Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | R | S | T | V | W | Z A adata (Heimdall.fc.Fc property) (Heimdall.fe.Fe property) (Heimdall.fg.Fg property) B binning() (Heimdall.fe.BinningFe method) (Heimdall.fe.ScBERTBinningFe method) BinningFe (class in Heimdall.fe) C check_flash_attn() (Heimdall.trainer.HeimdallTrainer method) CHECKPOINT_KEYS (Heimdall.trainer.HeimdallTrainer attribute) ChromosomeAwareFc (class in Heimdall.fc) ChromosomeBlockTailor (class in Heimdall.tailor) ChromosomeOrder (class in Heimdall.order) ChromosomeReduce (class in Heimdall.reduce) ChromosomeSumReduce (class in Heimdall.reduce) ChromosomeTailor (class in Heimdall.tailor) clear_cache_path() (Heimdall.task.Task method) collate() (Heimdall.task.Task method) CSVFg (class in Heimdall.fg) D data (Heimdall.task.PairedInstanceTask attribute) (Heimdall.task.SeqMaskedMLMTask attribute) (Heimdall.task.SingleInstanceTask attribute) (Heimdall.task.Task attribute) (Heimdall.trainer.HeimdallTrainer property) dataset_cfg (Heimdall.trainer.HeimdallTrainer property) dtype (Heimdall.models.HeimdallModel property) DummyFc (class in Heimdall.fc) E encode_cell() (Heimdall.models.HeimdallModel method) ExpressionOrder (class in Heimdall.order) extract_gene_positions() (Heimdall.fc.ChromosomeAwareFc method) F Fc (class in Heimdall.fc) fc_cfg (Heimdall.trainer.HeimdallTrainer property) Fe (class in Heimdall.fe) fe_cfg (Heimdall.trainer.HeimdallTrainer property) Fg (class in Heimdall.fg) fg_cfg (Heimdall.trainer.HeimdallTrainer property) fit() (Heimdall.trainer.HeimdallTrainer method) fit_model() (Heimdall.trainer.HeimdallTrainer method) forward() (Heimdall.models.HeimdallModel method) from_cache() (Heimdall.task.Task method) G gene_panel_idx (Heimdall.fe.Fe property) get_cache_path() (Heimdall.task.Task method) get_checkpoint_directory() (Heimdall.trainer.HeimdallTrainer method) get_inputs() (Heimdall.task.Task method) get_latest_checkpoint_path() (Heimdall.trainer.HeimdallTrainer method) get_outputs_and_loss() (Heimdall.trainer.HeimdallTrainer method) get_precomputed (Heimdall.trainer.HeimdallTrainer property) get_precomputed_outputs() (Heimdall.trainer.HeimdallTrainer method) get_pretrained_load_path() (Heimdall.trainer.HeimdallTrainer method) H head_config (Heimdall.task.PairedInstanceTask attribute) (Heimdall.task.SeqMaskedMLMTask attribute) (Heimdall.task.SingleInstanceTask attribute) (Heimdall.task.Task attribute) Heimdall module Heimdall.fc module Heimdall.fe module Heimdall.fg module Heimdall.models module Heimdall.order module Heimdall.reduce module Heimdall.tailor module Heimdall.task module Heimdall.trainer module HeimdallModel (class in Heimdall.models) HeimdallTrainer (class in Heimdall.trainer) I identity_valid_mask (Heimdall.fg.Fg property) IdentityFe (class in Heimdall.fe) IdentityFg (class in Heimdall.fg) IdentityReduce (class in Heimdall.reduce) idx (Heimdall.task.Task property) initialize_checkpointing() (Heimdall.trainer.HeimdallTrainer method) instantiate_loss_functions_from_config() (Heimdall.trainer.HeimdallTrainer method) interaction_type (Heimdall.task.Task attribute) iterate_dataloader() (Heimdall.trainer.HeimdallTrainer method) L label_col_name (Heimdall.task.Task attribute) label_obsm_name (Heimdall.task.Task attribute) labels (Heimdall.task.Task property) limit() (Heimdall.tailor.ChromosomeBlockTailor method) (Heimdall.tailor.ChromosomeTailor method) (Heimdall.tailor.ReorderTailor method) (Heimdall.tailor.Tailor method) (Heimdall.tailor.WeightedResampleTailor method) load_checkpoint() (Heimdall.trainer.HeimdallTrainer method) load_embeddings() (Heimdall.fg.CSVFg method) (Heimdall.fg.PretrainedFg method) (Heimdall.fg.TorchTensorFg method) load_from_cache() (Heimdall.fe.Fe method) (Heimdall.fg.Fg method) load_pretrained() (Heimdall.trainer.HeimdallTrainer method) load_trainer_state() (Heimdall.trainer.HeimdallTrainer method) local_cfg (Heimdall.trainer.HeimdallTrainer property) loss_config (Heimdall.task.PairedInstanceTask attribute) (Heimdall.task.SeqMaskedMLMTask attribute) (Heimdall.task.SingleInstanceTask attribute) (Heimdall.task.Task attribute) M mask_token (Heimdall.task.SeqMaskedMLMTask property) metrics (Heimdall.task.PairedInstanceTask attribute) (Heimdall.task.SeqMaskedMLMTask attribute) (Heimdall.task.SingleInstanceTask attribute) (Heimdall.task.Task attribute) model_cfg (Heimdall.trainer.HeimdallTrainer property) module Heimdall Heimdall.fc Heimdall.fe Heimdall.fg Heimdall.models Heimdall.order Heimdall.reduce Heimdall.tailor Heimdall.task Heimdall.trainer N num_tasks (Heimdall.task.Task property) O on_batch() (Heimdall.task.Task method) optimizer_cfg (Heimdall.trainer.HeimdallTrainer property) Order (class in Heimdall.order) P pad() (Heimdall.tailor.ChromosomeBlockTailor method) (Heimdall.tailor.ChromosomeTailor method) (Heimdall.tailor.ReorderTailor method) (Heimdall.tailor.Tailor method) (Heimdall.tailor.WeightedResampleTailor method) PairedInstanceTask (class in Heimdall.task) prepare_embedding_parameters() (Heimdall.fe.Fe method) (Heimdall.fg.Fg method) preprocess_embeddings() (Heimdall.fe.Fe method) (Heimdall.fg.Fg method) (Heimdall.fg.IdentityFg method) (Heimdall.fg.PretrainedFg method) PretrainedFg (class in Heimdall.fg) print_r0() (Heimdall.trainer.HeimdallTrainer method) PROPERTIES (Heimdall.task.Tasklist attribute) R RandomOrder (class in Heimdall.order) Reduce (class in Heimdall.reduce) reducer_config (Heimdall.task.Task attribute) ReorderTailor (class in Heimdall.tailor) S save_checkpoint() (Heimdall.trainer.HeimdallTrainer method) save_precomputed (Heimdall.trainer.HeimdallTrainer property) save_precomputed_outputs() (Heimdall.trainer.HeimdallTrainer method) save_umaps() (Heimdall.trainer.HeimdallTrainer method) ScBERTBinningFe (class in Heimdall.fe) scheduler_cfg (Heimdall.trainer.HeimdallTrainer property) SeqMaskedMLMTask (class in Heimdall.task) set_unique_properties() (Heimdall.task.Tasklist method) setup_class_names_and_num_labels() (Heimdall.trainer.HeimdallTrainer method) setup_labels() (Heimdall.task.PairedInstanceTask method) (Heimdall.task.SingleInstanceTask method) (Heimdall.task.Task method) shuffle (Heimdall.task.PairedInstanceTask attribute) (Heimdall.task.SeqMaskedMLMTask attribute) (Heimdall.task.SingleInstanceTask attribute) (Heimdall.task.Task attribute) SingleInstanceTask (class in Heimdall.task) splits (Heimdall.task.Task attribute) SumReduce (class in Heimdall.reduce) T Tailor (class in Heimdall.tailor) Task (class in Heimdall.task) task_type (Heimdall.task.PairedInstanceTask attribute) (Heimdall.task.SeqMaskedMLMTask attribute) (Heimdall.task.SingleInstanceTask attribute) (Heimdall.task.Task attribute) Tasklist (class in Heimdall.task) to_cache() (Heimdall.task.Task method) top_k (Heimdall.task.Task attribute) TorchTensorFg (class in Heimdall.fg) track_metric (Heimdall.task.Task attribute) train_epoch() (Heimdall.trainer.HeimdallTrainer method) train_split (Heimdall.task.Task attribute) trainer_cfg (Heimdall.trainer.HeimdallTrainer property) training (Heimdall.models.HeimdallModel attribute) V validate_model() (Heimdall.trainer.HeimdallTrainer method) W weighted_resampling() (Heimdall.tailor.ChromosomeTailor method) (Heimdall.tailor.WeightedResampleTailor method) WeightedResampleTailor (class in Heimdall.tailor) Z ZeroFe (class in Heimdall.fe)