Index

A

Autoencoder (class in rna_code.models.autoencoder)

B

BaseFeatureSelector (class in rna_code.data.feature_selection.base_feature_selector) BaseInterface (class in rna_code.data.interface.base_interface) BRCAInterface (class in rna_code.data.interface.BRCA_interface) build_decoder() (rna_code.models.autoencoder.Autoencoder method) (rna_code.models.cnn_ae.CNNAutoencoder method) (rna_code.models.mlp_ae.MLPAutoencoder method)

build_encoder() (rna_code.models.autoencoder.Autoencoder method) (rna_code.models.cnn_ae.CNNAutoencoder method) (rna_code.models.mlp_ae.MLPAutoencoder method)

C

CNNAutoencoder (class in rna_code.models.cnn_ae) compute_hopkins() (rna_code.utils.monitor_callback.MetricsComputer static method)

compute_metrics() (rna_code.utils.monitor_callback.MetricsComputer static method) configure_optimizers() (rna_code.models.autoencoder.Autoencoder method) CPTAC3Interface (class in rna_code.data.interface.cptac_3_interface)

D

dataset_plot() (in module rna_code.utils.visualization)

DatasetMerger (class in rna_code.utils.dataset_merger)

E

encode() (rna_code.models.autoencoder.Autoencoder method) encode_recon_dataset() (in module rna_code.utils.helpers)

entry_names (rna_code.data.interface.BRCA_interface.BRCAInterface property) (rna_code.data.interface.cptac_3_interface.CPTAC3Interface property) ExpressionSelector (class in rna_code.data.feature_selection.expression_selector)

F

find_subtypes() (rna_code.data.interface.BRCA_interface.BRCAInterface method) (rna_code.data.interface.cptac_3_interface.CPTAC3Interface method) forward() (rna_code.models.autoencoder.Autoencoder method) (rna_code.models.residual_stack.ResidualStack method) (rna_code.models.vector_quantizer.VectorQuantizer method) (rna_code.models.vq_conversion.vq_conversion method) (rna_code.models.vq_pre_residual_stack_decoder.vq_pre_residual_stack_decoder method)

G

generate_config() (in module rna_code.utils.helpers) generate_model() (rna_code.models.model_builder.ModelBuilder method)

get_encoded_data() (rna_code.utils.monitor_callback.MonitorCallback method) get_gene_names_from_file() (rna_code.data.interface.base_interface.BaseInterface static method)

I

intersect() (rna_code.utils.dataset_merger.DatasetMerger static method)

L

laplacian_score() (rna_code.data.feature_selection.laplacian_selector.LaplacianSelector method) LaplacianSelector (class in rna_code.data.feature_selection.laplacian_selector) LassoSelector (class in rna_code.data.feature_selection.lasso_selector)

load_patient_data() (rna_code.data.interface.base_interface.BaseInterface static method) load_patients() (rna_code.data.interface.BRCA_interface.BRCAInterface method) (rna_code.data.interface.cptac_3_interface.CPTAC3Interface method)

M

MADSelector (class in rna_code.data.feature_selection.mad_selector) MetricsComputer (class in rna_code.utils.monitor_callback) MLPAutoencoder (class in rna_code.models.mlp_ae) ModelBuilder (class in rna_code.models.model_builder) module rna_code rna_code.data rna_code.data.data_module rna_code.data.feature_selection rna_code.data.feature_selection.base_feature_selector rna_code.data.feature_selection.expression_selector rna_code.data.feature_selection.laplacian_selector rna_code.data.feature_selection.lasso_selector rna_code.data.feature_selection.mad_selector rna_code.data.interface rna_code.data.interface.base_interface rna_code.data.interface.BRCA_interface rna_code.data.interface.cptac_3_interface rna_code.models rna_code.models.autoencoder rna_code.models.cnn_ae rna_code.models.mlp_ae rna_code.models.model_builder rna_code.models.residual_stack rna_code.models.vector_quantizer rna_code.models.vq_conversion rna_code.models.vq_pre_residual_stack_decoder rna_code.utils rna_code.utils.dataset_merger rna_code.utils.helpers rna_code.utils.monitor_callback rna_code.utils.visualization

MonitorCallback (class in rna_code.utils.monitor_callback)

O

on_train_batch_end() (rna_code.utils.monitor_callback.MonitorCallback method)

on_train_epoch_end() (rna_code.utils.monitor_callback.MonitorCallback method)

P

post_training_animation() (in module rna_code.utils.visualization)

post_training_viz() (in module rna_code.utils.visualization)

R

reparameterize() (rna_code.models.autoencoder.Autoencoder method) ResidualStack (class in rna_code.models.residual_stack) retrieve_position() (rna_code.data.interface.base_interface.BaseInterface static method) rna_code module rna_code.data module rna_code.data.data_module module rna_code.data.feature_selection module rna_code.data.feature_selection.base_feature_selector module rna_code.data.feature_selection.expression_selector module rna_code.data.feature_selection.laplacian_selector module rna_code.data.feature_selection.lasso_selector module rna_code.data.feature_selection.mad_selector module rna_code.data.interface module rna_code.data.interface.base_interface module rna_code.data.interface.BRCA_interface module rna_code.data.interface.cptac_3_interface module

rna_code.models module rna_code.models.autoencoder module rna_code.models.cnn_ae module rna_code.models.mlp_ae module rna_code.models.model_builder module rna_code.models.residual_stack module rna_code.models.vector_quantizer module rna_code.models.vq_conversion module rna_code.models.vq_pre_residual_stack_decoder module rna_code.utils module rna_code.utils.dataset_merger module rna_code.utils.helpers module rna_code.utils.monitor_callback module rna_code.utils.visualization module

S

select_features() (rna_code.data.feature_selection.base_feature_selector.BaseFeatureSelector method) (rna_code.data.feature_selection.expression_selector.ExpressionSelector method) (rna_code.data.feature_selection.laplacian_selector.LaplacianSelector method) (rna_code.data.feature_selection.lasso_selector.LassoSelector method) (rna_code.data.feature_selection.mad_selector.MADSelector method)

setup() (rna_code.data.interface.BRCA_interface.BRCAInterface method) (rna_code.data.interface.cptac_3_interface.CPTAC3Interface method)

T

training_step() (rna_code.models.autoencoder.Autoencoder method)

U

union() (rna_code.utils.dataset_merger.DatasetMerger static method)

V

VectorQuantizer (class in rna_code.models.vector_quantizer)

vq_conversion (class in rna_code.models.vq_conversion) vq_pre_residual_stack_decoder (class in rna_code.models.vq_pre_residual_stack_decoder)