midaa
Let’s start with Multimodal Deep Archetypal Analysis
Finding your way in MIDAAs interface
MIDAA 101 (on 10X multiome)
Changelog
Contributing
Code of Conduct
API Reference
midaa
Index
Index
_
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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P
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R
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S
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T
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U
_
__getitem__() (midaa.MultiomeLoader.MultiOmeDataset method)
__len__() (midaa.MultiomeLoader.MultiOmeDataset method)
A
add_to_obs_adata() (in module midaa)
(in module midaa.Utils_parsers)
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)
,
[1]
(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)
compute_auxiliary_params_guide_input() (in module midaa.Utils_guide)
compute_auxiliary_params_guide_side() (in module midaa.Utils_guide)
compute_loss() (in module midaa.Likelihood)
compute_side_loss() (in module midaa.Likelihood)
compute_total_loss() (in module midaa.Likelihood)
create_z_fix() (in module midaa.Utils)
(in module Utils-checkpoint)
D
Decoder (class in midaa.Decoder)
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() (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)
guide() (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.MIDAA)
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_downstram
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.MIDAA.MIDAA method)
module
Encoder-checkpoint
Interface-checkpoint
midaa
midaa.DataGeneration
midaa.Decoder
midaa.Encoder
midaa.Interface
midaa.Likelihood
midaa.MIDAA
midaa.MultiomeLoader
midaa.Old_code
midaa.Plots
midaa.Utils
midaa.Utils_downstram
midaa.Utils_guide
midaa.Utils_model_stats
midaa.Utils_net
midaa.Utils_parsers
Utils-checkpoint
Utils_model_stats-checkpoint
Utils_net-checkpoint
MultiOmeDataset (class in midaa.MultiomeLoader)
P
plot_archetypes_proportion() (in module midaa.Plots)
plot_archetypes_simplex() (in module midaa)
(in module midaa.Plots)
plot_ELBO() (in module midaa)
(in module midaa.Plots)
plot_ELBO_across_runs() (in module midaa)
(in module midaa.Plots)
prepare_final_parameters() (in module Interface-checkpoint)
(in module midaa.Interface)
R
rank_features_by_arch() (in module midaa.Utils_downstram)
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_model_stats-checkpoint
module
Utils_net-checkpoint
module