"]:
vars_to_train = tf.trainable_variables()
print(vars_to_train)
# Training
start_t = time.time()
model.fit(train_data, valid_data)
train_time = time.time() - start_t
print(f"training time: {train_time}[sec]")
if valid_data.num > 0:
# Validation
start_t = time.time()
valid_cost, valid_metrics, prediction_data = model.pred_and_eval(
valid_data)
infer_time = time.time() - start_t
print(f"final cost = {valid_cost}\n"
f"{metric_name} = {valid_metrics[metric_name]}\n"
f"validation time: {infer_time}[sec]\n")
# Saving
if config["save_info_valid"] is not None:
result = {}
result["validation_cost"] = valid_cost
result["validation_accuracy"] = valid_metrics
result["train_time"] = train_time
result["infer_time"] = infer_time
if config["task"] != "link_prediction":
result["valid_metrics"] = compute_metrics(
config, info, prediction_data, valid_data.labels)
##
save_path = config["save_info_valid"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print(f"[SAVE] {save_path}")
with open(save_path, "w") as fp:
json.dump(result, fp, indent=4, cls=NumPyArangeEncoder)
if config["export_model"]:
try:
print(f"[SAVE] {config['export_model']}")
graph_def = graph_util.convert_variables_to_constants(
sess, graph.as_graph_def(), ['output'])
tf.train.write_graph(graph_def,
'.',
config["export_model"],
as_text=False)
except:
print('[ERROR] output has been not found')
if config["save_result_valid"] is not None:
filename = config["save_result_valid"]
save_prediction(filename, prediction_data)
if config["make_plot"]:
if config["task"] == "regression" or config[
"task"] == "regression_gmfe":
# plot_cost(config, valid_data, model)
plot_r2(config, valid_data.labels, np.array(prediction_data))
elif config["task"] == "link_prediction":
plot_cost(config, valid_data, model)
else:
plot_cost(config, valid_data, model)
plot_auc(config, valid_data.labels, np.array(prediction_data))
def train_cv(sess, graph, config):
all_data, info = load_data(
config, filename=config["dataset"],
prohibit_shuffle=True) # shuffle is done by KFold
model = CoreModel(sess, config, info)
load_model_py(model, config["model.py"])
# Training
if config["stratified_kfold"]:
print("[INFO] use stratified K-fold")
kf = StratifiedKFold(n_splits=config["k-fold_num"],
shuffle=config["shuffle_data"],
random_state=123)
else:
kf = KFold(n_splits=config["k-fold_num"],
shuffle=config["shuffle_data"],
random_state=123)
kf_count = 1
fold_data_list = []
output_data_list = []
if all_data["labels"] is not None:
split_base = all_data["labels"]
else:
split_base = all_data["label_list"][0]
if config["stratified_kfold"]:
split_base = np.argmax(split_base, axis=1)
score_metrics = []
if config["task"] == "regression":
metric_name = "mse"
elif config["task"] == "regression_gmfe":
metric_name = "gmfe"
else:
metric_name = "accuracy"
split_data_generator = kf.split(
split_base,
split_base) if config["stratified_kfold"] else kf.split(split_base)
for train_valid_list, test_list in split_data_generator:
print(f"starting fold: {kf_count}")
train_valid_data, test_data = split_data(
all_data,
indices_for_train_data=train_valid_list,
indices_for_valid_data=test_list)
train_data, valid_data = split_data(
train_valid_data, valid_data_rate=config["validation_data_rate"])
# Training
print(train_valid_list)
print(test_list)
start_t = time.time()
model.fit(train_data, valid_data, k_fold_num=kf_count)
train_time = time.time() - start_t
print(f"training time: {train_time}[sec]")
# Test
print("== valid data ==")
start_t = time.time()
valid_cost, valid_metrics, prediction_data = model.pred_and_eval(
valid_data)
infer_time = time.time() - start_t
print(f"final cost = {valid_cost}\n"
f"{metric_name} = {valid_metrics[metric_name]}\n"
f"infer time: {infer_time}[sec]\n")
print("== test data ==")
start_t = time.time()
test_cost, test_metrics, prediction_data = model.pred_and_eval(
test_data)
infer_time = time.time() - start_t
print(f"final cost = {test_cost}\n"
f"{metric_name} = {test_metrics[metric_name]}\n")
score_metrics.append(test_metrics[metric_name])
print(f"infer time: {infer_time}[sec]")
if config["export_model"]:
try:
name, ext = os.path.splitext(config["export_model"])
filename = name + "." + str(kf_count) + ext
print(f"[SAVE] {filename}")
graph_def = graph_util.convert_variables_to_constants(
sess, graph.as_graph_def(), ['output'])
tf.train.write_graph(graph_def, '.', filename, as_text=False)
except:
print('[ERROR] output has been not found')
if "save_edge_result_cv" in config:
output_data = model.output(test_data)
output_data_list.append(output_data)
# save fold data
fold_data = dotdict({})
fold_data.prediction_data = prediction_data
if all_data["labels"] is not None:
fold_data.test_labels = test_data.labels
else:
fold_data.test_labels = test_data.label_list
fold_data.test_data_idx = test_list
if config["task"] == "regression":
fold_data.training_mse = [
el["training_mse"] for el in model.training_metrics_list
]
fold_data.validation_mse = [
el["validation_mse"] for el in model.validation_metrics_list
]
elif config["task"] == "regression_gmfe":
fold_data.training_mse = [
el["training_gmfe"] for el in model.training_metrics_list
]
fold_data.validation_mse = [
el["validation_gmfe"] for el in model.validation_metrics_list
]
else:
fold_data.training_acc = [
el["training_accuracy"] for el in model.training_metrics_list
]
fold_data.validation_acc = [
el["validation_accuracy"]
for el in model.validation_metrics_list
]
fold_data.test_acc = test_metrics[metric_name]
fold_data.training_cost = model.training_cost_list
fold_data.validation_cost = model.validation_cost_list
fold_data.test_cost = test_cost
fold_data.train_time = train_time
fold_data.infer_time = infer_time
fold_data_list.append(fold_data)
kf_count += 1
print(f"cv {metric_name}(mean) = {np.mean(score_metrics)}\n"
f"cv {metric_name}(std.) = {np.std(score_metrics)}\n")
if "save_info_cv" in config and config["save_info_cv"] is not None:
save_path = config["save_info_cv"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print(f"[SAVE] {save_path}")
_, ext = os.path.splitext(save_path)
if ext == ".json":
with open(save_path, "w") as fp:
json.dump(fold_data_list, fp, indent=4, cls=NumPyArangeEncoder)
else:
joblib.dump(fold_data_list, save_path, compress=True)
#
if "save_edge_result_cv" in config and config[
"save_edge_result_cv"] is not None:
result_cv = []
for j, fold_data in enumerate(fold_data_list):
pred_score = np.array(fold_data.prediction_data)
true_label = np.array(fold_data.test_labels)
test_idx = fold_data.test_data_idx
score_list = []
for pair in true_label[0]:
i1, _, j1, i2, _, j2 = pair
s1 = pred_score[0, i1, j1]
s2 = pred_score[0, i2, j2]
score_list.append([s1, s2])
fold = {}
fold["output"] = output_data_list[j][0]
fold["score"] = np.array(score_list)
fold["test_data_idx"] = test_idx
result_cv.append(fold)
save_path = config["save_edge_result_cv"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print(f"[SAVE] {save_path}")
_, ext = os.path.splitext(save_path)
if ext == ".json":
with open(save_path, "w") as fp:
json.dump(result_cv, fp, indent=4, cls=NumPyArangeEncoder)
else:
joblib.dump(result_cv, save_path, compress=True)
#
if "save_result_cv" in config and config["save_result_cv"] is not None:
result_cv = []
for j, fold_data in enumerate(fold_data_list):
v = compute_metrics(config, info, fold_data.prediction_data,
fold_data.test_labels)
result_cv.append(v)
save_path = config["save_result_cv"]
print(f"[SAVE] {save_path}")
with open(save_path, "w") as fp:
json.dump(result_cv, fp, indent=4, cls=NumPyArangeEncoder)
#
for i, fold_data in enumerate(fold_data_list):
prefix = "fold" + str(i) + "_"
result_path = config["plot_path"]
os.makedirs(result_path, exist_ok=True)
if config["make_plot"]:
if config["task"] == "regression":
make_cost_acc_plot(fold_data.training_cost,
fold_data.validation_cost,
fold_data.training_mse,
fold_data.validation_mse,
result_path,
prefix=prefix)
pred_score = np.array(fold_data.prediction_data)
plot_r2(config,
fold_data.test_labels,
pred_score,
prefix=prefix)
elif config["task"] == "regression_gmfe":
make_cost_acc_plot(fold_data.training_cost,
fold_data.validation_cost,
fold_data.training_mse,
fold_data.validation_mse,
result_path,
prefix=prefix)
pred_score = np.array(fold_data.prediction_data)
plot_r2(config,
fold_data.test_labels,
pred_score,
prefix=prefix)
elif config["task"] == "link_prediction":
make_cost_acc_plot(fold_data.training_cost,
fold_data.validation_cost,
fold_data.training_acc,
fold_data.validation_acc,
result_path,
prefix=prefix)
else:
make_cost_acc_plot(fold_data.training_cost,
fold_data.validation_cost,
fold_data.training_acc,
fold_data.validation_acc,
result_path,
prefix=prefix)
pred_score = np.array(fold_data.prediction_data)
plot_auc(config,
fold_data.test_labels,
pred_score,
prefix=prefix)
def infer(sess, graph, config):
batch_size = config["batch_size"]
dataset_filename = config["dataset"]
if "dataset_test" in config:
dataset_filename = config["dataset_test"]
all_data, info = load_data(config, filename=dataset_filename)
model = CoreModel(sess, config, info)
load_model_py(model, config["model.py"], is_train=False)
# Initialize session
saver = tf.train.Saver()
#sess.run(tf.global_variables_initializer())
print("[LOAD]", config["load_model"])
saver.restore(sess, config["load_model"])
# Validation
start_t = time.time()
test_cost, test_metrics, prediction_data = model.pred_and_eval(all_data)
infer_time = time.time() - start_t
print("final cost =", test_cost)
print("accuracy =", test_metrics["accuracy"])
print("infer time:{0}".format(infer_time) + "[sec]")
if config["save_info_test"] is not None:
result = {}
result["test_cost"] = test_cost
result["test_accuracy"] = test_metrics
result["infer_time"] = infer_time
save_path = config["save_info_test"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print("[SAVE] ", save_path)
fp = open(save_path, "w")
json.dump(result, fp, indent=4, cls=NumPyArangeEncoder)
if config["save_result_test"] is not None:
filename = config["save_result_test"]
save_prediction(filename, prediction_data)
if config["make_plot"]:
plot_auc(config, all_data.labels, np.array(prediction_data))
if "save_edge_result_test" in config and config[
"save_edge_result_test"] is not None:
output_data = model.output(all_data)
pred_score = np.array(prediction_data)
true_label = np.array(all_data.label_list)
test_idx = all_data.test_data_idx
score_list = []
print(true_label.shape)
for pair in true_label[0]:
i1, _, j1, i2, _, j2 = pair
s1 = pred_score[0, i1, j1]
s2 = pred_score[0, i2, j2]
score_list.append([s1, s2])
fold = {}
fold["output"] = output_data[0]
fold["score"] = np.array(score_list)
save_path = config["save_edge_result_test"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print("[SAVE] ", save_path)
_, ext = os.path.splitext(save_path)
if ext == ".json":
fp = open(save_path, "w")
json.dump(fold, fp, indent=4, cls=NumPyArangeEncoder)
else:
joblib.dump(fold, save_path, compress=True)
def train_cv(sess, graph, config):
from sklearn.model_selection import KFold, StratifiedKFold
from kgcn.make_plots import make_auc_plot, make_cost_acc_plot
import sklearn
from sklearn.metrics import roc_curve, auc, accuracy_score, precision_recall_fscore_support
from scipy import interp
batch_size = config["batch_size"]
learning_rate = config["learning_rate"]
all_data, info = load_data(
config, filename=config["dataset"],
prohibit_shuffle=True) # shuffle is done by KFold
model = CoreModel(sess, config, info)
load_model_py(model, config["model.py"])
# Training
if config["stratified_kfold"]:
print("[INFO] use stratified K-fold")
kf = StratifiedKFold(n_splits=config["k-fold_num"],
shuffle=config["shuffle_data"],
random_state=123)
else:
kf = KFold(n_splits=config["k-fold_num"],
shuffle=config["shuffle_data"],
random_state=123)
kf_count = 1
fold_data_list = []
output_data_list = []
if all_data["labels"] is not None:
split_base = all_data["labels"]
else:
split_base = all_data["label_list"][0]
if config["stratified_kfold"]:
split_base = np.argmax(split_base, axis=1)
score_metrics = []
if config["task"] == "regression":
metric_name = "mse"
elif config["task"] == "regression_gmfe":
metric_name = "gmfe"
else:
metric_name = "accuracy"
split_data_generator = kf.split(
split_base,
split_base) if config["stratified_kfold"] else kf.split(split_base)
for train_valid_list, test_list in split_data_generator:
print("starting fold:{0}".format(kf_count))
train_valid_data, test_data = split_data(
all_data,
indices_for_train_data=train_valid_list,
indices_for_valid_data=test_list)
train_data, valid_data = split_data(
train_valid_data, valid_data_rate=config["validation_data_rate"])
# Training
print(train_valid_list)
print(test_list)
start_t = time.time()
model.fit(train_data, valid_data, k_fold_num=kf_count)
train_time = time.time() - start_t
print("traing time:{0}".format(train_time) + "[sec]")
# Test
print("== valid data ==")
start_t = time.time()
valid_cost, valid_metrics, prediction_data = model.pred_and_eval(
valid_data)
infer_time = time.time() - start_t
print("final cost =", valid_cost)
print("%s =%f" % (metric_name, valid_metrics[metric_name]))
print("infer time:{0}".format(infer_time) + "[sec]")
print("== test data ==")
start_t = time.time()
test_cost, test_metrics, prediction_data = model.pred_and_eval(
test_data)
infer_time = time.time() - start_t
print("final cost =", test_cost)
print("%s =%f" % (metric_name, test_metrics[metric_name]))
score_metrics.append(test_metrics[metric_name])
print("infer time:{0}".format(infer_time) + "[sec]")
if config["export_model"]:
try:
name, ext = os.path.splitext(config["export_model"])
filename = name + "." + str(kf_count) + ext
print("[SAVE]", filename)
graph_def = graph_util.convert_variables_to_constants(
sess, graph.as_graph_def(), ['output'])
tf.train.write_graph(graph_def, '.', filename, as_text=False)
except:
print('[ERROR] output has been not found')
if "save_edge_result_cv" in config:
output_data = model.output(test_data)
output_data_list.append(output_data)
# save fold data
fold_data = dotdict({})
fold_data.prediction_data = prediction_data
if all_data["labels"] is not None:
fold_data.test_labels = test_data.labels
else:
fold_data.test_labels = test_data.label_list
fold_data.test_data_idx = test_list
if config["task"] == "regression":
fold_data.training_mse = [
el["training_mse"] for el in model.training_metrics_list
]
fold_data.validation_mse = [
el["validation_mse"] for el in model.validation_metrics_list
]
elif config["task"] == "regression_gmfe":
fold_data.training_mse = [
el["training_gmfe"] for el in model.training_metrics_list
]
fold_data.validation_mse = [
el["validation_gmfe"] for el in model.validation_metrics_list
]
else:
fold_data.training_acc = [
el["training_accuracy"] for el in model.training_metrics_list
]
fold_data.validation_acc = [
el["validation_accuracy"]
for el in model.validation_metrics_list
]
fold_data.test_acc = test_metrics[metric_name]
fold_data.training_cost = model.training_cost_list
fold_data.validation_cost = model.validation_cost_list
fold_data.test_cost = test_cost
fold_data.train_time = train_time
fold_data.infer_time = infer_time
fold_data_list.append(fold_data)
kf_count += 1
print("cv %s(mean) =%f" % (metric_name, np.mean(score_metrics)))
print("cv %s(std.) =%f" % (metric_name, np.std(score_metrics)))
if "save_info_cv" in config and config["save_info_cv"] is not None:
save_path = config["save_info_cv"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print("[SAVE] ", save_path)
_, ext = os.path.splitext(save_path)
if ext == ".json":
fp = open(save_path, "w")
json.dump(fold_data_list, fp, indent=4, cls=NumPyArangeEncoder)
else:
joblib.dump(fold_data_list, save_path, compress=True)
##
if "save_edge_result_cv" in config and config[
"save_edge_result_cv"] is not None:
result_cv = []
for j, fold_data in enumerate(fold_data_list):
pred_score = np.array(fold_data.prediction_data)
true_label = np.array(fold_data.test_labels)
test_idx = fold_data.test_data_idx
score_list = []
for pair in true_label[0]:
i1, _, j1, i2, _, j2 = pair
s1 = pred_score[0, i1, j1]
s2 = pred_score[0, i2, j2]
score_list.append([s1, s2])
fold = {}
fold["output"] = output_data_list[j][0]
fold["score"] = np.array(score_list)
fold["test_data_idx"] = test_idx
result_cv.append(fold)
save_path = config["save_edge_result_cv"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print("[SAVE] ", save_path)
_, ext = os.path.splitext(save_path)
if ext == ".json":
fp = open(save_path, "w")
json.dump(result_cv, fp, indent=4, cls=NumPyArangeEncoder)
else:
joblib.dump(result_cv, save_path, compress=True)
#
#
if "save_result_cv" in config and config["save_result_cv"] is not None:
result_cv = []
for j, fold_data in enumerate(fold_data_list):
pred_score = np.array(fold_data.prediction_data)
if len(pred_score.shape) == 3: # multi-label-multi-task
# #data x # task x #class
# => this program supports only 2 labels
pred_score = pred_score[:, :, 1]
true_label = np.array(fold_data.test_labels)
# #data x # task x #class
if len(pred_score.shape) == 1:
pred_score = pred_score[:, np.newaxis]
if len(true_label.shape) == 1:
true_label = true_label[:, np.newaxis]
v = []
for i in range(info.label_dim):
el = {}
if config["task"] == "regression":
el["r2"] = sklearn.metrics.r2_score(
true_label[:, i], pred_score[:, i])
el["mse"] = sklearn.metrics.mean_squared_error(
true_label[:, i], pred_score[:, i])
elif config["task"] == "regression_gmfe":
el["gmfe"] = np.exp(
np.mean(np.log(true_label[:, i] / pred_score[:, i])))
else:
pred = np.zeros(pred_score.shape)
pred[pred_score > 0.5] = 1
fpr, tpr, _ = roc_curve(true_label[:, i],
pred_score[:, i],
pos_label=1)
roc_auc = auc(fpr, tpr)
acc = accuracy_score(true_label[:, i], pred[:, i])
scores = precision_recall_fscore_support(true_label[:, i],
pred[:, i],
average='binary')
el["auc"] = roc_auc
el["acc"] = acc
el["pre"] = scores[0]
el["rec"] = scores[1]
el["f"] = scores[2]
el["sup"] = scores[3]
v.append(el)
result_cv.append(v)
save_path = config["save_result_cv"]
print("[SAVE] ", save_path)
fp = open(save_path, "w")
json.dump(result_cv, fp, indent=4, cls=NumPyArangeEncoder)
#
for i, fold_data in enumerate(fold_data_list):
prefix = "fold" + str(i) + "_"
result_path = config["plot_path"]
os.makedirs(result_path, exist_ok=True)
if config["make_plot"]:
if config["task"] == "regression":
# plot cost
make_cost_acc_plot(fold_data.training_cost,
fold_data.validation_cost,
fold_data.training_mse,
fold_data.validation_mse,
result_path + prefix)
pred_score = np.array(fold_data.prediction_data)
plot_r2(config,
fold_data.test_labels,
pred_score,
prefix=prefix)
elif config["task"] == "regression_gmfe":
# plot cost
make_cost_acc_plot(fold_data.training_cost,
fold_data.validation_cost,
fold_data.training_mse,
fold_data.validation_mse,
result_path + prefix)
pred_score = np.array(fold_data.prediction_data)
plot_r2(config,
fold_data.test_labels,
pred_score,
prefix=prefix)
else:
# plot cost
make_cost_acc_plot(fold_data.training_cost,
fold_data.validation_cost,
fold_data.training_acc,
fold_data.validation_acc,
result_path + prefix)
# plot AUC
pred_score = np.array(fold_data.prediction_data)
plot_auc(config,
fold_data.test_labels,
pred_score,
prefix=prefix)
def train(sess, config):
if config["validation_dataset"] is None:
all_data, train_data, valid_data, info = load_and_split_data(
config,
filename=config["dataset"],
valid_data_rate=config["validation_data_rate"])
else:
print("[INFO] training")
train_data, info = load_data(config, filename=config["dataset"])
print("[INFO] validation")
valid_data, valid_info = load_data(
config, filename=config["validation_dataset"])
info["graph_node_num"] = max(info["graph_node_num"],
valid_info["graph_node_num"])
info["graph_num"] = info["graph_num"] + valid_info["graph_num"]
# train model
graph_index_list = []
for i in range(info["graph_num"]):
graph_index_list.append([i, i])
info.graph_index_list = graph_index_list
info.pos_weight = get_pos_weight(train_data)
info.norm = get_norm(train_data)
print(f"pos_weight={info.pos_weight}")
print(f"norm={info.norm}")
model = CoreModel(sess,
config,
info,
construct_feed_callback=construct_feed)
load_model_py(model, config["model.py"])
vars_to_train = tf.trainable_variables()
for v in vars_to_train:
print(v)
# Training
start_t = time.time()
model.fit(train_data, valid_data)
train_time = time.time() - start_t
print(f"training time:{train_time}[sec]")
# Validation
start_t = time.time()
validation_cost, validation_accuracy, validation_prediction_data = model.pred_and_eval(
valid_data)
training_cost, training_accuracy, training_prediction_data = model.pred_and_eval(
train_data)
infer_time = time.time() - start_t
print(f"final cost(training ) = {training_cost}\n"
f"accuracy (training ) = {training_accuracy['accuracy']}\n"
f"final cost(validation) = {validation_cost}\n"
f"accuracy (validation) = {validation_accuracy['accuracy']}\n"
f"infer time:{infer_time}[sec]\n")
# Saving
if config["save_info_valid"] is not None:
result = {}
result["validation_cost"] = validation_cost
result["validation_accuracy"] = validation_accuracy["accuracy"]
result["train_time"] = train_time
result["infer_time"] = infer_time
save_path = config["save_info_valid"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print(f"[SAVE] {save_path}")
with open(save_path, "w") as fp:
json.dump(result, fp, indent=4)
if config["save_info_train"] is not None:
result = {}
result["test_cost"] = training_cost
result["test_accuracy"] = training_accuracy["accuracy"]
result["train_time"] = train_time
save_path = config["save_info_train"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print(f"[SAVE] {save_path}")
with open(save_path, "w") as fp:
json.dump(result, fp, indent=4, cls=NumPyArangeEncoder)
if "reconstruction_valid" in config:
filename = config["reconstruction_valid"]
print(os.path.dirname(filename))
os.makedirs(os.path.dirname(filename), exist_ok=True)
print(f"[SAVE] {filename}")
joblib.dump(validation_prediction_data, filename)
if "reconstruction_train" in config:
filename = config["reconstruction_train"]
os.makedirs(os.path.dirname(filename), exist_ok=True)
print(f"[SAVE] {filename}")
joblib.dump(training_prediction_data, filename)
def train(sess, config):
batch_size = config["batch_size"]
learning_rate = config["learning_rate"]
all_data, train_data, valid_data, info = load_and_split_data(
config,
filename=config["dataset"],
valid_data_rate=config["validation_data_rate"])
# train model
graph_index_list = []
for i in range(all_data.num):
graph_index_list.append([i, i])
info.graph_index_list = graph_index_list
info.pos_weight = get_pos_weight(train_data)
info.norm = get_norm(train_data)
print("pos_weight=", info.pos_weight)
print("norm=", info.pos_weight)
model = CoreModel(sess,
config,
info,
construct_feed_callback=construct_feed)
model.build(importlib.import_module(config["model.py"]))
vars_to_train = tf.trainable_variables()
for v in vars_to_train:
print(v)
# Training
start_t = time.time()
model.fit(train_data, valid_data)
train_time = time.time() - start_t
print("traing time:{0}".format(train_time) + "[sec]")
# Validation
start_t = time.time()
validation_cost, validation_accuracy, validation_prediction_data = model.pred_and_eval(
valid_data)
training_cost, training_accuracy, training_prediction_data = model.pred_and_eval(
train_data)
infer_time = time.time() - start_t
print("final cost(training ) =", training_cost)
print("accuracy (training ) =", training_accuracy["accuracy"])
print("final cost(validation) =", validation_cost)
print("accuracy (validation) =", validation_accuracy["accuracy"])
print("infer time:{0}".format(infer_time) + "[sec]")
# Saving
if config["save_info_valid"] is not None:
result = {}
result["validation_cost"] = validation_cost
result["validation_accuracy"] = validation_accuracy["accuracy"]
result["train_time"] = train_time
result["infer_time"] = infer_time
save_path = config["save_info_valid"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print("[SAVE] ", save_path)
fp = open(save_path, "w")
json.dump(result, fp, indent=4)
if config["save_info_train"] is not None:
result = {}
result["test_cost"] = training_cost
result["test_accuracy"] = training_accuracy["accuracy"]
result["train_time"] = train_time
save_path = config["save_info_train"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print("[SAVE] ", save_path)
fp = open(save_path, "w")
json.dump(result, fp, indent=4, cls=NumPyArangeEncoder)
if "reconstruction_valid" in config:
filename = config["reconstruction_valid"]
print(os.path.dirname(filename))
os.makedirs(os.path.dirname(filename), exist_ok=True)
print("[SAVE]", filename)
joblib.dump(validation_prediction_data, filename)
if "reconstruction_train" in config:
filename = config["reconstruction_train"]
os.makedirs(os.path.dirname(filename), exist_ok=True)
print("[SAVE]", filename)
joblib.dump(training_prediction_data, filename)
def infer(sess, graph, config):
from sklearn.metrics import roc_curve, auc, accuracy_score, precision_recall_fscore_support
batch_size = config["batch_size"]
model = importlib.import_module(config["model.py"])
dataset_filename = config["dataset"]
if "dataset_test" in config:
dataset_filename = config["dataset_test"]
all_data, info = load_data(config, filename=dataset_filename)
model = CoreModel(sess, config, info)
load_model_py(model, config["model.py"], is_train=False)
# Initialize session
saver = tf.train.Saver()
#sess.run(tf.global_variables_initializer())
print("[LOAD]", config["load_model"])
saver.restore(sess, config["load_model"])
# Validation
start_t = time.time()
test_cost, test_metrics, prediction_data = model.pred_and_eval(all_data)
infer_time = time.time() - start_t
print("final cost =", test_cost)
print("accuracy =", test_metrics["accuracy"])
print("infer time:{0}".format(infer_time) + "[sec]")
if config["save_info_test"] is not None:
result = {}
result["test_cost"] = test_cost
result["test_accuracy"] = test_metrics
result["infer_time"] = infer_time
##
pred_score = np.array(prediction_data)
if len(pred_score.shape) == 3: # multi-label-multi-task
# #data x # task x #class
# => this program supports only 2 labels
pred_score = pred_score[:, :, 1]
true_label = np.array(all_data.labels)
# #data x # task x #class
if len(pred_score.shape) == 1:
pred_score = pred_score[:, np.newaxis]
if len(true_label.shape) == 1:
true_label = true_label[:, np.newaxis]
v = []
for i in range(info.label_dim):
el = {}
if config["task"] == "regression":
el["r2"] = sklearn.metrics.r2_score(true_label[:, i],
pred_score[:, i])
el["mse"] = sklearn.metrics.mean_squared_error(
true_label[:, i], pred_score[:, i])
elif config["task"] == "regression_gmfe":
el["gmfe"] = np.exp(
np.mean(np.log(true_label[:, i] / pred_score[:, i])))
else:
pred = np.zeros(pred_score.shape)
pred[pred_score > 0.5] = 1
fpr, tpr, _ = roc_curve(true_label[:, i],
pred_score[:, i],
pos_label=1)
roc_auc = auc(fpr, tpr)
acc = accuracy_score(true_label[:, i], pred[:, i])
scores = precision_recall_fscore_support(true_label[:, i],
pred[:, i],
average='binary')
el["auc"] = roc_auc
el["acc"] = acc
el["pre"] = scores[0]
el["rec"] = scores[1]
el["f"] = scores[2]
el["sup"] = scores[3]
v.append(el)
result["test_metrics"] = el
##
save_path = config["save_info_test"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print("[SAVE] ", save_path)
fp = open(save_path, "w")
json.dump(result, fp, indent=4, cls=NumPyArangeEncoder)
if config["save_result_test"] is not None:
filename = config["save_result_test"]
save_prediction(filename, prediction_data)
if config["make_plot"]:
plot_auc(config, all_data.labels, np.array(prediction_data))
if "save_edge_result_test" in config and config[
"save_edge_result_test"] is not None:
output_data = model.output(all_data)
pred_score = np.array(prediction_data)
true_label = np.array(all_data.label_list)
test_idx = all_data.test_data_idx
score_list = []
print(true_label.shape)
for pair in true_label[0]:
i1, _, j1, i2, _, j2 = pair
s1 = pred_score[0, i1, j1]
s2 = pred_score[0, i2, j2]
score_list.append([s1, s2])
fold = {}
fold["output"] = output_data[0]
fold["score"] = np.array(score_list)
save_path = config["save_edge_result_test"]
os.makedirs(os.path.dirname(save_path), exist_ok=True)
print("[SAVE] ", save_path)
_, ext = os.path.splitext(save_path)
if ext == ".json":
fp = open(save_path, "w")
json.dump(fold, fp, indent=4, cls=NumPyArangeEncoder)
else:
joblib.dump(fold, save_path, compress=True)
