Please use this identifier to cite or link to this item:
https://hdl.handle.net/11147/14420
Title: | Identifying promoter and enhancer sequences by graph convolutional networks | Authors: | Tenekeci,S. Tekir,S. |
Keywords: | Enhancer Graph convolutional networks Natural language processing Promoter Sequence analysis |
Publisher: | Elsevier Ltd | Abstract: | Identification of promoters, enhancers, and their interactions helps understand genetic regulation. This study proposes a graph-based semi-supervised learning model (GCN4EPI) for the enhancer-promoter classification problem. We adopt a graph convolutional network (GCN) architecture to integrate interaction information with sequence features. Nodes of the constructed graph hold word embeddings of DNA sequences while edges hold the Enhancer-Promoter Interaction (EPI) information. By means of semi-supervised learning, much less data (16%) and time are needed in model training. Comparisons on a benchmark dataset of six human cell lines show that the proposed approach outperforms the state-of-the-art methods by a large margin (10% higher F1 score) and has the fastest training time (up to 3 times). Moreover, GCN4EPI's performance on cross-cell line data is also better than the baselines (3% higher F1 score). Our qualitative analyses with graph explainability models prove that GCN4EPI learns from both text and graph structure. The results suggest that integrating interaction information with sequence features improves predictive performance and compensates for the number of training instances. © 2024 | URI: | https://doi.org/10.1016/j.compbiolchem.2024.108040 https://hdl.handle.net/11147/14420 |
ISSN: | 1476-9271 |
Appears in Collections: | Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection |
Show full item record
CORE Recommender
Items in GCRIS Repository are protected by copyright, with all rights reserved, unless otherwise indicated.