ANS‐SCMC: A matrix completion method based on adaptive neighbourhood similarity and sparse constraints for predicting microbe‐disease associations

The use of matrix completion methods to predict the association between microbes and diseases can effectively improve treatment efficiency. However, the similarity measures used in the existing methods are often influenced by various factors such as neighbourhood size, choice of similarity metric, or multiple parameters for similarity fusion, making it challenging. Additionally, matrix completion is currently limited by the sparsity of the initial association matrix, which restricts its predictive performance. To address these problems, we propose a matrix completion method based on adaptive neighbourhood similarity and sparse constraints (ANS-SCMC) for predict microbe-disease potential associations. Adaptive neighbourhood similarity learning dynamically uses the decomposition results as effective information for the next learning iteration by simultaneously performing local manifold structure learning and decomposition. This approach effectively preserves fine local structure information and avoids the influence of weight parameters directly involved in similarity measurement. Additionally, the sparse constraint-based matrix completion approach can better handle the sparsity challenge in the association matrix. Finally, the algorithm we proposed has achieved significantly higher predictive performance in the validation compared to several commonly used prediction methods proposed to date. Furthermore, in the case study, the prediction algorithm achieved an accuracy of up to 80% for the top 10 microbes associated with type 1 diabetes and 100% for Crohn's disease respectively.