Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | U | V | X | Z A add_module() (mmcontext.models.mmcontextencoder.MMContextEncoder method) annotate_omics_data() (mmcontext.eval.query_annotate.OmicsQueryAnnotator method), [1] apply() (mmcontext.models.mmcontextencoder.MMContextEncoder method) B bfloat16() (mmcontext.models.mmcontextencoder.MMContextEncoder method) bins (mmcontext.eval.label_similarity.LabelSimilarity attribute), [1] buffers() (mmcontext.models.mmcontextencoder.MMContextEncoder method) C cache_results (mmcontext.eval.label_similarity.LabelSimilarity attribute), [1] call_super_init (mmcontext.models.mmcontextencoder.MMContextEncoder attribute) children() (mmcontext.models.mmcontextencoder.MMContextEncoder method) compile() (mmcontext.models.mmcontextencoder.MMContextEncoder method) compute() (mmcontext.eval.label_similarity.LabelSimilarity method), [1] compute_average_scores() (mmcontext.eval.evaluate_scib.scibEvaluator method), [1] compute_metrics() (mmcontext.eval.evaluate_scib.scibEvaluator method), [1] compute_metrics_in_parallel() (mmcontext.eval.evaluate_scib.scibEvaluator method), [1] config_file_name (mmcontext.models.mmcontextencoder.MMContextEncoder attribute) config_keys (mmcontext.models.mmcontextencoder.MMContextEncoder attribute), [1] cpu() (mmcontext.models.mmcontextencoder.MMContextEncoder method) cuda() (mmcontext.models.mmcontextencoder.MMContextEncoder method) D double() (mmcontext.models.mmcontextencoder.MMContextEncoder method) dump_patches (mmcontext.models.mmcontextencoder.MMContextEncoder attribute) E eval() (mmcontext.models.mmcontextencoder.MMContextEncoder method) evaluate() (mmcontext.eval.evaluate_scib.scibEvaluator method), [1] extra_repr() (mmcontext.models.mmcontextencoder.MMContextEncoder method) F float() (mmcontext.models.mmcontextencoder.MMContextEncoder method) forward() (mmcontext.models.mmcontextencoder.MMContextEncoder method), [1] forward_kwargs (mmcontext.models.mmcontextencoder.MMContextEncoder attribute) G get_buffer() (mmcontext.models.mmcontextencoder.MMContextEncoder method) get_config_dict() (mmcontext.models.mmcontextencoder.MMContextEncoder method) get_extra_state() (mmcontext.models.mmcontextencoder.MMContextEncoder method) get_initial_embeddings() (mmcontext.models.mmcontextencoder.MMContextEncoder static method), [1] get_parameter() (mmcontext.models.mmcontextencoder.MMContextEncoder method) get_sentence_embedding_dimension() (mmcontext.models.mmcontextencoder.MMContextEncoder method), [1] get_submodule() (mmcontext.models.mmcontextencoder.MMContextEncoder method) H half() (mmcontext.models.mmcontextencoder.MMContextEncoder method) I ipu() (mmcontext.models.mmcontextencoder.MMContextEncoder method) L LabelSimilarity (class in mmcontext.eval.label_similarity) load() (mmcontext.models.mmcontextencoder.MMContextEncoder class method), [1] load_config() (mmcontext.models.mmcontextencoder.MMContextEncoder class method) load_dir_path() (mmcontext.models.mmcontextencoder.MMContextEncoder static method) load_file_path() (mmcontext.models.mmcontextencoder.MMContextEncoder static method) load_state_dict() (mmcontext.models.mmcontextencoder.MMContextEncoder method) load_torch_weights() (mmcontext.models.mmcontextencoder.MMContextEncoder class method) M mmcontext.eval module mmcontext.models module mmcontext.pp module MMContextEncoder (class in mmcontext.models.mmcontextencoder) MMContextProcessor (class in mmcontext.models.mmcontextencoder) module mmcontext.eval mmcontext.models mmcontext.pp modules() (mmcontext.models.mmcontextencoder.MMContextEncoder method) mtia() (mmcontext.models.mmcontextencoder.MMContextEncoder method) N name (mmcontext.eval.label_similarity.LabelSimilarity attribute), [1] named_buffers() (mmcontext.models.mmcontextencoder.MMContextEncoder method) named_children() (mmcontext.models.mmcontextencoder.MMContextEncoder method) named_modules() (mmcontext.models.mmcontextencoder.MMContextEncoder method) named_parameters() (mmcontext.models.mmcontextencoder.MMContextEncoder method) O OmicsQueryAnnotator (class in mmcontext.eval.query_annotate) P parameters() (mmcontext.models.mmcontextencoder.MMContextEncoder method) plot() (mmcontext.eval.label_similarity.LabelSimilarity method), [1] plot_only() (mmcontext.eval.label_similarity.LabelSimilarity method), [1] plot_query_scores_with_labels_umap() (in module mmcontext.pl.plotting) prepare_ds() (mmcontext.models.mmcontextencoder.MMContextEncoder method), [1] produces_plot (mmcontext.eval.label_similarity.LabelSimilarity attribute), [1] Q query_with_text() (mmcontext.eval.query_annotate.OmicsQueryAnnotator method), [1] R random_initial_embeddings() (mmcontext.models.mmcontextencoder.MMContextEncoder method), [1] register_backward_hook() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_buffer() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_forward_hook() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_forward_pre_hook() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_full_backward_hook() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_full_backward_pre_hook() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_initial_embeddings() (mmcontext.models.mmcontextencoder.MMContextEncoder method), [1] register_load_state_dict_post_hook() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_load_state_dict_pre_hook() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_module() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_parameter() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_state_dict_post_hook() (mmcontext.models.mmcontextencoder.MMContextEncoder method) register_state_dict_pre_hook() (mmcontext.models.mmcontextencoder.MMContextEncoder method) registered_data_origin (mmcontext.models.mmcontextencoder.MMContextEncoder attribute) (mmcontext.models.mmcontextencoder.MMContextEncoder property) registered_input_dim (mmcontext.models.mmcontextencoder.MMContextEncoder attribute) (mmcontext.models.mmcontextencoder.MMContextEncoder property) requires_grad_() (mmcontext.models.mmcontextencoder.MMContextEncoder method) requires_pair (mmcontext.eval.label_similarity.LabelSimilarity attribute), [1] S save() (mmcontext.models.mmcontextencoder.MMContextEncoder method), [1] save_config() (mmcontext.models.mmcontextencoder.MMContextEncoder method) save_in_root (mmcontext.models.mmcontextencoder.MMContextEncoder attribute) save_torch_weights() (mmcontext.models.mmcontextencoder.MMContextEncoder method) scibEvaluator (class in mmcontext.eval.evaluate_scib) set_extra_state() (mmcontext.models.mmcontextencoder.MMContextEncoder method) set_submodule() (mmcontext.models.mmcontextencoder.MMContextEncoder method) share_memory() (mmcontext.models.mmcontextencoder.MMContextEncoder method) similarity (mmcontext.eval.label_similarity.LabelSimilarity attribute), [1] skip_plotting (mmcontext.eval.label_similarity.LabelSimilarity attribute), [1] state_dict() (mmcontext.models.mmcontextencoder.MMContextEncoder method) T T_destination (mmcontext.models.mmcontextencoder.MMContextEncoder attribute) to() (mmcontext.models.mmcontextencoder.MMContextEncoder method) to_empty() (mmcontext.models.mmcontextencoder.MMContextEncoder method) tokenize() (mmcontext.models.mmcontextencoder.MMContextEncoder method), [1] (mmcontext.models.mmcontextencoder.MMContextProcessor method), [1] tokenizer (mmcontext.models.mmcontextencoder.MMContextEncoder attribute) (mmcontext.models.mmcontextencoder.MMContextEncoder property) train() (mmcontext.models.mmcontextencoder.MMContextEncoder method) training (mmcontext.models.mmcontextencoder.MMContextEncoder attribute) type() (mmcontext.models.mmcontextencoder.MMContextEncoder method) U umap_min_dist (mmcontext.eval.label_similarity.LabelSimilarity attribute), [1] umap_n_neighbors (mmcontext.eval.label_similarity.LabelSimilarity attribute), [1] umap_random_state (mmcontext.eval.label_similarity.LabelSimilarity attribute), [1] update_omics_lookup() (mmcontext.models.mmcontextencoder.MMContextProcessor method), [1] V VALID_DATA_ORIGINS (mmcontext.models.mmcontextencoder.MMContextEncoder attribute), [1] X xpu() (mmcontext.models.mmcontextencoder.MMContextEncoder method) Z zero_grad() (mmcontext.models.mmcontextencoder.MMContextEncoder method)