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Utils

utils.BRIDGE	BRIDGE model components: multimodal sequenc-structure network + supporting blocks.
utils.attribution_utils	Utilities for prediction, attribution, and visualization of nucleotide models.
utils.conv_layer	Convolutional building blocks used across BRIDGE and related models.
utils.dataloaders	FASTA + structure dataset readers (3-line records).
utils.datautils	General I/O and preprocessing utilities for BRIDGE-style datasets.
utils.FeatureEncoding	Hand-crafted sequence feature encoders.
utils.gen_transformer_embedding	Transformer embedding and attention extraction for k-mer tokenized sequences.
utils.metrics	Evaluation metrics utilities for BRIDGE experiments.
utils.resnet	(Deprecated) Residual and Squeeze-and-Excitation blocks kept for backward compatibility.
utils.structureFeatures	Secondary-structure feature utilities: RNAplfold profiles and per-base icSHAPE scores.
utils.train_loop	Training and evaluation loops for BRIDGE-style binary classification.
utils.utils	Dataset, encoding utilities, and learning-rate scheduling helpers for BRIDGE.
utils.variant	Variant-aware inference utilities for BRIDGE (GWAS / ribosnitches-style workflows).
utils.visualize	Saliency visualization utilities for BRIDGE models.
utils.motif_prior.motif_prior	Motif-prior generation and loading utilities (STREME-based pipeline wrapper).

Main

main

Motifs

motif_construction.run_finetune

Attention visualization + prediction export for HuggingFace sequence classifiers.

Variants

variant_aware

Unified variant-aware scoring entry point for BRIDGE.