MoAGL-SA: a multi-omics adaptive integration method with graph learning and self attention for cancer subtype classification
Lei Cheng, Qian Huang, Zhengqun Zhu, Yanan Li, Shuguang Ge, Longzhen Zhang, Ping Gong
Abstract
BACKGROUND: The integration of multi-omics data through deep learning has greatly improved cancer subtype classification, particularly in feature learning and multi-omics data integration. However, key challenges remain in embedding sample structure information into the feature space and designing flexible integration strategies. RESULTS: We propose MoAGL-SA, an adaptive multi-omics integration method based on graph learning and self-attention, to address these challenges. First, patient relationship graphs are generated from each omics dataset using graph learning. Next, three-layer graph convolutional networks are employed to extract omic-specific graph embeddings. Self-attention is then used to focus on the most relevant omics, adaptively assigning weights to different graph embeddings for multi-omics integration. Finally, cancer subtypes are classified using a softmax classifier. CONCLUSIONS: Experimental results show that MoAGL-SA outperforms several popular algorithms on datasets for breast invasive carcinoma, kidney renal papillary cell carcinoma, and kidney renal clear cell carcinoma. Additionally, MoAGL-SA successfully identifies key biomarkers for breast invasive carcinoma.