Minería de Reglas de Asociación en GPU

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

Accelerating binary biclustering on platforms with CUDA-enabled GPUs

© 2018 Elsevier B.V. All rights reserved. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/bync-nd/4.0/. This version of the article has been accepted for publication in Information Sciences. The Version of Record is available online at https://doi.org/10.1016/j.ins.2018.05.025This is a version of: J. González-Domínguez and R. R. Expósito, "Accelerating binary biclustering on platforms with CUDA-enabled GPUs", Information Sciences, Vol. 496, Sept. 2019, pp. 317-325, https://doi.org/10.1016/j.ins.2018.05.025[Abstract]: Data mining is nowadays essential in many scientific fields to extract valuable information from large input datasets and transform it into an understandable structure. For instance, biclustering techniques are very useful in identifying subsets of two-dimensional data where both rows and columns are correlated. However, some biclustering techniques have become extremely time-consuming when processing very large datasets, which nowadays prevents their use in many areas of research and industry (such as bioinformatics) that have experienced an explosive growth on the amount of available data. In this work we present CUBiBit, a tool that accelerates the search for relevant biclusters on binary data by exploiting the computational capabilities of CUDA-enabled GPUs as well as the several CPU cores available in most current systems. The experimental evaluation has shown that CUBiBit is up to 116 times faster than the fastest state-of-the-art tool, BiBit, in a system with two Intel Sandy Bridge processors (16 CPU cores) and three NVIDIA K20 GPUs. CUBiBit is publicly available to download from https://sourceforge.net/projects/cubibitThis work was supported by the Ministry of Economy, Industry and Competitiveness of Spain and FEDER funds of the European Union [grant TIN2016-75845-P (AEI/FEDER/UE)], as well as by Xunta de Galicia (Centro Singular de Investigacion de Galicia accreditation 2016-2019, ref. EDG431G/01).Xunta de Galicia; EDG431G/0

CUDA-JMI: Acceleration of feature selection on heterogeneous systems

©2019 Elsevier B.V. All rights reserved. This manuscript version is made available under the CC-BY-NC-ND 4.0 license https://creativecommons.org/licenses/bync-nd/4.0/. This version of the article has been accepted for publication in Future Generation Computer Systems. The Version of Record is available online at https://doi.org/10.1016/j.future.2019.08.031Versión final aceptada de: J. González-Domínguez, R. R. Expósito, and V. Bolón-Canedo, "CUDA-JMI: Acceleration of feature selection on heterogeneous systemss", Future Generation Computer Systems, Vol. 102, pp. 426-436, Jan. 2020, https://doi.org/10.1016/j.future.2019.08.031[Abstract]: Feature selection is a crucial step nowadays in machine learning and data analytics to remove irrelevant and redundant characteristics and thus to provide fast and reliable analyses. Many research works have focused on developing new methods that increase the global relevance of the subset of selected features while reducing the redundancy of information. However, those methods that select features with high relevance and low redundancy are extremely time-consuming when processing large datasets. In this work we present CUDA-JMI, a tool based on Joint Mutual Information that accelerates feature selection by exploiting the computational capabilities of modern heterogeneous systems that contain several CPU cores and GPU devices. The experimental evaluation has been carried out in three systems with different type and amount of CPUs and GPUs using five publicly available datasets from different fields. These results show that CUDA-JMI is significantly faster than its original sequential counterpart for all systems and input datasets. For instance, the runtime of CUDA-JMI is up to 52 times faster than an existing sequential JMI-based implementation in a machine with 24 CPU cores and two NVIDIA M60 boards (four GPUs). CUDA-JMI is publicly available to download from https://sourceforge.net/projects/cuda-jmiThis research has been partially funded by projects TIN2016-75845-P and TIN-2015-65069-C2-1-R of the Ministry of Economy, Industry and Competitiveness of Spain, as well as by Xunta de Galicia, Spain projects ED431D R2016/045, ED431G/01 and GRC2014/035, all of them partially funded by FEDER, Spain funds of the European Union.Xunta de Galicia; ED431D R2016/045Xunta de Galicia; ED431G/01Xunta de Galicia; GRC2014/03

Biomolecular Event Extraction using Natural Language Processing

Biomedical research and discoveries are communicated through scholarly publications and this literature is voluminous, rich in scientific text and growing exponentially by the day. Biomedical journals publish nearly three thousand research articles daily, making literature search a challenging proposition for researchers. Biomolecular events involve genes, proteins, metabolites, and enzymes that provide invaluable insights into biological processes and explain the physiological functional mechanisms. Text mining (TM) or extraction of such events automatically from big data is the only quick and viable solution to gather any useful information. Such events extracted from biological literature have a broad range of applications like database curation, ontology construction, semantic web search and interactive systems. However, automatic extraction has its challenges on account of ambiguity and the diverse nature of natural language and associated linguistic occurrences like speculations, negations etc., which commonly exist in biomedical texts and lead to erroneous elucidation. In the last decade, many strategies have been proposed in this field, using different paradigms like Biomedical natural language processing (BioNLP), machine learning and deep learning. Also, new parallel computing architectures like graphical processing units (GPU) have emerged as possible candidates to accelerate the event extraction pipeline. This paper reviews and provides a summarization of the key approaches in complex biomolecular big data event extraction tasks and recommends a balanced architecture in terms of accuracy, speed, computational cost, and memory usage towards developing a robust GPU-accelerated BioNLP system

Enhancing the scalability of a genetic algorithm to discover quantitative association rules in large-scale datasets

Association rule mining is a well-known methodology to discover significant and apparently hidden relations among attributes in a subspace of instances from datasets. Genetic algorithms have been extensively used to find interesting association rules. However, the rule-matching task of such techniques usually requires high computational and memory requirements. The use of efficient computational techniques has become a task of the utmost importance due to the high volume of generated data nowadays. Hence, this paper aims at improving the scalability of quantitative association rule mining techniques based on genetic algorithms to handle large-scale datasets without quality loss in the results obtained. For this purpose, a new representation of the individuals, new genetic operators and a windowing-based learning scheme are proposed to achieve successfully such challenging task. Specifically, the proposed techniques are integrated into the multi-objective evolutionary algorithm named QARGA-M to assess their performances. Both the standard version and the enhanced one of QARGA-M have been tested in several datasets that present different number of attributes and instances. Furthermore, the proposed methodologies have been integrated into other existing techniques based in genetic algorithms to discover quantitative association rules. The comparative analysis performed shows significant improvements of QARGA-M and other existing genetic algorithms in terms of computational costs without losing quality in the results when the proposed techniques are applied.Ministerio de Ciencia y Tecnología TIN2011- 28956-C02-02Junta de Andalucía TIC-7528Junta de Andalucía P12-TIC-1728Universidad Pablo de Olavide APPB81309

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

Exploring Decomposition for Solving Pattern Mining Problems

This article introduces a highly efficient pattern mining technique called Clustering-based Pattern Mining (CBPM). This technique discovers relevant patterns by studying the correlation between transactions in the transaction database based on clustering techniques. The set of transactions is first clustered, such that highly correlated transactions are grouped together. Next, we derive the relevant patterns by applying a pattern mining algorithm to each cluster. We present two different pattern mining algorithms, one applying an approximation-based strategy and another based on an exact strategy. The approximation-based strategy takes into account only the clusters, whereas the exact strategy takes into account both clusters and shared items between clusters. To boost the performance of the CBPM, a GPU-based implementation is investigated. To evaluate the CBPM framework, we perform extensive experiments on several pattern mining problems. The results from the experimental evaluation show that the CBPM provides a reduction in both the runtime and memory usage. Also, CBPM based on the approximate strategy provides good accuracy, demonstrating its effectiveness and feasibility. Our GPU implementation achieves significant speedup of up to 552× on a single GPU using big transaction databases.publishedVersio