https://hdl.handle.net/11000/459 2026-04-05T13:31:25Z https://hdl.handle.net/11000/39038 Título : Comparing the behaviour of basic linear algebra routines on multicore platforms Autor : Cuenca, Javier; García, Luis P.; Giménez, Domingo; Quesada-Martínez, Manuel Resumen : The use of an OpenMP compiler optimized for a multicore system could contribute to obtain programs with satisfactory execution time, but it is possible to have access in a system to more than one compiler, and different compilers optimize different parts of the code at different levels. In this paper, the influence of the compiler used on the performance of linear algebra routines is studied. From the results of the experiments carried out, we conclude a poly-compiling approach is necessary to decide automatically the best compiler. 2026-01-27T12:55:55Z https://hdl.handle.net/11000/39037 Título : Modelado y autooptimización en esquemas paralelos de backtracking Autor : Quesada-Martínez, Manuel; Giménez, Domingo Resumen : En este trabajo se estudia el modelado del tiempo de ejecuci´on de esquemas paralelos de backtracking. Se estudian diferentes esquemas de programaci ´on identificando par´ametros que influyen en el tiempo de ejecuci´on. Se propone una metodolog´ıa de optimizaci´on basada en la selecci´on autom´atica de par´ametros para obtener ejecuciones con un tiempo reducido. Se estudian las propiedades que deber´ıa tener un esquema algor´ıtmico secuencial de backtracking para poder realizar internamente la paralelizaci´on. De esta manera se pretende abstraer a los usuarios finales de las complejidades de la programaci´on paralela. 2026-01-27T12:53:34Z https://hdl.handle.net/11000/39036 Título : Analysis of the Influence of the Compiler on Multicore Performance Autor : Cuenca, Javier; García, Luis P; Giménez, Domingo; Quesada-Martínez, Manuel Resumen : The possibility of connecting several nodes in a network of processors has popularized parallel programming in the scientific community, but its use has been limited by the difficulty of message-passing programming. With the arrival of multicore processors, parallel programming has regained popularity. The use of an OpenMP compiler optimized for the multicore system in question is a good option, but it is possible to have access in a system to more than one compiler and different compilers can appropriately optimize different parts of the code. In this paper we study theoretically and experimentally the influence of the compiler on performance of routines. We conclude that a poly-compiling approach that decides the best compiler for each situation is necessary. 2026-01-27T12:52:56Z https://hdl.handle.net/11000/39035 Título : OBANSoft: integrated software for Bayesian statistics and high performance computing with R Autor : Quesada-Martínez, Manuel; Giménez, Domingo; Martínez, Asunción Resumen : Among all the applications for Bayesian analysis, there is none that integrates the whole process of Objective Bayesian Analysis. The aim of the “Software for Objective Bayesian Analysis” (OBANSoft) is to cover this gap. The first version includes the easiest models (Yang and Berger (1996)) but its design will allow for more complex algorithms in time. The statistics engine has been implemented using R. Implementing the algorithms with this language lets us take advantage of the increasing number of new routines that the R community is developing, so we can focus the effort on other purposes such as high performance computing. For this reason, OBANSoft has been designed taking into account that it is going to incorporate a variety of parallelism levels, and it will be the first R parallel in a shared memory architecture. Moreover, the heterogeneity of parallel architectures will obstruct non advance users in parallelism optimizing the performance of their programs without the help of an expert. Concerning parallel performance, OBANSoft is ready to include an auto tuning module that configures the best parameters to execute the parallel algorithms (Katagiri et al. (2004)). Although the statistics engine is developed in R, this is envolved in a top layer defined like a Java interface (using JRI to link them). This main layer coordinates the lower layers where the different engines based on several architectures are implemented. Indeed, this top layer will implement the auto-tuning algorithms. The final user will only use a desktop application that will solve a problem in the most efficient way for each platform. The first version is a complete and integrated Java Desktop Application (OBANSoft) implementing the first models used to teach Bayesian analysis (Quesada (2010)). All the models are implemented using R libraries that have been reorganized to compose our R engine. The SnowFall library (SnowFall (2011)) allows exploitation of parallelism in multicore systems. However, the performance of this library is not satisfactory enough and other parallelism strategies need to be considered. In conclusion, we have developed the base application where we are going to include more complex models with higher computational needs. Our concern is to implement and link the R engine with other parallel languages and high performance libraries (BLAS, OpenMP, MPI, CUDA, etc.). OBANSoft will assume all those new routines, including auto-tuning decisions. Our goal is to distance the final user from the problems of parallel computation. 2026-01-27T12:51:28Z https://hdl.handle.net/11000/39034 Título : Enrichment of OWL Ontologies: a method for defining axioms from labels Autor : Quesada-Martínez, Manuel; Fernández-Breis, Jesualdo Tomás; Stevens, Robert Resumen : An increasing interest has provoked the development of a significant number of ontologies, and many more are expected to be produced in the next years. A significant proportion of such ontologies have not been created by computer scientists or ontology engineers, but by domain experts. Many of such ontologies are rich in implicit knowledge, but are really basic taxonomies and controlled vocabularies, with little axiomatization. Many such ontologies have much information within the labels of the classes. There is a great deal of knowledge about the entities described within such labels and text definitions held on classes; these are useful for human users, but not for machine processing. In previous work we proposed a process for enriching ontologies which included the analysis of such labels, the identification of linguistic patterns and the design of knowledge patterns from them. However, such processes relied on manual intervention. In this paper we present a method and tool to guide the process of including axiomatisation in ontologies through the study of labels. This method guides domain experts in the definition of OWL axioms. The first step is the identification of linguistic patterns based on repetitions of sets of words. Second, the expert is provided with such patterns and recommendations about the existence of classes and properties in such labels by reusing existing ontologies. Third, the user is guided in the process of defining knowledge patterns that would code both the axioms to be added in the ontology and the classes that would be affected. Such axioms would also re-use existing ontologies. Such knowledge patterns are coded and executed using the Ontology Pre-Processor Language (OPPL), but our tool permits their definition without advanced knowledge of OPPL. Finally, we describe the application of the method and tool to the Molecular Function ontology of the Gene Ontology. 2026-01-27T12:50:53Z https://hdl.handle.net/11000/39033 Título : Extraction and Analysis of the Structure of Labels in Biomedical Ontologies Autor : Quesada-Martínez, Manuel; Fernández-Breis, Jesualdo Tomás; Stevens, Robert Resumen : The increasing interest in biomedical ontologies has provoked the development of a significant number of ontologies, and many more are expected to be produced in the near future. A significant proportion of such ontologies have not been created by computer scientists or ontology engineers, but by domain experts. Many such ontologies are rich in implicit knowledge, but are really just plain taxonomies and controlled vocabularies, with little axiomatization. Many of these ontologies have much information within the labels of the classes. There is a great deal of knowledge about the entities described within such labels and text definitions held on classes; these are useful for human users, but not for machine processing. In previous work we proposed a process for enriching ontologies, which included the analysis of such labels, the identification of lexical patterns and the design of corresponding knowledge patterns. However, this process relied on manual intervention. In this paper we present a method to analyze and extract unused information contained in the structure of the labels in biomedical ontologies. The aim of this method is to improve the source ontology. The first step is the identification of lexical patterns based on repetitions of sets of words. Second, such lexical patterns will be examined in existing biomedical ontologies to identify whether those patterns are referencing existing ontological entities. Finally, the results obtained with relevant biomedical ontologies are presented and discussed. 2026-01-27T12:50:18Z https://hdl.handle.net/11000/39032 Título : Analysis and Classification of Bio-ontologies by the Structure of their Labels Autor : Quesada-Martínez, Manuel; Fernández-Breis, Jesualdo Tomás; Stevens, Robert Resumen : The development and success of the Gene Ontology were key factors for attracting the interest of biomedical researchers and bioinformaticists to ontologies. In recent years, hundreds of biomedical ontologies have been produced, most of them developed in collaborative e orts and following a set of construction principles, including the use of a systematic naming convention and using descriptive labels. Such ontologies have been mainly used for supporting the annotation process, but more sophisticated uses would require such ontologies to have more axioms. In recent works, we have found that exploiting the structure of the labels could contribute to that axiomatic enrichment. Hence, in this work we perform a study of the labels of the ontologies available in BioPortal to classify them in terms of potential interest for their axiomatic enrichment. 2026-01-27T12:49:37Z https://hdl.handle.net/11000/39031 Título : Lexical Characterization and Analysis of the BioPortal Ontologies Autor : Quesada-Martínez, Manuel; Fernández-Breis, Jesualdo Tomás; Stevens, Robert Resumen : The increasing interest of the biomedical community in ontologies can be exemplified by the availability of hundreds of biomedical ontologies and controlled vocabularies, and by the international recommendations and efforts that suggest ontologies should play a critical role in the achievement of semantic interoperability in healthcare. However, many of the available biomedical ontologies are rich in human understandable labels, but are less rich in machine processable axioms, so their effectiveness for supporting advanced data analysis processes is limited. In this context, developing methods for analysing the labels and deriving axioms from them would contribute to make biomedical ontologies more useful. In fact, our recent work revealed that exploiting the regularities and structure of the labels could contribute to that axiomatic enrichment. In this paper, we present an approach for analysing and characterising biomedical ontologies from a lexical perspective, that is, by analysing the structure and content of the labels. This study has several goals: (1) characterization of the ontologies by the patterns found in their labels; (2) identifying which ones would be more appropriate for applying enrichment processes based on the labels; (3) inspecting how ontology re-use is being addressed for patterns found in more than one ontology. Our analysis method has been applied to BioPortal, which is likely to be the most popular repository of biomedical ontologies, containing more than two hundred resources. We have found that there is a high redundancy in the labels of the ontologies; it would be interesting to exploit the content and structure of the labels of many of them and that it seems that re-use is not always performed as it should be. Notas: Serie: Lecture Notes in Artificial Intelligence (LNAI) - 7885 2026-01-27T12:49:01Z https://hdl.handle.net/11000/39020 Título : OntoEnrich: A Platform for the Lexical Analysis of Ontologies Autor : Quesada-Martínez, Manuel; Fernández-Breis, Jesualdo Tomás; Stevens, Robert; Aussenac-Guilles, Nathalie Resumen : The content of the labels in ontologies is usually considered hidden semantics, because the domain knowledge of such labels is not available as logical axioms in the ontology. The use of systematic naming conventions as best practice for the design of the content of the labels generates labels with structural regularities, namely, lexical regularities. The structure and content of such regularities can help ontology engineers to increase the amount of machine-friendly content in ontologies, that is, to increase the number of logical axioms. In this paper we present a web platform based on the OntoEnrich framework, which detects and analyzes lexical regularities, providing a series of useful insights about the structure and content of the labels, which can be helpful for the study of the engineering of the ontologies and their axiomatic enrichment. Here, we describe its software architecture, and how it can be used for analyzing the labels of ontologies, which will be illustrated with some examples from our research studies. Notas: Lecture Notes in Artificial Intelligence (LNAI) - 8982 2026-01-26T11:33:25Z https://hdl.handle.net/11000/39019 Título : A Quality Assurance Workflow for Ontologies Based on Semantic Regularities Autor : Mikroyannidi, Eleni; Quesada-Martínez, Manuel; Tsarkov, Dmitry; Fernández-Breis, Jesualdo Tomás; Stevens, Robert; Palmisano, Ignazio Resumen : Syntactic regularities or syntactic patterns are sets of axioms in an OWL ontology with a regular structure. Detecting these patterns and reporting them in human readable form should help the understanding the authoring style of an ontology and is therefore useful in itself. However, pattern detection is sensitive to syntactic variations in the assertions; axioms that are semantically equivalent but syntactically different can reduce the effectiveness of the technique. Semantic regularity analysis focuses on the knowledge encoded in the ontology, rather than how it is spelled out, which is the focus of syntactic regularity analysis. Cluster analysis of the information provided by an OWL DL reasoner mitigates this sensitivity, providing measurable benefits over purely syntactic patterns - an example being patterns that are instantiated only in the entailments of an ontology. In this paper, we demonstrate, using SNOMED-CT, how the detection of semantic regularities in entailed axioms can be used in ontology quality assurance, in combination with lexical techniques. We also show how the detection of irregularities, i.e., deviations from a pattern, are useful for the same purpose. We evaluate and discuss the results of performing a semantic pattern inspection and we compare them against existing work on syntactic regularity detection. Systematic extraction of lexical, syntactic and semantic patterns is used and a quality assurance workflow that combines these patterns is presented. 2026-01-26T11:32:24Z