Index

_

_length (utils.utils.BaseRBPDataset attribute)

A

accuracy() (in module utils.metrics) ADPNet (class in utils.BRIDGE) ADPNetblock (class in utils.BRIDGE)

alt (variant_aware.ParsedHeader attribute) apply_complement() (in module utils.variant) attention_scores() (in module motif_construction.run_finetune) attribution() (in module utils.attribution_utils)

B

BaseRBPDataset (class in utils.utils) BRIDGE (class in utils.BRIDGE) bridge_cache (utils.variant.ModelHub attribute)

build_argparser() (in module variant_aware) build_dataset() (in module motif_construction.run_finetune) build_structure_tensor() (in module utils.structureFeatures) build_Transformer_embeddings() (in module utils.gen_transformer_embedding)

C

calculate_metrics() (in module utils.metrics) cell_line (variant_aware.ParsedHeader attribute) chrom (variant_aware.ParsedHeader attribute) coden() (in module utils.FeatureEncoding) concatenate() (in module utils.structureFeatures)

Conv1d (class in utils.conv_layer) Conv2d (class in utils.conv_layer) convert_one_hot() (in module utils.datautils) (in module utils.utils) convert_one_hot2() (in module utils.utils)

D

dealwithdata() (in module utils.FeatureEncoding) dealwithdata2() (in module utils.FeatureEncoding)

defineExperimentPaths() (in module utils.structureFeatures) device (utils.variant.ModelHub attribute) dpcp() (in module utils.FeatureEncoding)

E

end (variant_aware.ParsedHeader attribute)

extract_sequences_from_fa() (in module utils.motif_prior.motif_prior)

F

find_variant_index() (in module variant_aware) finished() (in module utils.datautils) fix_seed() (in module main) forward() (utils.BRIDGE.ADPNet method) (utils.BRIDGE.ADPNetblock method) (utils.BRIDGE.BRIDGE method) (utils.BRIDGE.multiscaleKAN method) (utils.conv_layer.Conv1d method) (utils.conv_layer.Conv2d method) (utils.conv_layer.SimpleConvKAN_1layer method) (utils.resnet.ResidualBlock1D method) (utils.resnet.ResidualBlock1D_ method) (utils.resnet.ResidualBlock2D method) (utils.resnet.ResidualBlock2D_ method) (utils.resnet.SEBlock method) (utils.resnet.SEBlock_ method)

frequency() (in module utils.FeatureEncoding)

G

gen_Transformer_embedding() (in module utils.gen_transformer_embedding) generateStructureFeatures() (in module utils.structureFeatures) get_1_trids() (in module utils.FeatureEncoding) get_2_trids() (in module utils.FeatureEncoding) get_3_trids() (in module utils.FeatureEncoding)

get_file_names() (in module utils.datautils) get_lr() (utils.utils.GradualWarmupScheduler method) get_motif_prior() (in module utils.motif_prior.motif_prior) get_motif_prior_matrix() (in module utils.motif_prior.motif_prior) get_nt_height() (in module utils.visualize) GradualWarmupScheduler (class in utils.utils)

H

header_raw (variant_aware.ParsedHeader attribute)

I

inference() (in module utils.visualize)

L

list_to_str() (in module utils.structureFeatures) load_bridge() (utils.variant.ModelHub method)

load_model() (in module utils.attribution_utils) load_tsv() (in module motif_construction.run_finetune) log_print() (in module main)

M

main module main() (in module main) (in module motif_construction.run_finetune) (in module variant_aware) make_attribution_figure() (in module utils.attribution_utils) make_directory() (in module utils.datautils) mat2str() (in module utils.datautils) md5() (in module utils.datautils) mk_dir() (in module utils.structureFeatures) modalities (utils.utils.BaseRBPDataset attribute), [1] (utils.utils.RBPInferDataset attribute) (utils.utils.RBPTrainDataset attribute) ModelHub (class in utils.variant) module main motif_construction.run_finetune utils.attribution_utils utils.BRIDGE utils.conv_layer utils.dataloaders utils.datautils utils.FeatureEncoding utils.gen_transformer_embedding utils.metrics utils.motif_prior.motif_prior utils.resnet utils.structureFeatures utils.train_loop utils.utils utils.variant utils.visualize variant_aware

motif_construction.run_finetune module multiscaleKAN (class in utils.BRIDGE) myDataset (class in utils.utils) myDataset2 (class in utils.utils)

N

nd() (in module utils.FeatureEncoding)

normalize_pwm() (in module utils.visualize)

O

open_output() (in module utils.variant)

P

param_num() (in module utils.utils) parse_header_catalog() (in module variant_aware) parse_protein_cell_line() (in module variant_aware) parse_variant_block() (in module utils.variant) parse_variant_block_flexible() (in module utils.variant) ParsedHeader (class in variant_aware) pearsonr() (in module utils.metrics) plot_saliency() (in module utils.visualize)

pr() (in module utils.metrics) predict() (in module utils.attribution_utils) predict_from_sequence() (in module utils.attribution_utils) process_sequences() (in module variant_aware) process_sequences_catalog_variants() (in module variant_aware) process_sequences_gwas() (in module variant_aware) processFastaFile() (in module utils.FeatureEncoding) protein (variant_aware.ParsedHeader attribute)

R

rbpformer_encode_batch() (in module utils.gen_transformer_embedding) RBPInferDataset (class in utils.utils) RBPTrainDataset (class in utils.utils) read_combined_profile() (in module utils.structureFeatures) read_csv() (in module utils.utils) read_csv_with_name() (in module utils.utils) read_fasta() (in module utils.dataloaders) (in module utils.variant) read_fasta_with_struct_single() (in module utils.dataloaders)

ref (variant_aware.ParsedHeader attribute) ResidualBlock1D (class in utils.resnet) ResidualBlock1D_ (class in utils.resnet) ResidualBlock2D (class in utils.resnet) ResidualBlock2D_ (class in utils.resnet) resolve_dynamic_model_name() (in module utils.utils) roc() (in module utils.metrics) rsquare() (in module utils.metrics) run_ribosnitches() (in module variant_aware) run_RNA() (in module utils.structureFeatures)

S

SEBlock (class in utils.resnet) SEBlock_ (class in utils.resnet) seq2kmer() (in module utils.gen_transformer_embedding) (in module utils.utils) seq_logo() (in module utils.visualize) sequence2int() (in module utils.attribution_utils) sequence2onehot() (in module utils.attribution_utils) sequences2inputs() (in module utils.attribution_utils)

SimpleConvKAN_1layer (class in utils.conv_layer) split_dataset() (in module utils.datautils) (in module utils.utils) start (variant_aware.ParsedHeader attribute) step() (utils.utils.GradualWarmupScheduler method) step_ReduceLROnPlateau() (utils.utils.GradualWarmupScheduler method) strand (variant_aware.ParsedHeader attribute) substitute_base() (in module utils.variant)

T

tokenizer (utils.variant.ModelHub attribute)

train() (in module utils.train_loop) transformer (utils.variant.ModelHub attribute)

U

utils.attribution_utils module utils.BRIDGE module utils.conv_layer module utils.dataloaders module utils.datautils module utils.FeatureEncoding module utils.gen_transformer_embedding module utils.metrics module

utils.motif_prior.motif_prior module utils.resnet module utils.structureFeatures module utils.train_loop module utils.utils module utils.variant module utils.visualize module

V

validate() (in module utils.train_loop) validate2() (in module utils.train_loop) validate_without_sigmoid() (in module utils.train_loop) var_pos (variant_aware.ParsedHeader attribute)

variant_aware module visualize_attribution_only() (in module utils.attribution_utils) visualize_track_attribution() (in module utils.attribution_utils)