SCCPMD: Probability matrix decomposition method subject to corrected similarity constraints for inferring long non-coding RNA-disease associations

• Published in: Frontiers in microbiology Vol. 13; p. 1093615
• Main Authors: Lin, Lieqing, Chen, Ruibin, Zhu, Yinting, Xie, Weijie, Jing, Huaiguo, Chen, Langcheng, Zou, Minqing
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 11.01.2023
• Subjects: associations prediction; constraint probability matrix decomposition; disease; lncRNA-long noncoding RNA; Microbiology; similarity correction; similarity correction; associations prediction; disease; lncRNA-long noncoding RNA; constraint probability matrix decomposition
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2022.1093615

Accumulating evidence has demonstrated various associations of long non-coding RNAs (lncRNAs) with human diseases, such as abnormal expression due to microbial influences that cause disease. Gaining a deeper understanding of lncRNA-disease associations is essential for disease diagnosis, treatment, and prevention. In recent years, many matrix decomposition methods have also been used to predict potential lncRNA-disease associations. However, these methods do not consider the use of microbe-disease association information to enrich disease similarity, and also do not make more use of similarity information in the decomposition process. To address these issues, we here propose a correction-based similarity-constrained probability matrix decomposition method (SCCPMD) to predict lncRNA-disease associations. The microbe-disease associations are first used to enrich the disease semantic similarity matrix, and then the logistic function is used to correct the lncRNA and disease similarity matrix, and then these two corrected similarity matrices are added to the probability matrix decomposition as constraints to finally predict the potential lncRNA-disease associations. The experimental results show that SCCPMD outperforms the five advanced comparison algorithms. In addition, SCCPMD demonstrated excellent prediction performance in a case study for breast cancer, lung cancer, and renal cell carcinoma, with prediction accuracy reaching 80, 100, and 100%, respectively. Therefore, SCCPMD shows excellent predictive performance in identifying unknown lncRNA-disease associations.