Index

B

BayesianOptimizer (class in parrot.bayesian_optimization) biophysics() (in module parrot.encode_sequence)

BRNN_MtM (class in parrot.brnn_architecture) BRNN_MtO (class in parrot.brnn_architecture)

C

compute_cv_loss() (parrot.bayesian_optimization.BayesianOptimizer method)

confusion_matrix() (in module parrot.brnn_plot)

D

decode() (parrot.encode_sequence.UserEncoder method)

E

encode() (parrot.encode_sequence.UserEncoder method)

eval_cv_brnns() (parrot.bayesian_optimization.BayesianOptimizer method)

F

forward() (parrot.brnn_architecture.BRNN_MtM method) (parrot.brnn_architecture.BRNN_MtO method)

I

initial_search() (parrot.bayesian_optimization.BayesianOptimizer method)

M

module parrot.bayesian_optimization parrot.brnn_architecture parrot.brnn_plot parrot.encode_sequence parrot.process_input_data parrot.py_predictor parrot.train_network

O

one_hot() (in module parrot.encode_sequence)

optimize() (parrot.bayesian_optimization.BayesianOptimizer method) output_predictions_to_file() (in module parrot.brnn_plot)

P

parrot.bayesian_optimization module parrot.brnn_architecture module parrot.brnn_plot module parrot.encode_sequence module parrot.process_input_data module

parrot.py_predictor module parrot.train_network module parse_encode_file() (in module parrot.encode_sequence) parse_file() (in module parrot.process_input_data) plot_precision_recall_curve() (in module parrot.brnn_plot) plot_roc_curve() (in module parrot.brnn_plot) predict() (parrot.py_predictor.Predictor method) Predictor (class in parrot.py_predictor)

R

read_split_file() (in module parrot.process_input_data) read_tsv_raw() (in module parrot.process_input_data) res_class_collate() (in module parrot.process_input_data) res_confusion_matrix() (in module parrot.brnn_plot)

res_regress_collate() (in module parrot.process_input_data) residue_regression_scatterplot() (in module parrot.brnn_plot) rev_biophysics() (in module parrot.encode_sequence) rev_one_hot() (in module parrot.encode_sequence)

S

seq_class_collate() (in module parrot.process_input_data) seq_regress_collate() (in module parrot.process_input_data) sequence_regression_scatterplot() (in module parrot.brnn_plot)

SequenceDataset (class in parrot.process_input_data) split_data() (in module parrot.process_input_data) split_data_cv() (in module parrot.process_input_data)

T

test_labeled_data() (in module parrot.train_network) test_unlabeled_data() (in module parrot.train_network)

train() (in module parrot.train_network) training_loss() (in module parrot.brnn_plot)

U

UserEncoder (class in parrot.encode_sequence)

V

vector_split() (in module parrot.process_input_data)

W

write_performance_metrics() (in module parrot.brnn_plot)