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ncem
Index
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Index
A
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C
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D
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E
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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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N
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O
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P
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R
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S
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T
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V
A
a (ncem.estimators.Estimator attribute)
ablation() (in module ncem.pl)
adj_type (ncem.estimators.Estimator attribute)
C
circular() (in module ncem.pl)
circular_rotated_labels() (in module ncem.pl)
cluster_freq() (in module ncem.pl)
complete_img_keys (ncem.estimators.Estimator attribute)
cond_depth (ncem.estimators.Estimator attribute)
cond_type (ncem.estimators.Estimator attribute)
copy_best_model() (ncem.train.GridSearchContainer method)
covar_selection (ncem.estimators.Estimator attribute)
cv_ids (ncem.train.GridSearchContainer attribute)
cv_keys (ncem.train.GridSearchContainer property)
D
differential_ncem() (in module ncem.tl)
differential_ncem_deconvoluted() (in module ncem.tl)
domains (ncem.estimators.Estimator attribute)
E
Estimator (class in ncem.estimators)
estimator (ncem.train.TrainModelCVAE attribute)
(ncem.train.TrainModelCVAEncem attribute)
(ncem.train.TrainModelED attribute)
(ncem.train.TrainModelEDncem attribute)
(ncem.train.TrainModelInteractions attribute)
(ncem.train.TrainModelLinear attribute)
EstimatorCVAE (class in ncem.estimators)
EstimatorCVAEncem (class in ncem.estimators)
EstimatorED (class in ncem.estimators)
EstimatorEDncem (class in ncem.estimators)
EstimatorGraph (class in ncem.estimators)
EstimatorInteractions (class in ncem.estimators)
EstimatorLinear (class in ncem.estimators)
EstimatorNoGraph (class in ncem.estimators)
evaluate_any() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
evaluate_any_posterior_sampling() (ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
evaluate_per_node_type() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
G
get_best_model_id() (ncem.train.GridSearchContainer method)
get_data() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
get_decoding_weights() (ncem.estimators.EstimatorEDncem method)
get_info() (ncem.train.GridSearchContainer method)
graph_covar (ncem.estimators.Estimator attribute)
graph_covar_names (ncem.estimators.Estimator attribute)
GridSearchContainer (class in ncem.train)
H
h_0 (ncem.estimators.Estimator attribute)
h_1 (ncem.estimators.Estimator attribute)
I
img_keys_all (ncem.estimators.Estimator property)
(ncem.estimators.EstimatorCVAE property)
(ncem.estimators.EstimatorCVAEncem property)
(ncem.estimators.EstimatorED property)
(ncem.estimators.EstimatorEDncem property)
(ncem.estimators.EstimatorGraph property)
(ncem.estimators.EstimatorInteractions property)
(ncem.estimators.EstimatorLinear property)
(ncem.estimators.EstimatorNoGraph property)
img_to_patient_dict (ncem.estimators.Estimator attribute)
init_estim() (ncem.train.TrainModelCVAE method)
(ncem.train.TrainModelCVAEncem method)
(ncem.train.TrainModelED method)
(ncem.train.TrainModelEDncem method)
(ncem.train.TrainModelInteractions method)
(ncem.train.TrainModelLinear method)
init_model() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
L
linear_ncem() (in module ncem.tl)
linear_ncem_deconvoluted() (in module ncem.tl)
load_gs() (ncem.train.GridSearchContainer method)
load_target_cell_evaluation() (ncem.train.GridSearchContainer method)
log_transform (ncem.estimators.Estimator attribute)
M
max_nodes (ncem.estimators.Estimator attribute)
model_type (ncem.estimators.Estimator attribute)
ModelCVAE (class in ncem.models)
ModelCVAEncem (class in ncem.models)
ModelED (class in ncem.models)
ModelEDncem (class in ncem.models)
ModelInteractions (class in ncem.models)
ModelLinear (class in ncem.models)
module
ncem.models
ncem.pl
ncem.tl
N
n_domains (ncem.estimators.Estimator attribute)
n_eval_nodes_per_graph (ncem.estimators.Estimator attribute)
n_features_0 (ncem.estimators.Estimator attribute)
n_features_1 (ncem.estimators.Estimator attribute)
n_features_standard (ncem.estimators.Estimator attribute)
n_features_type (ncem.estimators.Estimator attribute)
n_graph_covariates (ncem.estimators.Estimator attribute)
n_node_covariates (ncem.estimators.Estimator attribute)
ncem.models
module
ncem.pl
module
ncem.tl
module
node_covar (ncem.estimators.Estimator attribute)
node_feature_names (ncem.estimators.Estimator attribute)
node_type_names (ncem.estimators.Estimator attribute)
node_types (ncem.estimators.Estimator attribute)
nodes_idx_all (ncem.estimators.Estimator property)
(ncem.estimators.EstimatorCVAE property)
(ncem.estimators.EstimatorCVAEncem property)
(ncem.estimators.EstimatorED property)
(ncem.estimators.EstimatorEDncem property)
(ncem.estimators.EstimatorGraph property)
(ncem.estimators.EstimatorInteractions property)
(ncem.estimators.EstimatorLinear property)
(ncem.estimators.EstimatorNoGraph property)
nodes_idx_eval (ncem.estimators.Estimator attribute)
(ncem.estimators.EstimatorCVAE attribute)
(ncem.estimators.EstimatorCVAEncem attribute)
(ncem.estimators.EstimatorED attribute)
(ncem.estimators.EstimatorEDncem attribute)
(ncem.estimators.EstimatorGraph attribute)
(ncem.estimators.EstimatorInteractions attribute)
(ncem.estimators.EstimatorLinear attribute)
(ncem.estimators.EstimatorNoGraph attribute)
nodes_idx_test (ncem.estimators.Estimator attribute)
(ncem.estimators.EstimatorCVAE attribute)
(ncem.estimators.EstimatorCVAEncem attribute)
(ncem.estimators.EstimatorED attribute)
(ncem.estimators.EstimatorEDncem attribute)
(ncem.estimators.EstimatorGraph attribute)
(ncem.estimators.EstimatorInteractions attribute)
(ncem.estimators.EstimatorLinear attribute)
(ncem.estimators.EstimatorNoGraph attribute)
nodes_idx_train (ncem.estimators.Estimator attribute)
(ncem.estimators.EstimatorCVAE attribute)
(ncem.estimators.EstimatorCVAEncem attribute)
(ncem.estimators.EstimatorED attribute)
(ncem.estimators.EstimatorEDncem attribute)
(ncem.estimators.EstimatorGraph attribute)
(ncem.estimators.EstimatorInteractions attribute)
(ncem.estimators.EstimatorLinear attribute)
(ncem.estimators.EstimatorNoGraph attribute)
noise_structure() (in module ncem.pl)
O
output_layer (ncem.estimators.Estimator attribute)
P
patient_ids_bytarget (ncem.estimators.Estimator property)
(ncem.estimators.EstimatorCVAE property)
(ncem.estimators.EstimatorCVAEncem property)
(ncem.estimators.EstimatorED property)
(ncem.estimators.EstimatorEDncem property)
(ncem.estimators.EstimatorGraph property)
(ncem.estimators.EstimatorInteractions property)
(ncem.estimators.EstimatorLinear property)
(ncem.estimators.EstimatorNoGraph property)
patient_ids_unique (ncem.estimators.Estimator property)
(ncem.estimators.EstimatorCVAE property)
(ncem.estimators.EstimatorCVAEncem property)
(ncem.estimators.EstimatorED property)
(ncem.estimators.EstimatorEDncem property)
(ncem.estimators.EstimatorGraph property)
(ncem.estimators.EstimatorInteractions property)
(ncem.estimators.EstimatorLinear property)
(ncem.estimators.EstimatorNoGraph property)
plot_best_model_by_hyperparam() (ncem.train.GridSearchContainer method)
plot_target_cell_evaluation() (ncem.train.GridSearchContainer method)
predict() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
predict_embedding_any() (ncem.estimators.EstimatorEDncem method)
pretrain_decoder() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
R
run_ids_clean (ncem.train.GridSearchContainer attribute)
runparams (ncem.train.GridSearchContainer attribute)
S
save() (ncem.train.TrainModelCVAE method)
(ncem.train.TrainModelCVAEncem method)
(ncem.train.TrainModelED method)
(ncem.train.TrainModelEDncem method)
(ncem.train.TrainModelInteractions method)
(ncem.train.TrainModelLinear method)
save_time() (ncem.train.TrainModelCVAE method)
(ncem.train.TrainModelCVAEncem method)
(ncem.train.TrainModelED method)
(ncem.train.TrainModelEDncem method)
(ncem.train.TrainModelInteractions method)
(ncem.train.TrainModelLinear method)
select_cv() (ncem.train.GridSearchContainer method)
size_factors (ncem.estimators.Estimator attribute)
source_gs (ncem.train.GridSearchContainer attribute)
spline_differential_ncem() (in module ncem.tl)
spline_differential_ncem_deconvoluted() (in module ncem.tl)
spline_linear_ncem() (in module ncem.tl)
spline_linear_ncem_deconvoluted() (in module ncem.tl)
split_data_given() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
split_data_node() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
split_data_target_cell() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
steps_per_epoch (ncem.estimators.Estimator attribute)
T
target_cell_evals (ncem.train.GridSearchContainer attribute)
target_cell_indices (ncem.train.GridSearchContainer attribute)
target_cell_runparams (ncem.train.GridSearchContainer attribute)
train() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
train_aggressive() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
train_normal() (ncem.estimators.Estimator method)
(ncem.estimators.EstimatorCVAE method)
(ncem.estimators.EstimatorCVAEncem method)
(ncem.estimators.EstimatorED method)
(ncem.estimators.EstimatorEDncem method)
(ncem.estimators.EstimatorGraph method)
(ncem.estimators.EstimatorInteractions method)
(ncem.estimators.EstimatorLinear method)
(ncem.estimators.EstimatorNoGraph method)
TrainModelCVAE (class in ncem.train)
TrainModelCVAEncem (class in ncem.train)
TrainModelED (class in ncem.train)
TrainModelEDncem (class in ncem.train)
TrainModelInteractions (class in ncem.train)
TrainModelLinear (class in ncem.train)
V
validation_steps (ncem.estimators.Estimator attribute)
vi_model (ncem.estimators.Estimator attribute)
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