SGCL-LncLoc: an interpretable deep learning model for improving lncRNA subcellular localization prediction with supervised graph contrastive learning

Understanding the subcellular localization of long non-coding RNAs (lncRNAs) is crucial for unraveling their functional mechanisms. While previous computational methods have made progress in predicting lncRNA subcellular localization, most of them ignored the sequence order information by relying on k-mer frequency features to encode lncRNA sequences. Consequently, they faced limitations in accurately predicting the subcellular localization of lncRNAs.
In the study, we developed SGCL-LncLoc, a novel interpretable deep learning model based on supervised graph contrastive learning. SGCL-LncLoc transforms lncRNA sequences into de Bruijn graphs and uses the Word2Vec technique to learn the node representation of the graph. Then, SGCL-LncLoc applies graph convolutional networks to update the node representation and learn the comprehensive graph representation. Additionally, we proposed a computational method to map the attention weights of the graph nodes to the weights of nucleotides in the lncRNA sequence, allowing SGCL-LncLoc to serve as an interpretable deep learning model. Furthermore, SGCL-LncLoc employs a supervised contrastive learning strategy, which leverages the relationships between different samples and label information, guiding the model to enhance representation learning for lncRNAs. Extensive experimental results demonstrate that SGCL-LncLoc outperforms both machine learning and deep learning baseline models, highlighting the superiority of its network structure. Moreover, SGCL-LncLoc outperformers existing predictors, showing its capability for accurate lncRNA subcellular localization prediction. The ablation study confirms the contribution of each component in SGCL-LncLoc. Furthermore, we conducted a motif analysis, revealing that SGCL-LncLoc successfully captures known motifs associated with lncRNA subcellular localization. The SGCL-LncLoc web server is available at http://csuligroup.com:8000/SGCL-LncLoc. The source code can be obtained from https://github.com/CSUBioGroup/SGCL-LncLoc.