Discovering and Comparing Relational Knowledge, the Example of Pharmacogenomics

Article in Proceedings of the EKAW Doctoral Consortium 2018 co-located with the 21st International Conference on Knowledge Engineering and Knowledge Management (EKAW 2018)Pharmacogenomics (PGx) studies the influence of the genome in drug response, with knowledge units of the form of ternary relationships genomic variation-drug-phenotype. State-of-the-art PGx knowledge is available in the biomedical literature as well as in specialized knowledge bases. Additionally, Electronic Health Records of hospitals can be mined to discover such knowledge units that can then be compared with the state of the art, in order to confirm or temper relationships lacking validation or clinical counterpart. However, both discovering and comparing PGx relationships face multiple challenges: heterogeneous descriptions of knowledge units (languages, vocabularies and granularities), missing values and importance of the time dimension. In this research, we aim at proposing a framework based on Semantic Web technologies and Formal Concept Analysis to discover, represent and compare PGx knowledge units. We present the first results, consisting of creating an integrated knowledge base of PGx knowledge units from various sources and defining comparison methods, as well as the remaining issues to tackle

Découverte de définitions dans le web des données

In this thesis, we are interested in the web of data and knowledge units that can be possibly discovered inside. The web of data can be considered as a very large graph consisting of connected RDF triple databases. An RDF triple, denoted as (subject, predicate, object), represents a relation (i.e. the predicate) existing between two resources (i.e. the subject and the object). Resources can belong to one or more classes, where a class aggregates resources sharing common characteristics. Thus, these RDF triple databases can be seen as interconnected knowledge bases. Most of the time, these knowledge bases are collaboratively built thanks to human users. This is particularly the case of DBpedia, a central knowledge base within the web of data, which encodes Wikipedia content in RDF format. DBpedia is built from two types of Wikipedia data: on the one hand, (semi-)structured data such as infoboxes, and, on the other hand, categories, which are thematic clusters of manually generated pages. However, the semantics of categories in DBpedia, that is, the reason a human agent has bundled resources, is rarely made explicit. In fact, considering a class, a software agent has access to the resources that are regrouped together, i.e. the class extension, but it generally does not have access to the ``reasons'' underlying such a cluster, i.e. it does not have the class intension. Considering a category as a class of resources, we aim at discovering an intensional description of the category. More precisely, given a class extension, we are searching for the related intension. The pair (extension, intension) which is produced provides the final definition and the implementation of classification-based reasoning for software agents. This can be expressed in terms of necessary and sufficient conditions: if x belongs to the class C, then x has the property P (necessary condition), and if x has the property P, then it belongs to the class C (sufficient condition). Two complementary data mining methods allow us to materialize the discovery of definitions, the search for association rules and the search for redescriptions. In this thesis, we first present a state of the art about association rules and redescriptions. Next, we propose an adaptation of each data mining method for the task of definition discovery. Then we detail a set of experiments applied to DBpedia, and we qualitatively and quantitatively compare the two approaches. Finally, we discuss how discovered definitions can be added to DBpedia to improve its quality in terms of consistency and completeness.Dans cette thèse, nous nous intéressons au web des données et aux ``connaissances'' que potentiellement il renferme. Le web des données se présente comme un très grand graphe constitué de bases de triplets RDF connectées entre elles. Un triplet RDF, dénoté (sujet, prédicat, objet), représente une relation (le prédicat) qui existe entre deux ressources (le sujet et l'objet). Les ressources peuvent appartenir à une ou plusieurs classes, où une classe regroupe des ressources partageant des caractéristiques communes. Ainsi, ces bases de triplets RDF peuvent être vues comme des bases de connaissances interconnectées. La plupart du temps ces bases de connaissances sont construites de manière collaborative par des utilisateurs. C'est notamment le cas de DBpedia, une base de connaissances centrale dans le web des données, qui encode le contenu de Wikipédia au format RDF. DBpedia est construite à partir de deux types de données de Wikipédia : d'une part, des données (semi-)structurées telles que les infoboxes et d'autre part les catégories, qui sont des regroupements thématiques de pages générés manuellement. Cependant, la sémantique des catégories dans DBpedia, c'est-à-dire la raison pour laquelle un agent humain a regroupé des ressources, n'est pas explicite. De fait, en considérant une classe, un agent logiciel a accès aux ressources qui y sont regroupées --- il dispose de la définition dite en extension --- mais il n'a généralement pas accès aux ``motifs'' de ce regroupement --- il ne dispose pas de la définition dite en intension. Dans cette thèse, nous cherchons à associer une définition à une catégorie en l'assimilant à une classe de ressources. Plus précisément, nous cherchons à associer une intension à une classe donnée en extension. La paire (extension, intension) produite va fournir la définition recherchée et va autoriser la mise en œuvre d'un raisonnement par classification pour un agent logiciel. Cela peut s'exprimer en termes de conditions nécessaires et suffisantes : si x appartient à la classe C, alors x a la propriété P (condition nécessaire), et si x a la propriété P, alors il appartient à la classe C (condition suffisante). Deux méthodes de fouille de données complémentaires nous permettent de matérialiser la découverte de définitions, la fouille de règles d'association et la fouille de redescriptions. Dans le mémoire, nous présentons d'abord un état de l'art sur les règles d'association et les redescriptions. Ensuite, nous proposons une adaptation de chacune des méthodes pour finaliser la tâche de découverte de définitions. Puis nous détaillons un ensemble d'expérimentations menées sur DBpedia, où nous comparons qualitativement et quantitativement les deux approches. Enfin les définitions découvertes peuvent potentiellement être ajoutées à DBpedia pour améliorer sa qualité en termes de cohérence et de complétud

Front-Line Physicians' Satisfaction with Information Systems in Hospitals

Day-to-day operations management in hospital units is difficult due to continuously varying situations, several actors involved and a vast number of information systems in use. The aim of this study was to describe front-line physicians' satisfaction with existing information systems needed to support the day-to-day operations management in hospitals. A cross-sectional survey was used and data chosen with stratified random sampling were collected in nine hospitals. Data were analyzed with descriptive and inferential statistical methods. The response rate was 65 % (n = 111). The physicians reported that information systems support their decision making to some extent, but they do not improve access to information nor are they tailored for physicians. The respondents also reported that they need to use several information systems to support decision making and that they would prefer one information system to access important information. Improved information access would better support physicians' decision making and has the potential to improve the quality of decisions and speed up the decision making process.Peer reviewe

Bioinspired metaheuristic algorithms for global optimization

This paper presents concise comparison study of newly developed bioinspired algorithms for global optimization problems. Three different metaheuristic techniques, namely Accelerated Particle Swarm Optimization (APSO), Firefly Algorithm (FA), and Grey Wolf Optimizer (GWO) are investigated and implemented in Matlab environment. These methods are compared on four unimodal and multimodal nonlinear functions in order to find global optimum values. Computational results indicate that GWO outperforms other intelligent techniques, and that all aforementioned algorithms can be successfully used for optimization of continuous functions

Experimental Evaluation of Growing and Pruning Hyper Basis Function Neural Networks Trained with Extended Information Filter

In this paper we test Extended Information Filter (EIF) for sequential training of Hyper Basis Function Neural Networks with growing and pruning ability (HBF-GP). The HBF neuron allows different scaling of input dimensions to provide better generalization property when dealing with complex nonlinear problems in engineering practice. The main intuition behind HBF is in generalization of Gaussian type of neuron that applies Mahalanobis-like distance as a distance metrics between input training sample and prototype vector. We exploit concept of neuron’s significance and allow growing and pruning of HBF neurons during sequential learning process. From engineer’s perspective, EIF is attractive for training of neural networks because it allows a designer to have scarce initial knowledge of the system/problem. Extensive experimental study shows that HBF neural network trained with EIF achieves same prediction error and compactness of network topology when compared to EKF, but without the need to know initial state uncertainty, which is its main advantage over EKF

Anales del XIII Congreso Argentino de Ciencias de la Computación (CACIC)

Contenido: Arquitecturas de computadoras Sistemas embebidos Arquitecturas orientadas a servicios (SOA) Redes de comunicaciones Redes heterogéneas Redes de Avanzada Redes inalámbricas Redes móviles Redes activas Administración y monitoreo de redes y servicios Calidad de Servicio (QoS, SLAs) Seguridad informática y autenticación, privacidad Infraestructura para firma digital y certificados digitales Análisis y detección de vulnerabilidades Sistemas operativos Sistemas P2P Middleware Infraestructura para grid Servicios de integración (Web Services o .Net)Red de Universidades con Carreras en Informática (RedUNCI

Anales del XIII Congreso Argentino de Ciencias de la Computación (CACIC)

Contenido: Arquitecturas de computadoras Sistemas embebidos Arquitecturas orientadas a servicios (SOA) Redes de comunicaciones Redes heterogéneas Redes de Avanzada Redes inalámbricas Redes móviles Redes activas Administración y monitoreo de redes y servicios Calidad de Servicio (QoS, SLAs) Seguridad informática y autenticación, privacidad Infraestructura para firma digital y certificados digitales Análisis y detección de vulnerabilidades Sistemas operativos Sistemas P2P Middleware Infraestructura para grid Servicios de integración (Web Services o .Net)Red de Universidades con Carreras en Informática (RedUNCI