增强子
水准点(测量)
图形
计算机科学
人工智能
边距(机器学习)
编码
机器学习
生物
遗传学
理论计算机科学
基因
基因表达
大地测量学
地理
作者
Samet Tenekeci,Selma Tekir
标识
DOI:10.1016/j.compbiolchem.2024.108040
摘要
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.
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