Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure

Structuring Wikipedia Articles with Section Recommendations

Sections are the building blocks of Wikipedia articles. They enhance readability and can be used as a structured entry point for creating and expanding articles. Structuring a new or already existing Wikipedia article with sections is a hard task for humans, especially for newcomers or less experienced editors, as it requires significant knowledge about how a well-written article looks for each possible topic. Inspired by this need, the present paper defines the problem of section recommendation for Wikipedia articles and proposes several approaches for tackling it. Our systems can help editors by recommending what sections to add to already existing or newly created Wikipedia articles. Our basic paradigm is to generate recommendations by sourcing sections from articles that are similar to the input article. We explore several ways of defining similarity for this purpose (based on topic modeling, collaborative filtering, and Wikipedia's category system). We use both automatic and human evaluation approaches for assessing the performance of our recommendation system, concluding that the category-based approach works best, achieving precision@10 of about 80% in the human evaluation.Comment: SIGIR '18 camera-read

Discovering the Impact of Knowledge in Recommender Systems: A Comparative Study

Recommender systems engage user profiles and appropriate filtering techniques to assist users in finding more relevant information over the large volume of information. User profiles play an important role in the success of recommendation process since they model and represent the actual user needs. However, a comprehensive literature review of recommender systems has demonstrated no concrete study on the role and impact of knowledge in user profiling and filtering approache. In this paper, we review the most prominent recommender systems in the literature and examine the impression of knowledge extracted from different sources. We then come up with this finding that semantic information from the user context has substantial impact on the performance of knowledge based recommender systems. Finally, some new clues for improvement the knowledge-based profiles have been proposed.Comment: 14 pages, 3 tables; International Journal of Computer Science & Engineering Survey (IJCSES) Vol.2, No.3, August 201

Ontologies and Information Extraction

This report argues that, even in the simplest cases, IE is an ontology-driven process. It is not a mere text filtering method based on simple pattern matching and keywords, because the extracted pieces of texts are interpreted with respect to a predefined partial domain model. This report shows that depending on the nature and the depth of the interpretation to be done for extracting the information, more or less knowledge must be involved. This report is mainly illustrated in biology, a domain in which there are critical needs for content-based exploration of the scientific literature and which becomes a major application domain for IE

An Ontology-Based Recommender System with an Application to the Star Trek Television Franchise

Collaborative filtering based recommender systems have proven to be extremely successful in settings where user preference data on items is abundant. However, collaborative filtering algorithms are hindered by their weakness against the item cold-start problem and general lack of interpretability. Ontology-based recommender systems exploit hierarchical organizations of users and items to enhance browsing, recommendation, and profile construction. While ontology-based approaches address the shortcomings of their collaborative filtering counterparts, ontological organizations of items can be difficult to obtain for items that mostly belong to the same category (e.g., television series episodes). In this paper, we present an ontology-based recommender system that integrates the knowledge represented in a large ontology of literary themes to produce fiction content recommendations. The main novelty of this work is an ontology-based method for computing similarities between items and its integration with the classical Item-KNN (K-nearest neighbors) algorithm. As a study case, we evaluated the proposed method against other approaches by performing the classical rating prediction task on a collection of Star Trek television series episodes in an item cold-start scenario. This transverse evaluation provides insights into the utility of different information resources and methods for the initial stages of recommender system development. We found our proposed method to be a convenient alternative to collaborative filtering approaches for collections of mostly similar items, particularly when other content-based approaches are not applicable or otherwise unavailable. Aside from the new methods, this paper contributes a testbed for future research and an online framework to collaboratively extend the ontology of literary themes to cover other narrative content.Comment: 25 pages, 6 figures, 5 tables, minor revision