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
An in-depth evaluation of annotated transcription start sites in E. coli using deep learning
Jim Clauwaert, Gerben Menschaert, Willem Waegeman
To be submitted ---
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