In this modern era many educational institutes and business organisations are adopting the e-Learning approach as it provides an effective method for educating and testing their students and staff. The continuous development in the area of information technology and increasing use of the internet has resulted in a huge global market and rapid growth for e-Learning. Multiple Choice Tests (MCTs) are a popular form of assessment and are quite frequently used by many e-Learning applications as they are well adapted to assessing factual, conceptual and procedural information. In this thesis, we present an alternative to the lengthy and time-consuming activity of developing MCTs by proposing a Natural Language Processing (NLP) based approach that relies on semantic relations extracted using Information Extraction to automatically generate MCTs. Information Extraction (IE) is an NLP field used to recognise the most important entities present in a text, and the relations between those concepts, regardless of their surface realisations. In IE, text is processed at a semantic level that allows the partial representation of the meaning of a sentence to be produced. IE has two major subtasks: Named Entity Recognition (NER) and Relation Extraction (RE). In this work, we present two unsupervised RE approaches (surface-based and dependency-based). The aim of both approaches is to identify the most important semantic relations in a document without assigning explicit labels to them in order to ensure broad coverage, unrestricted to predefined types of relations. In the surface-based approach, we examined different surface pattern types, each implementing different assumptions about the linguistic expression of semantic relations between named entities while in the dependency-based approach we explored how dependency relations based on dependency trees can be helpful in extracting relations between named entities. Our findings indicate that the presented approaches are capable of achieving high precision rates. Our experiments make use of traditional, manually compiled corpora along with similar corpora automatically collected from the Web. We found that an automatically collected web corpus is still unable to ensure the same level of topic relevance as attained in manually compiled traditional corpora. Comparison between the surface-based and the dependency-based approaches revealed that the dependency-based approach performs better. Our research enabled us to automatically generate questions regarding the important concepts present in a domain by relying on unsupervised relation extraction approaches as extracted semantic relations allow us to identify key information in a sentence. The extracted patterns (semantic relations) are then automatically transformed into questions. In the surface-based approach, questions are automatically generated from sentences matched by the extracted surface-based semantic pattern which relies on a certain set of rules. Conversely, in the dependency-based approach questions are automatically generated by traversing the dependency tree of extracted sentence matched by the dependency-based semantic patterns. The MCQ systems produced from these surface-based and dependency-based semantic patterns were extrinsically evaluated by two domain experts in terms of questions and distractors readability, usefulness of semantic relations, relevance, acceptability of questions and distractors and overall MCQ usability. The evaluation results revealed that the MCQ system based on dependency-based semantic relations performed better than the surface-based one. A major outcome of this work is an integrated system for MCQ generation that has been evaluated by potential end users.

Thesis Title: Named Entity Recognition in the Biomedical Domain Named entity recognition (NER) is the task of information extraction that attempts to recognize and extract particular entities in a text. One of the issues that stems from NER is that its models are domain specific. The goal of the thesis is to focus on entities strictly from the biomedical domain. The other issue with NER comes the synonymous terms that may be linked to one entity, moreover they lead to issue of disambiguation of the entities. Due to the popularity of neural networks and their success in NLP tasks, the work should use a neural network architecture for the task of named entity disambiguation, which is described in the paper by Eshel et al [1]. One of the subtasks of the thesis is to map the words and entities to a vector space using word embeddings, which attempts to provide textual context similarity, and coherence [2]. The main output of the thesis will be a model that attempts to disambiguate entities of the biomedical domain, using scientific journals (PubMed and Embase) as the documents of our interest.

La quantité d'information disponible dans le domaine biomédical ne cesse d'augmenter. Pour que cette information soit facilement utilisable par les experts d'un domaine, il est nécessaire de l'extraire et de la structurer. Pour avoir des données structurées, il convient de détecter les relations existantes entre les entités dans les textes. Nos recherches se sont focalisées sur la question de l'extraction de relations complexes représentant des résultats expérimentaux, et sur la détection et la catégorisation de relations binaires entre des entités biomédicales. Nous nous sommes intéressée aux résultats expérimentaux présentés dans les articles scientifiques. Nous appelons résultat expérimental, un résultat quantitatif obtenu suite à une expérience et mis en relation avec les informations permettant de décrire cette expérience. Ces résultats sont importants pour les experts en biologie, par exemple pour faire de la modélisation. Dans le domaine de la physiologie rénale, une base de données a été créée pour centraliser ces résultats d'expérimentation, mais l'alimentation de la base est manuelle et de ce fait longue. Nous proposons une solution pour extraire automatiquement des articles scientifiques les connaissances pertinentes pour la base de données, c'est-à-dire des résultats expérimentaux que nous représentons par une relation n-aire. La méthode procède en deux étapes : extraction automatique des documents et proposition de celles-ci pour validation ou modification par l'expert via une interface. Nous avons également proposé une méthode à base d'apprentissage automatique pour l'extraction et la classification de relations binaires en domaine de spécialité. Nous nous sommes intéressée aux caractéristiques et variétés d'expressions des relations, et à la prise en compte de ces caractéristiques dans un système à base d'apprentissage. Nous avons étudié la prise en compte de la structure syntaxique de la phrase et la simplification de phrases dirigée pour la tâche d'extraction de relations. Nous avons en particulier développé une méthode de simplification à base d'apprentissage automatique, qui utilise en cascade plusieurs classifieurs. / The amount of available scientific literature is constantly growing. If the experts of a domain want to easily access this information, it must be extracted and structured. To obtain structured data, both entities and relations of the texts must be detected. Our research is about the problem of complex relation extraction which represent experimental results, and detection and classification of binary relations between biomedical entities. We are interested in experimental results presented in scientific papers. An experimental result is a quantitative result obtained by an experimentation and linked with information that describes this experimentation. These results are important for biology experts, for example for doing modelization. In the domain of renal physiology, a database was created to centralize these experimental results, but the base is manually populated, therefore the population takes a long time. We propose a solution to automatically extract relevant knowledge for the database from the scientific papers, that is experimental results which are represented by a n-ary relation. The method proceeds in two steps: automatic extraction from documents and proposal of information extracted for approval or modification by the experts via an interface. We also proposed a method based on machine learning for extraction and classification of binary relations in specialized domains. We focused on the variations of the expression of relations, and how to represent them in a machine learning system. We studied the way to take into account syntactic structure of the sentence and the sentence simplification guided by the task of relation extraction. In particular, we developed a simplification method based on machine learning, which uses a series of classifiers.

Made available in DSpace on 2016-06-02T19:05:46Z (GMT). No. of bitstreams: 1 3250.pdf: 4243437 bytes, checksum: 462620b959061657eacd8e13120fedb0 (MD5) Previous issue date: 2010-09-24 / Financiadora de Estudos e Projetos / There is a large volume of unstructured information (i.e., in text format) being published in electronic media, in digital libraries particularly. Thus, the human being becomes restricted to an amount of text that is able to process and to assimilate over time. In this dissertation is proposed a methodology for textual preprocessing to extract information about disease effects in the biomedical domain papers, in order to identify relevant information from a text, to structure and to store this information in a database to provide a future discovery of interesting relationships between the extracted information. The methodology consists of four steps: Data Entrance (Step 1), Sentence Classification (Step 2), Identification of Relevant Terms (Step 3) and Terms Management (Step 4). This methodology uses three information extraction approaches from the literature: machine learning approach, dictionary-based approach and rule-based approach. The first one is developed in Step 2, in which a supervised machine learning algorithm is responsible for classify the sentences. The second and third ones are developed in Step 3, in which a dictionary of terms validated by an expert and rules developed through regular expressions were used to identify relevant terms in sentences. The methodology validation was carried out through its instantiation to an area of the biomedical domain, more specifically using papers on Sickle Cell Anemia. Accordingly, two case studies were conducted in both Step 2 and in Step 3. The obtained accuracy in the sentence classification was above of 60% and F-measure for the negative effect class was above of 70%. These values correspond to the results achieved with the Support Vector Machine algorithm along with the use of the Noise Removal filter. The obtained F-measure with the identification of relevant terms was above of 85% for the fictitious extraction (i.e., manual classification performed by the expert) and above of 80% for the actual extraction (i.e., automatic classification performed by the classifier). The F-measure of the classifier above of 70% and F-measure of the actual extraction above 80% show the relevance of the sentence classification in the proposed methodology. Importantly to say that many false positives would be identified in full text papers without the sentence classification step. / Existe um grande volume de informação não estruturada (i.e., em formato textual) sendo publicada cada vez mais em meios eletrônicos, particularmente em bibliotecas digitais. Assim, com o passar do tempo, o ser humano fica cada vez mais restringido a uma limitada quantidade de texto que é capaz de processar e assimilar. No sentido de identificar as informações relevantes de um texto e com o objetivo de estruturar e armazenar essas informações em um banco de dados, a fim de propiciar uma futura descoberta de relacionamentos interessantes entre as informações extraídas, nesta dissertação é proposta uma metodologia de pré-processamento textual para extração de informação sobre efeitos de doenças em artigos científicos do domínio biomédico. A metodologia é composta por quatro etapas: Entrada de Dados (Etapa 1), Classificação de Sentenças (Etapa 2), Identificação de Termos Relevantes (Etapa 3) e Gerenciamento de Termos (Etapa 4). Esta metodologia utiliza três abordagens de extração de informação encontradas na literatura: abordagem baseada em aprendizado de máquina, abordagem baseada em dicionário e abordagem baseada em regras. A primeira abordagem é desenvolvida na Etapa 2, na qual um algoritmo de aprendizado de máquina supervisionado é responsável em classificar as sentenças. A segunda e a terceira abordagens são desenvolvidas na Etapa 3, na qual um dicionário de termos validados pelo especialista e regras desenvolvidas por meio de expressões regulares foram utilizados para identificar termos relevantes nas sentenças. A validação da metodologia foi realizada por meio de sua instanciação para uma área do domínio biomédico, mais especificamente usando artigos sobre a doença Anemia Falciforme. Nesse sentido, dois estudos de caso foram realizados tanto na Etapa 2 quanto na Etapa 3. O valor da acurácia obtida na classificação de sentenças foi acima de 60% e o valor da medida-F para a classe efeito negativo foi acima de 70%. Estes valores correspondem aos resultados alcançados com o algoritmo de aprendizado de máquina Support Vector Machine juntamente com a aplicação do filtro Remoção de Ruído. A medida-F obtida com a identificação de termos relevantes foi acima de 85% para a extração fictícia (i.e., classificação manual realizada pelo especialista) e acima de 80% para a extração real (i.e., classificação automática realizada pelo classificador). O valor de medida-F acima de 70% do classificador e o valor de medida-F acima de 80% da extração real mostra a relevância da classificação de sentenças na metodologia proposta. É importante ressaltar que sem a classificação de sentença, muitos falsos positivos seriam identificados nos artigos completos.

Made available in DSpace on 2016-06-02T19:05:56Z (GMT). No. of bitstreams: 1 4310.pdf: 3265738 bytes, checksum: 6650fb70eee9b096860bcac6b5ed596c (MD5) Previous issue date: 2012-02-24 / Currently in the medical field there is a large amount of unstructured information (i.e., in textual format). Regarding the large volume of data, it makes it impossible for doctors and specialists to analyze manually all the relevant literature, which requires techniques for automatically analyze the documents. In order to identify relevant information, as well as to structure and store them into a database and to enable future discovery of significant relationships, in this paper we propose a paragraph-based process to extract treatments from scientific papers in the biomedical domain. The hypothesis is that the initial search for sentences that have terms of complication improves the identification and extraction of terms of treatment. This happens because treatments mainly occur in the same sentence of a complication, or in nearby sentences in the same paragraph. Our methodology employs three approaches for information extraction: machine learning-based approach, for classifying sentences of interest that will have terms to be extracted; dictionary-based approach, which uses terms validated by an expert in the field; and rule-based approach. The methodology was validated as proof of concept, using papers from the biomedical domain, specifically, papers related to Sickle Cell Anemia disease. The proof of concept was performed in the classification of sentences and identification of relevant terms. The value obtained in the classification accuracy of sentences was 79% for the classifier of complication and 71% for the classifier of treatment. These values are consistent with the results obtained from the combination of the machine learning algorithm Support Vector Machine with the filter Noise Removal and Balancing of Classes. In the identification of relevant terms, the results of our methodology showed higher F-measure percentage (42%) compared to the manual classification (31%) and to the partial process, i.e., without using the classifier of complication (36%). Even with low percentage of recall, there was no impact observed on the extraction process, and, in addition, we were able to validate the hypothesis considered in this work. In other words, it was possible to obtain 100% of recall for different terms, thus not impacting the extraction process, and further the working hypothesis of this study was proven. / Atualmente na área médica existe uma grande quantidade de informações não estruturadas (i.e., em formato textual) sendo produzidas na literatura médica. Com o grande volume de dados, torna-se impossível que os médicos e especialistas da área analisem toda a literatura de forma manual, exigindo técnicas para automatizar a análise destes documentos. Com o intuito de identificar as informações relevantes, estruturar e armazenar estas informações em um banco de dados, para posteriormente identificar relacionamentos interessantes entre as informações extraídas, nesta dissertação é proposto um processo baseado em parágrafos para a extração de tratamentos de artigos científicos do domínio biomédico. A hipótese é que a busca inicial de sentenças que possuem termos de complicação melhora a eficiência na identificação e na extração de termos de tratamento. Isso acontece porque tratamentos ocorrem principalmente na mesma sentença de complicação ou em sentenças próximas no mesmo parágrafo. Esta metodologia utiliza três abordagens de extração de informação encontradas na literatura: abordagem baseada em aprendizado de máquina para classificar as sentenças de interesse; abordagem baseada em dicionário com termos validados pelo especialista da área e abordagem baseada em regras. A metodologia foi validada como prova de conceito, utilizando artigos do domínio biomédico, mais especificamente da doença Anemia Falciforme. A prova de conceito foi realizada na classificação de sentenças e identificação de termos relevantes. O valor da acurácia obtida na classificação de sentenças foi de 79% para o classificador de complicação e 71% para o classificador de tratamento. Estes valores condizem com os resultados obtidos com a combinação do algoritmo de aprendizado de máquina Support Vector Machine juntamente com a aplicação do filtro Remoção de Ruído e Balanceamento das Classes. Na identificação de termos relevantes, os resultados da metodologia proposta obteve percentual superior de 42% de medida-F comparado à classificação manual (31%) e comparado ao processo parcial, ou seja, sem utilizar o classificador de complicação (36%). Mesmo com a baixa revocação, foi possível obter 100% de revocação para os termos distintos de tratamento, não impactando o processo de extração, e portanto a hipótese considerada neste trabalho foi comprovada.

Made available in DSpace on 2016-06-02T19:06:20Z (GMT). No. of bitstreams: 1 6477.pdf: 3193803 bytes, checksum: 2bf85c80b2865f8b7efd9d6eeb6aa172 (MD5) Previous issue date: 2013-11-28 / Financiadora de Estudos e Projetos / Recently, there is an enormous amount of scientific material written in textual format and published in electronic ways (paper on proceedings and articles on journals). In the biomedical field, researchers need to analyse a vast amount of information in order to update their knowledges, in order to get more precise diagnostics and propose more modern and effective treatments. The task of getting knowledge is extremely onerous and the manual process to annotate relationships and to propose novel hypothesis for treatments becomes very slow and error-prone. In this sense, as a result of this master s research it is proposed a method to extract cause and effect semantic relationships in sentences of scientific papers of the biomedical domain. The goal of this work is to propose and implements a solution for: (1) to extract terms from the biomedical domain (genes, proteins, chemical components, structures and anatomical processes, cell components and strutures, and treatmens), (2) to identify existing relationships on the texts, from the extracted terms, and (3) to suggest a knowledge network based on the relations of cause and effect . Over the approach using textual patterns, our proposed method had extracted semantic relations with a precision of 94,83 %, recall of 98,10 %, F-measure of 96,43 %. / Atualmente, existe uma enorme quantidade de material científico escrito em formato textual e publicado em meios eletrônicos (artigos em anais de eventos e periódicos). Na área biomédica, pesquisadores necessitam assimilar uma grande parte deste conteúdo com a finalidade de se atualizarem e, por conseguinte realizarem diagnosticos mais precisos e aplicar tratamentos mais modernos e eficazes. A tarefa de obtenção de conhecimento é bastante onerosa e o processo manual para anotar relacionamentos e propor novas hipóteses de tratamentos torna-se muito lento. Neste sentido, como resultado desta pesquisa de mestrado, foi proposto um método para a extração de relacionamentos semânticos do tipo causa e efeito em artigos científicos do domínio biomédico. Mais especificamente, o objetivo deste trabalho é propor e implementar uma solução para (1) extrair termos do domínio biomédico de documentos científicos (genes, componentes químicos, proteínas, estruturas e processos anatômicos, componentes e estruturas celulares e tratamentos), (2) identificar relacionamentos existentes nos textos, com base nos termos extraídos, e (3) sugerir uma rede de conhecimento baseada nos relacionamentos extraídos. Através de uma abordagem utilizando regras e padrões textuais, o método proposto extraiu relacionamentos semânticos com uma precisão de 94,83 %, cobertura de 98,10 % e Medida-F de 96,43 %.