Index A | B | C | D | E | F | G | H | I | L | M | P | R | S | T | U | V A adata (topomics.models.MultimodalAmortizedLDA attribute) adata_manager (topomics.models.MultimodalAmortizedLDA attribute) B BaseTopicModel (class in topomics.models) basic_plot() (in module topomics.pl) basic_preproc() (in module topomics.pp) basic_tool() (in module topomics.tl) C cell_topic_distribution() (topomics.models.SVEM_LDA_Multi method) check_input() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) check_modalities_names() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) clear_metric_cache() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) convert_legacy_save() (topomics.models.MultimodalAmortizedLDA class method) cross_modality_score() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) D data_registry() (topomics.models.MultimodalAmortizedLDA method) deregister_manager() (topomics.models.MultimodalAmortizedLDA method) device (topomics.models.MultimodalAmortizedLDA attribute) diagnostics() (topomics.models.SVEM_LDA_Multi method) differential_abundance() (topomics.models.MultimodalAmortizedLDA method) E elaborate_example() (in module topomics.pp) F fit() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) from_data() (topomics.models.MultimodalAmortizedLDA class method) from_mudata() (topomics.models.MultimodalAmortizedLDA class method) G generate() (topomics.models.ShareTopic_LDA_Multi method) get_anndata_manager() (topomics.models.MultimodalAmortizedLDA method) get_cell_entropy() (topomics.models.MultimodalAmortizedLDA method) get_cell_topic_dist() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) get_elbo() (topomics.models.MultimodalAmortizedLDA method) get_entropy() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) get_entropy_weight() (topomics.models.MultimodalAmortizedLDA method) get_feature_topic_dist() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) get_from_registry() (topomics.models.MultimodalAmortizedLDA method) get_last_entropy() (topomics.models.MultimodalAmortizedLDA method) get_last_topic_variance() (topomics.models.MultimodalAmortizedLDA method) get_latent_representation() (topomics.models.MultimodalAmortizedLDA method) get_learned_dispersion() (topomics.models.MultimodalAmortizedLDA method) get_likelihood_per_modality() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) get_likelihood_weights() (topomics.models.MultimodalAmortizedLDA method) get_modality_weights() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) get_normalized_expression() (topomics.models.MultimodalAmortizedLDA method) get_normalized_function_name (topomics.models.MultimodalAmortizedLDA attribute) get_perplexity() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) get_perplexity_per_modality() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) get_setup_arg() (topomics.models.MultimodalAmortizedLDA method) get_state_registry() (topomics.models.MultimodalAmortizedLDA method) get_top_features_per_topic() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) get_topic_diversity() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) get_topic_variance() (topomics.models.MultimodalAmortizedLDA method) get_topic_variance_weight() (topomics.models.MultimodalAmortizedLDA method) get_var_names() (topomics.models.MultimodalAmortizedLDA method) H history (topomics.models.MultimodalAmortizedLDA attribute) I is_trained (topomics.models.MultimodalAmortizedLDA attribute) L load() (topomics.models.MultimodalAmortizedLDA class method) (topomics.models.ShareTopic_LDA_Multi class method) load_registry() (topomics.models.MultimodalAmortizedLDA static method) M MultimodalAmortizedLDA (class in topomics.models) P predict() (topomics.models.BaseTopicModel method) (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) (topomics.models.SVEM_LDA_Multi method) R register_manager() (topomics.models.MultimodalAmortizedLDA class method) registry (topomics.models.MultimodalAmortizedLDA attribute) run_id (topomics.models.MultimodalAmortizedLDA attribute) run_name (topomics.models.MultimodalAmortizedLDA attribute) S save() (topomics.models.MultimodalAmortizedLDA method) (topomics.models.ShareTopic_LDA_Multi method) setup_adata_dict() (topomics.models.MultimodalAmortizedLDA class method) setup_anndata() (topomics.models.MultimodalAmortizedLDA class method) setup_data() (topomics.models.MultimodalAmortizedLDA class method) setup_mudata() (topomics.models.MultimodalAmortizedLDA class method) setup_spatialdata() (topomics.models.MultimodalAmortizedLDA class method) ShareTopic_LDA_Multi (class in topomics.models) spatial (topomics.models.BaseTopicModel attribute) (topomics.models.MultimodalAmortizedLDA attribute) (topomics.models.ShareTopic_LDA_Multi attribute) (topomics.models.SVEM_LDA_Multi attribute) spatial() (in module topomics.pl) summary_string (topomics.models.MultimodalAmortizedLDA attribute) SVEM_LDA_Multi (class in topomics.models) T test_indices (topomics.models.MultimodalAmortizedLDA attribute) to_device() (topomics.models.MultimodalAmortizedLDA method) topic_by_feature() (topomics.models.SVEM_LDA_Multi method) train() (topomics.models.MultimodalAmortizedLDA method) train_indices (topomics.models.MultimodalAmortizedLDA attribute) transfer_fields() (topomics.models.MultimodalAmortizedLDA method) U update_setup_method_args() (topomics.models.MultimodalAmortizedLDA method) V validation_indices (topomics.models.MultimodalAmortizedLDA attribute) view_anndata_setup() (topomics.models.MultimodalAmortizedLDA method) view_registry() (topomics.models.MultimodalAmortizedLDA method) view_setup_args() (topomics.models.MultimodalAmortizedLDA static method) view_setup_method_args() (topomics.models.MultimodalAmortizedLDA method)