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

Knowledge management overview of feature selection problem in high-dimensional financial data: Cooperative co-evolution and Map Reduce perspectives

The term big data characterizes the massive amounts of data generation by the advanced technologies in different domains using 4Vs volume, velocity, variety, and veracity-to indicate the amount of data that can only be processed via computationally intensive analysis, the speed of their creation, the different types of data, and their accuracy. High-dimensional financial data, such as time-series and space-Time data, contain a large number of features (variables) while having a small number of samples, which are used to measure various real-Time business situations for financial organizations. Such datasets are normally noisy, and complex correlations may exist between their features, and many domains, including financial, lack the al analytic tools to mine the data for knowledge discovery because of the high-dimensionality. Feature selection is an optimization problem to find a minimal subset of relevant features that maximizes the classification accuracy and reduces the computations. Traditional statistical-based feature selection approaches are not adequate to deal with the curse of dimensionality associated with big data. Cooperative co-evolution, a meta-heuristic algorithm and a divide-And-conquer approach, decomposes high-dimensional problems into smaller sub-problems. Further, MapReduce, a programming model, offers a ready-To-use distributed, scalable, and fault-Tolerant infrastructure for parallelizing the developed algorithm. This article presents a knowledge management overview of evolutionary feature selection approaches, state-of-The-Art cooperative co-evolution and MapReduce-based feature selection techniques, and future research directions

Feature Selection and Classification of Microarray Data using MapReduce based ANOVA and K-Nearest Neighbor

AbstractThe major drawback of microarray data is the ‘curse of dimensionality problem’, this hinders the useful information of dataset and leads to computational instability. Therefore, selecting relevant genes is an imperative in microarray data analysis. Most of the existing schemes employ a two-phase processes: feature selection/extraction followed by classification. In this paper, a statistical test, ANOVA based on MapReduce is proposed to select the relevant features. After feature selection, MapReduce based K-Nearest Neighbor (K-NN) classifier is also proposed to classify the microarray data. These algorithms are successfully implemented on Hadoop framework and comparative analysis is done using various datasets

A Scalable and Effective Rough Set Theory based Approach for Big Data Pre-processing

International audienceA big challenge in the knowledge discovery process is to perform data pre-processing, specifically feature selection, on a large amount of data and high dimensional attribute set. A variety of techniques have been proposed in the literature to deal with this challenge with different degrees of success as most of these techniques need further information about the given input data for thresholding, need to specify noise levels or use some feature ranking procedures. To overcome these limitations, rough set theory (RST) can be used to discover the dependency within the data and reduce the number of attributes enclosed in an input data set while using the data alone and requiring no supplementary information. However, when it comes to massive data sets, RST reaches its limits as it is highly computationally expensive. In this paper, we propose a scalable and effective rough set theory-based approach for large-scale data pre-processing, specifically for feature selection, under the Spark framework. In our detailed experiments, data sets with up to 10,000 attributes have been considered, revealing that our proposed solution achieves a good speedup and performs its feature selection task well without sacrificing performance. Thus, making it relevant to big data

Analysis of Microarray Data using Machine Learning Techniques on Scalable Platforms

Microarray-based gene expression profiling has been emerged as an efficient technique for classification, diagnosis, prognosis, and treatment of cancer disease. Frequent changes in the behavior of this disease, generate a huge volume of data. The data retrieved from microarray cover its veracities, and the changes observed as time changes (velocity). Although, it is a type of high-dimensional data which has very large number of features rather than number of samples. Therefore, the analysis of microarray high-dimensional dataset in a short period is very much essential. It often contains huge number of data, only a fraction of which comprises significantly expressed genes. The identification of the precise and interesting genes which are responsible for the cause of cancer is imperative in microarray data analysis. Most of the existing schemes employ a two phase process such as feature selection/extraction followed by classification. Our investigation starts with the analysis of microarray data using kernel based classifiers followed by feature selection using statistical t-test. In this work, various kernel based classifiers like Extreme learning machine (ELM), Relevance vector machine (RVM), and a new proposed method called kernel fuzzy inference system (KFIS) are implemented. The proposed models are investigated using three microarray datasets like Leukemia, Breast and Ovarian cancer. Finally, the performance of these classifiers are measured and compared with Support vector machine (SVM). From the results, it is revealed that the proposed models are able to classify the datasets efficiently and the performance is comparable to the existing kernel based classifiers. As the data size increases, to handle and process these datasets becomes very bottleneck. Hence, a distributed and a scalable cluster like Hadoop is needed for storing (HDFS) and processing (MapReduce as well as Spark) the datasets in an efficient way. The next contribution in this thesis deals with the implementation of feature selection methods, which are able to process the data in a distributed manner. Various statistical tests like ANOVA, Kruskal-Wallis, and Friedman tests are implemented using MapReduce and Spark frameworks which are executed on the top of Hadoop cluster. The performance of these scalable models are measured and compared with the conventional system. From the results, it is observed that the proposed scalable models are very efficient to process data of larger dimensions (GBs, TBs, etc.), as it is not possible to process with the traditional implementation of those algorithms. After selecting the relevant features, the next contribution of this thesis is the scalable viii implementation of the proximal support vector machine classifier, which is an efficient variant of SVM. The proposed classifier is implemented on the two scalable frameworks like MapReduce and Spark and executed on the Hadoop cluster. The obtained results are compared with the results obtained using conventional system. From the results, it is observed that the scalable cluster is well suited for the Big data. Furthermore, it is concluded that Spark is more efficient than MapReduce due to its an intelligent way of handling the datasets through Resilient distributed dataset (RDD) as well as in-memory processing and conventional system to analyze the Big datasets. Therefore, the next contribution of the thesis is the implementation of various scalable classifiers base on Spark. In this work various classifiers like, Logistic regression (LR), Support vector machine (SVM), Naive Bayes (NB), K-Nearest Neighbor (KNN), Artificial Neural Network (ANN), and Radial basis function network (RBFN) with two variants hybrid and gradient descent learning algorithms are proposed and implemented using Spark framework. The proposed scalable models are executed on Hadoop cluster as well as conventional system and the results are investigated. From the obtained results, it is observed that the execution of the scalable algorithms are very efficient than conventional system for processing the Big datasets. The efficacy of the proposed scalable algorithms to handle Big datasets are investigated and compared with the conventional system (where data are not distributed, kept on standalone machine and processed in a traditional manner). The comparative analysis shows that the scalable algorithms are very efficient to process Big datasets on Hadoop cluster rather than the conventional system

Massively-Parallel Feature Selection for Big Data

We present the Parallel, Forward-Backward with Pruning (PFBP) algorithm for feature selection (FS) in Big Data settings (high dimensionality and/or sample size). To tackle the challenges of Big Data FS PFBP partitions the data matrix both in terms of rows (samples, training examples) as well as columns (features). By employing the concepts of $p$-values of conditional independence tests and meta-analysis techniques PFBP manages to rely only on computations local to a partition while minimizing communication costs. Then, it employs powerful and safe (asymptotically sound) heuristics to make early, approximate decisions, such as Early Dropping of features from consideration in subsequent iterations, Early Stopping of consideration of features within the same iteration, or Early Return of the winner in each iteration. PFBP provides asymptotic guarantees of optimality for data distributions faithfully representable by a causal network (Bayesian network or maximal ancestral graph). Our empirical analysis confirms a super-linear speedup of the algorithm with increasing sample size, linear scalability with respect to the number of features and processing cores, while dominating other competitive algorithms in its class

A Detailed Study of the Distributed Rough Set Based Locality Sensitive Hashing Feature Selection Technique

International audienceIn the context of big data, granular computing has recently been implemented by some mathematical tools, especially Rough Set Theory (RST). As a key topic of rough set theory, feature selection has been investigated to adapt the related granular concepts of RST to deal with large amounts of data, leading to the development of the distributed RST version. However, despite of its scalability, the distributed RST version faces a key challenge tied to the partitioning of the feature search space in the distributed environment while guaranteeing data dependency. Therefore, in this manuscript, we propose a new distributed RST version based on Locality Sensitive Hashing (LSH), named LSH-dRST, for big data feature selection. LSH-dRST uses LSH to match similar features into the same bucket and maps the generated buckets into partitions to enable the splitting of the universe in a more efficient way. More precisely, in this paper, we perform a detailed analysis of the performance of LSH-dRST by comparing it to the standard distributed RST version, which is based on a random partitioning of the universe. We demonstrate that our LSH-dRST is scalable when dealing with large amounts of data. We also demonstrate * This work is part of a project that has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 702527. 2 Z. Chelly Dagdia, C. Zarges / LSH-RST for an Efficient Big Data Pre-processing that LSH-dRST ensures the partitioning of the high dimensional feature search space in a more reliable way; hence better preserving data dependency in the distributed environment and ensuring a lower computational cost

PESSCARA: An Example Infrastructure for Big Data Research

Big data requires a flexible system for data management and curation which has to be intuitive, and it should also be able to execute non-linear analysis pipelines suitable to handle with the nature of big data. This is certainly true for medical images where the amount of data grows exponentially every year and the nature of images rapidly changes with technological advances and rapid genomic advances. In this chapter, we describe a system that provides flexible management for medical images plus a wide array of associated metadata, including clinical data, genomic data, and clinical trial information. The system consists of open-source Content Management System (CMS) that has a highly configurable workflow; has a single interface that can store, manage, enable curation, and retrieve imaging-based studies; and can handle the requirement for data auditing and project management. Furthermore, the system can be extended to interact with all the modern big data analysis technologies