A Semi-supervised Protein Complex Identification Algorithm Based on Sparseness Constraint

Abstract

Abstract Recognising protein complexes in protein interaction networks is crucial, but poses a major challenge due to the frequency of noisy interactions. These networks typically involve numerous protein complexes, with each protein generally only participating in a few complexes. Current recognition models often ignore this aspect. To address this problem, we present a semi-supervised protein complex identification algorithm that extends non-negative matrix factorization (NMF) with sparsity constraints. In contrast to conventional approaches that apply a global sparsity constraint to the entire matrix, our method imposes individual sparsity constraints on protein membership indicator vectors. This targeted strategy controls the algorithm more effectively. Our experimental results with yeast and human protein interaction networks show that our algorithm achieves higher accuracy in identifying protein complexes than leading contemporary methods.