This is a heavily adapted fork of the Transformer-XL repository (https://github.com/kimiyoung/transformer-xl)

This repository includes the code applied for the following two articles

1. ---

Novel transformer networks for improved sequence labeling in genomics

Jim Clauwaert, Willem Waegeman

https://ieeexplore.ieee.org/document/9246292

2. ---

Explainability in transformer models for functional genomics

Jim Clauwaert, Gerben Menschaert, Willem Waegeman

https://academic.oup.com/bib/article/22/5/bbab060/6214646?login=true ---

Novel transformer networks for improved sequence labeling in genomics

Data

data
├── eco_regulon
│   ├── eco_regulon_70.npy
├── eco_TIS
│   ├── eco_TIS.npy
├── eco_SMRTmeth
│   ├── eco_m4c.npy

Train models

run_m4c.sh
run_TIS.sh
run_TSS.sh

---

Explainability in transformer models for functional genomics

Data

data
├── eco_regulon
│   ├── eco_regulon_strong.npy
├── eco_capseq
│   ├── eco_rm_capseq.npy
├── eco_smrtcapseq
│   ├── eco_smrt_capseq.npy
├── eco_SEndseq
│   ├── eco_SEndseq.npy
├── eco_custom
│   ├── eco_custom.npy

Train models

run_regulon.sh
run_cappable.sh
run_smrtcappable.sh
run_send.sh
run_custom.sh