Index

A

add_active_gp_scores_to_obs() (nichecompass.models.NicheCompass method) add_gps_from_gp_dict_to_adata() (in module nichecompass.utils)

add_multimodal_mask_to_adata() (in module nichecompass.utils) AddOnMaskedLayer (class in nichecompass.nn)

B

BaseModuleMixin (class in nichecompass.modules)

C

compute_benchmarking_metrics() (in module nichecompass.benchmarking) compute_cas() (in module nichecompass.benchmarking) compute_cat_covariates_contrastive_loss() (in module nichecompass.modules) compute_clisis() (in module nichecompass.benchmarking) compute_communication_gp_network() (in module nichecompass.utils) compute_edge_recon_loss() (in module nichecompass.modules) compute_gcs() (in module nichecompass.benchmarking) compute_gp_gene_importances() (nichecompass.models.NicheCompass method) compute_gp_group_lasso_reg_loss() (in module nichecompass.modules)

compute_gp_l1_reg_loss() (in module nichecompass.modules) compute_gp_peak_importances() (nichecompass.models.NicheCompass method) compute_kl_reg_loss() (in module nichecompass.modules) compute_knn_graph_connectivities_and_distances() (in module nichecompass.benchmarking.utils) compute_mlami() (in module nichecompass.benchmarking) compute_nasw() (in module nichecompass.benchmarking) compute_omics_recon_nb_loss() (in module nichecompass.modules) CosineSimGraphDecoder (class in nichecompass.nn) create_new_color_dict() (in module nichecompass.utils)

E

edge_level_split() (in module nichecompass.data) Encoder (class in nichecompass.nn) eval_end() (nichecompass.train.Trainer method) eval_epoch() (nichecompass.train.Trainer method)

eval_metrics() (in module nichecompass.train) extract_gp_dict_from_collectri_tf_network() (in module nichecompass.utils) extract_gp_dict_from_nichenet_lrt_interactions() (in module nichecompass.utils) extract_gp_dict_from_omnipath_lr_interactions() (in module nichecompass.utils)

F

FCOmicsFeatureDecoder (class in nichecompass.nn) filter_and_combine_gp_dict_gps() (in module nichecompass.utils) forward() (nichecompass.modules.VGPGAE method) (nichecompass.nn.AddOnMaskedLayer method) (nichecompass.nn.CosineSimGraphDecoder method) (nichecompass.nn.Encoder method) (nichecompass.nn.FCOmicsFeatureDecoder method) (nichecompass.nn.MaskedLinear method) (nichecompass.nn.MaskedOmicsFeatureDecoder method) (nichecompass.nn.OneHopAttentionNodeLabelAggregator method) (nichecompass.nn.OneHopGCNNormNodeLabelAggregator method) (nichecompass.nn.OneHopSumNodeLabelAggregator method)

G

generate_enriched_gp_info_plots() (in module nichecompass.utils) generate_multimodal_mapping_dict() (in module nichecompass.utils) get_active_gp_mask() (nichecompass.modules.VGPGAE method) get_active_gps() (nichecompass.models.NicheCompass method) get_cat_covariates_embeds() (nichecompass.models.NicheCompass method) get_gene_annotations() (in module nichecompass.utils) get_gp_data() (nichecompass.models.NicheCompass method) get_gp_summary() (nichecompass.models.NicheCompass method)

get_gp_weights() (nichecompass.modules.VGPGAE method) get_latent_representation() (nichecompass.models.NicheCompass method) (nichecompass.modules.VGPGAE method) get_neighbor_importances() (nichecompass.models.NicheCompass method) get_omics_decoder_outputs() (nichecompass.models.NicheCompass method) (nichecompass.modules.VGPGAE method) get_recon_edge_probs() (nichecompass.models.NicheCompass method) get_unique_genes_from_gp_dict() (in module nichecompass.utils)

I

initialize_dataloaders() (in module nichecompass.data)

initialize_model() (in module nichecompass.models.utils) is_early_stopping() (nichecompass.train.Trainer method)

L

load() (nichecompass.models.NicheCompass class method) load_and_expand_state_dict() (nichecompass.modules.BaseModuleMixin method) (nichecompass.modules.VGPGAE method)

load_saved_files() (in module nichecompass.models.utils) load_spatial_adata_from_csv() (in module nichecompass.data) log_module_hyperparams_to_mlflow() (nichecompass.modules.VGPGAE method) loss() (nichecompass.modules.VGPGAE method)

M

MaskedLinear (class in nichecompass.nn) MaskedOmicsFeatureDecoder (class in nichecompass.nn) message() (nichecompass.nn.OneHopAttentionNodeLabelAggregator method) module nichecompass.benchmarking, [1] nichecompass.data, [1] nichecompass.models, [1] nichecompass.modules nichecompass.nn nichecompass.train nichecompass.utils, [1], [2]

N

NicheCompass (class in nichecompass.models) nichecompass.benchmarking module, [1] nichecompass.data module, [1] nichecompass.models module, [1] nichecompass.modules module

nichecompass.nn module nichecompass.train module nichecompass.utils module, [1], [2] node_level_split_mask() (in module nichecompass.data)

O

OneHopAttentionNodeLabelAggregator (class in nichecompass.nn)

OneHopGCNNormNodeLabelAggregator (class in nichecompass.nn) OneHopSumNodeLabelAggregator (class in nichecompass.nn)

P

plot_eval_metrics() (in module nichecompass.train)

prepare_data() (in module nichecompass.data)

R

reparameterize() (nichecompass.modules.VGAEModuleMixin method) (nichecompass.modules.VGPGAE method)

reset_parameters() (nichecompass.nn.OneHopAttentionNodeLabelAggregator method) run_differential_gp_tests() (nichecompass.models.NicheCompass method)

S

save() (nichecompass.models.NicheCompass method)

SpatialAnnTorchDataset (class in nichecompass.data)

T

train() (nichecompass.models.NicheCompass method) (nichecompass.train.Trainer method)

Trainer (class in nichecompass.train)

V

validate_var_names() (in module nichecompass.models.utils) VGAEModuleMixin (class in nichecompass.modules)

VGPGAE (class in nichecompass.modules) visualize_communication_gp_network() (in module nichecompass.utils)