Automated generation of computationally hard feature models using evolutionary algorithms

This is the post-print version of the final paper published in Expert Systems with Applications. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2014 Elsevier B.V.A feature model is a compact representation of the products of a software product line. The automated extraction of information from feature models is a thriving topic involving numerous analysis operations, techniques and tools. Performance evaluations in this domain mainly rely on the use of random feature models. However, these only provide a rough idea of the behaviour of the tools with average problems and are not sufficient to reveal their real strengths and weaknesses. In this article, we propose to model the problem of finding computationally hard feature models as an optimization problem and we solve it using a novel evolutionary algorithm for optimized feature models (ETHOM). Given a tool and an analysis operation, ETHOM generates input models of a predefined size maximizing aspects such as the execution time or the memory consumption of the tool when performing the operation over the model. This allows users and developers to know the performance of tools in pessimistic cases providing a better idea of their real power and revealing performance bugs. Experiments using ETHOM on a number of analyses and tools have successfully identified models producing much longer executions times and higher memory consumption than those obtained with random models of identical or even larger size.European Commission (FEDER), the Spanish Government and the Andalusian Government

Phenotypic characterization of oral streptococci by classical methods

The phenotypic characteristics of 215 strains of oral streptococci were compared on the basis of the results of sorbitol, raffinose and trehalose fermentation, ammonium from arginine production, aesculin hydrolysis, H2O2 production, susceptibility to 2 U bacitracin, and growth in 4% NaCl solution. Eleven different species were identified. Among the most noteworthy findings were the low number of H2O2-producing strains of Streptococcus sobrinus, the effective discrimination between Streptococcus sanguis and Streptococcus mitis on the basis of raffinose fermentation, and the phenotypic similarity between Streptococcus oralis and the former mutans group. To avoid the creation of new species, the term biotype is proposed to designate phenotypically distinct organisms which do not qualify as different species

FOM: A Framework for Metaheuristic Optimization

Most metaheuristic approaches for discrete optimization are usually implemented from scratch. In this paper, we introduce and discuss FOM, an object-oriented framework for metaheuristic optimization to be used as a general tool for the development and the implementation of metaheuristic algorithms. The basic idea behind the framework is to separate the problem side from the metaheuristic algorithms, allowing this to reuse different metaheuristic components in different problems. In addition to describing the design and functionality of the framework, we apply it to illustrative examples. Finally, we present our conclusions and discuss futures development

Extendiendo ABP con feedback ágil en la enseñanza de Ingeniería del Software

El Aprendizaje Basado en Proyectos (ABP) ha sido aplicado con éxito en diversas áreas de la docencia de la informática en el ámbito universitario. A su vez, a nivel industrial en el contexto de la ingeniería del software, las metodologías ágiles se han instaurado como la opción más utilizada para el desarrollo de proyectos gracias en parte a su promoción de un feedback temprano y continuo que ayuda a enfocar y adaptar el desarrollo a las necesidades del cliente. Este artículo presenta una experiencia piloto que aúna ambos conceptos, extendiendo el enfoque ABP para incorporar el ciclo de feedback rápido y continuo de las metodologías ágiles en la docencia de ingeniería del software. Dicho ciclo se incorpora mediante la aplicación de una evaluación continua de las tareas realizadas por el alumno, en base a un backlog de tareas semanales y a listas de verificación que permiten evaluar el trabajo realizado de manera objetiva. Los resultados obtenidos son prometedores, tanto en términos de la distribución de notas de los alumnos como en cuanto a la motivación de los alumnos con asignatura. Finalmente, se ha realizado un análisis pormenorizado de las numerosas métricas recolectadas de las distintas plataformas utilizadas que ha permitido un estudio de las tipologías de alumnos y la obtención de un conjunto de lecciones aprendidas que pueden ser aplicadas en el diseño de experiencias docentes similares.Project Based Learning (PBL) has been successfully applied in a number of scenarios as part of the Computer Science teaching. Alternatively, from the software industry point of view, agile methodologies represent a first class citizen being the most suitable choice in several cases as they boost an early customer feedback so it can be adapted to its needs. This paper presents a first experience combining PBL and Agile methodologies in Software Engineering course. Specifically, our approach combines the usage of a weekly backlog with a peer-reviewing process based on checklists that allow an accurate continuous evaluation of students performance. The results analysis of our experience shows an appropriate distribution of scores and a significant improvement in the student motivation. Additionally, we detail the analysis of a number of metrics in order to characterize some students patterns that support a list of lessons learned to potentially improve the teaching in similar courses

Aprendiendo a diseñar software usando juegos de mesa de licencia libre como enunciado de prácticas

El planteamiento de trabajos prácticos para el aprendizaje del diseño de software es una tarea compleja pues resulta necesario encontrar problemas de cierta envergadura, con puntos de variación y comportamientos complejos que eviten diseños triviales y que, además resulten motivadores para el alumno. En este artículo describimos nuestra experiencia de 3 años en el diseño, por parte del alumno, de software que implementa juegos de mesa. Los juegos de mesa cumplen los requisitos anteriores. Además, sus exhaustivas reglas son fácilmente usables como documentos de requisitos y la existencia de una amplia base de datos de juegos de licencia libre permite disponer con facilidad de multitud de problemas similares. Con este enfoque hemos mejorado significativamente el porcentaje de éxito de la asignatura

Clinical factors influencing long-term survival in a real-life cohort of early stage non-small-cell lung cancer patients in Spain

Funding Information: This work was supported in part by Centro de Matematica e Aplicaçoes, UID (MAT/00297/2020), Portuguese Foundation of Science and Technology. Acknowledgments Publisher Copyright: Copyright © 2023 Torrente, Sousa, Guerreiro, Franco, Hernández, Parejo, Sousa, Campo-Cañaveral, Pimentão and Provencio.Background: Current prognosis in oncology is reduced to the tumour stage and performance status, leaving out many other factors that may impact the patient´s management. Prognostic stratification of early stage non-small-cell lung cancer (NSCLC) patients with poor prognosis after surgery is of considerable clinical relevance. The objective of this study was to identify clinical factors associated with long-term overall survival in a real-life cohort of patients with stage I-II NSCLC and develop a prognostic model that identifies features associated with poor prognosis and stratifies patients by risk. Methods: This is a cohort study including 505 patients, diagnosed with stage I-II NSCLC, who underwent curative surgical procedures at a tertiary hospital in Madrid, Spain. Results: Median OS (in months) was 63.7 (95% CI, 58.7-68.7) for the whole cohort, 62.4 in patients submitted to surgery and 65 in patients submitted to surgery and adjuvant treatment. The univariate analysis estimated that a female diagnosed with NSCLC has a 0.967 (95% CI 0.936 - 0.999) probability of survival one year after diagnosis and a 0.784 (95% CI 0.712 - 0.863) five years after diagnosis. For males, these probabilities drop to 0.904 (95% CI 0.875 - 0.934) and 0.613 (95% CI 0.566 - 0.665), respectively. Multivariable analysis shows that sex, age at diagnosis, type of treatment, ECOG-PS, and stage are statistically significant variables (p1) while adjuvant chemotherapy is a good prognostic variable (HR<1). The prognostic model identified a high-risk profile defined by males over 71 years old, former smokers, treated with surgery, ECOG-PS 2. Conclusions: The results of the present study found that, overall, adjuvant chemotherapy was associated with the best long-term OS in patients with resected NSCLC. Age, stage and ECOG-PS were also significant factors to take into account when making decisions regarding adjuvant therapy.publishersversionpublishe

ALBACORE (Thunnus alalunga) REPRODUCTIVE BIOLOGY STUDY FOR THE NORTH ATLANTIC STOCK:YEARS 2020 AND 2021

The ICCAT North Atlantic Albacore (Thunnus alalunga) Research Program was established to enhance knowledge on albacore to provide more accurate scientific advice to the Commission. Funds are provided to the Albacore WG to develop research activities to accomplish several objectives. One of the research objectives is to increase knowledge on reproductive biology for the northern Atlantic stock, maturity schedules (L50) and egg production (size/age related fecundity. In March 2021, Terms of Reference were published by ICCAT. A Consortium integrated by Canada, Venezuela, Chinese-Taipei and Spain presented an offer to collect gonad samples and spines throughout the year and carry out the study of reproductive biology for North Atlantic albacore stock. Results of histological analysis: maturity stages, batch fecundity and seasonal area of spawners are presented as well as the age determined of partially collection of albacore spines. Analysis were done with the total albacore gonads samples collected in 2020 and 2021 for the reproductive biology study of northern albacore.

Invirtiendo las clases de laboratorio en Ingeniería Informática: Un enfoque ágil

En este artículo describimos nuestra experiencia al aplicar la metodología de clase invertida en la asignatura Arquitectura e Integración de Sistemas Software, de segundo curso del grado de Ingeniería del Software. Varios aspectos caracterizan este estudio frente a los trabajos relacionados. En primer lugar, la metodología fue aplicada en las clases prácticas de la asignatura, donde conseguimos aumentar el tiempo dedicado a la resolución de ejercicios en 24 minutos de media. En segundo lugar, la volatilidad del temario hizo necesario desarrollar una aproximación ágil a la metodología, en la que los profesores debían ser capaces de elaborar vídeos docentes de calidad en sus propios despachos y en unos pocos minutos. Este artículo resume algunas de las muchas lecciones aprendidas en relación a la elaboración del material. En tercer lugar, el estudio destaca también por el tamaño, habiéndose realizado a lo largo de dos cursos académicos, 2017 y 2018, involucrando a un total de 434 alumnos y 6 profesores. Los resultados del estudio, respaldados por un sólido análisis estadístico de los datos, demuestran la idoneidad de esta metodología para ser aplicada en las clases de laboratorio del área de Ingeniería del software.In this paper, we report our experience on flipping a second-year undergraduate course on software architecture and integration, taught in a Software Engineering degree. Several aspects characterize this study with respect to related works. In the first place, the methodology was applied in the practical classes of the course, where we managed to increase the time dedicated to exercises solving in 24 minutes on average. Second, due to the constant updates in tools and software used in the course, we applied an agile approach to the methodology, in which lecturers had to produce high-quality teaching videos in their own offices just in minutes. This paper summarizes some of the many lessons learned in this regard. Third, the study also stands out for its size, having been conducted over two academic courses, 2017 and 2018, involving a total amount of 434 students and 6 lecturers. The results of the study, backed by a solid statistical analysis of the data, demonstrate the suitability of this methodology to be applied in the laboratory classes in the Software Engineering area

Aprendiendo arquitectura software a partir de proyectos de código abierto en GitHub

La enseñanza de arquitectura del software supone todo un reto. Los conceptos teóricos son a menudo muy abstractos y los problemas arquitectónicos sólo son claramente visibles en aplicaciones de cierta envergadura. El reto es aún mayor cuando estos conceptos se enseñan en las primeras etapas del grado cuando los conocimientos de diseño y programación del alumnado aún son limitados. Para abordar este reto, inspirados por una propuesta llevada a cabo en la Delft University, decidimos adoptar un enfoque novedoso: enseñar arquitectura del software a través del análisis, evaluación y documentación de la arquitectura de proyectos existentes alojados en la plataforma GitHub. Para ello, fue necesario adaptar el método original, empleado a nivel de máster, a la asignatura objeto del estudio impartida durante el segundo curso de grado. Para evaluar este enfoque realizamos un total de 258 encuestas a estudiantes de dos cursos consecutivos. Los resultados del estudio, respaldados por un sólido análisis estadístico de los datos, demuestran la idoneidad de este método para la enseñanza de arquitectura del software en los primeros cursos de grado.Teaching software architecture is a challenge. Theoretical concepts are often very abstract and architectural problems are only clearly visible in applications of a certain magnitude. The challenge is even greater when these concepts are taught in the early stages of the bachelor’s degree when the students’ knowledge of design and programming is still limited. To address this challenge, inspired by a proposal carried out at Delft University, we decided to adopt a novel approach: teaching software architecture by analysing, evaluating and documenting the architecture of existing projects hosted on the GitHub platform. To do so, it was necessary to adapt the original method, used in a master course, to the course under study, taught during the second year of the bachelor’s degree. To evaluate this approach we conducted a total of 258 student surveys in two consecutive years. The results of the study, supported by a robust statistical analysis of the data, demonstrate the suitability of this method for teaching software architecture in the first years of the bachelor’s degree.Trabajo parcialmente financiado por el Dpto de Lenguajes y Sistemas de la Universidad de Sevilla y los proyectos TED2021-131023B-C21, TED2021-131023B-C22, PID2021-126227NB-C21, PID2021-126227NB-C22 financiados por MCIN/AEI/10.13039/501100011033/FEDER y por la Unión Europea NextGenerationEU/PRTR

A genome-wide association study suggests the HLA Class II region as the major susceptibility locus for IgA vasculitis.

The genetic component of Immunoglobulin-A (IgA) vasculitis is still far to be elucidated. To increase the current knowledge on the genetic component of this vasculitis we performed the first genome-wide association study (GWAS) on this condition. 308 IgA vasculitis patients and 1,018 healthy controls from Spain were genotyped by Illumina HumanCore BeadChips. Imputation of GWAS data was performed using the 1000 Genomes Project Phase III dataset as reference panel. After quality control filters and GWAS imputation, 285 patients and 1,006 controls remained in the datasets and were included in further analysis. Additionally, the human leukocyte antigen (HLA) region was comprehensively studied by imputing classical alleles and polymorphic amino acid positions. A linkage disequilibrium block of polymorphisms located in the HLA class II region surpassed the genome-wide level of significance (OR = 0.56, 95% CI = 0.46-0.68). Although no polymorphic amino acid positions were associated at the genome-wide level of significance, P-values of potential relevance were observed for the positions 13 and 11 of HLA-DRB1 (P = 6.67E-05, P = 1.88E-05, respectively). Outside the HLA, potential associations were detected, but none of them were close to the statistical significance. In conclusion, our study suggests that IgA vasculitis is an archetypal HLA class II disease