Validation of Electronic Health Record Phenotyping of Bipolar Disorder Cases and Controls

Objective: The study was designed to validate use of elec-tronic health records (EHRs) for diagnosing bipolar disorder and classifying control subjects. Method: EHR data were obtained from a health care system of more than 4.6 million patients spanning more than 20 years. Experienced clinicians reviewed charts to identify text features and coded data consistent or inconsistent with a diagnosis of bipolar disorder. Natural language processing was used to train a diagnostic algorithm with 95% specificity for classifying bipolar disorder. Filtered coded data were used to derive three additional classification rules for case subjects and one for control subjects. The positive predictive value (PPV) of EHR-based bipolar disorder and subphenotype di- agnoses was calculated against diagnoses from direct semi- structured interviews of 190 patients by trained clinicians blind to EHR diagnosis. Results: The PPV of bipolar disorder defined by natural language processing was 0.85. Coded classification based on strict filtering achieved a value of 0.79, but classifications based on less stringent criteria performed less well. No EHR- classified control subject received a diagnosis of bipolar dis- order on the basis of direct interview (PPV=1.0). For most subphenotypes, values exceeded 0.80. The EHR-based clas- sifications were used to accrue 4,500 bipolar disorder cases and 5,000 controls for genetic analyses. Conclusions: Semiautomated mining of EHRs can be used to ascertain bipolar disorder patients and control subjects with high specificity and predictive value compared with diagnostic interviews. EHRs provide a powerful resource for high-throughput phenotyping for genetic and clinical research.

Optimization and Applications of Large-Scale Biomedical Event Networks

The overwhelming amount and unprecedented speed of publication in the biomedical domain make it difficult for life science researchers to acquire and maintain a broad view of the field and gather all information that would be relevant for their research. As a response to this problem, the BioNLP (Biomedical Natural Language Processing) community of researches has emerged and strives to assist life science researchers by developing modern natural language processing (NLP), information extraction (IE) and information retrieval (IR) methods that can be applied at large-scale, to scan the whole publicly available biomedical literature and extract and aggregate the information found within, while automatically normalizing the variability of natural language statements. Among different tasks, biomedical event extraction has received much attention within BioNLP community recently. Biomedical event extraction constitutes the identification of biological processes and interactions described in biomedical literature, and their representation as a set of recursive event structures. The 2009–2013 series of BioNLP Shared Tasks on Event Extraction have given raise to a number of event extraction systems, several of which have been applied at a large scale (the full set of PubMed abstracts and PubMed Central Open Access full text articles), leading to creation of massive biomedical event databases, each of which containing millions of events. Sinece top-ranking event extraction systems are based on machine-learning approach and are trained on the narrow-domain, carefully selected Shared Task training data, their performance drops when being faced with the topically highly varied PubMed and PubMed Central documents. Specifically, false-positive predictions by these systems lead to generation of incorrect biomolecular events which are spotted by the end-users. This thesis proposes a novel post-processing approach, utilizing a combination of supervised and unsupervised learning techniques, that can automatically identify and filter out a considerable proportion of incorrect events from large-scale event databases, thus increasing the general credibility of those databases. The second part of this thesis is dedicated to a system we developed for hypothesis generation from large-scale event databases, which is able to discover novel biomolecular interactions among genes/gene-products. We cast the hypothesis generation problem as a supervised network topology prediction, i.e predicting new edges in the network, as well as types and directions for these edges, utilizing a set of features that can be extracted from large biomedical event networks. Routine machine learning evaluation results, as well as manual evaluation results suggest that the problem is indeed learnable. This work won the Best Paper Award in The 5th International Symposium on Languages in Biology and Medicine (LBM 2013).

Towards Proactive Context-aware Computing and Systems

A primary goal of context-aware systems is delivering the right information at the right place and right time to users in order to enable them to make effective decisions and improve their quality of life. There are three key requirements for achieving this goal: determining what information is relevant, personalizing it based on the users’ context (location, preferences, behavioral history etc.), and delivering it to them in a timely manner without an explicit request from them. These requirements create a paradigm that we term as “Proactive Context-aware Computing”. Most of the existing context-aware systems fulfill only a subset of these requirements. Many of these systems focus only on personalization of the requested information based on users’ current context. Moreover, they are often designed for specific domains. In addition, most of the existing systems are reactive - the users request for some information and the system delivers it to them. These systems are not proactive i.e. they cannot anticipate users’ intent and behavior and act proactively without an explicit request from them. In order to overcome these limitations, we need to conduct a deeper analysis and enhance our understanding of context-aware systems that are generic, universal, proactive and applicable to a wide variety of domains. To support this dissertation, we explore several directions. Clearly the most significant sources of information about users today are smartphones. A large amount of users’ context can be acquired through them and they can be used as an effective means to deliver information to users. In addition, social media such as Facebook, Flickr and Foursquare provide a rich and powerful platform to mine users’ interests, preferences and behavioral history. We employ the ubiquity of smartphones and the wealth of information available from social media to address the challenge of building proactive context-aware systems. We have implemented and evaluated a few approaches, including some as part of the Rover framework, to achieve the paradigm of Proactive Context-aware Computing. Rover is a context-aware research platform which has been evolving for the last 6 years. Since location is one of the most important context for users, we have developed ‘Locus’, an indoor localization, tracking and navigation system for multi-story buildings. Other important dimensions of users’ context include the activities that they are engaged in. To this end, we have developed ‘SenseMe’, a system that leverages the smartphone and its multiple sensors in order to perform multidimensional context and activity recognition for users. As part of the ‘SenseMe’ project, we also conducted an exploratory study of privacy, trust, risks and other concerns of users with smart phone based personal sensing systems and applications. To determine what information would be relevant to users’ situations, we have developed ‘TellMe’ - a system that employs a new, flexible and scalable approach based on Natural Language Processing techniques to perform bootstrapped discovery and ranking of relevant information in context-aware systems. In order to personalize the relevant information, we have also developed an algorithm and system for mining a broad range of users’ preferences from their social network profiles and activities. For recommending new information to the users based on their past behavior and context history (such as visited locations, activities and time), we have developed a recommender system and approach for performing multi-dimensional collaborative recommendations using tensor factorization. For timely delivery of personalized and relevant information, it is essential to anticipate and predict users’ behavior. To this end, we have developed a unified infrastructure, within the Rover framework, and implemented several novel approaches and algorithms that employ various contextual features and state of the art machine learning techniques for building diverse behavioral models of users. Examples of generated models include classifying users’ semantic places and mobility states, predicting their availability for accepting calls on smartphones and inferring their device charging behavior. Finally, to enable proactivity in context-aware systems, we have also developed a planning framework based on HTN planning. Together, these works provide a major push in the direction of proactive context-aware computing.

Exploration des réseaux de neurones à base d'autoencodeur dans le cadre de la modélisation des données textuelles

Depuis le milieu des années 2000, une nouvelle approche en apprentissage automatique, l'apprentissage de réseaux profonds (deep learning), gagne en popularité. En effet, cette approche a démontré son efficacité pour résoudre divers problèmes en améliorant les résultats obtenus par d'autres techniques qui étaient considérées alors comme étant l'état de l'art. C'est le cas pour le domaine de la reconnaissance d'objets ainsi que pour la reconnaissance de la parole. Sachant cela, l’utilisation des réseaux profonds dans le domaine du Traitement Automatique du Langage Naturel (TALN, Natural Language Processing) est donc une étape logique à suivre. Cette thèse explore différentes structures de réseaux de neurones dans le but de modéliser le texte écrit, se concentrant sur des modèles simples, puissants et rapides à entraîner.

Motor de recomendación construido sobre implicaciones

Este Trabajo Fin de Grado (TFG) tiene como objetivo la creación de un framework para su uso en sistemas de recomendación. Se ha realizado por dos personas en la modalidad de trabajo en equipo. Las tareas de este TFG están divididas en dos partes, una realizada conjuntamente y la otra de manera individual. La parte conjunta se centra en construir un sistema que sea capaz de, a partir de comentarios y opiniones sobre puntos de interés (POIs) y haciendo uso de la herramienta de procesamiento de lenguaje natural AlchemyAPI, construir contextos formales y contextos formales multivaluados. Para crear este último es necesario hacer uso de ontologías. El context formal multivaluado es el punto de partida de la segunda parte (individual), que consistirá en, haciendo uso del contexto multivaluado, obtener un conjunto de dependencias funcionales mediante la implementación en Java del algoritmo FDMine. Estas dependencias podrán ser usados en un motor de recomendación. El sistema se ha implementado como una aplicación web Java EE versión 6 y una API para trabajar con contextos formales multivaluados. Para el desarrollo web se han empleado tecnologías actuales como Spring y jQuery. Este proyecto se presenta como un trabajo inicial en el que se expondrán, además del sistema construido, diversos problemas relacionados con la creacion de conjuntos de datos validos. Por último, también se propondrán líneas para futuros TFGs.

Statistical Analysis of Text Summarization Evaluation

This dissertation applies statistical methods to the evaluation of automatic summarization using data from the Text Analysis Conferences in 2008-2011. Several aspects of the evaluation framework itself are studied, including the statistical testing used to determine significant differences, the assessors, and the design of the experiment. In addition, a family of evaluation metrics is developed to predict the score an automatically generated summary would receive from a human judge and its results are demonstrated at the Text Analysis Conference. Finally, variations on the evaluation framework are studied and their relative merits considered. An over-arching theme of this dissertation is the application of standard statistical methods to data that does not conform to the usual testing assumptions.

Testu arteko koherentziazko erlazio-egitura: lehen urratsak euskaraz

[EU]Testu bat koherente egiten duten arrazoiak ulertzea oso baliagarria da testuaren beraren ulermenerako, koherentzia eta koherentzia-erlazioak testu bat edo gehiago koherente diren ondorioztatzen laguntzen baitigu. Lan honetan gai bera duten testu ezberdinen arteko koherentziazko 3 Cross Document Structure Theory edo CST (Radev, 2000) erlazio aztertu eta sailkatu dira. Hori egin ahal izateko, euskaraz idatziriko gai berari buruzko testuak segmentatzeko eta beraien arteko erlazioak etiketatzeko gidalerroak proposatzen dira. 10 testuz osaturiko corpusa etiketatu da; horietako 3 cluster bi etiketatzailek aztertu dute. Etiketatzaileen arteko adostasunaren berri ematen dugu. Koherentzia-erlazioak garatzea oso garrantzitsua da Hizkuntzaren Prozesamenduko hainbat sistementzat, hala nola, informazioa erauzteko sistementzat, itzulpen automatikoarentzat, galde-erantzun sistementzat eta laburpen automatikoarentzat. Etorkizunean CSTko erlazio guztiak corpus esanguratsuan aztertuko balira, testuen arteko koherentzia- erlazioak euskarazko testuen prozesaketa automatikoa bideratzeko lehenengo pausua litzateke hemen egindakoa.

Image summarisation: human action description from static images

Dissertação de Mestrado, Processamento de Linguagem Natural e Indústrias da Língua, Faculdade de Ciências Humanas e Sociais, Universidade do Algarve, 2014

Automatic identification of whole-part relations in Portuguese

Dissertação de Mestrado, Ciências da Linguagem, Faculdade de Ciências Humanas e Sociais, Universidade do Algarve, 2014

Lexicon-grammar of Russian verbal idioms

Dissertação de Mestrado, Ciências da Linguagem, Faculdade de Ciências Humanas e Sociais, Universidade do Algarve, 2016

Développement d’un système d’appariement pour l’e-recrutement

Ce mémoire tente de répondre à une problématique très importante dans le domaine de recrutement : l’appariement entre offre d’emploi et candidats. Dans notre cas nous disposons de milliers d’offres d’emploi et de millions de profils ramassés sur les sites dédiés et fournis par un industriel spécialisé dans le recrutement. Les offres d’emploi et les profils de candidats sur les réseaux sociaux professionnels sont généralement destinés à des lecteurs humains qui sont les recruteurs et les chercheurs d’emploi. Chercher à effectuer une sélection automatique de profils pour une offre d’emploi se heurte donc à certaines difficultés que nous avons cherché à résoudre dans le présent mémoire. Nous avons utilisé des techniques de traitement automatique de la langue naturelle pour extraire automatiquement les informations pertinentes dans une offre d’emploi afin de construite une requête qui nous permettrait d’interroger notre base de données de profils. Pour valider notre modèle d’extraction de métier, de compétences et de d’expérience, nous avons évalué ces trois différentes tâches séparément en nous basant sur une référence cent offres d’emploi canadiennes que nous avons manuellement annotée. Et pour valider notre outil d’appariement nous avons fait évaluer le résultat de l’appariement de dix offres d’emploi canadiennes par un expert en recrutement.

Développement d’un système d’appariement pour l’e-recrutement

Ce mémoire tente de répondre à une problématique très importante dans le domaine de recrutement : l’appariement entre offre d’emploi et candidats. Dans notre cas nous disposons de milliers d’offres d’emploi et de millions de profils ramassés sur les sites dédiés et fournis par un industriel spécialisé dans le recrutement. Les offres d’emploi et les profils de candidats sur les réseaux sociaux professionnels sont généralement destinés à des lecteurs humains qui sont les recruteurs et les chercheurs d’emploi. Chercher à effectuer une sélection automatique de profils pour une offre d’emploi se heurte donc à certaines difficultés que nous avons cherché à résoudre dans le présent mémoire. Nous avons utilisé des techniques de traitement automatique de la langue naturelle pour extraire automatiquement les informations pertinentes dans une offre d’emploi afin de construite une requête qui nous permettrait d’interroger notre base de données de profils. Pour valider notre modèle d’extraction de métier, de compétences et de d’expérience, nous avons évalué ces trois différentes tâches séparément en nous basant sur une référence cent offres d’emploi canadiennes que nous avons manuellement annotée. Et pour valider notre outil d’appariement nous avons fait évaluer le résultat de l’appariement de dix offres d’emploi canadiennes par un expert en recrutement.

Criação de uma ontologia e respectiva povoação a partir do processamento de relatórios médicos

A evolução tecnológica tem provocado uma evolução na medicina, através de sistemas computacionais voltados para o armazenamento, captura e disponibilização de informações médicas. Os relatórios médicos são, na maior parte das vezes, guardados num texto livre não estruturado e escritos com vocabulário proprietário, podendo ocasionar falhas de interpretação. Através das linguagens da Web Semântica, é possível utilizar antologias como modo de estruturar e padronizar a informação dos relatórios médicos, adicionando¬ lhe anotações semânticas. A informação contida nos relatórios pode desta forma ser publicada na Web, permitindo às máquinas o processamento automático da informação. No entanto, o processo de criação de antologias é bastante complexo, pois existe o problema de criar uma ontologia que não cubra todo o domínio pretendido. Este trabalho incide na criação de uma ontologia e respectiva povoação, através de técnicas de PLN e Aprendizagem Automática que permitem extrair a informação dos relatórios médicos. Foi desenvolvida uma aplicação, que permite ao utilizador converter relatórios do formato digital para o formato OWL. ABSTRACT: Technological evolution has caused a medicine evolution through computer systems which allow storage, gathering and availability of medical information. Medical reports are, most of the times, stored in a non-structured free text and written in a personal way so that misunderstandings may occur. Through Semantic Web languages, it’s possible to use ontology as a way to structure and standardize medical reports information by adding semantic notes. The information in those reports can, by these means, be displayed on the web, allowing machines automatic information processing. However, the process of creating ontology is very complex, as there is a risk creating of an ontology that not covering the whole desired domain. This work is about creation of an ontology and its population through NLP and Machine Learning techniques to extract information from medical reports. An application was developed which allows the user to convert reports from digital for¬ mat to OWL format.

Using a Dialogue Manager to Improve Semantic Web Search

Question Answering systems that resort to the Semantic Web as a knowledge base can go well beyond the usual matching words in documents and, preferably, find a precise answer, without requiring user help to interpret the documents returned. In this paper, the authors introduce a Dialogue Manager that, through the analysis of the question and the type of expected answer, provides accurate answers to the questions posed in Natural Language. The Dialogue Manager not only represents the semantics of the questions, but also represents the structure of the discourse, including the user intentions and the questions context, adding the ability to deal with multiple answers and providing justified answers. The authors’ system performance is evaluated by comparing with similar question answering systems. Although the test suite is slight dimension, the results obtained are very promising.

Essays on Atypicality: A narrative perspective to illuminate how atypical actors can counter the disciplining effect of categories

Using Big Data and Natural Language Processing (NLP) tools, this dissertation investigates the narrative strategies that atypical actors can leverage to deal with the adverse reactions they often elicit. Extensive research shows that atypical actors, those who fail to abide by established contextual standards and norms, are subject to skepticism and face a higher risk of rejection. Indeed, atypical actors combine features and behaviors in unconventional ways, thereby generating confusion in the audience and instilling doubts about their propositions' legitimacy. However, the same atypicality is often cited as the precursor to socio-cultural innovation and a strategic act to expand the capacity for delivering valued goods and services. Contextualizing the conditions under which atypicality is celebrated or punished has been a significant theoretical challenge for scholars interested in reconciling this tension. Nevertheless, prior work has focused on audience side factors or on actor-side characteristics that are only scantily under an actor's control (e.g., status and reputation). This dissertation demonstrates that atypical actors can use strategically crafted narratives to mitigate against the audience’s negative response. In particular, when atypical actors evoke conventional features in their story, they are more likely to overcome the illegitimacy discount usually applied to them. Moreover, narratives become successful navigational devices for atypicality when atypical actors use a more abstract language. This simplifies classification and provides the audience with more flexibility to interpret and understand them.