Akira R. Kinjo

Akira R. Kinjo, Daphne Teck Ching Lai

With the membership function being strictly positive, the conventional fuzzy c-means clustering method sometimes causes imbalanced influence when clusters of vastly different sizes exist. That is, an outstandingly large cluster drags to its center all the other clusters, however far they are separated. To solve this problem, we propose a hybrid fuzzy-crisp clustering algorithm based on a target function combining linear and quadratic terms of the membership function. In this algorithm, the membership of a data point to a cluster is automatically set to exactly zero if the data point is ``sufficiently'' far from the cluster center. In this paper, we present a new algorithm for hybrid fuzzy-crisp clustering along with its geometric interpretation. The algorithm is tested on twenty simulated data generated and five real-world datasets from the UCI repository and compared with conventional fuzzy and crisp clustering methods. The proposed algorithm is demonstrated to outperform the conventional methods on imbalanced datasets and can be competitive on more balanced datasets.

Mona Alshahrani, Mohammed Asif Khan, Omar Maddouri et al.

Motivation: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of Semantic Web based knowledge bases in biology to use in machine learning and data analytics. Availability and Implementation: https://github.com/bio-ontology-research-group/walking-rdf-and-owl Contact: robert.hoehndorf@kaust.edu.sa