Index

A

Annotation (class in bend.utils.retrieve_from_bed)

AWDLSTMEmbedder (class in bend.utils.embedders)

B

base_model_prefix (bend.models.dilated_cnn.ConvNetPreTrainedModel attribute) BaseEmbedder (class in bend.utils.embedders) BaseTrainer (class in bend.utils.task_trainer) BCEWithLogitsLoss (class in bend.utils.task_trainer) bend module bend.io module, [1] bend.models module, [1] bend.models.dilated_cnn module bend.models.downstream module

bend.utils module bend.utils.data_downstream module bend.utils.download module bend.utils.embedders module bend.utils.retrieve_from_bed module bend.utils.sequences module bend.utils.task_trainer module

C

CaduceusEmbedder (class in bend.utils.embedders) CNN (class in bend.models.downstream) collate_fn_pad_to_longest() (in module bend.utils.data_downstream) config_class (bend.models.dilated_cnn.ConvNetPreTrainedModel attribute) ConvLayer (class in bend.models.dilated_cnn) ConvNetConfig (class in bend.models.dilated_cnn) ConvNetEmbedder (class in bend.utils.embedders)

ConvNetForMaskedLM (class in bend.models.dilated_cnn) ConvNetForSupervised (class in bend.models.downstream) ConvNetModel (class in bend.models.dilated_cnn) ConvNetOnlyMLMHead (class in bend.models.dilated_cnn) ConvNetPreTrainedModel (class in bend.models.dilated_cnn) count_nucleotides() (in module bend.utils.sequences) CrossEntropyLoss (class in bend.utils.task_trainer) CustomDataParallel (class in bend.models.downstream)

D

DNABert2Embedder (class in bend.utils.embedders) DNABertEmbedder (class in bend.utils.embedders)

download_model() (in module bend.utils.download) download_model_zenodo() (in module bend.utils.download)

E

embed() (bend.utils.embedders.AWDLSTMEmbedder method) (bend.utils.embedders.BaseEmbedder method) (bend.utils.embedders.CaduceusEmbedder method) (bend.utils.embedders.ConvNetEmbedder method) (bend.utils.embedders.DNABert2Embedder method) (bend.utils.embedders.DNABertEmbedder method) (bend.utils.embedders.GENALMEmbedder method) (bend.utils.embedders.GPNEmbedder method) (bend.utils.embedders.GROVEREmbedder method) (bend.utils.embedders.HyenaDNAEmbedder method) (bend.utils.embedders.NucleotideTransformerEmbedder method) (bend.utils.embedders.OneHotEmbedder method)

EncodeSequence (class in bend.utils.sequences) extend_segments() (bend.utils.retrieve_from_bed.Annotation method) extra_repr() (bend.models.dilated_cnn.OneHotEmbedding method)

F

forward() (bend.models.dilated_cnn.ConvLayer method) (bend.models.dilated_cnn.ConvNetForMaskedLM method) (bend.models.dilated_cnn.ConvNetModel method) (bend.models.dilated_cnn.ConvNetOnlyMLMHead method) (bend.models.dilated_cnn.OneHotEmbedding method) (bend.models.dilated_cnn.TransposeLayer method) (bend.models.downstream.CNN method) (bend.models.downstream.ConvNetForSupervised method) (bend.models.downstream.TransposeLayer method) (bend.models.downstream.UpsampleLayer method) (bend.utils.task_trainer.BCEWithLogitsLoss method) (bend.utils.task_trainer.CrossEntropyLoss method) (bend.utils.task_trainer.MSELoss method) (bend.utils.task_trainer.PoissonLoss method)

G

GENALMEmbedder (class in bend.utils.embedders) get_data() (in module bend.utils.data_downstream) get_dna_segment() (bend.utils.retrieve_from_bed.Annotation method)

get_item() (bend.utils.retrieve_from_bed.Annotation method) GPNEmbedder (class in bend.utils.embedders) GROVEREmbedder (class in bend.utils.embedders)

H

HyenaDNAEmbedder (class in bend.utils.embedders)

I

inverse_transform_integer() (bend.utils.sequences.EncodeSequence method)

L

load_model() (bend.utils.embedders.AWDLSTMEmbedder method) (bend.utils.embedders.BaseEmbedder method) (bend.utils.embedders.CaduceusEmbedder method) (bend.utils.embedders.ConvNetEmbedder method) (bend.utils.embedders.DNABert2Embedder method) (bend.utils.embedders.DNABertEmbedder method) (bend.utils.embedders.GENALMEmbedder method) (bend.utils.embedders.GPNEmbedder method) (bend.utils.embedders.GROVEREmbedder method) (bend.utils.embedders.HyenaDNAEmbedder method) (bend.utils.embedders.NucleotideTransformerEmbedder method)

M

max_match_tokenize() (bend.utils.embedders.GROVEREmbedder method) model_type (bend.models.dilated_cnn.ConvNetConfig attribute) module bend bend.io, [1] bend.models, [1] bend.models.dilated_cnn bend.models.downstream bend.utils bend.utils.data_downstream bend.utils.download bend.utils.embedders bend.utils.retrieve_from_bed bend.utils.sequences bend.utils.task_trainer

MSELoss (class in bend.utils.task_trainer)

N

NucleotideTransformerEmbedder (class in bend.utils.embedders)

O

OneHotEmbedder (class in bend.utils.embedders)

OneHotEmbedding (class in bend.models.dilated_cnn)

P

pad_to_longest() (in module bend.utils.data_downstream)

PoissonLoss (class in bend.utils.task_trainer)

R

reduce_last_dim() (bend.utils.sequences.EncodeSequence static method)

return_dataloader() (in module bend.utils.data_downstream)

T

test() (bend.utils.task_trainer.BaseTrainer method) train() (bend.utils.task_trainer.BaseTrainer method) train_epoch() (bend.utils.task_trainer.BaseTrainer method)

train_step() (bend.utils.task_trainer.BaseTrainer method) transform_integer() (bend.utils.sequences.EncodeSequence method) TransposeLayer (class in bend.models.dilated_cnn) (class in bend.models.downstream)

U

UpsampleLayer (class in bend.models.downstream)

V

validate() (bend.utils.task_trainer.BaseTrainer method)

W

worker_init_fn() (in module bend.utils.data_downstream)