No abstract

The BioJournalMonitor is a decision support system for the analysis of trends and topics in the biomedical literature. Its main goal is to identify potential diagnostic and therapeutic biomarkers for specific diseases. Several data sources are continuously integrated to provide the user with up-to-date information on current research in this field. State-of-theart text mining technologies are deployed to provide added value on top of the original content, including named entity detection, relation extraction, classification, clustering, ranking, summarization, and visualization. We present two novel technologies that are related to the analysis of temporal dynamics of text archives and associated ontologies. Currently, the MeSH ontology is used to annotate the scientific articles entering the PubMed database with medical terms. Both the maintenance of the ontology as well as the annotation of new articles is performed largely manually. We describe how probabilistic topic models can be used to annotate recent articles with the most likely MeSH terms. This provides our users with a competitive advantage because, when searching for MeSH terms, articles are found long before they are manually annotated. We further present a study on how to predict the inclusion of new terms in the MeSH ontology. The results suggest that early prediction of emerging trends is possible. The trend ranking functions are deployed in our system to enable interactive searches for the hottest new trends relating to a disease.

No abstract

In recent years, Bayesian networks became a popular framework to estimate the dependency structure of a set of variables. However, due to the NP-hardness of structure learning, this is a challenging task and typical state-of-the art algorithms fail to learn in domains with several thousands of variables. In this paper we introduce a novel algorithm, called substructure learning, that reduces the complexity of learning large networks by splitting this task into several small subtasks. Instead of learning one complete network, we estimate the network structure iteratively by learning small subnetworks. Results from several benchmark cases show that substructure learning efficiently reconstructs the network structure in large domains with high accuracy.