Index

B

beam_search() (reglm.lightning.LightningModel method)

C

CharDataset (class in reglm.dataset) compute_accuracy() (in module reglm.metrics)

compute_accuracy_on_dataset() (reglm.lightning.LightningModel method) configure_optimizers() (reglm.lightning.LightningModel method) (reglm.regression.EnformerModel method)

D

decode() (reglm.dataset.CharDataset method) (reglm.lightning.LightningModel method)

E

encode() (reglm.lightning.LightningModel method) encode_label() (reglm.dataset.CharDataset method) encode_labels() (reglm.lightning.LightningModel method)

encode_seq() (reglm.dataset.CharDataset method) encode_seqs() (reglm.lightning.LightningModel method) EnformerModel (class in reglm.regression) evolve() (in module reglm.evolve)

F

filter_base_probs() (reglm.lightning.LightningModel method) forward() (reglm.lightning.LightningModel method) (reglm.regression.EnformerModel method) (reglm.regression.MultiTaskEnformerModel method)

G

generate() (reglm.lightning.LightningModel method) generate_random_sequences() (in module reglm.interpret)

get_label_tokens() (in module reglm.utils) get_percentiles() (in module reglm.utils)

I

ISM() (in module reglm.interpret) ISM_at_pos() (in module reglm.interpret)

ISM_predict() (in module reglm.interpret) ISM_score() (in module reglm.interpret)

L

LightningModel (class in reglm.lightning)

load_pretrained_model() (in module reglm.lightning)

M

matrix_to_scores() (in module reglm.utils) module reglm reglm.dataset reglm.evolve reglm.interpret reglm.lightning reglm.metrics reglm.regression reglm.utils

motif_insert() (in module reglm.interpret) motif_likelihood() (in module reglm.interpret) MultiTaskEnformerModel (class in reglm.regression)

N

normalize_filtered_probs() (reglm.lightning.LightningModel method)

O

on_save_checkpoint() (reglm.lightning.LightningModel method)

P

P_labels_given_seqs() (reglm.lightning.LightningModel method) P_seqs() (reglm.lightning.LightningModel method) P_seqs_given_labels() (reglm.lightning.LightningModel method)

predict_on_dataset() (reglm.regression.EnformerModel method) (reglm.regression.MultiTaskEnformerModel method) probs_to_likelihood() (reglm.lightning.LightningModel method)

R

reglm module reglm.dataset module reglm.evolve module reglm.interpret module

reglm.lightning module reglm.metrics module reglm.regression module reglm.utils module

S

sample_idxs() (reglm.lightning.LightningModel method) scores_to_matrix() (in module reglm.utils)

SeqDataset (class in reglm.regression) seqs_to_idxs() (in module reglm.utils)

T

threshold_probs() (reglm.lightning.LightningModel method) tokenize() (in module reglm.utils) train_on_dataset() (reglm.lightning.LightningModel method) (reglm.regression.EnformerModel method)

training_step() (reglm.lightning.LightningModel method) (reglm.regression.EnformerModel method)

V

validation_epoch_end() (reglm.lightning.LightningModel method) (reglm.regression.EnformerModel method)

validation_step() (reglm.lightning.LightningModel method) (reglm.regression.EnformerModel method)