print("Training completed!")
os.makedirs("finetuning_bert")
model.save_pretrained("finetuning_bert")
tokenizer.save_pretrained("finetuning_bert")
#Evaulation
predictions = []
true_labels = []
model.eval()
for batch in validation_dataloader:
batch = tuple(t.to('cuda') for t in batch)
b_input_ids, b_input_mask, b_labels = batch
with torch.no_grad():
outputs = model(b_input_ids,
token_type_ids=None,
attention_mask=b_input_mask)
logits = outputs[0]
logits = logits.detach().cpu().numpy()
label_ids = b_labels.to('cpu').numpy()
predictions.append(logits)
true_labels.append(label_ids)
flat_predictions = [item for sublist in predictions for item in sublist]
flat_predictions = np.argmax(flat_predictions, axis=1).flatten()
flat_true_labels = [item for sublist in true_labels for item in sublist]
bert_evaluation_scores, bert_cm = evaluation.multilabel_evaluation(
flat_true_labels, flat_predictions, "SciBERT Embeddings Finetuning")
documentation_file_modelopt = open(
"classifier_optimization_finetuning_scibert.txt", "w+")
documentation_file_modelopt.write(bert_evaluation_scores)
documentation_file_modelopt.close()
"Random Undersampling")
sampling_strategies.append(triple_undersampled)
for sampling in sampling_strategies:
q_train_sample = sampling[0]
d_train_sample = sampling[1]
name = sampling[2]
documentation_file_modelopt.write(str(name) + "\n")
#Linear SVM model training and evaluation
print("SVM model evaluation")
classifier_svm = svm.LinearSVC()
classifier_svm.fit(np.asarray(q_train_sample), np.asarray(d_train_sample))
pred_svm = classifier_svm.predict(np.asarray(q_test))
#evaluate the model
svm_evaluation_scores, svm_cm = evaluation.multilabel_evaluation(
d_test, label_encoder.inverse_transform(pred_svm), "LinearSVM")
documentation_file_modelopt.write(svm_evaluation_scores)
# Random Forest: optimizing parameters with grid search
print("Random Forest model evaluation")
classifier_rf = RandomForestClassifier(class_weight='balanced',
max_depth=100)
classifier_rf.fit(np.asarray(q_train_sample), np.asarray(d_train_sample))
pred_rf = classifier_rf.predict(np.asarray(q_test))
#evaluate the model
rf_evaluation_scores, rf_cm = evaluation.multilabel_evaluation(
d_test, label_encoder.inverse_transform(pred_rf), "Random Forest")
documentation_file_modelopt.write(rf_evaluation_scores)
# Logistic Regression: optimizing parameters with grid search
print("Logistic Regression model evaluation")
}
cnn_scan = talos.Scan(x=X,
y=d_train_array,
model=cnn_optimization,
params=cnn_params,
experiment_name='CNN_Optimization',
round_limit=10,
fraction_limit=0.05)
cnn_analyze = talos.Analyze(cnn_scan)
documentation_file_parameteropt.write(
"CNN: Best parameters {}, reached score: {} \n".format(
cnn_analyze.best_params('accuracy', ['accuracy', 'loss', 'val_loss']),
cnn_analyze.high('accuracy')))
pred_cnn = talos.Predict(cnn_scan).predict(x_t, metric='val_f1score', asc=True)
#evaluate the model
cnn_evaluation_scores, cnn_cm = evaluation.multilabel_evaluation(
d_test_array, label_binarizer.inverse_transform(pred_cnn), "CNN")
documentation_file_modelopt.write(cnn_evaluation_scores)
#deploy best model
model_cnn = talos.Deploy(cnn_scan, "model_cnn_scibert", metric='val_accuracy')
#build LSTM model and evaluate the model
print("LSTM model evaluation")
def lstm_optimization(x_train, y_train, x_test, y_test, params):
"""Randomized search to optimize parameters of Neural Network."""
optimization_model = models.Sequential()
optimization_model.add(layers.LSTM(params['units'], return_sequences=True))
optimization_model.add(layers.LSTM(params['units'],
return_sequences=False))
optimization_model.add(layers.Dropout(0.5))
