Index

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__getitem__() (midaa.MultiomeLoader.MultiOmeDataset method) (MultiomeLoader-checkpoint.MultiOmicsDataset method) __init__-checkpoint module

__len__() (midaa.MultiomeLoader.MultiOmeDataset method) (MultiomeLoader-checkpoint.MultiOmicsDataset method)

A

add_to_obs_adata() (in module midaa) (in module midaa.Utils_parsers) (in module Utils_parsers-checkpoint)

B

build_conv_layer() (in module midaa.Utils_net) (in module Utils_net-checkpoint) build_conv_layer_reverse() (in module midaa.Utils_net) (in module Utils_net-checkpoint) build_last_layer_from_output_dist() (in module midaa.Utils_net) (in module Utils_net-checkpoint) build_last_layer_from_output_dist_conv() (in module midaa.Utils_net) (in module Utils_net-checkpoint) build_last_layer_from_output_dist_flat() (in module midaa.Utils_net) (in module Utils_net-checkpoint)

build_layer_general() (in module midaa.Utils_net) (in module Utils_net-checkpoint) build_multimodal_linear_decoder() (in module midaa.Utils_net) (in module Utils_net-checkpoint) build_multimodal_linear_encoder() (in module midaa.Utils_net) (in module Utils_net-checkpoint) build_sequential_layer() (in module midaa.Utils_net) (in module Utils_net-checkpoint)

C

calculate_BIC() (in module midaa.Utils_model_stats) (in module Utils_model_stats-checkpoint), [1] calculate_flattened_size() (in module midaa.Utils_net) (in module Utils_net-checkpoint) calculate_flattened_size_decoder() (in module midaa.Utils_net) (in module Utils_net-checkpoint) calculate_loss() (in module Interface-checkpoint) (in module midaa.Interface) calculate_number_of_params() (in module midaa.Utils_model_stats) (in module Utils_model_stats-checkpoint) compile_final_dict() (in module Interface-checkpoint) (in module midaa.Interface) compute_auxiliary_params_guide() (in module midaa.Utils_guide) (in module Utils_guide-checkpoint)

compute_auxiliary_params_guide_input() (in module midaa.Utils_guide) (in module Utils_guide-checkpoint) compute_auxiliary_params_guide_side() (in module midaa.Utils_guide) (in module Utils_guide-checkpoint) compute_feature_importance() (in module midaa) (in module midaa.Utils_downstream) (in module Utils_downstream-checkpoint) compute_loss() (in module midaa.Likelihood) compute_side_loss() (in module midaa.Likelihood) compute_total_loss() (in module midaa.Likelihood) correlation_by_archetype() (in module midaa) (in module midaa.Utils_downstream) (in module Utils_downstream-checkpoint) create_z_fix() (in module midaa.Utils) (in module Utils-checkpoint)

D

Decoder (class in Decoder-checkpoint) (class in midaa.Decoder) Decoder-checkpoint module

detach_or_iterate() (in module midaa.Utils) (in module Utils-checkpoint)

E

Encoder (class in Encoder-checkpoint) (class in midaa.Encoder)

Encoder-checkpoint module

F

find_matching_indexes() (in module midaa.Utils) (in module Utils-checkpoint) fit_MIDAA() (in module Interface-checkpoint) (in module midaa) (in module midaa.Interface)

forward() (Decoder-checkpoint.Decoder method) (Encoder-checkpoint.Encoder method) (midaa.Decoder.Decoder method) (midaa.Encoder.Encoder method)

G

generate_synthetic_data() (in module midaa) (in module midaa.DataGeneration) get_input_params_adata() (in module midaa) (in module midaa.Utils_parsers) (in module Utils_parsers-checkpoint)

guide() (MIDAA-checkpoint.MIDAA method) (midaa.MIDAA.MIDAA method)

H

handle_model_matrix() (in module Interface-checkpoint) (in module midaa.Interface)

handle_z() (in module Interface-checkpoint) (in module midaa.Interface)

I

initialize_params() (in module Interface-checkpoint) (in module midaa.Interface)

Interface-checkpoint module

L

load_model_from_state_dict() (in module Interface-checkpoint) (in module midaa) (in module midaa.Interface)

log_lk() (in module midaa.Utils_model_stats) (in module Utils_model_stats-checkpoint)

M

midaa module MIDAA (class in MIDAA-checkpoint) (class in midaa.MIDAA) MIDAA-checkpoint module midaa.DataGeneration module midaa.Decoder module midaa.Encoder module midaa.Interface module midaa.Likelihood module midaa.MIDAA module midaa.MultiomeLoader module midaa.Old_code module midaa.Plots module midaa.Utils module midaa.Utils_downstream module midaa.Utils_guide module midaa.Utils_model_stats module midaa.Utils_net module midaa.Utils_parsers module mix_weights() (in module midaa.Utils) (in module Utils-checkpoint)

model() (MIDAA-checkpoint.MIDAA method) (midaa.MIDAA.MIDAA method) module __init__-checkpoint Decoder-checkpoint Encoder-checkpoint Interface-checkpoint midaa MIDAA-checkpoint midaa.DataGeneration midaa.Decoder midaa.Encoder midaa.Interface midaa.Likelihood midaa.MIDAA midaa.MultiomeLoader midaa.Old_code midaa.Plots midaa.Utils midaa.Utils_downstream midaa.Utils_guide midaa.Utils_model_stats midaa.Utils_net midaa.Utils_parsers MultiomeLoader-checkpoint Plots-checkpoint Utils-checkpoint Utils_downstream-checkpoint Utils_guide-checkpoint Utils_model_stats-checkpoint Utils_net-checkpoint Utils_parsers-checkpoint MultiOmeDataset (class in midaa.MultiomeLoader) MultiomeLoader-checkpoint module MultiOmicsDataset (class in MultiomeLoader-checkpoint)

P

plot_archetypes_proportion() (in module midaa.Plots) (in module Plots-checkpoint) plot_archetypes_simplex() (in module midaa) (in module midaa.Plots) (in module Plots-checkpoint) plot_ELBO() (in module midaa) (in module midaa.Plots) (in module Plots-checkpoint)

plot_ELBO_across_runs() (in module midaa) (in module midaa.Plots) (in module Plots-checkpoint) Plots-checkpoint module prepare_final_parameters() (in module Interface-checkpoint) (in module midaa.Interface)

R

rank_features_by_arch() (in module midaa.Utils_downstream) (in module Utils_downstream-checkpoint)

retrieve_params() (in module midaa.Utils_model_stats) (in module Utils_model_stats-checkpoint)

S

sample_batch() (in module midaa.Utils) (in module Utils-checkpoint) sample_batch_aux() (in module midaa.Utils) (in module Utils-checkpoint) sample_batch_by_class_aux() (in module midaa.Utils) (in module Utils-checkpoint)

select_elements_at_indexes() (in module midaa.Utils) (in module Utils-checkpoint) select_elements_not_at_indexes() (in module midaa.Utils) (in module Utils-checkpoint)

T

to_cpu_ot_iterate() (in module midaa.Utils) (in module Utils-checkpoint)

training_loop() (in module Interface-checkpoint) (in module midaa.Interface)

U

Utils-checkpoint module Utils_downstream-checkpoint module Utils_guide-checkpoint module

Utils_model_stats-checkpoint module Utils_net-checkpoint module Utils_parsers-checkpoint module