Matching Biomedical Ontologies through Adaptive Multi-Modal Multi-Objective Evolutionary Algorithm

SIMPLE SUMMARY: Biomedical ontology matching is a large-scale multi-modal multi-objective optimization problem with sparse Pareto optimal solutions. To effectively address this challenging problem, this paper proposes an adaptive multi-modal multi-Objective Evolutionary Algorithm. First, a novel multi-objective optimization model is constructed to simultaneously optimize both the alignment’s f-measure and its conservativity. Then, a problem-specific algorithm is presented, which uses the guiding matrix to adaptively guide the algorithm’s convergence and diversity in both objective and decision spaces. The experimental results show that our approach is able to effectively solve the biomedical ontology matching problem and to provide more options for decision makers. ABSTRACT: To integrate massive amounts of heterogeneous biomedical data in biomedical ontologies and to provide more options for clinical diagnosis, this work proposes an adaptive Multi-modal Multi-Objective Evolutionary Algorithm (aMMOEA) to match two heterogeneous biomedical ontologies by finding the semantically identical concepts. In particular, we first propose two evaluation metrics on the alignment’s quality, which calculate the alignment’s statistical and its logical features, i.e., its f-measure and its conservativity. On this basis, we build a novel multi-objective optimization model for the biomedical ontology matching problem. By analyzing the essence of this problem, we point out that it is a large-scale Multi-modal Multi-objective Optimization Problem (MMOP) with sparse Pareto optimal solutions. Then, we propose a problem-specific aMMOEA to solve this problem, which uses the Guiding Matrix (GM) to adaptively guide the algorithm’s convergence and diversity in both objective and decision spaces. The experiment uses Ontology Alignment Evaluation Initiative (OAEI)’s biomedical tracks to test aMMOEA’s performance, and comparisons with two state-of-the-art MOEA-based matching techniques and OAEI’s participants show that aMMOEA is able to effectively determine diverse solutions for decision makers.