Hierarchical lifelong topic modeling using rules extracted from network communities.

Topic models extract latent concepts from texts in the form of topics. Lifelong topic models extend topic models by learning topics continuously based on accumulated knowledge from the past which is updated continuously as new information becomes available. Hierarchical topic modeling extends topic modeling by extracting topics and organizing them into a hierarchical structure. In this study, we combine the two and introduce hierarchical lifelong topic models. Hierarchical lifelong topic models not only allow to examine the topics at different levels of granularity but also allows to continuously adjust the granularity of the topics as more information becomes available. A fundamental issue in hierarchical lifelong topic modeling is the extraction of rules that are used to preserve the hierarchical structural information among the rules and will continuously update based on new information. To address this issue, we introduce a network communities based rule mining approach for hierarchical lifelong topic models (NHLTM). The proposed approach extracts hierarchical structural information among the rules by representing textual documents as graphs and analyzing the underlying communities in the graph. Experimental results indicate improvement of the hierarchical topic structures in terms of topic coherence that increases from general to specific topics.

A three-way approach for protein function classification.

The knowledge of protein functions plays an essential role in understanding biological cells and has a significant impact on human life in areas such as personalized medicine, better crops and improved therapeutic interventions. Due to expense and inherent difficulty of biological experiments, intelligent methods are generally relied upon for automatic assignment of functions to proteins. The technological advancements in the field of biology are improving our understanding of biological processes and are regularly resulting in new features and characteristics that better describe the role of proteins. It is inevitable to neglect and overlook these anticipated features in designing more effective classification techniques. A key issue in this context, that is not being sufficiently addressed, is how to build effective classification models and approaches for protein function prediction by incorporating and taking advantage from the ever evolving biological information. In this article, we propose a three-way decision making approach which provides provisions for seeking and incorporating future information. We considered probabilistic rough sets based models such as Game-Theoretic Rough Sets (GTRS) and Information-Theoretic Rough Sets (ITRS) for inducing three-way decisions. An architecture of protein functions classification with probabilistic rough sets based three-way decisions is proposed and explained. Experiments are carried out on Saccharomyces cerevisiae species dataset obtained from Uniprot database with the corresponding functional classes extracted from the Gene Ontology (GO) database. The results indicate that as the level of biological information increases, the number of deferred cases are reduced while maintaining similar level of accuracy.