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

Deciphering clinical text: concept recognition in primary care text notes

Electronic patient records, containing data about the health and care of a patient, are a valuable source of information for longitudinal clinical studies. The General Practice Research Database (GPRD) has collected patient records from UK primary care practices since the late 1980s. These records contain both structured data (in the form of codes and numeric values) and free text notes. While the structured data have been used extensively in clinical studies, there are significant practical obstacles in extracting information from the free text notes. The main obstacles are data access restrictions, due to the presence of sensitive information, and the specific language of medical practitioners, which renders standard language processing tools ineffective. The aim of this research is to investigate approaches for computer analysis of free text notes. The research involved designing a primary care text corpus (the Harvey Corpus) annotated with syntactic chunks and clinically-relevant semantic entities, developing a statistical chunking model, and devising a novel method for applying machine learning for entity recognition based on chunk annotation. The tools produced would facilitate reliable information extraction from primary care patient records, needed for the development of clinically-related research. The three medical concept types targeted in this thesis could contribute to epidemiological studies by enhancing the detection of co-morbidities, and better analysing the descriptions of patient experiences and treatments. The main contributions of the research reported in this thesis are: guidelines for chunk and concept annotation of clinical text, an approach to maximising agreement between human annotators, the Harvey Corpus, a method for using a standard part-of-speech tagging model in clinical text chunking, and a novel approach to recognising clinically relevant medical concepts

In Search of Meaning:Lessons, Resources and Next Steps for Computational Analysis of Financial Discourse

We critically assess mainstream accounting and finance research applying methods from computational linguistics (CL) to study financial discourse. We also review common themes and innovations in the literature and assess the incremental contributions of work applying CL methods over manual content analysis. Key conclusions emerging from our analysis are: (a) accounting and finance research is behind the curve in terms of CL methods generally and word sense disambiguation in particular; (b) implementation issues mean the proposed benefits of CL are often less pronounced than proponents suggest; (c) structural issues limit practical relevance; and (d) CL methods and high quality manual analysis represent complementary approaches to analyzing financial discourse. We describe four CL tools that have yet to gain traction in mainstream AF research but which we believe offer promising ways to enhance the study of meaning in financial discourse. The four approaches are named entity recognition, summarization, semantics and corpus linguistics

Semantic Feature Extraction Using Multi-Sense Embeddings and Lexical Chains

The relationship between words in a sentence often tell us more about the underlying semantic content of a document than its actual words individually. Natural language understanding has seen an increasing effort in the formation of techniques that try to produce non-trivial features, in the last few years, especially after robust word embeddings models became prominent, when they proved themselves able to capture and represent semantic relationships from massive amounts of data. These new dense vector representations indeed leverage the baseline in natural language processing, but they still fall short in dealing with intrinsic issues in linguistics, such as polysemy and homonymy. Systems that make use of natural language at its core, can be affected by a weak semantic representation of human language, resulting in inaccurate outcomes based on poor decisions. In this subject, word sense disambiguation and lexical chains have been exploring alternatives to alleviate several problems in linguistics, such as semantic representation, definitions, differentiation, polysemy, and homonymy. However, little effort is seen in combining recent advances in token embeddings (e.g. words, documents) with word sense disambiguation and lexical chains. To collaborate in building a bridge between these areas, this work proposes a collection of algorithms to extract semantic features from large corpora as its main contributions, named MSSA, MSSA-D, MSSA-NR, FLLC II, and FXLC II. The MSSA techniques focus on disambiguating and annotating each word by its specific sense, considering the semantic effects of its context. The lexical chains group derive the semantic relations between consecutive words in a document in a dynamic and pre-defined manner. These original techniques' target is to uncover the implicit semantic links between words using their lexical structure, incorporating multi-sense embeddings, word sense disambiguation, lexical chains, and lexical databases. A few natural language problems are selected to validate the contributions of this work, in which our techniques outperform state-of-the-art systems. All the proposed algorithms can be used separately as independent components or combined in one single system to improve the semantic representation of words, sentences, and documents. Additionally, they can also work in a recurrent form, refining even more their results.Ph.D.College of Engineering & Computer ScienceUniversity of Michigan-Dearbornhttps://deepblue.lib.umich.edu/bitstream/2027.42/149647/1/Terry Ruas Final Dissertation.pdfDescription of Terry Ruas Final Dissertation.pdf : Dissertatio

Practical Natural Language Processing for Low-Resource Languages.

As the Internet and World Wide Web have continued to gain widespread adoption, the linguistic diversity represented has also been growing. Simultaneously the field of Linguistics is facing a crisis of the opposite sort. Languages are becoming extinct faster than ever before and linguists now estimate that the world could lose more than half of its linguistic diversity by the year 2100. This is a special time for Computational Linguistics; this field has unprecedented access to a great number of low-resource languages, readily available to be studied, but needs to act quickly before political, social, and economic pressures cause these languages to disappear from the Web. Most work in Computational Linguistics and Natural Language Processing (NLP) focuses on English or other languages that have text corpora of hundreds of millions of words. In this work, we present methods for automatically building NLP tools for low-resource languages with minimal need for human annotation in these languages. We start first with language identification, specifically focusing on word-level language identification, an understudied variant that is necessary for processing Web text and develop highly accurate machine learning methods for this problem. From there we move onto the problems of part-of-speech tagging and dependency parsing. With both of these problems we extend the current state of the art in projected learning to make use of multiple high-resource source languages instead of just a single language. In both tasks, we are able to improve on the best current methods. All of these tools are practically realized in the "Minority Language Server," an online tool that brings these techniques together with low-resource language text on the Web. The Minority Language Server, starting with only a few words in a language can automatically collect text in a language, identify its language and tag its parts of speech. We hope that this system is able to provide a convincing proof of concept for the automatic collection and processing of low-resource language text from the Web, and one that can hopefully be realized before it is too late.PhDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113373/1/benking_1.pd

Mining the Medical and Patent Literature to Support Healthcare and Pharmacovigilance

Recent advancements in healthcare practices and the increasing use of information technology in the medical domain has lead to the rapid generation of free-text data in forms of scientific articles, e-health records, patents, and document inventories. This has urged the development of sophisticated information retrieval and information extraction technologies. A fundamental requirement for the automatic processing of biomedical text is the identification of information carrying units such as the concepts or named entities. In this context, this work focuses on the identification of medical disorders (such as diseases and adverse effects) which denote an important category of concepts in the medical text. Two methodologies were investigated in this regard and they are dictionary-based and machine learning-based approaches. Futhermore, the capabilities of the concept recognition techniques were systematically exploited to build a semantic search platform for the retrieval of e-health records and patents. The system facilitates conventional text search as well as semantic and ontological searches. Performance of the adapted retrieval platform for e-health records and patents was evaluated within open assessment challenges (i.e. TRECMED and TRECCHEM respectively) wherein the system was best rated in comparison to several other competing information retrieval platforms. Finally, from the medico-pharma perspective, a strategy for the identification of adverse drug events from medical case reports was developed. Qualitative evaluation as well as an expert validation of the developed system's performance showed robust results. In conclusion, this thesis presents approaches for efficient information retrieval and information extraction from various biomedical literature sources in the support of healthcare and pharmacovigilance. The applied strategies have potential to enhance the literature-searches performed by biomedical, healthcare, and patent professionals. The applied strategies have potential to enhance the literature-searches performed by biomedical, healthcare, and patent professionals. This can promote the literature-based knowledge discovery, improve the safety and effectiveness of medical practices, and drive the research and development in medical and healthcare arena

Empirical studies on word representations

One of the most fundamental tasks in natural language processing is representing words with mathematical objects (such as vectors). The word representations, which are most often estimated from data, allow capturing the meaning of words. They enable comparing words according to their semantic similarity, and have been shown to work extremely well when included in complex real-world applications. A large part of our work deals with ways of estimating word representations directly from large quantities of text. Our methods exploit the idea that words which occur in similar contexts have a similar meaning. How we define the context is an important focus of our thesis. The context can consist of a number of words to the left and to the right of the word in question, but, as we show, obtaining context words via syntactic links (such as the link between the verb and its subject) often works better. We furthermore investigate word representations that accurately capture multiple meanings of a single word. We show that translation of a word in context contains information that can be used to disambiguate the meaning of that word