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Installation
Usage
Benchmarking tokenizers for cross-tissue generalization
Implementing a novel scFM tokenizer
API
Heimdall.trainer.HeimdallTrainer
Heimdall.trainer.HeimdallTrainer.check_flash_attn
Heimdall.trainer.HeimdallTrainer.fit
Heimdall.trainer.HeimdallTrainer.fit_model
Heimdall.trainer.HeimdallTrainer.get_checkpoint_directory
Heimdall.trainer.HeimdallTrainer.get_latest_checkpoint_path
Heimdall.trainer.HeimdallTrainer.get_outputs_and_loss
Heimdall.trainer.HeimdallTrainer.get_precomputed_outputs
Heimdall.trainer.HeimdallTrainer.get_pretrained_load_path
Heimdall.trainer.HeimdallTrainer.initialize_checkpointing
Heimdall.trainer.HeimdallTrainer.instantiate_loss_functions_from_config
Heimdall.trainer.HeimdallTrainer.iterate_dataloader
Heimdall.trainer.HeimdallTrainer.load_checkpoint
Heimdall.trainer.HeimdallTrainer.load_pretrained
Heimdall.trainer.HeimdallTrainer.load_trainer_state
Heimdall.trainer.HeimdallTrainer.print_r0
Heimdall.trainer.HeimdallTrainer.save_checkpoint
Heimdall.trainer.HeimdallTrainer.save_precomputed_outputs
Heimdall.trainer.HeimdallTrainer.save_umaps
Heimdall.trainer.HeimdallTrainer.setup_class_names_and_num_labels
Heimdall.trainer.HeimdallTrainer.train_epoch
Heimdall.trainer.HeimdallTrainer.validate_model
Heimdall.fg.Fg
Heimdall.fg.Fg.load_from_cache
Heimdall.fg.Fg.prepare_embedding_parameters
Heimdall.fg.Fg.preprocess_embeddings
Heimdall.fg.IdentityFg
Heimdall.fg.PretrainedFg
Heimdall.fg.TorchTensorFg
Heimdall.fg.CSVFg
Heimdall.fe.Fe
Heimdall.fe.Fe.load_from_cache
Heimdall.fe.Fe.prepare_embedding_parameters
Heimdall.fe.Fe.preprocess_embeddings
Heimdall.fe.IdentityFe
Heimdall.fe.ZeroFe
Heimdall.fe.BinningFe
Heimdall.fe.ScBERTBinningFe
Heimdall.fc.Fc
Heimdall.fc.DummyFc
Heimdall.fc.ChromosomeAwareFc
Heimdall.order.Order
Heimdall.order.ExpressionOrder
Heimdall.order.RandomOrder
Heimdall.order.ChromosomeOrder
Heimdall.tailor.Tailor
Heimdall.tailor.ReorderTailor
Heimdall.tailor.ChromosomeTailor
Heimdall.tailor.WeightedResampleTailor
Heimdall.tailor.ChromosomeBlockTailor
Heimdall.reduce.Reduce
Heimdall.reduce.IdentityReduce
Heimdall.reduce.SumReduce
Heimdall.reduce.ChromosomeReduce
Heimdall.reduce.ChromosomeSumReduce
Heimdall.task.Task
Heimdall.task.Task.clear_cache_path
Heimdall.task.Task.collate
Heimdall.task.Task.from_cache
Heimdall.task.Task.get_cache_path
Heimdall.task.Task.get_inputs
Heimdall.task.Task.on_batch
Heimdall.task.Task.setup_labels
Heimdall.task.Task.to_cache
Heimdall.task.SingleInstanceTask
Heimdall.task.SingleInstanceTask.setup_labels
Heimdall.task.PairedInstanceTask
Heimdall.task.PairedInstanceTask.setup_labels
Heimdall.task.SeqMaskedMLMTask
Heimdall.task.Tasklist
Heimdall.task.Tasklist.set_unique_properties
Heimdall.models.HeimdallModel
Heimdall.models.HeimdallModel.encode_cell
Heimdall.models.HeimdallModel.forward
.rst
.pdf
Heimdall.task.SeqMaskedMLMTask.shuffle
Contents
SeqMaskedMLMTask.shuffle
Heimdall.task.SeqMaskedMLMTask.shuffle
#
SeqMaskedMLMTask.
shuffle
#
Contents
SeqMaskedMLMTask.shuffle