BioEve Search: A Novel Framework to Facilitate Interactive Literature Search

Background. Recent advances in computational and biological methods in last two decades have remarkably changed the scale of biomedical research and with it began the unprecedented growth in both the production of biomedical data and amount of published literature discussing it. An automated extraction system coupled with a cognitive search and navigation service over these document collections would not only save time and effort, but also pave the way to discover hitherto unknown information implicitly conveyed in the texts. Results. We developed a novel framework (named “BioEve”) that seamlessly integrates Faceted Search (Information Retrieval) with Information Extraction module to provide an interactive search experience for the researchers in life sciences. It enables guided step-by-step search query refinement, by suggesting concepts and entities (like genes, drugs, and diseases) to quickly filter and modify search direction, and thereby facilitating an enriched paradigm where user can discover related concepts and keywords to search while information seeking. Conclusions. The BioEve Search framework makes it easier to enable scalable interactive search over large collection of textual articles and to discover knowledge hidden in thousands of biomedical literature articles with ease

Optimizing scoring functions and indexes for proximity search in type-annotated corpora

We introduce a new, powerful class of text proximity queries: find an instance of a given "answer type" (person, place, distance) near "selector" tokens matching given literals or satisfying given ground predicates. An example query is type=distance NEAR Hamburg Munich. Nearness is defined as a flexible, trainable parameterized aggregation function of the selectors, their frequency in the corpus, and their distance from the candidate answer. Such queries provide a key data reduction step for information extraction, data integration, question answering, and other text-processing applications. We describe the architecture of a next-generation information retrieval engine for such applications, and investigate two key technical problems faced in building it. First, we propose a new algorithm that estimates a scoring function from past logs of queries and answer spans. Plugging the scoring function into the query processor gives high accuracy: typically, an answer is found at rank 2-4. Second, we exploit the skew in the distribution over types seen in query logs to optimize the space required by the new index structures required by our system. Extensive performance studies with a 10GB, 2-million document TREC corpus and several hundred TREC queries show both the accuracy and the efficiency of our system. From an initial 4.3GB index using 18,000 types from WordNet, we can discard 88% of the space, while inflating query times by a factor of only 1.9. Our final index overhead is only 20% of the total index space needed

Towards a Query Optimizer for Text-Centric Tasks

Text is ubiquitous and, not surprisingly, many important applications rely on textual data for a variety of tasks. As a notable example, information extraction applications derive structured relations from unstructured text; as another example, focused crawlers explore the Web to locate pages about specific topics. Execution plans for text-centric tasks follow two general paradigms for processing a text database: either we can scan, or “crawl,” the text database or, alternatively, we can exploit search engine indexes and retrieve the documents of interest via carefully crafted queries constructed in task-specific ways. The choice between crawl- and query-based execution plans can have a substantial impact on both execution time and output “completeness” (e.g., in terms of recall). Nevertheless, this choice is typically ad hoc and based on heuristics or plain intuition. In this article, we present fundamental building blocks to make the choice of execution plans for text-centric tasks in an informed, cost-based way. Towards this goal, we show how to analyze query- and crawl-based plans in terms of both execution time and output completeness. We adapt results from random-graph theory and statistics to develop a rigorous cost model for the execution plans. Our cost model reflects the fact that the performance of the plans depends on fundamental task-specific properties of the underlying text databases. We identify these properties and present efficient techniques for estimating the associated parameters of the cost model.We also present two optimization approaches for text-centric tasks that rely on the cost-model parameters and select efficient execution plans. Overall, our optimization approaches help build efficient execution plans for a task, resulting in significant efficiency and output completeness benefits. We complement our results with a large-scale experimental evaluation for three important text-centric tasks and over multiple real-life data sets.NYU, Stern School of Business, IOMS Department, Center for Digital Economy Researc

Scalable and Declarative Information Extraction in a Parallel Data Analytics System

Informationsextraktions (IE) auf sehr großen Datenmengen erfordert hochkomplexe, skalierbare und anpassungsfähige Systeme. Obwohl zahlreiche IE-Algorithmen existieren, ist die nahtlose und erweiterbare Kombination dieser Werkzeuge in einem skalierbaren System immer noch eine große Herausforderung. In dieser Arbeit wird ein anfragebasiertes IE-System für eine parallelen Datenanalyseplattform vorgestellt, das für konkrete Anwendungsdomänen konfigurierbar ist und für Textsammlungen im Terabyte-Bereich skaliert. Zunächst werden konfigurierbare Operatoren für grundlegende IE- und Web-Analytics-Aufgaben definiert, mit denen komplexe IE-Aufgaben in Form von deklarativen Anfragen ausgedrückt werden können. Alle Operatoren werden hinsichtlich ihrer Eigenschaften charakterisiert um das Potenzial und die Bedeutung der Optimierung nicht-relationaler, benutzerdefinierter Operatoren (UDFs) für Data Flows hervorzuheben. Anschließend wird der Stand der Technik in der Optimierung nicht-relationaler Data Flows untersucht und herausgearbeitet, dass eine umfassende Optimierung von UDFs immer noch eine Herausforderung ist. Darauf aufbauend wird ein erweiterbarer, logischer Optimierer (SOFA) vorgestellt, der die Semantik von UDFs mit in die Optimierung mit einbezieht. SOFA analysiert eine kompakte Menge von Operator-Eigenschaften und kombiniert eine automatisierte Analyse mit manuellen UDF-Annotationen, um die umfassende Optimierung von Data Flows zu ermöglichen. SOFA ist in der Lage, beliebige Data Flows aus unterschiedlichen Anwendungsbereichen logisch zu optimieren, was zu erheblichen Laufzeitverbesserungen im Vergleich mit anderen Techniken führt. Als Viertes wird die Anwendbarkeit des vorgestellten Systems auf Korpora im Terabyte-Bereich untersucht und systematisch die Skalierbarkeit und Robustheit der eingesetzten Methoden und Werkzeuge beurteilt um schließlich die kritischsten Herausforderungen beim Aufbau eines IE-Systems für sehr große Datenmenge zu charakterisieren.Information extraction (IE) on very large data sets requires highly complex, scalable, and adaptive systems. Although numerous IE algorithms exist, their seamless and extensible combination in a scalable system still is a major challenge. This work presents a query-based IE system for a parallel data analysis platform, which is configurable for specific application domains and scales for terabyte-sized text collections. First, configurable operators are defined for basic IE and Web Analytics tasks, which can be used to express complex IE tasks in the form of declarative queries. All operators are characterized in terms of their properties to highlight the potential and importance of optimizing non-relational, user-defined operators (UDFs) for dataflows. Subsequently, we survey the state of the art in optimizing non-relational dataflows and highlight that a comprehensive optimization of UDFs is still a challenge. Based on this observation, an extensible, logical optimizer (SOFA) is introduced, which incorporates the semantics of UDFs into the optimization process. SOFA analyzes a compact set of operator properties and combines automated analysis with manual UDF annotations to enable a comprehensive optimization of data flows. SOFA is able to logically optimize arbitrary data flows from different application areas, resulting in significant runtime improvements compared to other techniques. Finally, the applicability of the presented system to terabyte-sized corpora is investigated. Hereby, we systematically evaluate scalability and robustness of the employed methods and tools in order to pinpoint the most critical challenges in building an IE system for very large data sets

Graph-based Interactive Bibliographic Information Retrieval Systems

In the big data era, we have witnessed the explosion of scholarly literature. This explosion has imposed challenges to the retrieval of bibliographic information. Retrieval of intended bibliographic information has become challenging due to the overwhelming search results returned by bibliographic information retrieval systems for given input queries. At the same time, users’ bibliographic information needs have become more specific such that only information that best matches their needs is seen as relevant. Current bibliographic information retrieval systems such as Web of Science, Scopus, and Google Scholar have become an unalienable component in searching bibliographic data. However, these systems have limited support of complex bibliographic queries. For example, a query- “papers on information retrieval, which were cited by John’s papers that had been presented in SIGIR” is an ordinary information need that researchers may have, but is not appropriately representable in these systems. In addition, these systems only support search for papers and do not support other bibliographic entities such as authors and terms as the final search results. Therefore, in this dissertation, we propose several bibliographic information retrieval systems that can address complex bibliographic queries. We propose form-, natural language-, and visual graph-based systems that allow users to formulate bibliographic queries in a variety of ways. The form-based system allows users to formulate queries by selecting forms and input values in those selected forms. In the natural language-based system, users formulate queries using a natural language. Users formulate queries by drawing nodes and links in the visual graph-based system. These systems are based on a graph model to enhance retrieval efficiency and provides interfaces for users to formulate queries interactively. Through a system-centered evaluation, we find that our graph-based system took less time to process complex queries than a relational-entity-based system (two secs vs. several mins on average). In addition, our visual graph-based system can deal with the representation of advanced queries such as bibliographic coupling, paper co-citation, and author co-citation, while current bibliographic information systems do not support these queries. A user-centered evaluation reveals that participants rated the natural language-based system the most useful, easy to use, and easy to learn. Participants also reported that the form-based system was easier to learn than the visual graph-based system. Based on the results of a usability evaluation, we find that the form-based system is preferred for low-complexity tasks while the visual graph-based system is preferred for high-complexity tasks. The strength of the natural language-based system is that no additional effort is needed to formulate more complex queries. The proposed systems are effective and efficient solutions for addressing complex bibliographic information needs. In addition, we believe the experimental design and results shown in this paper can serve as a useful guideline and benchmark for future studies.Ph.D., Information Studies -- Drexel University, 201

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

A Search Engine for Natural Language Applications ABSTRACT

Many modern natural language-processing applications utilize search engines to locate large numbers of Web documents or to compute statistics over the Web corpus. Yet Web search engines are designed and optimized for simple human queries—they are not well suited to support such applications. As a result, these applications are forced to issue millions of successive queries resulting in unnecessary search engine load and in slow applications with limited scalability. In response, this paper introduces the Bindings Engine (be), which supports queries containing typed variables and string-processing functions. For example, in response to the query “powerful 〈noun〉 ” be will return all the nouns in its index that immediately follow the word “powerful”, sorted by frequency. In response to the query “Cities such as ProperNoun(Head(〈NounPhrase〉))”, be will return a list of proper nouns likely to be city names. be’s novel neighborhood index enables it to do so with O(k) random disk seeks and O(k) serial disk reads, where k is the number of non-variable terms in its query. As a result, be can yield several orders of magnitude speedup for largescale language-processing applications. The main cost is a modest increase in space to store the index. We report on experiments validating these claims, and analyze how be’s space-time tradeoff scales with the size of its index and the number of variable types. Finally, we describe how a bebased application extracts thousands of facts from the Web at interactive speeds in response to simple user queries