Information Extraction from Biomedical Text Using Machine Learning

Inadequate drug experimental data and the use of unlicensed drugs may cause adverse drug reactions, especially in pediatric populations. Every year the U.S. Food and Drug Administration approves human prescription drugs for marketing. The labels associated with these drugs include information about clinical trials and drug response in pediatric population. In order for doctors to make an informed decision about the safety and effectiveness of these drugs for children, there is a need to analyze complex and often unstructured drug labels. In this work, first, an exploratory analysis of drug labels using a Natural Language Processing pipeline is performed. Second, Machine Learning algorithms have been employed to build baseline binary classification models to identify pediatric text in unstructured drug labels. Third, a series of experiments have been executed to evaluate the accuracy of the model. The prototype is able to classify pediatrics-related text with a recall of 0.93 and precision of 0.86

Self-disclosure model for classifying & predicting text-based online disclosure

Les médias sociaux et les sites de réseaux sociaux sont devenus des babillards numériques pour les internautes à cause de leur évolution accélérée. Comme ces sites encouragent les consommateurs à exposer des informations personnelles via des profils et des publications, l'utilisation accrue des médias sociaux a généré des problèmes d’invasion de la vie privée. Des chercheurs ont fait de nombreux efforts pour détecter l'auto-divulgation en utilisant des techniques d'extraction d'informations. Des recherches récentes sur l'apprentissage automatique et les méthodes de traitement du langage naturel montrent que la compréhension du sens contextuel des mots peut entraîner une meilleure précision que les méthodes d'extraction de données traditionnelles. Comme mentionné précédemment, les utilisateurs ignorent souvent la quantité d'informations personnelles publiées dans les forums en ligne. Il est donc nécessaire de détecter les diverses divulgations en langage naturel et de leur donner le choix de tester la possibilité de divulgation avant de publier. Pour ce faire, ce travail propose le « SD_ELECTRA », un modèle de langage spécifique au contexte. Ce type de modèle détecte les divulgations d'intérêts, de données personnelles, d'éducation et de travail, de relations, de personnalité, de résidence, de voyage et d'accueil dans les données des médias sociaux. L'objectif est de créer un modèle linguistique spécifique au contexte sur une plate-forme de médias sociaux qui fonctionne mieux que les modèles linguistiques généraux. De plus, les récents progrès des modèles de transformateurs ont ouvert la voie à la formation de modèles de langage à partir de zéro et à des scores plus élevés. Les résultats expérimentaux montrent que SD_ELECTRA a surpassé le modèle de base dans toutes les métriques considérées pour la méthode de classification de texte standard. En outre, les résultats montrent également que l'entraînement d'un modèle de langage avec un corpus spécifique au contexte de préentraînement plus petit sur un seul GPU peut améliorer les performances. Une application Web illustrative est conçue pour permettre aux utilisateurs de tester les possibilités de divulgation dans leurs publications sur les réseaux sociaux. En conséquence, en utilisant l'efficacité du modèle suggéré, les utilisateurs pourraient obtenir un apprentissage en temps réel sur l'auto-divulgation.Social media and social networking sites have evolved into digital billboards for internet users due to their rapid expansion. As these sites encourage consumers to expose personal information via profiles and postings, increased use of social media has generated privacy concerns. There have been notable efforts from researchers to detect self-disclosure using Information extraction (IE) techniques. Recent research on machine learning and natural language processing methods shows that understanding the contextual meaning of the words can result in better accuracy than traditional data extraction methods. Driven by the facts mentioned earlier, users are often ignorant of the quantity of personal information published in online forums, there is a need to detect various disclosures in natural language and give them a choice to test the possibility of disclosure before posting. For this purpose, this work proposes "SD_ELECTRA," a context-specific language model to detect Interest, Personal, Education and Work, Relationship, Personality, Residence, Travel plan, and Hospitality disclosures in social media data. The goal is to create a context-specific language model on a social media platform that performs better than the general language models. Moreover, recent advancements in transformer models paved the way to train language models from scratch and achieve higher scores. Experimental results show that SD_ELECTRA has outperformed the base model in all considered metrics for the standard text classification method. In addition, the results also show that training a language model with a smaller pre-training context-specific corpus on a single GPU can improve its performance. An illustrative web application designed allows users to test the disclosure possibilities in their social media posts. As a result, by utilizing the efficiency of the suggested model, users would be able to get real-time learning on self-disclosure

Geospatial database generation from digital newspapers: use case for risk and disaster domains.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies.The generation of geospatial databases is expensive in terms of time and money. Many geospatial users still lack spatial data. Geographic Information Extraction and Retrieval systems can alleviate this problem. This work proposes a method to populate spatial databases automatically from the Web. It applies the approach to the risk and disaster domain taking digital newspapers as a data source. News stories on digital newspapers contain rich thematic information that can be attached to places. The use case of automating spatial database generation is applied to Mexico using placenames. In Mexico, small and medium disasters occur most years. The facts about these are frequently mentioned in newspapers but rarely stored as records in national databases. Therefore, it is difficult to estimate human and material losses of those events. This work present two ways to extract information from digital news using natural languages techniques for distilling the text, and the national gazetteer codes to achieve placename-attribute disambiguation. Two outputs are presented; a general one that exposes highly relevant news, and another that attaches attributes of interest to placenames. The later achieved a 75% rate of thematic relevance under qualitative analysis

BlogForever D2.6: Data Extraction Methodology

This report outlines an inquiry into the area of web data extraction, conducted within the context of blog preservation. The report reviews theoretical advances and practical developments for implementing data extraction. The inquiry is extended through an experiment that demonstrates the effectiveness and feasibility of implementing some of the suggested approaches. More specifically, the report discusses an approach based on unsupervised machine learning that employs the RSS feeds and HTML representations of blogs. It outlines the possibilities of extracting semantics available in blogs and demonstrates the benefits of exploiting available standards such as microformats and microdata. The report proceeds to propose a methodology for extracting and processing blog data to further inform the design and development of the BlogForever platform

Semantic Knowledge Graphs for the News: A Review

ICT platforms for news production, distribution, and consumption must exploit the ever-growing availability of digital data. These data originate from different sources and in different formats; they arrive at different velocities and in different volumes. Semantic knowledge graphs (KGs) is an established technique for integrating such heterogeneous information. It is therefore well-aligned with the needs of news producers and distributors, and it is likely to become increasingly important for the news industry. This article reviews the research on using semantic knowledge graphs for production, distribution, and consumption of news. The purpose is to present an overview of the field; to investigate what it means; and to suggest opportunities and needs for further research and development.publishedVersio

Choriented Maps: Visualizing SDG Data on Mobile Devices

Choropleth maps and graduated symbol maps are often used to visualize quantitative geographic data. However, as the number of classes grows, distinguishing between adjacent classes increasingly becomes challenging. To mitigate this issue, this work introduces two new visualization types: choriented maps (maps that use colour and orientation as variables to encode geographic information) and choriented mobile (an optimization of choriented maps for mobile devices). The maps were evaluated in a graphical perception study featuring the comparison of SDG (Sustainable Development Goal) data for several European countries. Choriented maps and choriented mobile visualizations resulted in comparable, sometimes better effectiveness and confidence scores than choropleth and graduated symbol maps. Choriented maps and choriented mobile visualizations also performed well regarding efficiency overall and performed worse only than graduated symbol maps. These results suggest that the use of colour and orientation as visual variables in combination can improve the selectivity of map symbols and user performance during the exploration of geographic data in some scenarios.Comment: Accepted for publication in the Cartographic Journa

Ranking for Scalable Information Extraction

Information extraction systems are complex software tools that discover structured information in natural language text. For instance, an information extraction system trained to extract tuples for an Occurs-in(Natural Disaster, Location) relation may extract the tuple from the sentence: "A tsunami swept the coast of Hawaii." Having information in structured form enables more sophisticated querying and data mining than what is possible over the natural language text. Unfortunately, information extraction is a time-consuming task. For example, a state-of-the-art information extraction system to extract Occurs-in tuples may take up to two hours to process only 1,000 text documents. Since document collections routinely contain millions of documents or more, improving the efficiency and scalability of the information extraction process over these collections is critical. As a significant step towards this goal, this dissertation presents approaches for (i) enabling the deployment of efficient information extraction systems and (ii) scaling the information extraction process to large volumes of text. To enable the deployment of efficient information extraction systems, we have developed two crucial building blocks for this task. As a first contribution, we have created REEL, a toolkit to easily implement, evaluate, and deploy full-fledged relation extraction systems. REEL, in contrast to existing toolkits, effectively modularizes the key components involved in relation extraction systems and can integrate other long-established text processing and machine learning toolkits. To define a relation extraction system for a new relation and text collection, users only need to specify the desired configuration, which makes REEL a powerful framework for both research and application building. As a second contribution, we have addressed the problem of building representative extraction task-specific document samples from collections, a step often required by approaches for efficient information extraction. Specifically, we devised fully automatic document sampling techniques for information extraction that can produce better-quality document samples than the state-of-the-art sampling strategies; furthermore, our techniques are substantially more efficient than the existing alternative approaches. To scale the information extraction process to large volumes of text, we have developed approaches that address the efficiency and scalability of the extraction process by focusing the extraction effort on the collections, documents, and sentences worth processing for a given extraction task. For collections, we have studied both (adaptations of) state-of-the art approaches for estimating the number of documents in a collection that lead to the extraction of tuples as well as information extraction-specific approaches. Using these estimations we can identify the collections worth processing and ignore the rest, for efficiency. For documents, we have developed an adaptive document ranking approach that relies on learning-to-rank techniques to prioritize the documents that are likely to produce tuples for an extraction task of choice. Our approach revises the (learned) ranking decisions periodically as the extraction process progresses and new characteristics of the useful documents are revealed. Finally, for sentences, we have developed an approach based on the sparse group selection problem that identifies sentences|modeled as groups of words|that best characterize the extraction task. Beyond identifying sentences worth processing, our approach aims at selecting sentences that lead to the extraction of unseen, novel tuples. Our approaches are lightweight and efficient, and dramatically improve the efficiency and scalability of the information extraction process. We can often complete the extraction task by focusing on just a very small fraction of the available text, namely, the text that contains relevant information for the extraction task at hand. Our approaches therefore constitute a substantial step towards efficient and scalable information extraction over large volumes of text

Automatic Extraction and Assessment of Entities from the Web

The search for information about entities, such as people or movies, plays an increasingly important role on the Web. This information is still scattered across many Web pages, making it more time consuming for a user to find all relevant information about an entity. This thesis describes techniques to extract entities and information about these entities from the Web, such as facts, opinions, questions and answers, interactive multimedia objects, and events. The findings of this thesis are that it is possible to create a large knowledge base automatically using a manually-crafted ontology. The precision of the extracted information was found to be between 75–90 % (facts and entities respectively) after using assessment algorithms. The algorithms from this thesis can be used to create such a knowledge base, which can be used in various research fields, such as question answering, named entity recognition, and information retrieval

Bootstrapping named entity resources for adaptive question answering systems

Los Sistemas de Búsqueda de Respuestas (SBR) amplían las capacidades de un buscador de información tradicional con la capacidad de encontrar respuestas precisas a las preguntas del usuario. El objetivo principal es facilitar el acceso a la información y disminuir el tiempo y el esfuerzo que el usuario debe emplear para encontrar una información concreta en una lista de documentos relevantes. En esta investigación se han abordado dos trabajos relacionados con los SBR. La primera parte presenta una arquitectura para SBR en castellano basada en la combinación y adaptación de diferentes técnicas de Recuperación y de Extracción de Información. Esta arquitectura está integrada por tres módulos principales que incluyen el análisis de la pregunta, la recuperación de pasajes relevantes y la extracción y selección de respuestas. En ella se ha prestado especial atención al tratamiento de las Entidades Nombradas puesto que, con frecuencia, son el tema de las preguntas o son buenas candidatas como respuestas. La propuesta se ha encarnado en el SBR del grupo MIRACLE que ha sido evaluado de forma independiente durante varias ediciones en la tarea compartida CLEF@QA, parte del foro de evaluación competitiva Cross-Language Evaluation Forum (CLEF). Se describen aquí las participaciones y los resultados obtenidos entre 2004 y 2007. El SBR de MIRACLE ha obtenido resultados moderados en el desempeño de la tarea con tasas de respuestas correctas entre el 20% y el 30%. Entre los resultados obtenidos destacan los de la tarea principal de 2005 y la tarea piloto de Búsqueda de Respuestas en tiempo real de 2006, RealTimeQA. Esta última tarea, además de requerir respuestas correctas incluía el tiempo de respuesta como un factor adicional en la evaluación. Estos resultados respaldan la validez de la arquitectura propuesta como una alternativa viable para los SBR sobre colecciones textuales y también corrobora resultados similares para el inglés y otras lenguas. Por otro lado, el análisis de los resultados a lo largo de las diferentes ediciones de CLEF así como la comparación con otros SBR apunta nuevos problemas y retos. Según nuestra experiencia, los sistemas de QA son más complicados de adaptar a otros dominios y lenguas que los sistemas de Recuperación de Información. Este problema viene heredado del uso de herramientas complejas de análisis de lenguaje como analizadores morfológicos, sintácticos y semánticos. Entre estos últimos se cuentan las herramientas para el Reconocimiento y Clasificación de Entidades Nombradas (NERC en inglés) así como para la Detección y Clasificación de Relaciones (RDC en inglés). Debido a la di cultad de adaptación del SBR a distintos dominios y colecciones, en la segunda parte de esta tesis se investiga una propuesta diferente basada en la adquisición de conocimiento mediante métodos de aprendizaje ligeramente supervisado. El objetivo de esta investigación es adquirir recursos semánticos útiles para las tareas de NERC y RDC usando colecciones de textos no anotados. Además, se trata de eliminar la dependencia de herramientas de análisis lingüístico con el fin de facilitar que las técnicas sean portables a diferentes dominios e idiomas. En primer lugar, se ha realizado un estudio de diferentes algoritmos para NERC y RDC de forma semisupervisada a partir de unos pocos ejemplos (bootstrapping). Este trabajo propone primero una arquitectura común y compara diferentes funciones que se han usado en la evaluación y selección de resultados intermedios, tanto instancias como patrones. La principal propuesta es un nuevo algoritmo que permite la adquisición simultánea e iterativa de instancias y patrones asociados a una relación. Incluye también la posibilidad de adquirir varias relaciones de forma simultánea y mediante el uso de la hipótesis de exclusividad obtener mejores resultados. Como característica distintiva el algoritmo explora la colección de textos con una estrategia basada en indización, que permite adquirir conocimiento de grandes colecciones. La estrategia de selección de candidatos y la evaluación se basan en la construcción de un grafo de instancias y patrones, que justifica nuestro método para la selección de candidatos. Este procedimiento es semejante al frente de exploración de una araña web y permite encontrar las instancias más parecidas a las semillas con las evidencias disponibles. Este algoritmo se ha implementado en el sistema SPINDEL y para su evaluación se ha comenzado con el caso concreto de la adquisición de recursos para las clases de Entidades Nombradas más comunes, Persona, Lugar y Organización. El objetivo es adquirir nombres asociados a cada una de las categorías así como patrones contextuales que permitan detectar menciones asociadas a una clase. Se presentan resultados para la adquisición de dos idiomas distintos, castellano e inglés, y para el castellano, en dos dominios diferentes, noticias y textos de una enciclopedia colaborativa, Wikipedia. En ambos casos el uso de herramientas de análisis lingüístico se ha limitado de acuerdo con el objetivo de avanzar hacia la independencia de idioma. Las listas adquiridas mediante bootstrapping parten de menos de 40 semillas por clase y obtienen del orden de 30.000 instancias de calidad variable. Además se obtienen listas de patrones indicativos asociados a cada clase de entidad. La evaluación indirecta confirma la utilidad de ambos recursos en la clasificación de Entidades Nombradas usando un enfoque simple basado únicamente en diccionarios. La mejor configuración obtiene para la clasificación en castellano una medida F de 67,17 y para inglés de 55,99. Además se confirma la utilidad de los patrones adquiridos que en ambos casos ayudan a mejorar la cobertura. El módulo requiere menor esfuerzo de desarrollo que los enfoques supervisados, si incluimos la necesidad de anotación, aunque su rendimiento es inferior por el momento. En definitiva, esta investigación constituye un primer paso hacia el desarrollo de aplicaciones semánticas como los SBR que requieran menos esfuerzo de adaptación a un dominio o lenguaje nuevo.-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Question Answering (QA) systems add new capabilities to traditional search engines with the ability to find precise answers to user questions. Their objective is to enable easier information access by reducing the time and effort that the user requires to find a concrete information among a list of relevant documents. In this thesis we have carried out two works related with QA systems. The first part introduces an architecture for QA systems for Spanish which is based on the combination and adaptation of different techniques from Information Retrieval (IR) and Information Extraction (IE). This architecture is composed by three modules that include question analysis, relevant passage retrieval and answer extraction and selection. The appropriate processing of Named Entities (NE) has received special attention because of their importance as question themes and candidate answers. The proposed architecture has been implemented as part of the MIRACLE QA system. This system has taken part in independent evaluations like the CLEF@QA track in the Cross-Language Evaluation Forum (CLEF). Results from 2004 to 2007 campaigns as well as the details and the evolution of the system have been described in deep. The MIRACLE QA system has obtained moderate performance with a first answer accuracy ranging between 20% and 30%. Nevertheless, it is important to highlight the results obtained in the 2005 main QA task and the RealTimeQA pilot task in 2006. The last one included response time as an important additional variable of the evaluation. These results back the proposed architecture as an option for QA from textual collection and confirm similar findings obtained for English and other languages. On the other hand, the analysis of the results along evaluation campaigns and the comparison with other QA systems point problems with current systems and new challenges. According to our experience, it is more dificult to tailor QA systems to different domains and languages than IR systems. The problem is inherited by the use of complex language analysis tools like POS taggers, parsers and other semantic analyzers, like NE Recognition and Classification (NERC) and Relation Detection and Characterization (RDC) tools. The second part of this thesis tackles this problem and proposes a different approach to adapting QA systems for di erent languages and collections. The proposal focuses on acquiring knowledge for the semantic analyzers based on lightly supervised approaches. The goal is to obtain useful resources that help to perform NERC or RDC using as few annotated resources as possible. Besides, we try to avoid dependencies from other language analysis tools with the purpose that these methods apply to different languages and domains. First of all, we have study previous work on building NERC and RDC modules with few supervision, particularly bootstrapping methods. We propose a common framework for different bootstrapping systems that help to unify different evaluation functions for intermediate results. The main proposal is a new algorithm that is able to simultaneously acquire instances and patterns associated to a relation of interest. It also uses mutual exclusion among relations to reduce concept drift and achieve better results. A distinctive characteristic is that it uses a query based exploration strategy of the text collection which enables their use for larger collections. Candidate selection and evaluation are based on incrementally building a graph of instances and patterns which also justifies our evaluation function. The discovery approach is analogous to the front of exploration in a web crawler and it is able to find the most similar instances to the available seeds. This algorithm has been implemented in the SPINDEL system. We have selected for evaluation the task of acquiring resources for the most common NE classes, Person, Location and Organization. The objective is to acquire name instances that belong to any of the classes as well as contextual patterns that help to detect mentions of NE that belong to that class. We present results for the acquisition of resources from raw text from two different languages, Spanish and English. We also performed experiments for Spanish in two different collections, news and texts from a collaborative encyclopedia, Wikipedia. Both cases are tackled with limited language analysis tools and resources. With an initial list of 40 instance seeds, the bootstrapping process is able to acquire large name lists containing up to 30.000 instances with a variable quality. Besides, large lists of indicative patterns are obtained too. Our indirect evaluation confirms the utility of both resources to classify NE using a simple dictionary recognition approach. Best results for Spanish obtained a F-score of 67,17 and for English this value is 55,99. The module requires much less development effort than annotation for supervised algorithms although the performance is not in pair yet. This research is a first step towards the development of semantic applications like QA for a new language or domain with no annotated corpora that requires less adaptation effort