NP-BERT: A Two-Staged BERT Based Nucleosome Positioning Prediction Architecture for Multiple Species

Ahtisham Fazeel, Ahtisham Fazeel, Areeb Agha, Andreas Dengel, Andreas Dengel, Sheraz Ahmed

2023

Abstract

Nucleosomes are complexes of histone and DNA base pairs in which DNA is wrapped around histone proteins to achieve compactness. Nucleosome positioning is associated with various biological processes such as DNA replication, gene regulation, DNA repair, and its dysregulation can lead to various diseases such as sepsis, and tumor. Since nucleosome positioning can be determined only to a limited extent in wet lab experiments, various artificial intelligence-based methods have been proposed to identify nucleosome positioning. Existing predictors/tools do not provide consistent performance, especially when evaluated on 12 publicly available benchmark datasets. Given such limitation, this study proposes a nucleosome positioning predictor, namely NP-BERT. NP-BERT is extensively evaluated in different settings on 12 publicly available datasets from 4 different species. Evaluation results reveal that NP-BERT achieves significant performance on all datasets, and beats state-of-the-art methods on 8/12 datasets, and achieves equivalent performance on 2 datasets. The codes and datasets used in this study are provided in https://github.com/FAhtisham/Nucleosome-position-prediction.

Paper Citation

in Harvard Style

Fazeel A., Agha A., Dengel A. and Ahmed S. (2023). NP-BERT: A Two-Staged BERT Based Nucleosome Positioning Prediction Architecture for Multiple Species. In Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2023) - Volume 3: BIOINFORMATICS; ISBN 978-989-758-631-6, SciTePress, pages 175-187. DOI: 10.5220/0011679200003414

in Bibtex Style

@conference{bioinformatics23,
author={Ahtisham Fazeel and Areeb Agha and Andreas Dengel and Sheraz Ahmed},
title={NP-BERT: A Two-Staged BERT Based Nucleosome Positioning Prediction Architecture for Multiple Species},
booktitle={Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2023) - Volume 3: BIOINFORMATICS},
year={2023},
pages={175-187},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0011679200003414},
isbn={978-989-758-631-6},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 16th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2023) - Volume 3: BIOINFORMATICS
TI - NP-BERT: A Two-Staged BERT Based Nucleosome Positioning Prediction Architecture for Multiple Species
SN - 978-989-758-631-6
AU - Fazeel A.
AU - Agha A.
AU - Dengel A.
AU - Ahmed S.
PY - 2023
SP - 175
EP - 187
DO - 10.5220/0011679200003414
PB - SciTePress