Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data

Mass spectrometry (MS) data provide a promising strategy for biomarker discovery. For this purpose, the detection of relevant peakbins in MS data is currently under intense research. Data from mass spectrometry are challenging to analyze because of their high dimensionality and the generally low number of samples available. To tackle this problem, the scientific community is becoming increasingly interested in applying feature subset selection techniques based on specialized machine learning algorithms. In this paper, we present a performance comparison of some metaheuristics: best first (BF), genetic algorithm (GA), scatter search (SS) and variable neighborhood search (VNS). Up to now, all the algorithms, except for GA, have been first applied to detect relevant peakbins in MS data. All these metaheuristic searches are embedded in two different filter and wrapper schemes coupled with Naive Bayes and SVM classifiers

An evolutionary algorithm to discover quantitative association rules in multidimensional time series

An evolutionary approach for finding existing relationships among several variables of a multidimensional time series is presented in this work. The proposed model to discover these relationships is based on quantitative association rules. This algorithm, called QARGA (Quantitative Association Rules by Genetic Algorithm), uses a particular codification of the individuals that allows solving two basic problems. First, it does not perform a previous attribute discretization and, second, it is not necessary to set which variables belong to the antecedent or consequent. Therefore, it may discover all underlying dependencies among different variables. To evaluate the proposed algorithm three experiments have been carried out. As initial step, several public datasets have been analyzed with the purpose of comparing with other existing evolutionary approaches. Also, the algorithm has been applied to synthetic time series (where the relationships are known) to analyze its potential for discovering rules in time series. Finally, a real-world multidimensional time series composed by several climatological variables has been considered. All the results show a remarkable performance of QARGA.Ministerio de Ciencia y Tecnología TIN2007- 68084-C02-02Junta de Andalucia P07-TIC- 0261

Holistic, data-driven, service and supply chain optimisation: linked optimisation.

The intensity of competition and technological advancements in the business environment has made companies collaborate and cooperate together as a means of survival. This creates a chain of companies and business components with unified business objectives. However, managing the decision-making process (like scheduling, ordering, delivering and allocating) at the various business components and maintaining a holistic objective is a huge business challenge, as these operations are complex and dynamic. This is because the overall chain of business processes is widely distributed across all the supply chain participants; therefore, no individual collaborator has a complete overview of the processes. Increasingly, such decisions are automated and are strongly supported by optimisation algorithms - manufacturing optimisation, B2B ordering, financial trading, transportation scheduling and allocation. However, most of these algorithms do not incorporate the complexity associated with interacting decision-making systems like supply chains. It is well-known that decisions made at one point in supply chains can have significant consequences that ripple through linked production and transportation systems. Recently, global shocks to supply chains (COVID-19, climate change, blockage of the Suez Canal) have demonstrated the importance of these interdependencies, and the need to create supply chains that are more resilient and have significantly reduced impact on the environment. Such interacting decision-making systems need to be considered through an optimisation process. However, the interactions between such decision-making systems are not modelled. We therefore believe that modelling such interactions is an opportunity to provide computational extensions to current optimisation paradigms. This research study aims to develop a general framework for formulating and solving holistic, data-driven optimisation problems in service and supply chains. This research achieved this aim and contributes to scholarship by firstly considering the complexities of supply chain problems from a linked problem perspective. This leads to developing a formalism for characterising linked optimisation problems as a model for supply chains. Secondly, the research adopts a method for creating a linked optimisation problem benchmark by linking existing classical benchmark sets. This involves using a mix of classical optimisation problems, typically relating to supply chain decision problems, to describe different modes of linkages in linked optimisation problems. Thirdly, several techniques for linking supply chain fragmented data have been proposed in the literature to identify data relationships. Therefore, this thesis explores some of these techniques and combines them in specific ways to improve the data discovery process. Lastly, many state-of-the-art algorithms have been explored in the literature and these algorithms have been used to tackle problems relating to supply chain problems. This research therefore investigates the resilient state-of-the-art optimisation algorithms presented in the literature, and then designs suitable algorithmic approaches inspired by the existing algorithms and the nature of problem linkages to address different problem linkages in supply chains. Considering research findings and future perspectives, the study demonstrates the suitability of algorithms to different linked structures involving two sub-problems, which suggests further investigations on issues like the suitability of algorithms on more complex structures, benchmark methodologies, holistic goals and evaluation, processmining, game theory and dependency analysis

Minería de Reglas de Asociación en GPU

Premio extraordinario de Trabajo Fin de Máster curso 2012-2013.Sistemas Inteligentes

Evolutionary Algorithms to Discover Quantitative Association Rules

Premio Extraordinario de Doctorado U

Computational and human-based methods for knowledge discovery over knowledge graphs

The modern world has evolved, accompanied by the huge exploitation of data and information. Daily, increasing volumes of data from various sources and formats are stored, resulting in a challenging strategy to manage and integrate them to discover new knowledge. The appropriate use of data in various sectors of society, such as education, healthcare, e-commerce, and industry, provides advantages for decision support in these areas. However, knowledge discovery becomes challenging since data may come from heterogeneous sources with important information hidden. Thus, new approaches that adapt to the new challenges of knowledge discovery in such heterogeneous data environments are required. The semantic web and knowledge graphs (KGs) are becoming increasingly relevant on the road to knowledge discovery. This thesis tackles the problem of knowledge discovery over KGs built from heterogeneous data sources. We provide a neuro-symbolic artificial intelligence system that integrates symbolic and sub-symbolic frameworks to exploit the semantics encoded in a KG and its structure. The symbolic system relies on existing approaches of deductive databases to make explicit, implicit knowledge encoded in a KG. The proposed deductive database $DS$ can derive new statements to ego networks given an abstract target prediction. Thus, $DS$ minimizes data sparsity in KGs. In addition, a sub-symbolic system relies on knowledge graph embedding (KGE) models. KGE models are commonly applied in the KG completion task to represent entities in a KG in a low-dimensional vector space. However, KGE models are known to suffer from data sparsity, and a symbolic system assists in overcoming this fact. The proposed approach discovers knowledge given a target prediction in a KG and extracts unknown implicit information related to the target prediction. As a proof of concept, we have implemented the neuro-symbolic system on top of a KG for lung cancer to predict polypharmacy treatment effectiveness. The symbolic system implements a deductive system to deduce pharmacokinetic drug-drug interactions encoded in a set of rules through the Datalog program. Additionally, the sub-symbolic system predicts treatment effectiveness using a KGE model, which preserves the KG structure. An ablation study on the components of our approach is conducted, considering state-of-the-art KGE methods. The observed results provide evidence for the benefits of the neuro-symbolic integration of our approach, where the neuro-symbolic system for an abstract target prediction exhibits improved results. The enhancement of the results occurs because the symbolic system increases the prediction capacity of the sub-symbolic system. Moreover, the proposed neuro-symbolic artificial intelligence system in Industry 4.0 (I4.0) is evaluated, demonstrating its effectiveness in determining relatedness among standards and analyzing their properties to detect unknown relations in the I4.0KG. The results achieved allow us to conclude that the proposed neuro-symbolic approach for an abstract target prediction improves the prediction capability of KGE models by minimizing data sparsity in KGs

A Mono- and Multi-objective Approach for Recommending Software Refactoring

Les systèmes logiciels sont devenus de plus en plus répondus et importants dans notre société. Ainsi, il y a un besoin constant de logiciels de haute qualité. Pour améliorer la qualité de logiciels, l’une des techniques les plus utilisées est le refactoring qui sert à améliorer la structure d'un programme tout en préservant son comportement externe. Le refactoring promet, s'il est appliqué convenablement, à améliorer la compréhensibilité, la maintenabilité et l'extensibilité du logiciel tout en améliorant la productivité des programmeurs. En général, le refactoring pourra s’appliquer au niveau de spécification, conception ou code. Cette thèse porte sur l'automatisation de processus de recommandation de refactoring, au niveau code, s’appliquant en deux étapes principales: 1) la détection des fragments de code qui devraient être améliorés (e.g., les défauts de conception), et 2) l'identification des solutions de refactoring à appliquer. Pour la première étape, nous traduisons des régularités qui peuvent être trouvés dans des exemples de défauts de conception. Nous utilisons un algorithme génétique pour générer automatiquement des règles de détection à partir des exemples de défauts. Pour la deuxième étape, nous introduisons une approche se basant sur une recherche heuristique. Le processus consiste à trouver la séquence optimale d'opérations de refactoring permettant d'améliorer la qualité du logiciel en minimisant le nombre de défauts tout en priorisant les instances les plus critiques. De plus, nous explorons d'autres objectifs à optimiser: le nombre de changements requis pour appliquer la solution de refactoring, la préservation de la sémantique, et la consistance avec l’historique de changements. Ainsi, réduire le nombre de changements permets de garder autant que possible avec la conception initiale. La préservation de la sémantique assure que le programme restructuré est sémantiquement cohérent. De plus, nous utilisons l'historique de changement pour suggérer de nouveaux refactorings dans des contextes similaires. En outre, nous introduisons une approche multi-objective pour améliorer les attributs de qualité du logiciel (la flexibilité, la maintenabilité, etc.), fixer les « mauvaises » pratiques de conception (défauts de conception), tout en introduisant les « bonnes » pratiques de conception (patrons de conception).Software systems have become prevalent and important in our society. There is a constant need for high-quality software. Hence, to improve software quality, one of the most-used techniques is the refactoring which improves design structure while preserving the external behavior. Refactoring has promised, if applied well, to improve software readability, maintainability and extendibility while increasing the speed at which programmers can write and maintain their code. In general, refactoring can be performed in various levels such as the requirement, design, or code level. In this thesis, we mainly focus on the source code level where automated refactoring recommendation can be performed through two main steps: 1) detection of code fragments that need to be improved/fixed (e.g., code-smells), and 2) identification of refactoring solutions to achieve this goal. For the code-smells identification step, we translate regularities that can be found in such code-smell examples into detection rules. To this end, we use genetic programming to automatically generate detection rules from examples of code-smells. For the refactoring identification step, a search-based approach is used. The process aims at finding the optimal sequence of refactoring operations that improve software quality by minimizing the number of detected code-smells while prioritizing the most critical ones. In addition, we explore other objectives to optimize using a multi-objective approach: the code changes needed to apply refactorings, semantics preservation, and the consistency with development change history. Hence, reducing code changes allows us to keep as much as possible the initial design. On the other hand, semantics preservation insures that the refactored program is semantically coherent, and that it models correctly the domain-semantics. Indeed, we use knowledge from historical code change to suggest new refactorings in similar contexts. Furthermore, we introduce a novel multi-objective approach to improve software quality attributes (i.e., flexibility, maintainability, etc.), fix “bad” design practices (i.e., code-smells) while promoting “good” design practices (i.e., design patterns)