Semantic lifting and reasoning on the personalised activity big data repository for healthcare research

The fast growing markets of smart health monitoring devices and mobile applications provide opportunities for common citizens to have capability for understanding and managing their own health situations. However, there are many challenges for data engineering and knowledge discovery research to enable efficient extraction of knowledge from data that is collected from heterogonous devices and applications with big volumes and velocity. This paper presents research that initially started with the EC MyHealthAvatar project and is under continual improvement following the project’s completion. The major contribution of the work is a comprehensive big data and semantic knowledge discovery framework which integrates data from varied data resources. The framework applies hybrid database architecture of NoSQL and RDF repositories with introductions for semantic oriented data mining and knowledge lifting algorithms. The activity stream data is collected through Kafka’s big data processing component. The motivation of the research is to enhance the knowledge management, discovery capabilities and efficiency to support further accurate health risk analysis and lifestyle summarisation

Examining the Application of Modular and Contextualised Ontology in Query Expansions for Information Retrieval

This research considers the ongoing challenge of semantics-based search from the perspective of how to exploit Semantic Web languages for search in the current Web environment. The purpose of the PhD was to use ontology-based query expansion (OQE) to improve search effectiveness by increasing search precision, i.e. retrieving relevant documents in the topmost ranked positions in a returned document list. Query experiments have required a novel search tool that can combine Semantic Web technologies in an otherwise traditional IR process using a Web document collection

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

Context-based understanding of food-related queries using a culinary knowledge model

Dietary practices are governed by a mix of ethnographic aspects, such as social, cultural and environmental factors. These aspects need to be taken into consideration during an analysis of food-related queries. Queries are usually ambiguous. It is essential to understand, analyse and refine the queries for better search and retrieval. The work is focused on identifying the explicit, implicit and hidden facets of a query, taking into consideration the context – culinary domain. This article proposes a technique for query understanding, analysis and refinement based on a domain specific knowledge model. Queries are conceptualised by mapping the query term to concepts defined in the model. This allows an understanding of the semantic point of view of a query and an ability to determine the meaning of its terms and their interrelatedness. The knowledge model acts as a backbone providing the context for query understanding, analysis and refinement and outperforms other models, such as Schema.org, BBC Food Ontology and Recipe Ontology

User-centered semantic dataset retrieval

Finding relevant research data is an increasingly important but time-consuming task in daily research practice. Several studies report on difficulties in dataset search, e.g., scholars retrieve only partial pertinent data, and important information can not be displayed in the user interface. Overcoming these problems has motivated a number of research efforts in computer science, such as text mining and semantic search. In particular, the emergence of the Semantic Web opens a variety of novel research perspectives. Motivated by these challenges, the overall aim of this work is to analyze the current obstacles in dataset search and to propose and develop a novel semantic dataset search. The studied domain is biodiversity research, a domain that explores the diversity of life, habitats and ecosystems. This thesis has three main contributions: (1) We evaluate the current situation in dataset search in a user study, and we compare a semantic search with a classical keyword search to explore the suitability of semantic web technologies for dataset search. (2) We generate a question corpus and develop an information model to figure out on what scientific topics scholars in biodiversity research are interested in. Moreover, we also analyze the gap between current metadata and scholarly search interests, and we explore whether metadata and user interests match. (3) We propose and develop an improved dataset search based on three components: (A) a text mining pipeline, enriching metadata and queries with semantic categories and URIs, (B) a retrieval component with a semantic index over categories and URIs and (C) a user interface that enables a search within categories and a search including further hierarchical relations. Following user centered design principles, we ensure user involvement in various user studies during the development process

Enterprise search and discovery capability: the factors and generative mechanisms for user satisfaction.

Many organizations are re-creating the 'Google-like' experience behind their firewall to exploit their information. However, surveys show dissatisfaction with enterprise search is commonplace. No prior study has investigated unsolicited user feedback from an enterprise search user interface to understand the underlying reasons for dissatisfaction. A mixed methods longitudinal study was undertaken analysing feedback from over 1,000 users and interviewing search service staff in a multinational corporation. Results show that 62% of dissatisfaction events were due to human (information & search literacy) rather than technology factors. Cognitive biases and the 'Google Habitus' influence expectations and information behaviour, and are postulated as deep underlying generative mechanisms. The current literature focuses on 'structure' (technology and information quality) as the reason for enterprise search satisfaction, agency (search literacy) appears downplayed. Organizations which emphasise 'systems thinking' and bimodal approaches towards search strategy and information behaviour may improve capabilities

Utilizing ChatGPT to Enhance Clinical Trial Enrollment

Clinical trials are a critical component of evaluating the effectiveness of new medical interventions and driving advancements in medical research. Therefore, timely enrollment of patients is crucial to prevent delays or premature termination of trials. In this context, Electronic Health Records (EHRs) have emerged as a valuable tool for identifying and enrolling eligible participants. In this study, we propose an automated approach that leverages ChatGPT, a large language model, to extract patient-related information from unstructured clinical notes and generate search queries for retrieving potentially eligible clinical trials. Our empirical evaluation, conducted on two benchmark retrieval collections, shows improved retrieval performance compared to existing approaches when several general-purposed and task-specific prompts are used. Notably, ChatGPT-generated queries also outperform human-generated queries in terms of retrieval performance. These findings highlight the potential use of ChatGPT to enhance clinical trial enrollment while ensuring the quality of medical service and minimizing direct risks to patients.Comment: Under Revie