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

A survey on sentiment analysis in Urdu: A resource-poor language

© 2020 Background/introduction: The dawn of the internet opened the doors to the easy and widespread sharing of information on subject matters such as products, services, events and political opinions. While the volume of studies conducted on sentiment analysis is rapidly expanding, these studies mostly address English language concerns. The primary goal of this study is to present state-of-art survey for identifying the progress and shortcomings saddling Urdu sentiment analysis and propose rectifications. Methods: We described the advancements made thus far in this area by categorising the studies along three dimensions, namely: text pre-processing lexical resources and sentiment classification. These pre-processing operations include word segmentation, text cleaning, spell checking and part-of-speech tagging. An evaluation of sophisticated lexical resources including corpuses and lexicons was carried out, and investigations were conducted on sentiment analysis constructs such as opinion words, modifiers, negations. Results and conclusions: Performance is reported for each of the reviewed study. Based on experimental results and proposals forwarded through this paper provides the groundwork for further studies on Urdu sentiment analysis

Multiword expressions at length and in depth

The annual workshop on multiword expressions takes place since 2001 in conjunction with major computational linguistics conferences and attracts the attention of an ever-growing community working on a variety of languages, linguistic phenomena and related computational processing issues. MWE 2017 took place in Valencia, Spain, and represented a vibrant panorama of the current research landscape on the computational treatment of multiword expressions, featuring many high-quality submissions. Furthermore, MWE 2017 included the first shared task on multilingual identification of verbal multiword expressions. The shared task, with extended communal work, has developed important multilingual resources and mobilised several research groups in computational linguistics worldwide. This book contains extended versions of selected papers from the workshop. Authors worked hard to include detailed explanations, broader and deeper analyses, and new exciting results, which were thoroughly reviewed by an internationally renowned committee. We hope that this distinctly joint effort will provide a meaningful and useful snapshot of the multilingual state of the art in multiword expressions modelling and processing, and will be a point point of reference for future work

Clefts in context : A QUD-perspective on c'est / il y a utterances in spoken French

In this paper we present the results of a pragmatic analysis of French full clefts and monoclausal c'est/il y a utterances (e.g. c'est la femme qui l'a tué 'it's the wife who killed him' vs. c'est la femme 'it's the wife' respectively in answer to the question 'who killed him?'), when these structures are used as pragmatic strategies to focalize the subject in spoken French. Unlike full cleft sentences, monoclausal c'est and il y a utterances have received less attention in the literature, especially with regard to focus and its realization in spontaneous speech. Investigating the opposition between full clefts and monoclausal forms as well as the questions that these clefts answer allows us to arrive at a more precise understanding of the discourse functions of these structures and the pragmatic contexts in which they are felicitous. The corpus that is used (sgs, spontaneous spoken French) contains many question-answer pairs due to its interactive setup, thus enabling a clear analysis of the types of Question Under Discussion that the clefts answer. The data show that monoclausal utterances are more likely to answer highly active QUDs, whereas full clefts are more likely to answer less active QUDs. The level of activation is determined in terms of proximity and implicitness of the QUD (immediately-preceding the cleft, further away or implicit), and - when the question is uttered explicitly - modality (wh or yes/no) also plays a role

Introducción de la formación de palabras a través de corpus nativos para favorecer la profundidad de vocabulario en alumnado de inglés como segunda lengua en Educación Secundaria

ABSTRACT: This paper analyses the types and different possibilities offered by linguistic corpora, aiming to evaluate the benefits and constraints of their direct use in the classroom. Once this has been described, I inspect the concepts of word, vocabulary and lexical unit. Furthermore, I turn to morphology to examine the processes of affixation and derivation in word formation, and more specifically, how these two processes are approached in the language education curricula in Spain. Finally, I explore the pedagogical bases and most common approaches to learning vocabulary in English, among which we can find the direct use of corpora in the classroom through Data-Driven Learning. To put these elements into practice, the last part of this paper is based on the creation of a learning unit aimed for upper secondary English learners with an intermediate level within the Spanish curricular framework.RESUMEN: En el presente trabajo se analizan los tipos y las diferentes posibilidades ofrecidas por los corpus lingüísticos, con el objetivo de evaluar los beneficios y desventajas de su uso directo en el aula. Una vez esto ha sido descrito, se inspeccionan los conceptos de palabra, vocabulario y unidad léxica. Además, se examinan los procesos de afijación y derivación en la formación de palabras y cómo se tratan estos dos procesos en el currículum de educación de lenguas en España. Finalmente, se exploran las bases pedagógicas y los enfoques más comunes del aprendizaje de vocabulario en inglés, entre los cuales se encuentra el uso directo de los corpus en el aula a través del Data-Driven Learning. Para poner estos elementos en práctica, la última parte de este trabajo está basada en la creación de una unidad didáctica dirigida a estudiantes de inglés de la etapa de Bachillerato con un nivel intermedio de inglés, en el contexto del marco curricular español.Máster en Aprendizaje y Enseñanza de Segundas Lenguas / Second Language Learning and Teachin

Improving Search via Named Entity Recognition in Morphologically Rich Languages – A Case Study in Urdu

University of Minnesota Ph.D. dissertation. February 2018. Major: Computer Science. Advisors: Vipin Kumar, Blake Howald. 1 computer file (PDF); xi, 236 pages.Search is not a solved problem even in the world of Google and Bing's state of the art engines. Google and similar search engines are keyword based. Keyword-based searching suffers from the vocabulary mismatch problem -- the terms in document and user's information request don't overlap. For example, cars and automobiles. This phenomenon is called synonymy. Similarly, the user's term may be polysemous -- a user is inquiring about a river's bank, but documents about financial institutions are matched. Vocabulary mismatch exacerbated when the search occurs in Morphological Rich Language (MRL). Concept search techniques like dimensionality reduction do not improve search in Morphological Rich Languages. Names frequently occur news text and determine the "what," "where," "when," and "who" in the news text. Named Entity Recognition attempts to recognize names automatically in text, but these techniques are far from mature in MRL, especially in Arabic Script languages. Urdu is one the focus MRL of this dissertation among Arabic, Farsi, Hindi, and Russian, but it does not have the enabling technologies for NER and search. A corpus, stop word generation algorithm, a light stemmer, a baseline, and NER algorithm is created so the NER-aware search can be accomplished for Urdu. This dissertation demonstrates that NER-aware search on Arabic, Russian, Urdu, and English shows significant improvement over baseline. Furthermore, this dissertation highlights the challenges for researching in low-resource MRL languages

The TXM Portal Software giving access to Old French Manuscripts Online

Texte intégral en ligne : http://www.lrec-conf.org/proceedings/lrec2012/workshops/13.ProceedingsCultHeritage.pdfInternational audiencehttp://www.lrec-conf.org/proceedings/lrec2012/workshops/13.ProceedingsCultHeritage.pdf This paper presents the new TXM software platform giving online access to Old French Text Manuscripts images and tagged transcriptions for concordancing and text mining. This platform is able to import medieval sources encoded in XML according to the TEI Guidelines for linking manuscript images to transcriptions, encode several diplomatic levels of transcription including abbreviations and word level corrections. It includes a sophisticated tokenizer able to deal with TEI tags at different levels of linguistic hierarchy. Words are tagged on the fly during the import process using IMS TreeTagger tool with a specific language model. Synoptic editions displaying side by side manuscript images and text transcriptions are automatically produced during the import process. Texts are organized in a corpus with their own metadata (title, author, date, genre, etc.) and several word properties indexes are produced for the CQP search engine to allow efficient word patterns search to build different type of frequency lists or concordances. For syntactically annotated texts, special indexes are produced for the Tiger Search engine to allow efficient syntactic concordances building. The platform has also been tested on classical Latin, ancient Greek, Old Slavonic and Old Hieroglyphic Egyptian corpora (including various types of encoding and annotations)