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
Novel transformer networks for improved sequence labeling in genomics
Jim Clauwaert, Willem Waegeman
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 ---
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
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