Adverse Drug Event Detection, Causality Inference, Patient Communication and Translational Research

Adverse drug events (ADEs) are injuries resulting from a medical intervention related to a drug. ADEs are responsible for nearly 20% of all the adverse events that occur in hospitalized patients. ADEs have been shown to increase the cost of health care and the length of stays in hospital. Therefore, detecting and preventing ADEs for pharmacovigilance is an important task that can improve the quality of health care and reduce the cost in a hospital setting. In this dissertation, we focus on the development of ADEtector, a system that identifies ADEs and medication information from electronic medical records and the FDA Adverse Event Reporting System reports. The ADEtector system employs novel natural language processing approaches for ADE detection and provides a user interface to display ADE information. The ADEtector employs machine learning techniques to automatically processes the narrative text and identify the adverse event (AE) and medication entities that appear in that narrative text. The system will analyze the entities recognized to infer the causal relation that exists between AEs and medications by automating the elements of Naranjo score using knowledge and rule based approaches. The Naranjo Adverse Drug Reaction Probability Scale is a validated tool for finding the causality of a drug induced adverse event or ADE. The scale calculates the likelihood of an adverse event related to drugs based on a list of weighted questions. The ADEtector also presents the user with evidence for ADEs by extracting figures that contain ADE related information from biomedical literature. A brief summary is generated for each of the figures that are extracted to help users better comprehend the figure. This will further enhance the user experience in understanding the ADE information better. The ADEtector also helps patients better understand the narrative text by recognizing complex medical jargon and abbreviations that appear in the text and providing definitions and explanations for them from external knowledge resources. This system could help clinicians and researchers in discovering novel ADEs and drug relations and also hypothesize new research questions within the ADE domain

Measuring Semantic Textual Similarity and Automatic Answer Assessment in Dialogue Based Tutoring Systems

This dissertation presents methods and resources proposed to improve onmeasuring semantic textual similarity and their applications in student responseunderstanding in dialogue based Intelligent Tutoring Systems. In order to predict the extent of similarity between given pair of sentences,we have proposed machine learning models using dozens of features, such as thescores calculated using optimal multi-level alignment, vector based compositionalsemantics, and machine translation evaluation methods. Furthermore, we haveproposed models towards adding an interpretation layer on top of similaritymeasurement systems. Our models on predicting and interpreting the semanticsimilarity have been the top performing systems in SemEval (a premier venue for thesemantic evaluation) for the last three years. The correlations between our models\u27predictions and the human judgments were above 0.80 for several datasets while ourmodels being very robust than many other top performing systems. Moreover, wehave proposed Bayesian. We have also proposed a novel Neural Network based word representationmapping approach which allows us to map the vector based representation of a wordfound in one model to the another model where the word representation is missing,effectively pooling together the vocabularies and corresponding representationsacross models. Our experiments show that the model coverage increased by few toseveral times depending on which model\u27s vocabulary is taken as a reference. Also,the transformed representations were well correlated to the native target modelvectors showing that the mapped representations can be used with condence tosubstitute the missing word representations in the target model. models to adapt similarity models across domains. Furthermore, we have proposed methods to improve open-ended answersassessment in dialogue based tutoring systems which is very challenging because ofthe variations in student answers which often are not self contained and need thecontextual information (e.g., dialogue history) in order to better assess theircorrectness. In that, we have proposed Probabilistic Soft Logic (PSL) modelsaugmenting semantic similarity information with other knowledge. To detect intra- and inter-sentential negation scope and focus in tutorialdialogs, we have developed Conditional Random Fields (CRF) models. The resultsindicate that our approach is very effective in detecting negation scope and focus intutorial dialogue context and can be further developed to augment the naturallanguage understanding systems. Additionally, we created resources (datasets, models, and tools) for fosteringresearch in semantic similarity and student response understanding inconversational tutoring systems

言語学的特徴を用いた述部の正規化と同義性判定

京都大学0048新制・課程博士博士(情報学)甲第17991号情博第513号新制||情||91(附属図書館)80835京都大学大学院情報学研究科知能情報学専攻(主査)教授 黒橋 禎夫, 教授 石田 亨, 教授 河原 達也学位規則第4条第1項該当Doctor of InformaticsKyoto UniversityDFA

Confluence of Vision and Natural Language Processing for Cross-media Semantic Relations Extraction

In this dissertation, we focus on extracting and understanding semantically meaningful relationships between data items of various modalities; especially relations between images and natural language. We explore the ideas and techniques to integrate such cross-media semantic relations for machine understanding of large heterogeneous datasets, made available through the expansion of the World Wide Web. The datasets collected from social media websites, news media outlets and blogging platforms usually contain multiple modalities of data. Intelligent systems are needed to automatically make sense out of these datasets and present them in such a way that humans can find the relevant pieces of information or get a summary of the available material. Such systems have to process multiple modalities of data such as images, text, linguistic features, and structured data in reference to each other. For example, image and video search and retrieval engines are required to understand the relations between visual and textual data so that they can provide relevant answers in the form of images and videos to the users\u27 queries presented in the form of text. We emphasize the automatic extraction of semantic topics or concepts from the data available in any form such as images, free-flowing text or metadata. These semantic concepts/topics become the basis of semantic relations across heterogeneous data types, e.g., visual and textual data. A classic problem involving image-text relations is the automatic generation of textual descriptions of images. This problem is the main focus of our work. In many cases, large amount of text is associated with images. Deep exploration of linguistic features of such text is required to fully utilize the semantic information encoded in it. A news dataset involving images and news articles is an example of this scenario. We devise frameworks for automatic news image description generation based on the semantic relations of images, as well as semantic understanding of linguistic features of the news articles

Knowledge Modelling and Learning through Cognitive Networks

One of the most promising developments in modelling knowledge is cognitive network science, which aims to investigate cognitive phenomena driven by the networked, associative organization of knowledge. For example, investigating the structure of semantic memory via semantic networks has illuminated how memory recall patterns influence phenomena such as creativity, memory search, learning, and more generally, knowledge acquisition, exploration, and exploitation. In parallel, neural network models for artificial intelligence (AI) are also becoming more widespread as inferential models for understanding which features drive language-related phenomena such as meaning reconstruction, stance detection, and emotional profiling. Whereas cognitive networks map explicitly which entities engage in associative relationships, neural networks perform an implicit mapping of correlations in cognitive data as weights, obtained after training over labelled data and whose interpretation is not immediately evident to the experimenter. This book aims to bring together quantitative, innovative research that focuses on modelling knowledge through cognitive and neural networks to gain insight into mechanisms driving cognitive processes related to knowledge structuring, exploration, and learning. The book comprises a variety of publication types, including reviews and theoretical papers, empirical research, computational modelling, and big data analysis. All papers here share a commonality: they demonstrate how the application of network science and AI can extend and broaden cognitive science in ways that traditional approaches cannot

Temporality and modality in entailment graph induction

The ability to draw inferences is core to semantics and the field of Natural Language Processing. Answering a seemingly simple question like ‘Did Arsenal play Manchester yesterday’ from textual evidence that says ‘Arsenal won against Manchester yesterday’ requires modeling the inference that ‘winning’ entails ‘playing’. One way of modeling this type of lexical semantics is with Entailment Graphs, collections of meaning postulates that can be learned in an unsupervised way from large text corpora. In this work, we explore the role that temporality and linguistic modality can play in inducing Entailment Graphs. We identify inferences that were previously not supported by Entailment Graphs (such as that ‘visiting’ entails an ‘arrival’ before the visit) and inferences that were likely to be learned incorrectly (such as that ‘winning’ entails ‘losing’). Temporality is shown to be useful in alleviating these challenges, in the Entailment Graph representation as well as the learning algorithm. An exploration of linguistic modality in the training data shows, counterintuitively, that there is valuable signal in modalized predications. We develop three datasets for evaluating a system’s capability of modeling these inferences, which were previously underrepresented in entailment rule evaluations. Finally, in support of the work on modality, we release a relation extraction system that is capable of annotating linguistic modality, together with a comprehensive modality lexicon

Enhancing the interactivity of a clinical decision support system by using knowledge engineering and natural language processing

Mental illness is a serious health problem and it affects many people. Increasingly,Clinical Decision Support Systems (CDSS) are being used for diagnosis and it is important to improve the reliability and performance of these systems. Missing a potential clue or a wrong diagnosis can have a detrimental effect on the patient's quality of life and could lead to a fatal outcome. The context of this research is the Galatean Risk and Safety Tool (GRiST), a mental-health-risk assessment system. Previous research has shown that success of a CDSS depends on its ease of use, reliability and interactivity. This research addresses these concerns for the GRiST by deploying data mining techniques. Clinical narratives and numerical data have both been analysed for this purpose.Clinical narratives have been processed by natural language processing (NLP)technology to extract knowledge from them. SNOMED-CT was used as a reference ontology and the performance of the different extraction algorithms have been compared. A new Ensemble Concept Mining (ECM) method has been proposed, which may eliminate the need for domain specific phrase annotation requirements. Word embedding has been used to filter phrases semantically and to build a semantic representation of each of the GRiST ontology nodes.The Chi-square and FP-growth methods have been used to find relationships between GRiST ontology nodes. Interesting patterns have been found that could be used to provide real-time feedback to clinicians. Information gain has been used efficaciously to explain the differences between the clinicians and the consensus risk. A new risk management strategy has been explored by analysing repeat assessments. A few novel methods have been proposed to perform automatic background analysis of the patient data and improve the interactivity and reliability of GRiST and similar systems

Text complexity and text simplification in the crisis management domain

Due to the fact that emergency situations can lead to substantial losses, both financial and in terms of human lives, it is essential that texts used in a crisis situation be clearly understandable. This thesis is concerned with the study of the complexity of the crisis management sub-language and with methods to produce new, clear texts and to rewrite pre-existing crisis management documents which are too complex to be understood. By doing this, this interdisciplinary study makes several contributions to the crisis management field. First, it contributes to the knowledge of the complexity of the texts used in the domain, by analysing the presence of a set of written language complexity issues derived from the psycholinguistic literature in a novel corpus of crisis management documents. Second, since the text complexity analysis shows that crisis management documents indeed exhibit high numbers of text complexity issues, the thesis adapts to the English language controlled language writing guidelines which, when applied to the crisis management language, reduce its complexity and ambiguity, leading to clear text documents. Third, since low quality of communication can have fatal consequences in emergency situations, the proposed controlled language guidelines and a set of texts which were re-written according to them are evaluated from multiple points of view. In order to achieve that, the thesis both applies existing evaluation approaches and develops new methods which are more appropriate for the task. These are used in two evaluation experiments – evaluation on extrinsic tasks and evaluation of users’ acceptability. The evaluations on extrinsic tasks (evaluating the impact of the controlled language on text complexity, reading comprehension under stress, manual translation, and machine translation tasks) Text Complexity and Text Simplification in the Crisis Management domain 4 show a positive impact of the controlled language on simplified documents and thus ensure the quality of the resource. The evaluation of users’ acceptability contributes additional findings about manual simplification and helps to determine directions for future implementation. The thesis also gives insight into reading comprehension, machine translation, and cross-language adaptability, and provides original contributions to machine translation, controlled languages, and natural language generation evaluation techniques, which make it valuable for several scientific fields, including Linguistics, Psycholinguistics, and a number of different sub-fields of NLP.EThOS - Electronic Theses Online ServiceGBUnited Kingdo