BIOMedical search engine framework: lightweight and customized implementation of domain-specific biomedical search engines

The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef

Modelado y Comparación de Colecciones en la Web Semántica

En esta tesis se estudia la representación, modelado y comparación de colecciones mediante el uso de ontologías en el ámbito de la Web Semántica. Las colecciones, entendidas como agrupaciones de objetos o elementos con entidad propia, son construcciones que aparecen frecuentemente en prácticamente todos los dominios del mundo real, y por tanto, es imprescindible disponer de conceptualizaciones de estas estructuras abstractas y de representaciones de estas conceptualizaciones en los sistemas informáticos, que definan adecuadamente su semántica. Mientras que en muchos ámbitos de la Informática y la Inteligencia Artificial, como por ejemplo la programación, las bases de datos o la recuperación de información, las colecciones han sido ampliamente estudiadas y se han desarrollado representaciones que responden a multitud de conceptualizaciones, en el ámbito de la Web Semántica, sin embargo, su estudio ha sido bastante limitado. De hecho hasta la fecha existen pocas propuestas de representación de colecciones mediante ontologías, y las que hay sólo cubren algunos tipos de colecciones y presentan importantes limitaciones. Esto impide la representación adecuada de colecciones y dificulta otras tareas comunes como la comparación de colecciones, algo crítico en operaciones habituales como las búsquedas semánticas o el enlazado de datos en la Web Semántica. Para solventar este problema esta tesis hace una propuesta de modelización de colecciones basada en una nueva clasificación de colecciones de acuerdo a sus características estructurales (homogeneidad, unicidad, orden y cardinalidad). Esta clasificación permite definir una taxonomía con hasta 16 tipos de colecciones distintas. Entre otras ventajas, esta nueva clasificación permite aprovechar la semántica de las propiedades estructurales de cada tipo de colección para realizar comparaciones utilizando las funciones de similitud y disimilitud más apropiadas. De este modo, la tesis desarrolla además un nuevo catálogo de funciones de similitud para las distintas colecciones, donde se han recogido las funciones de (di)similitud más conocidas y también algunas nuevas. Esta propuesta se ha implementado mediante dos ontologías paralelas, la ontología E-Collections, que representa los distintos tipos de colecciones de la taxonomía y su axiomática, y la ontología SIMEON (Similarity Measures Ontology) que representa los tipos de funciones de (di)similitud para cada tipo de colección. Gracias a estas ontologías, para comparar dos colecciones, una vez representadas como instancias de la clase más apropiada de la ontología E-Collections, automáticamente se sabe qué funciones de (di)similitud de la ontología SIMEON pueden utilizarse para su comparación. Abstract This thesis studies the representation, modeling and comparison of collections in the Semantic Web using ontologies. Collections, understood as groups of objects or elements with their own identities, are constructions that appear frequently in almost all areas of the real world. Therefore, it is essential to have conceptualizations of these abstract structures and representations of these conceptualizations in computer systems, that define their semantic properly. While in many areas of Computer Science and Artificial Intelligence, such as Programming, Databases or Information Retrieval, the collections have been extensively studied and there are representations that match many conceptualizations, in the field Semantic Web, however, their study has been quite limited. In fact, there are few representations of collections using ontologies so far, and they only cover some types of collections and have important limitations. This hinders a proper representation of collections and other common tasks like comparing collections, something critical in usual operations such as semantic search or linking data on the Semantic Web. To solve this problem this thesis makes a proposal for modelling collections based on a new classification of collections according to their structural characteristics (homogeneity, uniqueness, order and cardinality). This classification allows to define a taxonomy with up to 16 different types of collections. Among other advantages, this new classification can leverage the semantics of the structural properties of each type of collection to make comparisons using the most appropriate (dis)similarity functions. Thus, the thesis also develops a new catalog of similarity functions for the different types of collections. This catalog contains the most common (dis)similarity functions as well as new ones. This proposal is implemented through two parallel ontologies, the E-Collections ontology that represents the different types of collections in the taxonomy and their axiomatic, and the SIMEON ontology (Similarity Measures Ontology) that represents the types of (dis)similarity functions for each type of collection. Thanks to these ontologies, to compare two collections, once represented as instances of the appropriate class of E-Collections ontology, we can know automatically which (dis)similarity functions of the SIMEON ontology are suitable for the comparison. Finally, the feasibility and usefulness of this modeling and comparison of collections proposal is proved in the field of oenology, applying both E-Collections and SIMEON ontologies to the representation and comparison of wines with the E-Baco ontology.

Indexação e pesquisa de informação com base em ontologias interligadas

Tecnologias da Web Semântica como RDF, OWL e SPARQL sofreram nos últimos anos um forte crescimento e aceitação. Projectos como a DBPedia e Open Street Map começam a evidenciar o verdadeiro potencial da Linked Open Data. No entanto os motores de pesquisa semânticos ainda estão atrasados neste crescendo de tecnologias semânticas. As soluções disponíveis baseiam-se mais em recursos de processamento de linguagem natural. Ferramentas poderosas da Web Semântica como ontologias, motores de inferência e linguagens de pesquisa semântica não são ainda comuns. Adicionalmente a esta realidade, existem certas dificuldades na implementação de um Motor de Pesquisa Semântico. Conforme demonstrado nesta dissertação, é necessária uma arquitectura federada de forma a aproveitar todo o potencial da Linked Open Data. No entanto um sistema federado nesse ambiente apresenta problemas de performance que devem ser resolvidos através de cooperação entre fontes de dados. O standard actual de linguagem de pesquisa na Web Semântica, o SPARQL, não oferece um mecanismo para cooperação entre fontes de dados. Esta dissertação propõe uma arquitectura federada que contém mecanismos que permitem cooperação entre fontes de dados. Aborda o problema da performance propondo um índice gerido de forma centralizada assim como mapeamentos entre os modelos de dados de cada fonte de dados. A arquitectura proposta é modular, permitindo um crescimento de repositórios e funcionalidades simples e de forma descentralizada, à semelhança da Linked Open Data e da própria World Wide Web. Esta arquitectura trabalha com pesquisas por termos em linguagem natural e também com inquéritos formais em linguagem SPARQL. No entanto os repositórios considerados contêm apenas dados em formato RDF. Esta dissertação baseia-se em múltiplas ontologias partilhadas e interligadas.

Search adaptations and the challenges of the web

Search has become a hot topic in Internet computing, with rival search engines battling to become the de facto Web portal, harnessing search algorithms to wade through information on a scale undreamed of by early information retrieval (IR) pioneers. This article examines how search has matured from its roots in specialized IR systems to become a key foundation of the Web. The authors describe new challenges posed by the Web's scale, and show how search is changing the nature of the Web as much as the Web has changed the nature of search

Self-supervised information retrieval: a novel approach based on Deep Metric Learning and Neural Language Models

Most of the existing open-source search engines, utilize keyword or tf-idf based techniques to find relevant documents and web pages relative to an input query. Although these methods, with the help of a page rank or knowledge graphs, proved to be effective in some cases, they often fail to retrieve relevant instances for more complicated queries that would require a semantic understanding to be exploited. In this Thesis, a self-supervised information retrieval system based on transformers is employed to build a semantic search engine over the library of Gruppo Maggioli company. Semantic search or search with meaning can refer to an understanding of the query, instead of simply finding words matches and, in general, it represents knowledge in a way suitable for retrieval. We chose to investigate a new self-supervised strategy to handle the training of unlabeled data based on the creation of pairs of ’artificial’ queries and the respective positive passages. We claim that by removing the reliance on labeled data, we may use the large volume of unlabeled material on the web without being limited to languages or domains where labeled data is abundant.

Ethics in the flesh: formalizing moral values in embodied cognition

Values are beliefs or principles that are deemed significant or desirable within a specific society or culture, serving as the fundamental underpinnings for ethical and socio-behavioral norms. The objective of this research is to explore the domain encompassing moral, cultural, and individual values. To achieve this, we employ an ontological approach to formally represent the semantic relations within the value domain. The theoretical framework employed adopts Fillmore’s frame semantics, treating values as semantic frames. A value situation is thus characterized by the co-occurrence of specific semantic roles fulfilled within a given event or circumstance. Given the intricate semantics of values as abstract entities with high social capital, our investigation extends to two interconnected domains. The first domain is embodied cognition, specifically image schemas, which are cognitive patterns derived from sensorimotor experiences that shape our conceptualization of entities in the world. The second domain pertains to emotions, which are inherently intertwined with the realm of values. Consequently, our approach endeavors to formalize the semantics of values within an embodied cognition framework, recognizing values as emotional-laden semantic frames. The primary ontologies proposed in this work are: (i) ValueNet, an ontology network dedicated to the domain of values; (ii) ISAAC, the Image Schema Abstraction And Cognition ontology; and (iii) EmoNet, an ontology for theories of emotions. The knowledge formalization adheres to established modeling practices, including the reuse of semantic web resources such as WordNet, VerbNet, FrameNet, DBpedia, and alignment to foundational ontologies like DOLCE, as well as the utilization of Ontology Design Patterns. These ontological resources are operationalized through the development of a fully explainable frame-based detector capable of identifying values, emotions, and image schemas generating knowledge graphs from from natural language, leveraging the semantic dependencies of a sentence, and allowing non trivial higher layer knowledge inferences.

Direct search optimization application programming interface with remote access

Search Optimization methods are needed to solve optimization problems where the objective function and/or constraints functions might be non differentiable, non convex or might not be possible to determine its analytical expressions either due to its complexity or its cost (monetary, computational, time,...). Many optimization problems in engineering and other fields have these characteristics, because functions values can result from experimental or simulation processes, can be modelled by functions with complex expressions or by noise functions and it is impossible or very difficult to calculate their derivatives. Direct Search Optimization methods only use function values and do not need any derivatives or approximations of them. In this work we present a Java API that including several methods and algorithms, that do not use derivatives, to solve constrained and unconstrained optimization problems. Traditional API access, by installing it on the developer and/or user computer, and remote API access to it, using Web Services, are also presented. Remote access to the API has the advantage of always allow the access to the latest version of the API. For users that simply want to have a tool to solve Nonlinear Optimization Problems and do not want to integrate these methods in applications, also two applications were developed. One is a standalone Java application and the other a Web-based application, both using the developed API.

Substrats neuronaux du traitement visuel et sémantique des mots dans le vieillissement normal : apports de la MEG

Bien que l’on ait longtemps considéré que les substrats cérébraux de la mémoire sémantique (MS) demeuraient intacts au cours du vieillissement normal (VN), en raison d’une préservation de la performance des personnes âgées à des épreuves sémantiques, plusieurs études récentes suggèrent que des modifications cérébrales sous-tendant le traitement sémantique opèrent au cours du vieillissement. Celles-ci toucheraient principalement les régions responsables des aspects exécutifs du traitement sémantique, impliqués dans les processus de recherche, de sélection et de manipulation stratégique de l’information sémantique. Cependant, les mécanismes spécifiques régissant la réorganisation cérébrale du traitement sémantique au cours du VN demeurent méconnus, notamment en raison de divergences méthodologiques entre les études. De plus, des données de la littérature suggèrent que des modifications cérébrales associées au vieillissement pourraient également avoir lieu en relation avec les aspects perceptifs visuels du traitement des mots. Puisque le processus de lecture des mots représente un processus interactif et dynamique entre les fonctions perceptuelles de bas niveau et les fonctions de plus haut niveau tel que la MS, il pourrait exister des modifications liées à l’âge au plan des interactions cérébrales entre les aspects perceptifs et sémantiques du traitement des mots. Dans son ensemble, l’objectif de la présente thèse était de caractériser les modifications cérébrales ainsi que le décours temporel du signal cérébral qui sont associés au traitement sémantique ainsi qu’au traitement perceptif des mots en lien avec le VN, ainsi que les relations et les modulations entre les processus sémantiques et perceptifs au cours du VN, en utilisant la magnétoencéphalographie (MEG) comme technique d’investigation. Dans un premier temps (chapitre 2), les patrons d’activation cérébrale d’un groupe de participants jeunes et d’un groupe de participants âgés sains ont été comparés alors qu’ils effectuaient une tâche de jugement sémantique sur des mots en MEG, en se concentrant sur le signal autour de la N400, une composante associée au traitement sémantique. Les résultats démontrent que des modifications cérébrales liées à l’âge touchent principalement les structures impliquées dans les aspects exécutifs du traitement sémantique. Une activation plus importante du cortex préfrontal inférieur (IPC) a été observée chez les participants jeunes que chez les participants âgés, alors que ces derniers activaient davantage les régions temporo-pariétales que les jeunes adultes. Par ailleurs, le lobe temporal antérieur (ATL) gauche, considéré comme une région centrale et amodale du traitement sémantique, était également davantage activé par les participants âgés que par les jeunes adultes. Dans un deuxième temps (chapitre 3), les patrons d’activation cérébrale d’un groupe de participants jeunes et d’un groupe de participants âgés sains ont été comparés en se concentrant sur le signal associé au traitement perceptif visuel, soit dans les 200 premières millisecondes du traitement des mots. Les résultats montrent que des modifications cérébrales liées à l’âge touchent le gyrus fusiforme mais aussi le réseau sémantique, avec une plus grande activation pour le groupe de participants âgés, malgré une absence de différence d’activation dans le cortex visuel extrastrié entre les deux groupes. Les implications théoriques des résultats de ces deux études sont ensuite discutées, et les limites et perspectives futures sont finalement adressées (chapitre 4).

Common Craft

Common craft make short videos which explain in simple terms some common concepts and technologies used in learning and teaching. These are available through The Common Craft Store, which offers versions of videos that are: Downloadable files Presentation-quality Licensed for workplace use You can find the free, online versions of the videos on The Common Craft Show. Topics include phishing, RSS, wikis, Twitter, social networking, social bookmarking, web search strategies, social media, podcasting, sharing photos online and many more.

Os synsets de verbos do português com o SE inerente e os seus equivalentes do inglês

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A scalable approach for content based image retrieval in cloud datacenter

The emergence of cloud datacenters enhances the capability of online data storage. Since massive data is stored in datacenters, it is necessary to effectively locate and access interest data in such a distributed system. However, traditional search techniques only allow users to search images over exact-match keywords through a centralized index. These techniques cannot satisfy the requirements of content based image retrieval (CBIR). In this paper, we propose a scalable image retrieval framework which can efficiently support content similarity search and semantic search in the distributed environment. Its key idea is to integrate image feature vectors into distributed hash tables (DHTs) by exploiting the property of locality sensitive hashing (LSH). Thus, images with similar content are most likely gathered into the same node without the knowledge of any global information. For searching semantically close images, the relevance feedback is adopted in our system to overcome the gap between low-level features and high-level features. We show that our approach yields high recall rate with good load balance and only requires a few number of hops.

Desarrollo de una aplicación para la escalada y oferta de servicios web

El autor de este proyecto es miembro reciente de la asociación SoloBoulder, dedicada a la modalidad de escalada boulder, noticias y actualidad, contenido multimedia, promoción de un equipo de escaladores y defensa de valores medioambientales en la montaña. El principal canal de distribución de contenidos es una página web existente previa a este proyecto. La asociación ha detectado una escasez y mala calidad de recursos en internet en cuanto a guías de zonas donde poder practicar el boulder. Tal circunstancia impulsa la iniciativa de este proyecto fin de carrera. El objetivo general es el desarrollo de una nueva aplicación que proporcione a los usuarios a nivel mundial una guía interactiva de boulder y otros puntos de interés, una red social que permita la creación cooperativa y orgánica de contenido, y servicios web para el consumo de la información desde otras plataformas u organizaciones. El nuevo software desarrollado es independiente de la página web de SoloBoulder previa. No obstante, ambas partes se integran bajo el mismo domino web y aspecto. La nueva aplicación ofrece a escaladores y turistas un servicio informativo e interactivo de calidad, con el que se espera aumentar el número de visitas en todo el sitio web y poder ampliar la difusión de valores medioambientales, diversificar las zonas de boulder y regular las masificadas, favorecer el deporte y brindar al escalador una oportunidad de autopromoción personal. Una gran motivación para el autor también es el proceso de investigación y formación en tecnologías, patrones arquitecturales de diseño y metodologías de trabajo adaptadas a las tendencias actuales en la ingeniería de software, con especial curiosidad hacia el mundo web. A este respecto podemos destacar: metodología de trabajo en proyectos, análisis de proyectos, arquitecturas de software, diseño de software, bases de datos, programación y buenas prácticas, seguridad, interfaz gráfica web, diseño gráfico, Web Performance Optimization, Search Engine Optimization, etc. En resumen, este proyecto constituye un aprendizaje y puesta en práctica de diversos conocimientos adquiridos durante la ejecución del mismo, así como afianzamiento de materias estudiadas en la carrera. Además, el producto desarrollado ofrece un servicio de calidad a los usuarios y favorece el deporte y la autopromoción del escalador. ABSTRACT. The author of this Project is recent member of the association SoloBoulder, dedicated to a rock climbing discipline called bouldering, news, multimedia content, promotion of a team of climbers and defense of environmental values in the mountain. The main content distribution channel is a web page existing previous to this project. The association has detected scarcity and bad quality of resources on the internet about guides of bouldering areas. This circumstance motivates the initiative of this project. The general objective is the development of a new application which provides a worldwide, interactive bouldering guide, including other points of interest, a social network which allows the cooperative and organic creation of content, and web services for consumption of information from other platforms or organizations. The new software developed is independent of the previous SoloBoulder web page. However, both parts are integrated under the same domain and appearance. The new application offers to climbers and tourists a quality informative and interactive service, with which we hope to increase the number of visits in the whole web site and be able to expand the dissemination of environmental values, diversify boulder areas and regulate the overcrowded ones, encourage sport and offer to the climber an opportunity of self-promotion. A strong motivation for the author is also the process of investigation and education in technologies, architectural design patterns and working methodologies adapted to the actual trends in software engineering, with special curiosity about the web world. In this regard we could highlight: project working methodologies, project analysis, software architectures, software design, data bases, programming and good practices, security, graphic web interface, graphic design, Web Performance Optimization, Search Engine Optimization, etc. To sum up, this project constitutes learning and practice of diverse knowledge acquired during its execution, as well as consolidation of subjects studied in the degree. In addition, the product developed offers a quality service to the users and favors the sport and the selfpromotion of the climber.

Prueba de concepto de expansión de consultas basada en ontologías de dominio financiero

Este trabajo presenta el uso de una ontología en el dominio financiero para la expansión de consultas con el fin de mejorar los resultados de un sistema de recuperación de información (RI) financiera. Este sistema está compuesto por una ontología y un índice de Lucene que permite recuperación de conceptos identificados mediante procesamiento de lenguaje natural. Se ha llevado a cabo una evaluación con un conjunto limitado de consultas y los resultados indican que la ambigüedad sigue siendo un problema al expandir la consulta. En ocasiones, la elección de las entidades adecuadas a la hora de expandir las consultas (filtrando por sector, empresa, etc.) permite resolver esa ambigüedad.

A comparative evaluation of term recognition algorithms

Automatic Term Recognition (ATR) is a fundamental processing step preceding more complex tasks such as semantic search and ontology learning. From a large number of methodologies available in the literature only a few are able to handle both single and multi-word terms. In this paper we present a comparison of five such algorithms and propose a combined approach using a voting mechanism. We evaluated the six approaches using two different corpora and show how the voting algorithm performs best on one corpus (a collection of texts from Wikipedia) and less well using the Genia corpus (a standard life science corpus). This indicates that choice and design of corpus has a major impact on the evaluation of term recognition algorithms. Our experiments also showed that single-word terms can be equally important and occupy a fairly large proportion in certain domains. As a result, algorithms that ignore single-word terms may cause problems to tasks built on top of ATR. Effective ATR systems also need to take into account both the unstructured text and the structured aspects and this means information extraction techniques need to be integrated into the term recognition process.