Clustering approaches for visual knowledge exploration in molecular interaction networks

• Published in: BMC bioinformatics Vol. 19; no. 1; p. 308
• Main Authors: Ostaszewski, Marek, Kieffer, Emmanuel, Danoy, Grégoire, Schneider, Reinhard, Bouvry, Pascal
• Format: Journal Article
• Language: English
• Published: England BioMed Central 29-08-2018; BMC
• Subjects: Algorithms; Benchmarks; Bi-level optimization; Bioinformatics; Cluster Analysis; Clustering; Computational Biology - methods; Computer applications; Computer Graphics; Data Mining - methods; Databases, Factual; Datasets; Disease; Enrichment; Euclidean geometry; Evolutionary algorithms; Exploration; Gene mapping; Gene Regulatory Networks; Genetic algorithms; Humans; Information sources; Kinases; Knowledge discovery; Knowledge management; Molecular diagrams; Molecular interactions; Multiple myeloma; Ontology; Optimization; Repositories; Shortest-path problems; Molecular diagrams; Knowledge discovery; Evolutionary algorithms; Bi-level optimization; Ontology; Clustering
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-018-2314-z

Biomedical knowledge grows in complexity, and becomes encoded in network-based repositories, which include focused, expert-drawn diagrams, networks of evidence-based associations and established ontologies. Combining these structured information sources is an important computational challenge, as large graphs are difficult to analyze visually.
We investigate knowledge discovery in manually curated and annotated molecular interaction diagrams. To evaluate similarity of content we use: i) Euclidean distance in expert-drawn diagrams, ii) shortest path distance using the underlying network and iii) ontology-based distance. We employ clustering with these metrics used separately and in pairwise combinations. We propose a novel bi-level optimization approach together with an evolutionary algorithm for informative combination of distance metrics. We compare the enrichment of the obtained clusters between the solutions and with expert knowledge. We calculate the number of Gene and Disease Ontology terms discovered by different solutions as a measure of cluster quality. Our results show that combining distance metrics can improve clustering accuracy, based on the comparison with expert-provided clusters. Also, the performance of specific combinations of distance functions depends on the clustering depth (number of clusters). By employing bi-level optimization approach we evaluated relative importance of distance functions and we found that indeed the order by which they are combined affects clustering performance. Next, with the enrichment analysis of clustering results we found that both hierarchical and bi-level clustering schemes discovered more Gene and Disease Ontology terms than expert-provided clusters for the same knowledge repository. Moreover, bi-level clustering found more enriched terms than the best hierarchical clustering solution for three distinct distance metric combinations in three different instances of disease maps.
In this work we examined the impact of different distance functions on clustering of a visual biomedical knowledge repository. We found that combining distance functions may be beneficial for clustering, and improve exploration of such repositories. We proposed bi-level optimization to evaluate the importance of order by which the distance functions are combined. Both combination and order of these functions affected clustering quality and knowledge recognition in the considered benchmarks. We propose that multiple dimensions can be utilized simultaneously for visual knowledge exploration.