Multi-Objective Genetic Programming for Feature Extraction and Data Visualization

Feature extraction transforms high dimensional data into a new subspace of lower dimensionalitywhile keeping the classification accuracy. Traditional algorithms do not consider the multi-objective nature of this task. Data transformations should improve the classification performance on the new subspace, as well as to facilitate data visualization, which has attracted increasing attention in recent years. Moreover, new challenges arising in data mining, such as the need to deal with imbalanced data sets call for new algorithms capable of handling this type of data. This paper presents a Pareto-basedmulti-objective genetic programming algorithm for feature extraction and data visualization. The algorithm is designed to obtain data transformations that optimize the classification and visualization performance both on balanced and imbalanced data. Six classification and visualization measures are identified as objectives to be optimized by the multi-objective algorithm. The algorithm is evaluated and compared to 11 well-known feature extraction methods, and to the performance on the original high dimensional data. Experimental results on 22 balanced and 20 imbalanced data sets show that it performs very well on both types of data, which is its significant advantage over existing feature extraction algorithms

Probabilistic grammatical model of protein language and its application to helix-helix contact site classification

BACKGROUND: Hidden Markov Models power many state‐of‐the‐art tools in the field of protein bioinformatics. While excelling in their tasks, these methods of protein analysis do not convey directly information on medium‐ and long‐range residue‐residue interactions. This requires an expressive power of at least context‐free grammars. However, application of more powerful grammar formalisms to protein analysis has been surprisingly limited. RESULTS: In this work, we present a probabilistic grammatical framework for problem‐specific protein languages and apply it to classification of transmembrane helix‐helix pairs configurations. The core of the model consists of a probabilistic context‐free grammar, automatically inferred by a genetic algorithm from only a generic set of expert‐based rules and positive training samples. The model was applied to produce sequence based descriptors of four classes of transmembrane helix‐helix contact site configurations. The highest performance of the classifiers reached AUCROC of 0.70. The analysis of grammar parse trees revealed the ability of representing structural features of helix‐helix contact sites. CONCLUSIONS: We demonstrated that our probabilistic context‐free framework for analysis of protein sequences outperforms the state of the art in the task of helix‐helix contact site classification. However, this is achieved without necessarily requiring modeling long range dependencies between interacting residues. A significant feature of our approach is that grammar rules and parse trees are human‐readable. Thus they could provide biologically meaningful information for molecular biologists

Grammar-based evolutionary approach for automated workflow composition with domain-specific operators and ensemble diversity

The process of extracting valuable and novel insights from raw data involves a series of complex steps. In the realm of Automated Machine Learning (AutoML), a significant research focus is on automating aspects of this process, specifically tasks like selecting algorithms and optimising their hyper-parameters. A particularly challenging task in AutoML is automatic workflow composition (AWC). AWC aims to identify the most effective sequence of data preprocessing and ML algorithms, coupled with their best hyper-parameters, for a specific dataset. However, existing AWC methods are limited in how many and in what ways they can combine algorithms within a workflow. Addressing this gap, this paper introduces EvoFlow, a grammar-based evolutionary approach for AWC. EvoFlow enhances the flexibility in designing workflow structures, empowering practitioners to select algorithms that best fit their specific requirements. EvoFlow stands out by integrating two innovative features. First, it employs a suite of genetic operators, designed specifically for AWC, to optimise both the structure of workflows and their hyper-parameters. Second, it implements a novel updating mechanism that enriches the variety of predictions made by different workflows. Promoting this diversity helps prevent the algorithm from overfitting. With this aim, EvoFlow builds an ensemble whose workflows differ in their misclassified instances. To evaluate EvoFlow's effectiveness, we carried out empirical validation using a set of classification benchmarks. We begin with an ablation study to demonstrate the enhanced performance attributable to EvoFlow's unique components. Then, we compare EvoFlow with other AWC approaches, encompassing both evolutionary and non-evolutionary techniques. Our findings show that EvoFlow's specialised genetic operators and updating mechanism substantially outperform current leading methods[..]Comment: 32 pages, 7 figures, 6 tables, journal pape

Automated Machine Learning for Multi-Label Classification

Automated machine learning (AutoML) aims to select and configure machine learning algorithms and combine them into machine learning pipelines tailored to a dataset at hand. For supervised learning tasks, most notably binary and multinomial classification, aka single-label classification (SLC), such AutoML approaches have shown promising results. However, the task of multi-label classification (MLC), where data points are associated with a set of class labels instead of a single class label, has received much less attention so far. In the context of multi-label classification, the data-specific selection and configuration of multi-label classifiers are challenging even for experts in the field, as it is a high-dimensional optimization problem with multi-level hierarchical dependencies. While for SLC, the space of machine learning pipelines is already huge, the size of the MLC search space outnumbers the one of SLC by several orders. In the first part of this thesis, we devise a novel AutoML approach for single-label classification tasks optimizing pipelines of machine learning algorithms, consisting of two algorithms at most. This approach is then extended first to optimize pipelines of unlimited length and eventually configure the complex hierarchical structures of multi-label classification methods. Furthermore, we investigate how well AutoML approaches that form the state of the art for single-label classification tasks scale with the increased problem complexity of AutoML for multi-label classification. In the second part, we explore how methods for SLC and MLC could be configured more flexibly to achieve better generalization performance and how to increase the efficiency of execution-based AutoML systems

A grammar-based technique for genetic search and optimization

The genetic algorithm (GA) is a robust search technique which has been theoretically and empirically proven to provide efficient search for a variety of problems. Due largely to the semantic and expressive limitations of adopting a bitstring representation, however, the traditional GA has not found wide acceptance in the Artificial Intelligence community. In addition, binary chromosones can unevenly weight genetic search, reduce the effectiveness of recombination operators, make it difficult to solve problems whose solution schemata are of high order and defining length, and hinder new schema discovery in cases where chromosome-wide changes are required.;The research presented in this dissertation describes a grammar-based approach to genetic algorithms. Under this new paradigm, all members of the population are strings produced by a problem-specific grammar. Since any structure which can be expressed in Backus-Naur Form can thus be manipulated by genetic operators, a grammar-based GA strategy provides a consistent methodology for handling any population structure expressible in terms of a context-free grammar.;In order to lend theoretical support to the development of the syntactic GA, the concept of a trace schema--a similarity template for matching the derivation traces of grammar-defined rules--was introduced. An analysis of the manner in which a grammar-based GA operates yielded a Trace Schema Theorem for rule processing, which states that above-average trace schemata containing relatively few non-terminal productions are sampled with increasing frequency by syntactic genetic search. Schemata thus serve as the building blocks in the construction of the complex rule structures manipulated by syntactic GAs.;As part of the research presented in this dissertation, the GEnetic Rule Discovery System (GERDS) implementation of the grammar-based GA was developed. A comparison between the performance of GERDS and the traditional GA showed that the class of problems solvable by a syntactic GA is a superset of the class solvable by its binary counterpart, and that the added expressiveness greatly facilitates the representation of GA problems. to strengthen that conclusion, several experiments encompassing diverse domains were performed with favorable results

Using Dimensional Aware Genetic Programming to find interpretable Dispatching Rules for the Job Shop Scheduling Problem

Dispatching Rules (DRs) have been used in several applications in manufacturing systems. They assign priority to jobs in a queue choosing the next job to be executed. As they are challenging to design, genetic programming (GP) is being used to find better performative DRs. In GP, several different DRs are evolved, and due to some operations and selection processes inspired in nature, the DRs improve. However, little research has been done in trying to reach small and interpretable DRs. Usually, these generated expressions tend to become extremely large, with a couple of hundred terms or more. This work will innovate by using CFG (context-free grammars) methods, particularly CFG-GP and GE (Grammar Evolution), for reaching DRs which are dimensional aware. These methods will be compared as they have several distinct characteristics and were never used for this problem. The objective is that by forcing the syntax of the DRs to be correct, it will be possible to reach smaller and more interpretable DRs. Furthermore, an enumerator was made that found the best possible expression for a small DRs size, which will serve as a baseline to evaluate how well the different algorithms can explore these spaces and give the best possible DRs for a specific size. The results show a significant performance improvement in using DAGP methods for this problem. Moreover, GP/GE and CFG-GP can explore the small DRs optimally or close to optimally, managing to find the best small DRs

Nuevos retos en clasificación asociativa: Big Data y aplicaciones

La clasificación asociativa surge como resultado de la unión de dos importantes ámbitos del aprendizaje automático. Por un lado la tarea descriptiva de extracción de reglas de asociación, como mecanismo para obtener información previamente desconocida e interesante de un conjunto de datos, combinado con una tarea predictiva, como es la clasificación, que permite en base a un conjunto de variables explicativas y previamente conocidas realizar una predicción sobre una variable de interés o predictiva. Los objetivos de esta tesis doctoral son los siguientes: 1) El estudio y el análisis del estado del arte de tanto la extracción de reglas de asociación como de la clasificación asociativa; 2) La propuesta de nuevos modelos de clasificación asociativa así como de extracción de reglas de asociación teniendo en cuenta la obtención de modelos que sean precisos, interpretables, eficientes así como flexibles para poder introducir conocimiento subjetivo en éstos. 3) Adicionalmente, y dado la gran cantidad de datos que cada día se genera en las últimas décadas, se prestará especial atención al tratamiento de grandes cantidades datos, también conocido como Big Data. En primer lugar, se ha analizado el estado del arte tanto de clasificación asociativa como de la extracción de reglas de asociación. En este sentido, se ha realizado un estudio y análisis exhaustivo de la bibliografía de los trabajos relacionados para poder conocer con gran nivel de detalle el estado del arte. Como resultado, se ha permitido sentar las bases para la consecución de los demás objetivos así como detectar que dentro de la clasificación asociativa se requería de algún mecanismo que facilitara la unificación de comparativas así como que fueran lo más completas posibles. Para tal fin, se ha propuesto una herramienta de software que cuenta con al menos un algoritmo de todas las categorías que componen la taxonomía actual. Esto permitirá dentro de las investigaciones del área, realizar comparaciones más diversas y completas que hasta el momento se consideraba una tarea en el mejor de los casos muy ardua, al no estar disponibles muchos de los algoritmos en un formato ejecutable ni mucho menos como código abierto. Además, esta herramienta también dispone de un conjunto muy diverso de métricas que permite cuantificar la calidad de los resultados desde diferentes perspectivas. Esto permite conseguir clasificadores lo más completos posibles, así como para unificar futuras comparaciones con otras propuestas. En segundo lugar, y como resultado del análisis previo, se ha detectado que las propuestas actuales no permiten escalar, ni horizontalmente, ni verticalmente, las metodologías sobre conjuntos de datos relativamente grandes. Dado el creciente interés, tanto del mundo académico como del industrial, de aumentar la capacidad de cómputo a ingentes cantidades de datos, se ha considerado interesante continuar esta tesis doctoral realizando un análisis de diferentes propuestas sobre Big Data. Para tal fin, se ha comenzado realizando un análisis pormenorizado de los últimos avances para el tratamiento de tal cantidad de datos. En este respecto, se ha prestado especial atención a la computación distribuida ya que ha demostrado ser el único procedimiento que permite el tratamiento de grandes cantidades de datos sin la realización de técnicas de muestreo. En concreto, se ha prestado especial atención a las metodologías basadas en MapReduce que permite la descomposición de problemas complejos en fracciones divisibles y paralelizables, que posteriormente pueden ser agrupadas para obtener el resultado final. Como resultado de este objetivo se han propuesto diferentes algoritmos que permiten el tratamiento de grandes cantidades de datos, sin la pérdida de precisión ni interpretabilidad. Todos los algoritmos propuestos se han diseñado para que puedan funcionar sobre las implementaciones de código abierto más conocidas de MapReduce. En tercer y último lugar, se ha considerado interesante realizar una propuesta que mejore el estado del arte de la clasificación asociativa. Para tal fin, y dado que las reglas de asociación son la base y factores determinantes para los clasificadores asociativos, se ha comenzado realizando una nueva propuesta para la extracción de reglas de asociación. En este aspecto, se ha combinado el uso de los últimos avances en computación distribuida, como MapReduce, con los algoritmos evolutivos que han demostrado obtener excelentes resultados en el área. En particular, se ha hecho uso de programación genética gramatical por su flexibilidad para codificar las soluciones, así como introducir conocimiento subjetivo en el proceso de búsqueda a la vez que permiten aliviar los requisitos computacionales y de memoria. Este nuevo algoritmo, supone una mejora significativa de la extracción de reglas de asociación ya que ha demostrado obtener mejores resultados que las propuestas existentes sobre diferentes tipos de datos así como sobre diferentes métricas de interés, es decir, no sólo obtiene mejores resultados sobre Big Data, sino que se ha comparado en su versión secuencial con los algoritmos existentes. Una vez que se ha conseguido este algoritmo que permite extraer excelentes reglas de asociación, se ha adaptado para la obtención de reglas de asociación de clase así como para obtener un clasificador a partir de tales reglas. De nuevo, se ha hecho uso de programación genética gramatical para la obtención del clasificador de forma que se permite al usuario no sólo introducir conocimiento subjetivo en las propias formas de las reglas, sino también en la forma final del clasificador. Esta nueva propuesta también se ha comparado con los algoritmos existentes de clasificación asociativa forma secuencial para garantizar que consigue diferencias significativas respecto a éstos en términos de exactitud, interpretabilidad y eficiencia. Adicionalmente, también se ha comparado con otras propuestas específicas de Big Data demostrado obtener excelentes resultados a la vez que mantiene un compromiso entre los objetivos conflictivos de interpretabilidad, exactitud y eficiencia. Esta tesis doctoral se ha desarrollado bajo un entorno experimental apropiado, haciendo uso de diversos conjunto de datos incluyendo tanto datos de pequeña dimensionalidad como Big Data. Además, todos los conjuntos de datos usados están publicados libremente y conforman un conglomerado de diversas dimensionalidades, número de instancias y de clases. Todos los resultados obtenidos se han comparado con el estado de arte correspondiente, y se ha hecho uso de tests estadísticos no paramétricos para comprobar que las diferencias encontradas son significativas desde un punto de vista estadístico, y no son fruto del azar. Adicionalmente, todas las comparaciones realizadas consideran diferentes perspectivas, es decir, se ha analizado rendimiento, eficiencia, precisión así como interpretabilidad en cada uno de los estudios.This Doctoral Thesis aims at solving the challenging problem of associative classification and its application on very large datasets. First, associative classification state-of-art has been studied and analyzed, and a new tool covering the whole taxonomy of algorithms as well as providing many different measures has been proposed. The goal of this tool is two-fold: 1) unification of comparisons, since existing works compare with very different measures; 2) providing a unique tool which has at least one algorithm of each category forming the taxonomy. This tool is a very important advancement in the field, since until the moment the whole taxonomy has not been covered due to that many algorithms have not been released as open source nor they were available to be run. Second, AC has been analyzed on very large quantities of data. In this regard, many different platforms for distributed computing have been studied and different proposals have been developed on them. These proposals enable to deal with very large data in a efficient way scaling up the load on very different compute nodes. Third, as one of the most important part of the associative classification is to extract high quality rules, it has been proposed a novel grammar-guided genetic programming algorithm which enables to obtain interesting association rules with regard to different metrics and in different kinds of data, including truly Big Data datasets. This proposal has proved to obtain very good results in terms of both quality and interpretability, at the same time of providing a very flexible way of representing the solutions and enabling to introduce subjective knowledge in the search process. Then, a novel algorithm has been proposed for associative classification using a non-trivial adaptation of the aforementioned algorithm to obtain the rules forming the classifier. This methodology is also based on grammar-guided genetic programming enabling user not only to constrain the form of the rules, but the final form of the classifier. Results have proved that this algorithm obtains very accurate classifiers at the same time of maintaining a good level of interpretability. All the methodologies proposed along this Thesis has been evaluated using a proper experimental framework, using a varied set of datasets including both classical and Big Data dataset, and analyzing different metrics to quantify the quality of the algorithms with regard to different perspectives. Results have been compared with state-of-the-art and they have been verified by means of non-parametric statistical tests proving that the proposed methods overcome to existing approaches

A systematic literature review on the semi-automatic configuration of extended product lines

Product line engineering has become essential in mass customisation given its ability to reduce production costs and time to market, and to improve product quality and customer satisfaction. In product line literature, mass customisation is known as product configuration. Currently, there are multiple heterogeneous contributions in the product line configuration domain. However, a secondary study that shows an overview of the progress, trends, and gaps faced by researchers in this domain is still missing. In this context, we provide a comprehensive systematic literature review to discover which approaches exist to support the configuration process of extended product lines and how these approaches perform in practice. Extend product lines consider non-functional properties in the product line modelling. We compare and classify a total of 66 primary studies from 2000 to 2016. Mainly, we give an in-depth view of techniques used by each work, how these techniques are evaluated and their main shortcomings. As main results, our review identified (i) the need to improve the quality of the evaluation of existing approaches, (ii) a lack of hybrid solutions to support multiple configuration constraints, and (iii) a need to improve scalability and performance conditions