Learning Language from a Large (Unannotated) Corpus

A novel approach to the fully automated, unsupervised extraction of dependency grammars and associated syntax-to-semantic-relationship mappings from large text corpora is described. The suggested approach builds on the authors' prior work with the Link Grammar, RelEx and OpenCog systems, as well as on a number of prior papers and approaches from the statistical language learning literature. If successful, this approach would enable the mining of all the information needed to power a natural language comprehension and generation system, directly from a large, unannotated corpus.Comment: 29 pages, 5 figures, research proposa

Ontology Enrichment from Free-text Clinical Documents: A Comparison of Alternative Approaches

While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships, as well as difficulty in updating the ontology as domain knowledge changes. Methodologies developed in the fields of Natural Language Processing (NLP), Information Extraction (IE), Information Retrieval (IR), and Machine Learning (ML) provide techniques for automating the enrichment of ontology from free-text documents. In this dissertation, I extended these methodologies into biomedical ontology development. First, I reviewed existing methodologies and systems developed in the fields of NLP, IR, and IE, and discussed how existing methods can benefit the development of biomedical ontologies. This previously unconducted review was published in the Journal of Biomedical Informatics. Second, I compared the effectiveness of three methods from two different approaches, the symbolic (the Hearst method) and the statistical (the Church and Lin methods), using clinical free-text documents. Third, I developed a methodological framework for Ontology Learning (OL) evaluation and comparison. This framework permits evaluation of the two types of OL approaches that include three OL methods. The significance of this work is as follows: 1) The results from the comparative study showed the potential of these methods for biomedical ontology enrichment. For the two targeted domains (NCIT and RadLex), the Hearst method revealed an average of 21% and 11% new concept acceptance rates, respectively. The Lin method produced a 74% acceptance rate for NCIT; the Church method, 53%. As a result of this study (published in the Journal of Methods of Information in Medicine), many suggested candidates have been incorporated into the NCIT; 2) The evaluation framework is flexible and general enough that it can analyze the performance of ontology enrichment methods for many domains, thus expediting the process of automation and minimizing the likelihood that key concepts and relationships would be missed as domain knowledge evolves

Knowledge-based methods for automatic extraction of domain-specific ontologies

Semantic web technology aims at developing methodologies for representing large amount of knowledge in web accessible form. The semantics of knowledge should be easy to interpret and understand by computer programs, so that sharing and utilizing knowledge across the Web would be possible. Domain specific ontologies form the basis for knowledge representation in the semantic web. Research on automated development of ontologies from texts has become increasingly important because manual construction of ontologies is labor intensive and costly, and, at the same time, large amount of texts for individual domains is already available in electronic form. However, automatic extraction of domain specific ontologies is challenging due to the unstructured nature of texts and inherent semantic ambiguities in natural language. Moreover, the large size of texts to be processed renders full-fledged natural language processing methods infeasible. In this dissertation, we develop a set of knowledge-based techniques for automatic extraction of ontological components (concepts, taxonomic and non-taxonomic relations) from domain texts. The proposed methods combine information retrieval metrics, lexical knowledge-base(like WordNet), machine learning techniques, heuristics, and statistical approaches to meet the challenge of the task. These methods are domain-independent and automatic approaches. For extraction of concepts, the proposed WNSCA+{PE, POP} method utilizes the lexical knowledge base WordNet to improve precision and recall over the traditional information retrieval metrics. A WordNet-based approach, the compound term heuristic, and a supervised learning approach are developed for taxonomy extraction. We also developed a weighted word-sense disambiguation method for use with the WordNet-based approach. An unsupervised approach using log-likelihood ratios is proposed for extracting non-taxonomic relations. Further more, a supervised approach is investigated to learn the semantic constraints for identifying relations from prepositional phrases. The proposed methods are validated by experiments with the Electronic Voting and the Tender Offers, Mergers, and Acquisitions domain corpus. Experimental results and comparisons with some existing approaches clearly indicate the superiority of our methods. In summary, a good combination of information retrieval, lexical knowledge base, statistics and machine learning methods in this study has led to the techniques efficient and effective for extracting ontological components automatically

Entity-centric knowledge discovery for idiosyncratic domains

Technical and scientific knowledge is produced at an ever-accelerating pace, leading to increasing issues when trying to automatically organize or process it, e.g., when searching for relevant prior work. Knowledge can today be produced both in unstructured (plain text) and structured (metadata or linked data) forms. However, unstructured content is still themost dominant formused to represent scientific knowledge. In order to facilitate the extraction and discovery of relevant content, new automated and scalable methods for processing, structuring and organizing scientific knowledge are called for. In this context, a number of applications are emerging, ranging fromNamed Entity Recognition (NER) and Entity Linking tools for scientific papers to specific platforms leveraging information extraction techniques to organize scientific knowledge. In this thesis, we tackle the tasks of Entity Recognition, Disambiguation and Linking in idiosyncratic domains with an emphasis on scientific literature. Furthermore, we study the related task of co-reference resolution with a specific focus on named entities. We start by exploring Named Entity Recognition, a task that aims to identify the boundaries of named entities in textual contents. We propose a newmethod to generate candidate named entities based on n-gram collocation statistics and design several entity recognition features to further classify them. In addition, we show how the use of external knowledge bases (either domain-specific like DBLP or generic like DBPedia) can be leveraged to improve the effectiveness of NER for idiosyncratic domains. Subsequently, we move to Entity Disambiguation, which is typically performed after entity recognition in order to link an entity to a knowledge base. We propose novel semi-supervised methods for word disambiguation leveraging the structure of a community-based ontology of scientific concepts. Our approach exploits the graph structure that connects different terms and their definitions to automatically identify the correct sense that was originally picked by the authors of a scientific publication. We then turn to co-reference resolution, a task aiming at identifying entities that appear using various forms throughout the text. We propose an approach to type entities leveraging an inverted index built on top of a knowledge base, and to subsequently re-assign entities based on the semantic relatedness of the introduced types. Finally, we describe an application which goal is to help researchers discover and manage scientific publications. We focus on the problem of selecting relevant tags to organize collections of research papers in that context. We experimentally demonstrate that the use of a community-authored ontology together with information about the position of the concepts in the documents allows to significantly increase the precision of tag selection over standard methods

Graph-based approaches to word sense induction

This thesis is a study of Word Sense Induction (WSI), the Natural Language Processing (NLP) task of automatically discovering word meanings from text. WSI is an open problem in NLP whose solution would be of considerable benefit to many other NLP tasks. It has, however, has been studied by relatively few NLP researchers and often in set ways. Scope therefore exists to apply novel methods to the problem, methods that may improve upon those previously applied. This thesis applies a graph-theoretic approach to WSI. In this approach, word senses are identifed by finding particular types of subgraphs in word co-occurrence graphs. A number of original methods for constructing, analysing, and partitioning graphs are introduced, with these methods then incorporated into graphbased WSI systems. These systems are then shown, in a variety of evaluation scenarios, to return results that are comparable to those of the current best performing WSI systems. The main contributions of the thesis are a novel parameter-free soft clustering algorithm that runs in time linear in the number of edges in the input graph, and novel generalisations of the clustering coeficient (a measure of vertex cohesion in graphs) to the weighted case. Further contributions of the thesis include: a review of graph-based WSI systems that have been proposed in the literature; analysis of the methodologies applied in these systems; analysis of the metrics used to evaluate WSI systems, and empirical evidence to verify the usefulness of each novel method introduced in the thesis for inducing word senses