Knowledge representation and text mining in biomedical, healthcare, and political domains

Knowledge representation and text mining can be employed to discover new knowledge and develop services by using the massive amounts of text gathered by modern information systems. The applied methods should take into account the domain-specific nature of knowledge. This thesis explores knowledge representation and text mining in three application domains. Biomolecular events can be described very precisely and concisely with appropriate representation schemes. Protein–protein interactions are commonly modelled in biological databases as binary relationships, whereas the complex relationships used in text mining are rich in information. The experimental results of this thesis show that complex relationships can be reduced to binary relationships and that it is possible to reconstruct complex relationships from mixtures of linguistically similar relationships. This encourages the extraction of complex relationships from the scientific literature even if binary relationships are required by the application at hand. The experimental results on cross-validation schemes for pair-input data help to understand how existing knowledge regarding dependent instances (such those concerning protein–protein pairs) can be leveraged to improve the generalisation performance estimates of learned models. Healthcare documents and news articles contain knowledge that is more difficult to model than biomolecular events and tend to have larger vocabularies than biomedical scientific articles. This thesis describes an ontology that models patient education documents and their content in order to improve the availability and quality of such documents. The experimental results of this thesis also show that the Recall-Oriented Understudy for Gisting Evaluation measures are a viable option for the automatic evaluation of textual patient record summarisation methods and that the area under the receiver operating characteristic curve can be used in a large-scale sentiment analysis. The sentiment analysis of Reuters news corpora suggests that the Western mainstream media portrays China negatively in politics-related articles but not in general, which provides new evidence to consider in the debate over the image of China in the Western media

An ontology-based semantic building post-occupancy evaluation framework and its application

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonCatering to sustainable development in Architecture, Engineering and Construction (AEC) industry, many building performance evaluation (BPE) schemas have been developed to support building assessment and aim to narrow down the performance gap. Post-Occupancy Evaluation (POE), viewed as a sub-process of BPE, is a systematic method to obtain feedback on building performance in use. However, building evaluation is a complex and knowledge-intensive process with scattered and fragmented knowledge, it is time-consuming and error-prone to acquire explicit knowledge. Benefiting from the advantages of Semantic Web technology in knowledge conceptualization, ontology, as the core of the Semantic Web, has been widely taken as an effective method for knowledge management, information representation and extraction, and logical inference in the AEC industry, especially in the BPE field. However, most of the existing ontologies in the AEC industry are lightweight ontologies that mainly focus on building a structured system to represent the specific domain knowledge or information, without developing formal axioms and constraints to provide higher expressivity. Moreover, the research focus of ontology in building assessment is mainly on energy-related fields, and there is not a comprehensive POE ontology yet, especially with the focus on building occupant satisfaction, which is the starting point of this research. This research develops an ontology-based post-occupancy evaluation framework dedicated to building performance assessment, with the ultimate aim of optimizing building operation and improving building occupants' use experience quality and well-being. In the developed framework, a heavyweight ontology is developed to structure the fragmented building performance assessment knowledge in the POE domain. In POE ontology, the building occupants' needs for building performance are generalized and classified, and the corresponded building performance assessment knowledge is formalized. In addition, a set of SWRL (Semantic Web Rule Language) rules and SQWRL (Semantic Query-Enhanced Web Rule Language) query rules are developed based on the benchmarking evaluation axioms to enable automatic rule-based reasoning and query in different identified application scenarios. This ontology model enables effective POE-related knowledge retrieving and sharing, and promotes its implementation in the POE domain. To validate the developed framework, a case study is carried out facilitated by the Building Use Studies (BUS) Methodology to illustrate its feasibility and effectiveness in different application scenarios. This research concludes that the proposed ontology-based POE framework has the capability to conduct a multi-objective and multi-criteria POE assessment at the building operation stage and provide a multi-criteria optimised solution

Large-scale event extraction from literature with multi-level gene normalization

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons -Attribution - Share Alike (CC BY-SA) license

Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1