Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | V | W | X | Z _ __init__() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) A add_module() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) adversarial() (ladder.models.scvi_variants.Patches method), [1] anndata (ladder.scripts.workflows.BaseWorkflow attribute) AnndataConverter (class in ladder.data.real_data) apply() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) B BaseWorkflow (class in ladder.scripts.workflows) batch_key (ladder.scripts.workflows.BaseWorkflow attribute) batch_mapping (ladder.scripts.workflows.BaseWorkflow attribute) bfloat16() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) buffers() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) C calc_asw() (in module ladder.scripts.metrics) call_super_init (ladder.models.scvi_variants.Patches attribute) (ladder.models.scvi_variants.SCANVI attribute) (ladder.models.scvi_variants.SCVI attribute) cell_type_label_key (ladder.scripts.workflows.BaseWorkflow attribute) children() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) compile() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) config (ladder.scripts.workflows.BaseWorkflow attribute) construct_labels() (in module ladder.data.real_data) converter (ladder.scripts.workflows.BaseWorkflow attribute) cpu() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) CrossConditionWorkflow (class in ladder.scripts.workflows) cuda() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) D dataset (ladder.scripts.workflows.BaseWorkflow attribute) df_view (ladder.data.real_data.MetadataConverter attribute) distrib_dataset() (in module ladder.data.real_data) double() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) dump_patches (ladder.models.scvi_variants.Patches attribute) (ladder.models.scvi_variants.SCANVI attribute) (ladder.models.scvi_variants.SCVI attribute) E eval() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) evaluate_reconstruction() (ladder.scripts.workflows.BaseWorkflow method), [1] (ladder.scripts.workflows.CrossConditionWorkflow method) (ladder.scripts.workflows.InterpretableWorkflow method) evaluate_separability() (ladder.scripts.workflows.BaseWorkflow method), [1] (ladder.scripts.workflows.CrossConditionWorkflow method) (ladder.scripts.workflows.InterpretableWorkflow method) evaluate_transfer() (ladder.scripts.workflows.CrossConditionWorkflow method), [1] extra_repr() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) F factors (ladder.scripts.workflows.BaseWorkflow attribute) float() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) forward() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) G gen_profile_reproduction() (in module ladder.scripts.metrics) generate() (ladder.models.scvi_variants.Patches method), [1] (ladder.models.scvi_variants.SCANVI method), [1] (ladder.models.scvi_variants.SCVI method), [1] get_buffer() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) get_common_loadings() (ladder.scripts.workflows.InterpretableWorkflow method), [1] get_conditional_loadings() (ladder.scripts.workflows.InterpretableWorkflow method), [1] get_data() (in module ladder.data.builtin_data) get_device() (in module ladder.scripts.training) get_extra_state() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) get_normalized_profile() (in module ladder.scripts.metrics) get_parameter() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) get_reproduction_error() (in module ladder.scripts.metrics) get_submodule() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) get_weights() (ladder.models.scvi_variants.Patches method), [1] (ladder.models.scvi_variants.SCANVI method), [1] (ladder.models.scvi_variants.SCVI method), [1] guide() (ladder.models.scvi_variants.Patches method), [1] (ladder.models.scvi_variants.SCANVI method), [1] (ladder.models.scvi_variants.SCVI method), [1] H half() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) I InterpretableWorkflow (class in ladder.scripts.workflows) ipu() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) K kmeans_ari() (in module ladder.scripts.metrics) kmeans_nmi() (in module ladder.scripts.metrics) knn_error() (in module ladder.scripts.metrics) L l_mean (ladder.scripts.workflows.BaseWorkflow attribute) l_scale (ladder.scripts.workflows.BaseWorkflow attribute) label_style (ladder.scripts.workflows.BaseWorkflow attribute) ladder.data.builtin_data module ladder.data.real_data module ladder.models.scvi_variants module ladder.scripts.metrics module ladder.scripts.training module ladder.scripts.workflows module, [1], [2] latent_dim (ladder.scripts.workflows.BaseWorkflow attribute) len_attrs (ladder.scripts.workflows.BaseWorkflow attribute) levels (ladder.scripts.workflows.BaseWorkflow attribute) load() (ladder.models.scvi_variants.Patches method), [1] (ladder.models.scvi_variants.SCANVI method), [1] (ladder.models.scvi_variants.SCVI method), [1] load_model() (ladder.scripts.workflows.BaseWorkflow method), [1] (ladder.scripts.workflows.CrossConditionWorkflow method) (ladder.scripts.workflows.InterpretableWorkflow method) load_state_dict() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) M map_to_anndat() (ladder.data.real_data.AnndataConverter method) map_to_df() (ladder.data.real_data.AnndataConverter method) (ladder.data.real_data.MetadataConverter method) MetadataConverter (class in ladder.data.real_data) METRICS_REG (ladder.scripts.workflows.BaseWorkflow attribute) (ladder.scripts.workflows.CrossConditionWorkflow attribute) (ladder.scripts.workflows.InterpretableWorkflow attribute) minibatch_size (ladder.scripts.workflows.BaseWorkflow attribute) model (ladder.scripts.workflows.BaseWorkflow attribute) model() (ladder.models.scvi_variants.Patches method), [1] (ladder.models.scvi_variants.SCANVI method), [1] (ladder.models.scvi_variants.SCVI method), [1] model_type (ladder.scripts.workflows.BaseWorkflow attribute) module ladder.data.builtin_data ladder.data.real_data ladder.models.scvi_variants ladder.scripts.metrics ladder.scripts.training ladder.scripts.workflows, [1], [2] modules() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) mtia() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) N named_buffers() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) named_children() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) named_modules() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) named_parameters() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) num_cols (ladder.data.real_data.MetadataConverter attribute) O OPT_CLASS1 (ladder.scripts.workflows.BaseWorkflow attribute) (ladder.scripts.workflows.CrossConditionWorkflow attribute) (ladder.scripts.workflows.InterpretableWorkflow attribute) OPT_CLASS2 (ladder.scripts.workflows.BaseWorkflow attribute) (ladder.scripts.workflows.CrossConditionWorkflow attribute) (ladder.scripts.workflows.InterpretableWorkflow attribute) OPT_DEFAULTS (ladder.scripts.workflows.BaseWorkflow attribute) (ladder.scripts.workflows.CrossConditionWorkflow attribute) (ladder.scripts.workflows.InterpretableWorkflow attribute) OPT_LIST (ladder.scripts.workflows.BaseWorkflow attribute) (ladder.scripts.workflows.CrossConditionWorkflow attribute) (ladder.scripts.workflows.InterpretableWorkflow attribute) optim_args (ladder.scripts.workflows.BaseWorkflow attribute) P parameters() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) Patches (class in ladder.models.scvi_variants) plot_loss() (ladder.scripts.workflows.BaseWorkflow method), [1] (ladder.scripts.workflows.CrossConditionWorkflow method) (ladder.scripts.workflows.InterpretableWorkflow method) predictive (ladder.scripts.workflows.BaseWorkflow attribute) prep_model() (ladder.scripts.workflows.BaseWorkflow method), [1] (ladder.scripts.workflows.CrossConditionWorkflow method) (ladder.scripts.workflows.InterpretableWorkflow method) preprocess_anndata() (in module ladder.data.real_data) R random_seed (ladder.scripts.workflows.BaseWorkflow attribute) reconstruction (ladder.scripts.workflows.BaseWorkflow attribute) register_backward_hook() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_buffer() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_forward_hook() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_forward_pre_hook() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_full_backward_hook() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_full_backward_pre_hook() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_load_state_dict_post_hook() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_load_state_dict_pre_hook() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_module() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_parameter() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_state_dict_post_hook() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) register_state_dict_pre_hook() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) requires_grad_() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) run_model() (ladder.scripts.workflows.BaseWorkflow method), [1] (ladder.scripts.workflows.CrossConditionWorkflow method) (ladder.scripts.workflows.InterpretableWorkflow method) S save() (ladder.models.scvi_variants.Patches method), [1] (ladder.models.scvi_variants.SCANVI method), [1] (ladder.models.scvi_variants.SCVI method), [1] save_model() (ladder.scripts.workflows.BaseWorkflow method), [1] (ladder.scripts.workflows.CrossConditionWorkflow method) (ladder.scripts.workflows.InterpretableWorkflow method) SCANVI (class in ladder.models.scvi_variants) SCVI (class in ladder.models.scvi_variants) SEP_METRICS_REG (ladder.scripts.workflows.BaseWorkflow attribute) (ladder.scripts.workflows.CrossConditionWorkflow attribute) (ladder.scripts.workflows.InterpretableWorkflow attribute) set_extra_state() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) set_submodule() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) share_memory() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) state_dict() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) T T_destination (ladder.models.scvi_variants.Patches attribute) (ladder.models.scvi_variants.SCANVI attribute) (ladder.models.scvi_variants.SCVI attribute) test_loss (ladder.scripts.workflows.BaseWorkflow attribute) test_set (ladder.scripts.workflows.BaseWorkflow attribute) to() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) to_empty() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) train() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) train_loss (ladder.scripts.workflows.BaseWorkflow attribute) train_pyro() (in module ladder.scripts.training) train_pyro_disjoint_param() (in module ladder.scripts.training) train_set (ladder.scripts.workflows.BaseWorkflow attribute) training (ladder.models.scvi_variants.Patches attribute) (ladder.models.scvi_variants.SCANVI attribute) (ladder.models.scvi_variants.SCVI attribute) type() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) V verbose (ladder.scripts.workflows.BaseWorkflow attribute) W w_dim (ladder.scripts.workflows.BaseWorkflow attribute) write_embeddings() (ladder.scripts.workflows.BaseWorkflow method), [1] (ladder.scripts.workflows.CrossConditionWorkflow method) (ladder.scripts.workflows.InterpretableWorkflow method) X xpu() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method) Z zero_grad() (ladder.models.scvi_variants.Patches method) (ladder.models.scvi_variants.SCANVI method) (ladder.models.scvi_variants.SCVI method)