Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Learning from Multi-Class Imbalanced Big Data with Apache Spark

With data becoming a new form of currency, its analysis has become a top priority in both academia and industry, furthering advancements in high-performance computing and machine learning. However, these large, real-world datasets come with additional complications such as noise and class overlap. Problems are magnified when with multi-class data is presented, especially since many of the popular algorithms were originally designed for binary data. Another challenge arises when the number of examples are not evenly distributed across all classes in a dataset. This often causes classifiers to favor the majority class over the minority classes, leading to undesirable results as learning from the rare cases may be the primary goal. Many of the classic machine learning algorithms were not designed for multi-class, imbalanced data or parallelism, and so their effectiveness has been hindered. This dissertation addresses some of these challenges with in-depth experimentation using novel implementations of machine learning algorithms using Apache Spark, a distributed computing framework based on the MapReduce model designed to handle very large datasets. Experimentation showed that many of the traditional classifier algorithms do not translate well to a distributed computing environment, indicating the need for a new generation of algorithms targeting modern high-performance computing. A collection of popular oversampling methods, originally designed for small binary class datasets, have been implemented using Apache Spark for the first time to improve parallelism and add multi-class support. An extensive study on how instance level difficulty affects the learning from large datasets was also performed

An insight into imbalanced Big Data classification: outcomes and challenges

Big Data applications are emerging during the last years, and researchers from many disciplines are aware of the high advantages related to the knowledge extraction from this type of problem. However, traditional learning approaches cannot be directly applied due to scalability issues. To overcome this issue, the MapReduce framework has arisen as a “de facto” solution. Basically, it carries out a “divide-and-conquer” distributed procedure in a fault-tolerant way to adapt for commodity hardware. Being still a recent discipline, few research has been conducted on imbalanced classification for Big Data. The reasons behind this are mainly the difficulties in adapting standard techniques to the MapReduce programming style. Additionally, inner problems of imbalanced data, namely lack of data and small disjuncts, are accentuated during the data partitioning to fit the MapReduce programming style. This paper is designed under three main pillars. First, to present the first outcomes for imbalanced classification in Big Data problems, introducing the current research state of this area. Second, to analyze the behavior of standard pre-processing techniques in this particular framework. Finally, taking into account the experimental results obtained throughout this work, we will carry out a discussion on the challenges and future directions for the topic.This work has been partially supported by the Spanish Ministry of Science and Technology under Projects TIN2014-57251-P and TIN2015-68454-R, the Andalusian Research Plan P11-TIC-7765, the Foundation BBVA Project 75/2016 BigDaPTOOLS, and the National Science Foundation (NSF) Grant IIS-1447795

Exploring and Evaluating the Scalability and Efficiency of Apache Spark using Educational Datasets

Research into the combination of data mining and machine learning technology with web-based education systems (known as education data mining, or EDM) is becoming imperative in order to enhance the quality of education by moving beyond traditional methods. With the worldwide growth of the Information Communication Technology (ICT), data are becoming available at a significantly large volume, with high velocity and extensive variety. In this thesis, four popular data mining methods are applied to Apache Spark, using large volumes of datasets from Online Cognitive Learning Systems to explore the scalability and efficiency of Spark. Various volumes of datasets are tested on Spark MLlib with different running configurations and parameter tunings. The thesis convincingly presents useful strategies for allocating computing resources and tuning to take full advantage of the in-memory system of Apache Spark to conduct the tasks of data mining and machine learning. Moreover, it offers insights that education experts and data scientists can use to manage and improve the quality of education, as well as to analyze and discover hidden knowledge in the era of big data

SOUL: Scala Oversampling and Undersampling Library for imbalance classification

This work has been supported by the research project TIN2017-89517-P, by the UGR research contract OTRI 3940 and by a research scholarship, given to the authors Nestor Rodriguez and David Lopez by the University of Granada, Spain.The improvements in technology and computation have promoted a global adoption of Data Science. It is devoted to extracting significant knowledge from high amounts of information by means of the application of Artificial Intelligence and Machine Learning tools. Among the different tasks within Data Science, classification is probably the most widespread overall. Focusing on the classification scenario, we often face some datasets in which the number of instances for one of the classes is much lower than that of the remaining ones. This issue is known as the imbalanced classification problem, and it is mainly related to the need for boosting the recognition of the minority class examples. In spite of a large number of solutions that were proposed in the specialized literature to address imbalanced classification, there is a lack of open-source software that compiles the most relevant ones in an easy-to-use and scalable way. In this paper, we present a novel software approach named as SOUL, which stands for Scala Oversampling and Undersampling Library for imbalanced classification. The main capabilities of this new library include a large number of different data preprocessing techniques, efficient execution of these approaches, and a graphical environment to contrast the output for the different preprocessing solutions.UGR research contract OTRI 3940University of Granada, SpainTIN2017-89517-

Block size estimation for data partitioning in HPC applications using machine learning techniques

The extensive use of HPC infrastructures and frameworks for running data-intensive applications has led to a growing interest in data partitioning techniques and strategies. In fact, finding an effective partitioning, i.e. a suitable size for data blocks, is a key strategy to speed-up parallel data-intensive applications and increase scalability. This paper describes a methodology for data block size estimation in HPC applications, which relies on supervised machine learning techniques. The implementation of the proposed methodology was evaluated using as a testbed dislib, a distributed computing library highly focused on machine learning algorithms built on top of the PyCOMPSs framework. We assessed the effectiveness of our solution through an extensive experimental evaluation considering different algorithms, datasets, and infrastructures, including the MareNostrum 4 supercomputer. The results we obtained show that the methodology is able to efficiently determine a suitable way to split a given dataset, thus enabling the efficient execution of data-parallel applications in high performance environments

Big data analytics: a predictive analysis applied to cybersecurity in a financial organization

Project Work presented as partial requirement for obtaining the Master’s degree in Information Management, with a specialization in Knowledge Management and Business IntelligenceWith the generalization of the internet access, cyber attacks have registered an alarming growth in frequency and severity of damages, along with the awareness of organizations with heavy investments in cybersecurity, such as in the financial sector. This work is focused on an organization’s financial service that operates on the international markets in the payment systems industry. The objective was to develop a predictive framework solution responsible for threat detection to support the security team to open investigations on intrusive server requests, over the exponentially growing log events collected by the SIEM from the Apache Web Servers for the financial service. A Big Data framework, using Hadoop and Spark, was developed to perform classification tasks over the financial service requests, using Neural Networks, Logistic Regression, SVM, and Random Forests algorithms, while handling the training of the imbalance dataset through BEV. The main conclusions over the analysis conducted, registered the best scoring performances for the Random Forests classifier using all the preprocessed features available. Using the all the available worker nodes with a balanced configuration of the Spark executors, the most performant elapsed times for loading and preprocessing of the data were achieved using the column-oriented ORC with native format, while the row-oriented CSV format performed the best for the training of the classifiers.Com a generalização do acesso à internet, os ciberataques registaram um crescimento alarmante em frequência e severidade de danos causados, a par da consciencialização das organizações, com elevados investimentos em cibersegurança, como no setor financeiro. Este trabalho focou-se no serviço financeiro de uma organização que opera nos mercados internacionais da indústria de sistemas de pagamento. O objetivo consistiu no desenvolvimento uma solução preditiva responsável pela detecção de ameaças, por forma a dar suporte à equipa de segurança na abertura de investigações sobre pedidos intrusivos no servidor, relativamente aos exponencialmente crescentes eventos de log coletados pelo SIEM, referentes aos Apache Web Servers, para o serviço financeiro. Uma solução de Big Data, usando Hadoop e Spark, foi desenvolvida com o objectivo de executar tarefas de classificação sobre os pedidos do serviço financeiros, usando os algoritmos Neural Networks, Logistic Regression, SVM e Random Forests, solucionando os problemas associados ao treino de um dataset desequilibrado através de BEV. As principais conclusões sobre as análises realizadas registaram os melhores resultados de classificação usando o algoritmo Random Forests com todas as variáveis pré-processadas disponíveis. Usando todos os nós do cluster e uma configuração balanceada dos executores do Spark, os melhores tempos para carregar e pré-processar os dados foram obtidos usando o formato colunar ORC nativo, enquanto o formato CSV, orientado a linhas, apresentou os melhores tempos para o treino dos classificadores