Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | V | X | Z A adata (amici.AMICI property) adata_manager (amici.AMICI property) add_caching_hooks() (amici.AMICIModule method) add_module() (amici.AMICIModule method) AMICI (class in amici) AMICIAblationModule (class in amici.interpretation) AMICIAttentionModule (class in amici.interpretation) AMICICounterfactualAttentionModule (class in amici.interpretation) AMICIExplainedVarianceModule (class in amici.interpretation) AMICIModule (class in amici) apply() (amici.AMICIModule method) AttentionPenaltyMonitor (class in amici.callbacks) B bfloat16() (amici.AMICIModule method) buffers() (amici.AMICIModule method) C cache_some() (amici.AMICIModule method) calculate_counterfactual_attention_at_distances() (amici.interpretation.AMICICounterfactualAttentionModule method) check_and_add_hook() (amici.AMICIModule method) check_hooks_to_add() (amici.AMICIModule method) children() (amici.AMICIModule method) compile() (amici.AMICIModule method) compute() (amici.interpretation.AMICIAblationModule class method) (amici.interpretation.AMICIAttentionModule class method) (amici.interpretation.AMICICounterfactualAttentionModule class method) (amici.interpretation.AMICIExplainedVarianceModule class method) compute_communication_hubs() (amici.interpretation.AMICIAttentionModule method) compute_max_explained_variance_head() (amici.interpretation.AMICIExplainedVarianceModule method) convert_legacy_save() (amici.AMICI class method) cpu() (amici.AMICIModule method) cuda() (amici.AMICIModule method) D deregister_manager() (amici.AMICI method) device (amici.AMICI property) double() (amici.AMICIModule method) E eval() (amici.AMICIModule method) extra_repr() (amici.AMICIModule method) F float() (amici.AMICIModule method) forward() (amici.AMICIModule method) G generative() (amici.AMICIModule method) get_anndata_manager() (amici.AMICI method) get_attention_patterns() (amici.AMICI method) get_buffer() (amici.AMICIModule method) get_caching_hooks() (amici.AMICIModule method) get_counterfactual_attention_patterns() (amici.AMICI method) get_elbo() (amici.AMICI method) get_expl_variance_scores() (amici.AMICI method) get_extra_state() (amici.AMICIModule method) get_from_registry() (amici.AMICI method) get_gene_residual_contributions() (amici.AMICI method) get_interaction_circos_plot() (amici.interpretation.AMICIAblationModule method) get_latent_representation() (amici.AMICI method) get_marginal_ll() (amici.AMICI method) get_neighbor_ablation_scores() (amici.AMICI method) get_parameter() (amici.AMICIModule method) get_reconstruction_error() (amici.AMICI method) get_submodule() (amici.AMICIModule method) H half() (amici.AMICIModule method) history (amici.AMICI property) hooks() (amici.AMICIModule method) I inference() (amici.AMICIModule method) ipu() (amici.AMICIModule method) is_count_data() (in module amici.tools) is_trained (amici.AMICI property) L load() (amici.AMICI class method) load_object() (amici.interpretation.AMICIAblationModule class method) load_registry() (amici.AMICI static method) load_state_dict() (amici.AMICIModule method) (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) loss() (amici.AMICIModule method) M ModelInterpretationLogging (class in amici.callbacks) modules() (amici.AMICIModule method) mtia() (amici.AMICIModule method) N named_buffers() (amici.AMICIModule method) named_children() (amici.AMICIModule method) named_modules() (amici.AMICIModule method) named_parameters() (amici.AMICIModule method) O on_after_backward() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_before_backward() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_before_optimizer_step() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_before_zero_grad() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_exception() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_fit_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_fit_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_load() (amici.AMICIModule method) on_load_checkpoint() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_predict_batch_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_predict_batch_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_predict_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_predict_epoch_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_predict_epoch_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_predict_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_sanity_check_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_sanity_check_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_save_checkpoint() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_test_batch_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_test_batch_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_test_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_test_epoch_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_test_epoch_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_test_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_train_batch_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_train_batch_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_train_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_train_epoch_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_train_epoch_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_train_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_validation_batch_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_validation_batch_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_validation_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_validation_epoch_end() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_validation_epoch_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) on_validation_start() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) P parameters() (amici.AMICIModule method) plot_attention_summary() (amici.interpretation.AMICIAttentionModule method) plot_counterfactual_attention_summary() (amici.interpretation.AMICICounterfactualAttentionModule method) plot_explained_variance_barplot() (amici.interpretation.AMICIExplainedVarianceModule method) plot_featurewise_ablation_heatmap() (amici.interpretation.AMICIAblationModule method) plot_featurewise_contributions_dotplot() (amici.interpretation.AMICIAblationModule method) plot_featurewise_contributions_heatmap() (amici.interpretation.AMICIAblationModule method) plot_featurewise_explained_variance_heatmap() (amici.interpretation.AMICIExplainedVarianceModule method) plot_interaction_directed_graph() (amici.interpretation.AMICIAblationModule method) plot_interaction_weight_heatmap() (amici.interpretation.AMICIAblationModule method) plot_length_scale_distribution() (amici.interpretation.AMICICounterfactualAttentionModule method) plot_neighbor_ablation_scores() (amici.interpretation.AMICIAblationModule method) R register_backward_hook() (amici.AMICIModule method) register_buffer() (amici.AMICIModule method) register_forward_hook() (amici.AMICIModule method) register_forward_pre_hook() (amici.AMICIModule method) register_full_backward_hook() (amici.AMICIModule method) register_full_backward_pre_hook() (amici.AMICIModule method) register_load_state_dict_post_hook() (amici.AMICIModule method) register_load_state_dict_pre_hook() (amici.AMICIModule method) register_manager() (amici.AMICI class method) register_module() (amici.AMICIModule method) register_parameter() (amici.AMICIModule method) register_state_dict_post_hook() (amici.AMICIModule method) register_state_dict_pre_hook() (amici.AMICIModule method) requires_grad_() (amici.AMICIModule method) run_with_cache() (amici.AMICIModule method) run_with_hooks() (amici.AMICIModule method) S sample() (amici.AMICIModule method) save() (amici.AMICI method) (amici.interpretation.AMICIAttentionModule method) (amici.interpretation.AMICICounterfactualAttentionModule method) (amici.interpretation.AMICIExplainedVarianceModule method) save_object() (amici.interpretation.AMICIAblationModule method) set_extra_state() (amici.AMICIModule method) set_submodule() (amici.AMICIModule method) setup() (amici.AMICIModule method) (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) setup_anndata() (amici.AMICI class method) share_memory() (amici.AMICIModule method) state_dict() (amici.AMICIModule method) (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) state_key (amici.callbacks.AttentionPenaltyMonitor property) (amici.callbacks.ModelInterpretationLogging property) summary_string (amici.AMICI property) T teardown() (amici.callbacks.AttentionPenaltyMonitor method) (amici.callbacks.ModelInterpretationLogging method) test_indices (amici.AMICI property) to() (amici.AMICIModule method) to_device() (amici.AMICI method) to_empty() (amici.AMICIModule method) train() (amici.AMICI method) (amici.AMICIModule method) train_indices (amici.AMICI property) type() (amici.AMICIModule method) V validation_indices (amici.AMICI property) view_anndata_setup() (amici.AMICI method) view_setup_args() (amici.AMICI static method) X xpu() (amici.AMICIModule method) Z zero_grad() (amici.AMICIModule method)