Ontology-Based Clinical Information Extraction Using SNOMED CT

Extracting and encoding clinical information captured in unstructured clinical documents with standard medical terminologies is vital to enable secondary use of clinical data from practice. SNOMED CT is the most comprehensive medical ontology with broad types of concepts and detailed relationships and it has been widely used for many clinical applications. However, few studies have investigated the use of SNOMED CT in clinical information extraction. In this dissertation research, we developed a fine-grained information model based on the SNOMED CT and built novel information extraction systems to recognize clinical entities and identify their relations, as well as to encode them to SNOMED CT concepts. Our evaluation shows that such ontology-based information extraction systems using SNOMED CT could achieve state-of-the-art performance, indicating its potential in clinical natural language processing

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

Hybrid fuzzy multi-objective particle swarm optimization for taxonomy extraction

Ontology learning refers to an automatic extraction of ontology to produce the ontology learning layer cake which consists of five kinds of output: terms, concepts, taxonomy relations, non-taxonomy relations and axioms. Term extraction is a prerequisite for all aspects of ontology learning. It is the automatic mining of complete terms from the input document. Another important part of ontology is taxonomy, or the hierarchy of concepts. It presents a tree view of the ontology and shows the inheritance between subconcepts and superconcepts. In this research, two methods were proposed for improving the performance of the extraction result. The first method uses particle swarm optimization in order to optimize the weights of features. The advantage of particle swarm optimization is that it can calculate and adjust the weight of each feature according to the appropriate value, and here it is used to improve the performance of term and taxonomy extraction. The second method uses a hybrid technique that uses multi-objective particle swarm optimization and fuzzy systems that ensures that the membership functions and fuzzy system rule sets are optimized. The advantage of using a fuzzy system is that the imprecise and uncertain values of feature weights can be tolerated during the extraction process. This method is used to improve the performance of taxonomy extraction. In the term extraction experiment, five extracted features were used for each term from the document. These features were represented by feature vectors consisting of domain relevance, domain consensus, term cohesion, first occurrence and length of noun phrase. For taxonomy extraction, matching Hearst lexico-syntactic patterns in documents and the web, and hypernym information form WordNet were used as the features that represent each pair of terms from the texts. These two proposed methods are evaluated using a dataset that contains documents about tourism. For term extraction, the proposed method is compared with benchmark algorithms such as Term Frequency Inverse Document Frequency, Weirdness, Glossary Extraction and Term Extractor, using the precision performance evaluation measurement. For taxonomy extraction, the proposed methods are compared with benchmark methods of Feature-based and weighting by Support Vector Machine using the f-measure, precision and recall performance evaluation measurements. For the first method, the experiment results concluded that implementing particle swarm optimization in order to optimize the feature weights in terms and taxonomy extraction leads to improved accuracy of extraction result compared to the benchmark algorithms. For the second method, the results concluded that the hybrid technique that uses multi-objective particle swarm optimization and fuzzy systems leads to improved performance of taxonomy extraction results when compared to the benchmark methods, while adjusting the fuzzy membership function and keeping the number of fuzzy rules to a minimum number with a high degree of accuracy

Data Visualization Collection. How graphical representation can inspect and communicate sustainability through systemic design.

Big data are totally changing the business rules, the society, as well as the perception of ourself. The need of a big data oriented culture is becoming essential for everything that has an informative asset. Furthermore, technological innovation offers products and features unique that can help to convey values and meanings, for the purpose of communication based on increasingly strong interaction between people. In a world where everything is consumed in a short time, it is important to turn information as visual as possible, making simple what is complex. The visualization becomes a medium for increasing cognitive perception of the beholder, easing reasoning and storing of the information represented, showing patterns and relationships, known or not, maybe not easily visible without the aid of a visual representation of information

A framework for analyzing changes in health care lexicons and nomenclatures

Ontologies play a crucial role in current web-based biomedical applications for capturing contextual knowledge in the domain of life sciences. Many of the so-called bio-ontologies and controlled vocabularies are known to be seriously defective from both terminological and ontological perspectives, and do not sufficiently comply with the standards to be considered formai ontologies. Therefore, they are continuously evolving in order to fix the problems and provide valid knowledge. Moreover, many problems in ontology evolution often originate from incomplete knowledge about the given domain. As our knowledge improves, the related definitions in the ontologies will be altered. This problem is inadequately addressed by available tools and algorithms, mostly due to the lack of suitable knowledge representation formalisms to deal with temporal abstract notations, and the overreliance on human factors. Also most of the current approaches have been focused on changes within the internal structure of ontologies, and interactions with other existing ontologies have been widely neglected. In this research, alter revealing and classifying some of the common alterations in a number of popular biomedical ontologies, we present a novel agent-based framework, RLR (Represent, Legitimate, and Reproduce), to semi-automatically manage the evolution of bio-ontologies, with emphasis on the FungalWeb Ontology, with minimal human intervention. RLR assists and guides ontology engineers through the change management process in general, and aids in tracking and representing the changes, particularly through the use of category theory. Category theory has been used as a mathematical vehicle for modeling changes in ontologies and representing agents' interactions, independent of any specific choice of ontology language or particular implementation. We have also employed rule-based hierarchical graph transformation techniques to propose a more specific semantics for analyzing ontological changes and transformations between different versions of an ontology, as well as tracking the effects of a change in different levels of abstractions. Thus, the RLR framework enables one to manage changes in ontologies, not as standalone artifacts in isolation, but in contact with other ontologies in an openly distributed semantic web environment. The emphasis upon the generality and abstractness makes RLR more feasible in the multi-disciplinary domain of biomedical Ontology change management

Towards Personalized and Human-in-the-Loop Document Summarization

The ubiquitous availability of computing devices and the widespread use of the internet have generated a large amount of data continuously. Therefore, the amount of available information on any given topic is far beyond humans' processing capacity to properly process, causing what is known as information overload. To efficiently cope with large amounts of information and generate content with significant value to users, we require identifying, merging and summarising information. Data summaries can help gather related information and collect it into a shorter format that enables answering complicated questions, gaining new insight and discovering conceptual boundaries. This thesis focuses on three main challenges to alleviate information overload using novel summarisation techniques. It further intends to facilitate the analysis of documents to support personalised information extraction. This thesis separates the research issues into four areas, covering (i) feature engineering in document summarisation, (ii) traditional static and inflexible summaries, (iii) traditional generic summarisation approaches, and (iv) the need for reference summaries. We propose novel approaches to tackle these challenges, by: i)enabling automatic intelligent feature engineering, ii) enabling flexible and interactive summarisation, iii) utilising intelligent and personalised summarisation approaches. The experimental results prove the efficiency of the proposed approaches compared to other state-of-the-art models. We further propose solutions to the information overload problem in different domains through summarisation, covering network traffic data, health data and business process data.Comment: PhD thesi