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embedding_file = args.embedding_file
k_folds = list(map(int, args.k_folds.split(",")))
print("args is : {}".format(args))
print(
"Local devices are : {}, \n\n Available gpus are : {}".format(
device_lib.list_local_devices(), K.tensorflow_backend._get_available_gpus()
)
)
# prepare output path
if not os.path.exists(output_path):
os.makedirs(output_path, exist_ok=True)
# Get a crystal graph with cutoff radius A
cg = CrystalGraph(
bond_convertor=GaussianDistance(np.linspace(0, radius + 1, 100), 0.5),
cutoff=radius,
)
if graph_file is not None:
# load graph data
with gzip.open(graph_file, "rb") as f:
valid_graph_dict = pickle.load(f)
idx_list = list(range(len(valid_graph_dict)))
valid_idx_list = [
idx for idx, graph in valid_graph_dict.items() if graph is not None
]
else:
# load structure data
with gzip.open(args.input_file, "rb") as f:
df = pd.DataFrame(pickle.load(f))[["structure", prop_col]]
act=act,
is_classification=is_classification,
l2_coef=l2_coef,
dropout=dropout,
dropout_on_predict=dropout_on_predict)
# Compile the model with the optimizer
loss = 'binary_crossentropy' if is_classification else loss
opt_params = {'lr': lr}
if optimizer_kwargs is not None:
opt_params.update(optimizer_kwargs)
model.compile(Adam(**opt_params), loss, metrics=metrics)
if graph_converter is None:
graph_converter = CrystalGraph(cutoff=4, bond_converter=GaussianDistance(np.linspace(0, 5, 100), 0.5))
super().__init__(model=model, target_scaler=target_scaler, graph_converter=graph_converter)
act=act,
is_classification=is_classification,
l2_coef=l2_coef,
dropout=dropout,
dropout_on_predict=dropout_on_predict)
# Compile the model with the optimizer
loss = 'binary_crossentropy' if is_classification else loss
opt_params = {'lr': lr}
if optimizer_kwargs is not None:
opt_params.update(optimizer_kwargs)
model.compile(Adam(**opt_params), loss, metrics=metrics)
if graph_converter is None:
graph_converter = CrystalGraph(cutoff=4, bond_converter=GaussianDistance(np.linspace(0, 5, 100), 0.5))
super().__init__(model=model, target_scaler=target_scaler, graph_converter=graph_converter)