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

Multilevel Weighted Support Vector Machine for Classification on Healthcare Data with Missing Values

This work is motivated by the needs of predictive analytics on healthcare data as represented by Electronic Medical Records. Such data is invariably problematic: noisy, with missing entries, with imbalance in classes of interests, leading to serious bias in predictive modeling. Since standard data mining methods often produce poor performance measures, we argue for development of specialized techniques of data-preprocessing and classification. In this paper, we propose a new method to simultaneously classify large datasets and reduce the effects of missing values. It is based on a multilevel framework of the cost-sensitive SVM and the expected maximization imputation method for missing values, which relies on iterated regression analyses. We compare classification results of multilevel SVM-based algorithms on public benchmark datasets with imbalanced classes and missing values as well as real data in health applications, and show that our multilevel SVM-based method produces fast, and more accurate and robust classification results.Comment: arXiv admin note: substantial text overlap with arXiv:1503.0625

Gait-based Gender Classification Considering Resampling and Feature Selection

Two intrinsic data characteristics that arise in many domains are the class imbalance and the high dimensionality, which pose new challenges that should be addressed. When using gait for gender classification, benchmarking public databases and renowned gait representations lead to these two problems, but they have not been jointly studied in depth. This paper is a preliminary study that pursues to investigate the benefits of using several techniques to tackle the aforementioned problems either singly or in combination, and also to evaluate the order of application that leads to the best classification performance. Experimental results show the importance of jointly managing both problems for gait-based gender classification. In particular, it seems that the best strategy consists of applying resampling followed by feature selection

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