def general_training_target_test(data_path,
model_id,
data_id,
output,
n_patients,
target_icu=None):
"""
Train on all ICU and evaluate on test ICU
"""
auc = []
try:
print("\n\n\n=== General training ===")
folds = load_data(data_path, data_id, [1, 2, 3, 4], n_patients)
for fold, (x_train, y_train, x_val, y_val, x_test, y_test,
icu_ids_train, icu_ids_val,
icu_ids_test) in enumerate(folds):
layers, freezable = models.create_freezable_layers(
model_id, x_train.shape[1], x_train.shape[2])
checkpoint, early_stopping, model = models.create_model(
"mt-" + model_id + "-" + data_id, layers)
model.fit(x_train,
y_train,
epochs=n_epochs,
validation_data=(x_val, y_val),
callbacks=[early_stopping, checkpoint])
icu_test_list = [
target_icu
] if target_icu is not None else np.unique(icu_ids_test)
icu_auc = []
score, general_score = models.evaluate_model(
"mt-" + model_id + "-" + data_id, x_test, y_test)
print("\n\n=== General Score - \tFold %d - \tAUC %f" %
(fold, general_score))
for test_icu in icu_test_list:
score, auc_score = models.evaluate_model(
"mt-" + model_id + "-" + data_id,
x_test[icu_ids_test == test_icu],
y_test[icu_ids_test == test_icu])
icu_auc.append(auc_score)
print("\n=== ICU Test %d - \tFold %d - \tAUC %f" %
(test_icu, fold, auc_score))
output.write(
"Mixed-%d,%d,%d,%d,%f,%f,%f,%f,%f,%f\n" %
(test_icu, fold, np.count_nonzero(y_test == 0),
np.count_nonzero(y_test == 1), score[0], score[1],
score[2], score[3], score[4], auc_score))
auc.append(icu_auc)
except Exception as e:
print(e)
avg_auc = np.array(auc).mean(axis=0).tolist()
return avg_auc
def mixed(model_id, data_id, output, n_patients, feature_sequence):
folds = load_data(data_id, [1, 2, 3, 4], n_patients, feature_sequence)
for fold, (x_train, y_train, x_val, y_val, x_test, y_test, icu_ids_train,
icu_ids_val, icu_ids_test) in enumerate(folds):
layers, freezable = models.create_freezable_layers(
model_id, x_train.shape[1], x_train.shape[2])
checkpoint, early_stopping, model = models.create_model(
"mt-" + model_id + "-" + data_id, layers)
model.fit(x_train,
y_train,
epochs=n_epochs,
validation_data=(x_val, y_val),
callbacks=[early_stopping, checkpoint])
score, auc_score = models.evaluate_model(
"mt-" + model_id + "-" + data_id, x_test, y_test)
print("ALL " + "," + str(auc_score))
output.write(str(fold) + "," + str(auc_score))
for test_icu in np.unique(icu_ids_test):
score, auc_score = models.evaluate_model(
"mt-" + model_id + "-" + data_id,
x_test[icu_ids_test == test_icu],
y_test[icu_ids_test == test_icu])
print("ICU " + str(test_icu) + "," + str(auc_score))
output.write("," + str(auc_score))
output.write("\n")
def test_model(model, test_data, transformation_type=TRANSFORMATION.clean):
X, Y = test_data
print('Transforming test data set...')
X = transform(X, transformation_type)
print('Testing model [{}]...'.format(transformation_type))
models.evaluate_model(model, X, Y)
del X, Y
def train_on_target(data_path, model_id, data_id, output, n_patients):
"""
Train and evaluate only on target ICU
"""
auc = []
try:
icu_types = [1, 2, 3, 4]
for held_out_icu in icu_types:
print("=== Target: " + str(held_out_icu) + " ===")
folds = load_data(data_path, data_id, [held_out_icu], n_patients)
fold_auc = []
for fold, (x_train, y_train, x_val, y_val, x_test, y_test,
icu_ids_train, icu_ids_val,
icu_ids_test) in enumerate(folds):
layers, freezable = models.create_freezable_layers(
model_id, x_train.shape[1], x_train.shape[2])
print("=== Train on Target ===")
checkpoint, early_stopping, model = models.create_model(
"fc-" + model_id + "-" + data_id + "-" + str(held_out_icu),
layers)
model.fit(x_train,
y_train,
epochs=n_epochs,
validation_data=(x_val, y_val),
callbacks=[early_stopping, checkpoint])
score, auc_score = models.evaluate_model(
"fc-" + model_id + "-" + data_id + "-" + str(held_out_icu),
x_test, y_test)
fold_auc.append(auc_score)
print("=== Fold: " + str(fold) + ",Loss: " + str(score[0]) +
",Acc: " + str(score[1]) + ",Prec: " + str(score[2]) +
",Rec: " + str(score[3]) + ",F1: " + str(score[4]) +
",AUC: " + str(auc_score) + " ====")
output.write(
"Target-%d,%d,%d,%d,%f,%f,%f,%f,%f,%f\n" %
(held_out_icu, fold, np.count_nonzero(y_test == 0),
np.count_nonzero(y_test == 1), score[0], score[1],
score[2], score[3], score[4], auc_score))
auc.append(fold_auc)
except Exception as e:
print(e)
avg_auc = np.array(auc).mean(axis=1).tolist()
return avg_auc
def general_training(data_path, model_id, data_id, output, n_patients):
"""
Train and evaluate on all ICU
"""
auc = []
try:
print("=== General training and testing ===")
folds = load_data(data_path, data_id, [1, 2, 3, 4], n_patients)
for fold, (x_train, y_train, x_val, y_val, x_test, y_test,
icu_ids_train, icu_ids_val,
icu_ids_test) in enumerate(folds):
layers, freezable = models.create_freezable_layers(
model_id, x_train.shape[1], x_train.shape[2])
checkpoint, early_stopping, model = models.create_model(
"mtt-" + model_id + "-" + data_id, layers)
model.fit(x_train,
y_train,
epochs=n_epochs,
validation_data=(x_val, y_val),
callbacks=[early_stopping, checkpoint])
score, auc_score = models.evaluate_model(
"mtt-" + model_id + "-" + data_id, x_test, y_test)
auc.append(auc_score)
print("=== General Test, Fold: " + str(fold) + ",Loss: " +
str(score[0]) + ",Acc: " + str(score[1]) + ",Prec: " +
str(score[2]) + ",Rec: " + str(score[3]) + ",F1: " +
str(score[4]) + ",AUC: " + str(auc_score) + " ====")
output.write("General-Test-%d,%d,%d,%f,%f,%f,%f,%f,%f\n" %
(fold, np.count_nonzero(y_test == 0),
np.count_nonzero(y_test == 1), score[0], score[1],
score[2], score[3], score[4], auc_score))
except Exception as e:
print(e)
avg_auc = np.array(auc).mean().tolist()
return avg_auc
def train_pipeline(training_pipeline_params: TrainingPipelineParams):
logger.info(f"Start training with params: {training_pipeline_params}")
load_data(training_pipeline_params.input_data_path,
training_pipeline_params.input_data_url)
data = read_data(training_pipeline_params.input_data_path)
logger.info(f"Raw data shape: {data.shape}")
train_df, val_df = split_train_val_data(
data, training_pipeline_params.splitting_params)
logger.info(f"Train df shape: {train_df.shape}")
logger.info(f"Val df shape: {val_df.shape}")
pipeline = build_transformer(training_pipeline_params.feature_params)
pipeline.fit(train_df)
logger.info(f"Transform fitted.")
train_features = make_features(pipeline, train_df)
train_target = extract_target(train_df,
training_pipeline_params.feature_params)
logger.info(f"Train features shape: {train_features.shape}")
val_features = make_features(pipeline, val_df)
val_target = extract_target(val_df,
training_pipeline_params.feature_params)
logger.info(f"Val features shape: {train_features.shape}")
model = get_model(training_pipeline_params.train_params)
model = train_model(train_features, train_target, model)
logger.info(f"Model trained.")
predictions = predict_model(val_features, model)
metrics = evaluate_model(predictions, val_target)
path_to_model = save_artifacts(metrics, model, pipeline,
training_pipeline_params)
return path_to_model, metrics
train_list, val_list, test_list, model_type, config_dict)
test_loader = loader_dict['test']
if ablate == "F":
mask = np.isin(qty_full, force_features, invert=False)
test_loader.dataset.mask_labels(mask)
if ablate == "P":
mask = np.isin(qty_full, pos_features, invert=False)
test_loader.dataset.mask_labels(mask)
if use_predlist:
predictions = predlist[i]
else:
#plt.close('all')
predictions = mdl.evaluate_model(model,
test_loader,
model_type=model_type,
encode=encode)
predictions_list.append(predictions)
np.savetxt('encodings_031621/encode_' + str(i + 1) + '.txt',
predictions) # uncomment to save encodings.
else:
for i, (test, condition) in enumerate(
zip(test_list_full, condition_list), 0):
test_list = [test]
loader_dict, loader_sizes = dat.init_dataset(
train_list, val_list, test_list, model_type, config_dict)
test_loader = loader_dict['test']
dataset_mean = np.loadtxt('train_dataset_mean.dat')
dataset_stdev = np.loadtxt('train_dataset_sd.dat')
'crop_list': None,
'trans_function': None
}
loader_dict, loader_sizes = dat.init_dataset(train_list, val_list, test_list,
model_type, config_dict)
test_loader = loader_dict["test"]
test_loader.dataset.mean = mean1
test_loader.dataset.stdev = std1
test_loader.dataset.label_array = test_loader.dataset.raw_label_array
test_loader.dataset.normalize_state(mean1, std1)
model = mdl.StateModel(54, 3)
model.load_state_dict(torch.load("best_modelweights_S_PSM1.dat"))
predictions1 = mdl.evaluate_model(model, test_loader, model_type=model_type)
np.savetxt("dual_PSM1_1.pred", predictions1)
#%% Do this for PSM2
file_dir = '../experiment_data' # define the file directory for dataset
model_type = "S"
train_list = [1, 3, 5, 7, 8, 10, 12, 14, 15, 17, 19, 21]
val_list = [1]
test_list = [1]
config_dict = {
'file_dir': file_dir,
'include_torque': False,
'spatial_forces': False,
'custom_state': None,
def domain_adaptation(data_path,
model_id,
data_id,
output,
n_patients,
shuffle,
use_target,
target_icu=None):
"""
Train on all ICU, fine tunning and evaluate on target ICU
"""
auc = []
try:
icu_types = [1, 2, 3, 4]
target_icu_list = [target_icu] if target_icu is not None else icu_types
for held_out_icu in target_icu_list:
icus = list(icu_types)
if not use_target:
icus.remove(held_out_icu)
folds = load_data(data_path, data_id, icus, n_patients)
icu_folds = load_data(data_path, data_id, [held_out_icu],
n_patients)
model_name = "ft-" + model_id + "-" + data_id + "-" + str(
held_out_icu)
fold_auc = []
for fold in range(k_fold):
x_train, y_train, x_val, y_val, x_test, y_test, icu_ids_train, icu_ids_val, icu_ids_test = folds[
fold]
print("=== Held out: " + str(held_out_icu) + " ===")
layers, freezable = models.create_freezable_layers(
model_id, x_train.shape[1], x_train.shape[2])
print("=== General training ===")
checkpoint, early_stopping, model = models.create_model(
model_name, layers)
model.fit(x_train,
y_train,
epochs=n_epochs,
validation_data=(x_val, y_val),
callbacks=[early_stopping, checkpoint])
if use_target:
score, auc_score_gt = models.evaluate_model(
model_name, x_test[icu_ids_test == held_out_icu],
y_test[icu_ids_test == held_out_icu])
else:
score, auc_score_gt = models.evaluate_model(
model_name, x_test, y_test)
print("=== Fine tuning ===")
model = models.get_model(model_name)
# layers = model.layers
x_icu_train, y_icu_train, x_val, y_val, x_icu_test, y_icu_test, icu_ids_train, icu_ids_val, icu_ids_test = icu_folds[
fold]
checkpoint, early_stopping, new_model = models.create_model(
model_name, model.layers, freezable, shuffle)
new_model.fit(x_icu_train,
y_icu_train,
epochs=n_epochs,
validation_data=(x_val, y_val),
callbacks=[early_stopping, checkpoint])
score, auc_score = models.evaluate_model(
model_name, x_icu_test, y_icu_test)
fold_auc.append([auc_score_gt, auc_score])
print("\n=== ICU %d - \tFold %d - \tAUC GT %f - \tAUC FT %f" %
(held_out_icu, fold, auc_score_gt, auc_score))
y_zero_count = np.count_nonzero(y_icu_test == 0)
y_one_count = np.count_nonzero(y_icu_test == 1)
output.write("DA-%d-%s-%s,%d,%d,%d,%f,%f,%f,%f,%f,%f\n" %
(held_out_icu, shuffle, use_target, fold,
y_zero_count, y_one_count, score[0], score[1],
score[2], score[3], score[4], auc_score))
auc.append(fold_auc)
except Exception as e:
print(e)
avg_auc = np.array(auc).mean(axis=1)
auc_df = pd.DataFrame(avg_auc.mean(axis=1))
print(auc_df)
return avg_auc.tolist()
def run_ablations(model, num_ablations):
'''set up some persistent tracking variables'''
remove_features = [] # list of features we are removing
metrics_list = [] # list storing dictionary of performance metrics
# feature indexes
full_state_index = np.arange(7, 61)
input_state = 54
# create loss function
criterion = nn.MSELoss(reduction='sum')
# define optimization method
optimizer = opt.Adam(model.parameters(), lr=0.01)
param_count = []
param_count.append(count_params(model))
current_feature_list = np.array(qty)
# create the dataloader
dataloaders, dataset_sizes = dat.init_dataset(train_list, val_list,
val_list, model_type,
config_dict)
print('evaluating full model predictions...')
predictions = mdl.evaluate_model(model,
dataloaders['test'],
model_type=model_type,
no_pbar=True)
# compute the loss statistics
print('computing full model performance metrics...')
metrics = model_eval.compute_loss_metrics(
predictions, dataloaders['test'].dataset.label_array[:, 1:4])
metrics_list.append(metrics)
print('Performance Summary of Full Model:')
print(metrics)
print('Running ablation study on model type:' + model_type)
for iteration in range(num_ablations):
print('-' * 10)
print('Begin ablation run: {}/{}'.format(iteration + 1, num_ablations))
print('-' * 10)
# compute the backprop values:
gbp_data = model_eval.compute_GBP(model,
dataloaders['test'],
num_state_inputs=input_state,
model_type=model_type,
no_pbar=True)
# evaluate means
df_gbp_means = model_eval.compute_and_plot_gbp(gbp_data,
current_feature_list,
True,
suppress_plots=True)
# group by feature type and rank by value
df_gbp_means = df_gbp_means.groupby('feature').mean().sort_values(
by='gbp', ascending=False).reset_index()
# get top ranking value and append to removal list
feature_to_remove = df_gbp_means.iloc[0, 0]
print("removing " + feature_to_remove + "...")
remove_features.append(feature_to_remove)
# create the mask
mask = np.isin(qty, remove_features, invert=True)
# mask the full state vector in config_dict global variable
config_dict['custom_state'] = full_state_index[mask]
current_feature_list = np.array(qty)[
mask] #update the current feature list
# decrease the input dimension of the model by one
input_state = input_state - 1
# redefine the models
print('redefining model with input state dims: {}'.format(input_state))
if model_type == "VS":
model = mdl.StateVisionModel(30,
input_state,
3,
feature_extract=feat_extract)
elif model_type == "S":
model = mdl.StateModel(input_state, 3)
# recalculate the number of parameters
param_count.append(count_params(model))
# redefine the optimizer
optimizer = opt.Adam(model.parameters(), lr=0.01)
# redefine the dataloader
dataloaders, dataset_sizes = dat.init_dataset(train_list, val_list,
val_list, model_type,
config_dict)
# retrain the model
model, train_history, val_history = mdl.train_model(
model,
criterion,
optimizer,
dataloaders,
dataset_sizes,
num_epochs=50,
model_type=model_type,
weight_file=weight_file,
no_pbar=True)
print('retraining completed')
# do inference
print('evaluating model predictions...')
predictions = mdl.evaluate_model(model,
dataloaders['test'],
model_type=model_type,
no_pbar=True)
# compute the loss statistics
print('computing performance metrics...')
metrics = model_eval.compute_loss_metrics(
predictions, dataloaders['test'].dataset.label_array[:, 1:4])
metrics_list.append(metrics)
print('Performance Summary:')
print(metrics)
return remove_features, param_count, metrics_list