Concept graphs: Applications to biomedical text categorization and concept extraction

As science advances, the underlying literature grows rapidly providing valuable knowledge mines for researchers and practitioners. The text content that makes up these knowledge collections is often unstructured and, thus, extracting relevant or novel information could be nontrivial and costly. In addition, human knowledge and expertise are being transformed into structured digital information in the form of vocabulary databases and ontologies. These knowledge bases hold substantial hierarchical and semantic relationships of common domain concepts. Consequently, automating learning tasks could be reinforced with those knowledge bases through constructing human-like representations of knowledge. This allows developing algorithms that simulate the human reasoning tasks of content perception, concept identification, and classification. This study explores the representation of text documents using concept graphs that are constructed with the help of a domain ontology. In particular, the target data sets are collections of biomedical text documents, and the domain ontology is a collection of predefined biomedical concepts and relationships among them. The proposed representation preserves those relationships and allows using the structural features of graphs in text mining and learning algorithms. Those features emphasize the significance of the underlying relationship information that exists in the text content behind the interrelated topics and concepts of a text document. The experiments presented in this study include text categorization and concept extraction applied on biomedical data sets. The experimental results demonstrate how the relationships extracted from text and captured in graph structures can be used to improve the performance of the aforementioned applications. The discussed techniques can be used in creating and maintaining digital libraries through enhancing indexing, retrieval, and management of documents as well as in a broad range of domain-specific applications such as drug discovery, hypothesis generation, and the analysis of molecular structures in chemoinformatics

From Frequency to Meaning: Vector Space Models of Semantics

Computers understand very little of the meaning of human language. This profoundly limits our ability to give instructions to computers, the ability of computers to explain their actions to us, and the ability of computers to analyse and process text. Vector space models (VSMs) of semantics are beginning to address these limits. This paper surveys the use of VSMs for semantic processing of text. We organize the literature on VSMs according to the structure of the matrix in a VSM. There are currently three broad classes of VSMs, based on term-document, word-context, and pair-pattern matrices, yielding three classes of applications. We survey a broad range of applications in these three categories and we take a detailed look at a specific open source project in each category. Our goal in this survey is to show the breadth of applications of VSMs for semantics, to provide a new perspective on VSMs for those who are already familiar with the area, and to provide pointers into the literature for those who are less familiar with the field

Distantly Supervised Web Relation Extraction for Knowledge Base Population

Extracting information from Web pages for populating large, cross-domain knowledge bases requires methods which are suitable across domains, do not require manual effort to adapt to new domains, are able to deal with noise, and integrate information extracted from different Web pages. Recent approaches have used existing knowledge bases to learn to extract information with promising results, one of those approaches being distant supervision. Distant supervision is an unsupervised method which uses background information from the Linking Open Data cloud to automatically label sentences with relations to create training data for relation classifiers. In this paper we propose the use of distant supervision for relation extraction from the Web. Although the method is promising, existing approaches are still not suitable for Web extraction as they suffer from three main issues: data sparsity, noise and lexical ambiguity. Our approach reduces the impact of data sparsity by making entity recognition tools more robust across domains and extracting relations across sentence boundaries using unsupervised co- reference resolution methods. We reduce the noise caused by lexical ambiguity by employing statistical methods to strategically select training data. To combine information extracted from multiple sources for populating knowledge bases we present and evaluate several information integration strategies and show that those benefit immensely from additional relation mentions extracted using co-reference resolution, increasing precision by 8%. We further show that strategically selecting training data can increase precision by a further 3%

Doctor of Philosophy

dissertationDisease-specific ontologies, designed to structure and represent the medical knowledge about disease etiology, diagnosis, treatment, and prognosis, are essential for many advanced applications, such as predictive modeling, cohort identification, and clinical decision support. However, manually building disease-specific ontologies is very labor-intensive, especially in the process of knowledge acquisition. On the other hand, medical knowledge has been documented in a variety of biomedical knowledge resources, such as textbook, clinical guidelines, research articles, and clinical data repositories, which offers a great opportunity for an automated knowledge acquisition. In this dissertation, we aim to facilitate the large-scale development of disease-specific ontologies through automated extraction of disease-specific vocabularies from existing biomedical knowledge resources. Three separate studies presented in this dissertation explored both manual and automated vocabulary extraction. The first study addresses the question of whether disease-specific reference vocabularies derived from manual concept acquisition can achieve a near-saturated coverage (or near the greatest possible amount of disease-pertinent concepts) by using a small number of literature sources. Using a general-purpose, manual acquisition approach we developed, this study concludes that a small number of expert-curated biomedical literature resources can prove sufficient for acquiring near-saturated disease-specific vocabularies. The second and third studies introduce automated techniques for extracting disease-specific vocabularies from both MEDLINE citations (title and abstract) and a clinical data repository. In the second study, we developed and assessed a pipeline-based system which extracts disease-specific treatments from PubMed citations. The system has achieved a mean precision of 0.8 for the top 100 extracted treatment concepts. In the third study, we applied classification models to reduce irrelevant disease-concepts associations extracted from MEDLINE citations and electronic medical records. This study suggested the combination of measures of relevance from disparate sources to improve the identification of true-relevant concepts through classification and also demonstrated the generalizability of the studied classification model to new diseases. With the studies, we concluded that existing biomedical knowledge resources are valuable sources for extracting disease-concept associations, from which classification based on statistical measures of relevance could assist a semi-automated generation of disease-specific vocabularies