def test_saliency(self):
bcn = BaseConvNet(min_filters=4, filter_growth_rate=1.5, min_data_width=8,
dense_neurons=8, output_type="sigmoid")
bcn.build_network(self.x_shape, 1)
sal = bcn.saliency(self.x_ds)
assert sal.max() > 0
self.assertListEqual(list(sal.shape[1:]), list(self.x.shape))
def test_network_build(self):
bcn = BaseConvNet(min_filters=4, filter_growth_rate=1.5, min_data_width=8,
dense_neurons=4, output_type="sigmoid")
bcn.build_network(self.x_shape, 1)
assert bcn.model_.layers[1].output.shape[-1] == bcn.min_filters
assert bcn.model_.layers[-6].output.shape[1] == bcn.min_data_width
return
def main():
# Parse arguments
parser = argparse.ArgumentParser()
parser.add_argument("config", help="Name of the config file.")
parser.add_argument("-t",
"--train",
action="store_true",
help="Run neural network training.")
parser.add_argument("-i",
"--interp",
action="store_true",
help="Run interpretation.")
parser.add_argument("-p",
"--plot",
action="store_true",
help="Plot interpretation results.")
args = parser.parse_args()
if not exists(args.config):
raise FileNotFoundError(args.config + " not found.")
with open(args.config, "r") as config_file:
config = yaml.load(config_file, Loader=yaml.Loader)
# Load training data
print(
f"Loading training data period: {config['train_start_date']} to {config['train_end_date']}"
)
input = {}
output = {}
out_max = {}
labels = {}
meta = {}
meta_df = {}
input_combined = {}
input_scaled = {}
scale_values = {}
predictions = {}
modes = ["train", "val", "test"]
# Load training, validation, and testing data
for mode in modes:
input[mode], output[mode], meta[mode] = load_patch_files(
config[mode + "_start_date"], config[mode + "_end_date"],
config["data_path"], config["input_variables"],
config["output_variables"], config["meta_variables"],
config["patch_radius"])
input_combined[mode] = combine_patch_data(input[mode],
config["input_variables"])
if mode == "train":
input_scaled[mode], scale_values[mode] = min_max_scale(
input_combined[mode])
else:
input_scaled[mode], scale_values[mode] = min_max_scale(
input_combined[mode], scale_values["train"])
out_max[mode] = storm_max_value(
output[mode][config["output_variables"][0]], meta[mode]["masks"])
meta_df[mode] = get_meta_scalars(meta[mode])
print(meta_df[mode].columns)
if config["classifier"]:
labels[mode] = np.where(
out_max[mode] >= config["classifier_threshold"], 1, 0)
else:
labels[mode] = out_max[mode]
if not exists(config["out_path"]):
makedirs(config["out_path"])
scale_values["train"].to_csv(join(config["out_path"], "scale_values.csv"),
index_label="variable")
if "get_visible_devices" in dir(tf.config.experimental):
gpus = tf.config.experimental.get_visible_devices("GPU")
else:
gpus = tf.config.get_visible_devices("GPU")
for device in gpus:
tf.config.experimental.set_memory_growth(device, True)
models = {}
neuron_activations = {}
neuron_scores = {}
saliency = {}
if args.train:
print("Begin model training")
for mode in modes:
predictions[mode] = pd.DataFrame(0,
index=meta_df[mode].index,
columns=list(
config["models"].keys()))
predictions[mode] = pd.merge(meta_df[mode],
predictions[mode],
left_index=True,
right_index=True)
for model_name, model_config in config["models"].items():
model_out_path = join(config["out_path"], model_name)
if not exists(model_out_path):
makedirs(model_out_path)
scale_values["train"].to_csv(join(
model_out_path, "scale_values_" + model_name + ".csv"),
index_label="variable")
models[model_name] = BaseConvNet(**model_config)
models[model_name].fit(input_scaled["train"].values,
labels["train"],
val_x=input_scaled["val"].values,
val_y=labels["val"])
models[model_name].save_model(model_out_path, model_name)
for mode in modes:
predictions[mode].loc[:,
model_name] = models[model_name].predict(
input_scaled[mode].values)
for mode in modes:
predictions[mode].to_csv(join(config["out_path"],
f"predictions_{mode}.csv"),
index_label="index")
print("Calculate metrics")
if config["classifier"]:
model_scores = classifier_metrics(
labels["test"],
predictions["test"][list(config["models"].keys())])
model_scores.to_csv(join(config["out_path"],
"model_test_scores.csv"),
index_label="model_name")
if args.interp:
for model_name, model_config in config["models"].items():
if model_name not in models.keys():
model_out_path = join(config["out_path"], model_name)
models[model_name] = load_conv_net(model_out_path, model_name)
neuron_columns = [
f"neuron_{n:03d}"
for n in range(models[model_name].dense_neurons)
]
neuron_activations[model_name] = {}
neuron_scores[model_name] = pd.DataFrame(0,
columns=neuron_columns,
index=modes)
saliency[model_name] = {}
for mode in modes:
neuron_activations[model_name][mode] = pd.merge(
meta_df[mode],
pd.DataFrame(0,
columns=neuron_columns,
index=meta_df[mode].index),
left_index=True,
right_index=True)
neuron_activations[model_name][
mode].loc[:, neuron_columns] = models[
model_name].output_hidden_layer(
input_scaled[mode].values)
neuron_activations[model_name][mode].to_csv(
join(config["out_path"],
f"neuron_activations_{model_name}_{mode}.csv"),
index_label="index")
saliency[model_name][mode] = models[model_name].saliency(
input_scaled[mode])
saliency[model_name][mode].to_netcdf(join(
config["out_path"],
f"neuron_saliency_{model_name}_{mode}.nc"),
encoding={
"saliency": {
"zlib": True,
"complevel": 4,
"shuffle": True
}
})
if config["classifier"]:
neuron_scores[model_name].loc[mode] = score_neurons(
labels[mode], neuron_activations[model_name][mode]
[neuron_columns].values)
else:
neuron_scores[model_name].loc[mode] = score_neurons(
labels[mode],
neuron_activations[model_name][mode]
[neuron_columns].values,
metric="r")
neuron_scores[model_name].to_csv(join(
config["out_path"], f"neuron_scores_{model_name}.csv"),
index_label="mode")
if args.plot:
for model_name, model_config in config["models"].items():
if model_name not in models.keys():
model_out_path = join(config["out_path"], model_name)
models[model_name] = load_conv_net(model_out_path, model_name)
neuron_activations[model_name] = {}
neuron_scores[model_name] = pd.read_csv(join(
config["out_path"], f"neuron_scores_{model_name}.csv"),
index_col="mode")
saliency[model_name] = {}
for mode in modes:
if mode not in neuron_activations[model_name].keys():
neuron_activations[model_name][mode] = pd.read_csv(
join(config["out_path"],
f"neuron_activations_{model_name}_{mode}.csv"),
index_col="index")
saliency[model_name][mode] = xr.open_dataarray(
join(config["out_path"],
f"neuron_saliency_{model_name}_{mode}.nc"))
for variable_name in config["input_variables"]:
plot_neuron_composites(
config["out_path"], model_name + "_" + mode,
input_combined[mode],
neuron_activations[model_name][mode].values,
neuron_scores[model_name].loc[mode].values,
variable_name)
plot_saliency_composites(
config["out_path"], model_name + "_" + mode,
saliency[model_name][mode],
neuron_activations[model_name][mode].values,
neuron_scores[model_name].loc[mode].values,
variable_name)
return
def main():
# Parse arguments
parser = argparse.ArgumentParser()
parser.add_argument("config", help="Name of the config file.")
parser.add_argument("-t", "--train", action="store_true", help="Run neural network training.")
parser.add_argument("-i", "--interp", action="store_true", help="Run interpretation.")
parser.add_argument("-u", "--train_gmm", action="store_true", help="Run unsupervised model training.")
parser.add_argument("-p", "--plot", action="store_true", help="Plot interpretation results.")
parser.add_argument("-p2", "--plot2", action="store_true", help="Plot additional interpretation results.")
args = parser.parse_args()
if not exists(args.config):
raise FileNotFoundError(args.config + " not found.")
with open(args.config, "r") as config_file:
config = yaml.load(config_file, Loader=yaml.Loader)
np.random.seed(config["random_seed"])
random.seed(config["random_seed"])
tf.random.set_seed(config["random_seed"])
# Load training data
print(f"Loading training data period: {config['train_start_date']} to {config['train_end_date']}")
data_input = {}
output = {}
out_max = {}
labels = {}
meta = {}
meta_df = {}
input_combined = {}
input_scaled = {}
scale_values = {}
predictions = {}
if exists('mask') in config:
mask = config['mask']
else:
mask = False
modes = ["train", "val", "test"]
# Load training, validation, and testing data
for mode in modes:
data_input[mode], output[mode], meta[mode] = load_patch_files(config[mode + "_start_date"],
config[mode + "_end_date"],
None,
config["data_path"],
config["input_variables"],
config["output_variables"],
config["meta_variables"],
config["patch_radius"],
mask)
input_combined[mode] = combine_patch_data(data_input[mode], config["input_variables"])
if mode == "train":
input_scaled[mode], scale_values[mode] = min_max_scale(input_combined[mode])
else:
input_scaled[mode], scale_values[mode] = min_max_scale(input_combined[mode], scale_values["train"])
out_max[mode] = storm_max_value(output[mode][config["output_variables"][0]], meta[mode]["masks"])
meta_df[mode] = get_meta_scalars(meta[mode])
print(meta_df[mode].columns)
if config["classifier"]:
labels[mode] = np.where(out_max[mode] >= config["classifier_threshold"], 1, 0)
else:
labels[mode] = out_max[mode]
del data_input, out_max
for folder in ['models', 'plots', 'data', 'metrics', 'labels']:
makedirs(join(config["out_path"], folder), exist_ok=True)
with open(join(config['out_path'], 'full_config.yml'), "w") as config_file:
yaml.dump(config, config_file)
if "get_visible_devices" in dir(tf.config.experimental):
gpus = tf.config.experimental.get_visible_devices("GPU")
else:
gpus = tf.config.get_visible_devices("GPU")
for device in gpus:
tf.config.experimental.set_memory_growth(device, True)
models = {}
neuron_activations = {}
neuron_scores = {}
saliency = {}
if args.train:
print("Begin model training")
for mode in modes:
predictions[mode] = pd.DataFrame(0, index=meta_df[mode].index,
columns=list(config["models"].keys()))
predictions[mode] = pd.merge(meta_df[mode], predictions[mode], left_index=True, right_index=True)
for model_name, model_config in config["models"].items():
model_out_path = join(config["out_path"], "models", model_name)
if not exists(model_out_path):
makedirs(model_out_path)
scale_values["train"].to_csv(join(model_out_path, "scale_values_" + model_name + ".csv"),
index_label="variable")
models[model_name] = BaseConvNet(**model_config)
models[model_name].fit(input_scaled["train"].values, labels["train"],
val_x=input_scaled["val"].values, val_y=labels["val"])
models[model_name].save_model(model_out_path, model_name)
for mode in modes:
predictions[mode].loc[:, model_name] = models[model_name].predict(input_scaled[mode].values)
for mode in modes:
predictions[mode].to_csv(
join(config["out_path"], "metrics", f"predictions_{mode}.csv"), index_label="index")
print("Calculate metrics")
if config["classifier"]:
model_scores = classifier_metrics(labels["test"], predictions["test"][list(config["models"].keys())])
model_scores.to_csv(join(config["out_path"], "metrics", "model_test_scores.csv"), index_label="model_name")
if args.interp:
for model_name, model_config in config["models"].items():
if model_name not in models.keys():
model_out_path = join(config["out_path"], "models", model_name)
models[model_name] = load_conv_net(model_out_path, model_name)
neuron_columns = [f"neuron_{n:03d}" for n in range(models[model_name].dense_neurons)]
neuron_activations[model_name] = {}
neuron_scores[model_name] = pd.DataFrame(0, columns=neuron_columns, index=modes)
saliency[model_name] = {}
for mode in modes:
neuron_activations[model_name][mode] = pd.merge(meta_df[mode], pd.DataFrame(0, columns=neuron_columns,
index=meta_df[mode].index),
left_index=True, right_index=True)
neuron_activations[model_name][mode].loc[:, neuron_columns] = models[model_name].output_hidden_layer(
input_scaled[mode].values)
neuron_activations[model_name][mode].to_csv(join(config["out_path"], "data",
f"neuron_activations_{model_name}_{mode}.csv"),
index_label="index")
saliency[model_name][mode] = models[model_name].saliency(input_scaled[mode])
saliency[model_name][mode].to_netcdf(join(config["out_path"], "data",
f"neuron_saliency_{model_name}_{mode}.nc"),
encoding={"saliency": {"zlib": True,
"complevel": 4,
"shuffle": True,
"least_significant_digit": 3}})
if config["classifier"]:
neuron_scores[model_name].loc[mode] = score_neurons(labels[mode],
neuron_activations[model_name][mode][
neuron_columns].values)
else:
neuron_scores[model_name].loc[mode] = score_neurons(labels[mode],
neuron_activations[model_name][mode][
neuron_columns].values,
metric="r")
del saliency[model_name][mode]
neuron_scores[model_name].to_csv(join(config["out_path"], "metrics",
f"neuron_scores_{model_name}.csv"), index_label="mode")
del models[model_name], neuron_activations[model_name]
if args.train_gmm:
print('Begin Training Gaussian Mixture Model(s)')
cluster_df = {}
GMM = {}
for model_name, model_config in config["models"].items():
for mode in modes:
neuron_activations[model_name] = {}
neuron_activations[model_name][mode] = pd.read_csv(join(config["out_path"], "data",
f"neuron_activations_{model_name}_{mode}.csv"))
X = neuron_activations[model_name][mode].loc[
:, neuron_activations[model_name][mode].columns.str.contains('neuron')]
for GMM_mod_name, GMM_config in config["GMM_models"].items():
if mode == "train":
GMM[GMM_mod_name] = GaussianMixture(**GMM_config).fit(X)
cluster_df[GMM_mod_name] = {}
cluster_df[GMM_mod_name][mode] = pd.DataFrame(GMM[GMM_mod_name].predict_proba(X),
columns=[f"cluster {i}" for i in range(
GMM_config['n_components'])])
cluster_df[GMM_mod_name][mode]['label prob'] = cluster_df[GMM_mod_name][mode].max(axis=1)
cluster_df[GMM_mod_name][mode]['label'] = GMM[GMM_mod_name].predict(X)
neuron_activations[model_name][mode].merge(
cluster_df[GMM_mod_name][mode], right_index=True, left_index=True).to_csv(join(
config["out_path"], "data", f"{model_name}_{GMM_mod_name}_{mode}_clusters.csv"), index=False)
joblib.dump(GMM[GMM_mod_name], join(
config["out_path"], "models", f'{model_name}_{GMM_mod_name}.mod'))
if args.plot:
print("Begin plotting")
if "plot_kwargs" not in config.keys():
config["plot_kwargs"] = {}
for model_name, model_config in config["models"].items():
print(model_name)
if model_name not in models.keys():
model_out_path = join(config["out_path"], "models", model_name)
models[model_name] = load_conv_net(model_out_path, model_name)
neuron_activations[model_name] = {}
neuron_scores[model_name] = pd.read_csv(join(config["out_path"], "metrics",
f"neuron_scores_{model_name}.csv"), index_col="mode")
saliency[model_name] = {}
for mode in modes:
print(mode)
if mode not in neuron_activations[model_name].keys():
neuron_activations[model_name][mode] = pd.read_csv(join(config["out_path"], "data",
f"neuron_activations_{model_name}_{mode}.csv"),
index_col="index")
saliency[model_name][mode] = xr.open_dataarray(join(config["out_path"], "data",
f"neuron_saliency_{model_name}_{mode}.nc"))
for variable_name in config["input_variables"]:
print(variable_name)
if variable_name not in config["plot_kwargs"].keys():
plot_kwargs = None
else:
plot_kwargs = config["plot_kwargs"][variable_name]
plot_out_path = join(config["out_path"], "plots")
plot_neuron_composites(plot_out_path,
model_name + "_" + mode,
input_combined[mode],
neuron_activations[model_name][mode].values,
neuron_scores[model_name].loc[mode].values,
variable_name, plot_kwargs=plot_kwargs)
plot_saliency_composites(plot_out_path,
model_name + "_" + mode,
saliency[model_name][mode], neuron_activations[model_name][mode].values,
neuron_scores[model_name].loc[mode].values,
variable_name)
plot_top_activations(plot_out_path,
model_name + "_" + mode,
input_combined[mode], meta_df[mode],
neuron_activations[model_name][mode],
neuron_scores[model_name].loc[mode].values,
saliency[model_name][mode],
variable_name, plot_kwargs=plot_kwargs)
del saliency[model_name][mode]
if args.plot2:
print("Additional Plotting...")
for model_name in config["models"].keys():
for mode in ["val"]:
for GMM_mod_name, GMM_config in config["GMM_models"].items():
plot_out_path = join(config["out_path"], "plots", model_name, GMM_mod_name)
if not exists(plot_out_path):
makedirs(plot_out_path, exist_ok=True)
cluster_df = pd.read_csv(join(
config["out_path"], "data", f"{model_name}_{GMM_mod_name}_{mode}_clusters.csv"))
plot_prob_dist(cluster_df, plot_out_path, GMM_mod_name, GMM_config["n_components"])
plot_prob_cdf(cluster_df, plot_out_path, GMM_mod_name, GMM_config["n_components"])
cape_shear_modes(cluster_df, plot_out_path, config["data_path"], mode, model_name,
gmm_name=GMM_mod_name, cluster=True, num_storms=1000)
spatial_neuron_activations(cluster_df, plot_out_path, mode, model_name,
gmm_name=GMM_mod_name, cluster=True)
diurnal_neuron_activations(cluster_df, plot_out_path, mode, model_name,
gmm_name=GMM_mod_name, cluster=True)
for prob_type in ['highest', 'lowest']:
plot_storm_clusters(config['data_path'], plot_out_path, cluster_df,
n_storms=25,
patch_radius=config["patch_radius"],
prob_type=prob_type,
seed=config["random_seed"])
return