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

StackInsights: Cognitive Learning for Hybrid Cloud Readiness

Hybrid cloud is an integrated cloud computing environment utilizing a mix of public cloud, private cloud, and on-premise traditional IT infrastructures. Workload awareness, defined as a detailed full range understanding of each individual workload, is essential in implementing the hybrid cloud. While it is critical to perform an accurate analysis to determine which workloads are appropriate for on-premise deployment versus which workloads can be migrated to a cloud off-premise, the assessment is mainly performed by rule or policy based approaches. In this paper, we introduce StackInsights, a novel cognitive system to automatically analyze and predict the cloud readiness of workloads for an enterprise. Our system harnesses the critical metrics across the entire stack: 1) infrastructure metrics, 2) data relevance metrics, and 3) application taxonomy, to identify workloads that have characteristics of a) low sensitivity with respect to business security, criticality and compliance, and b) low response time requirements and access patterns. Since the capture of the data relevance metrics involves an intrusive and in-depth scanning of the content of storage objects, a machine learning model is applied to perform the business relevance classification by learning from the meta level metrics harnessed across stack. In contrast to traditional methods, StackInsights significantly reduces the total time for hybrid cloud readiness assessment by orders of magnitude

Visual Integration of Data and Model Space in Ensemble Learning

Ensembles of classifier models typically deliver superior performance and can outperform single classifier models given a dataset and classification task at hand. However, the gain in performance comes together with the lack in comprehensibility, posing a challenge to understand how each model affects the classification outputs and where the errors come from. We propose a tight visual integration of the data and the model space for exploring and combining classifier models. We introduce a workflow that builds upon the visual integration and enables the effective exploration of classification outputs and models. We then present a use case in which we start with an ensemble automatically selected by a standard ensemble selection algorithm, and show how we can manipulate models and alternative combinations.Comment: 8 pages, 7 picture

Classification under Streaming Emerging New Classes: A Solution using Completely Random Trees

This paper investigates an important problem in stream mining, i.e., classification under streaming emerging new classes or SENC. The common approach is to treat it as a classification problem and solve it using either a supervised learner or a semi-supervised learner. We propose an alternative approach by using unsupervised learning as the basis to solve this problem. The SENC problem can be decomposed into three sub problems: detecting emerging new classes, classifying for known classes, and updating models to enable classification of instances of the new class and detection of more emerging new classes. The proposed method employs completely random trees which have been shown to work well in unsupervised learning and supervised learning independently in the literature. This is the first time, as far as we know, that completely random trees are used as a single common core to solve all three sub problems: unsupervised learning, supervised learning and model update in data streams. We show that the proposed unsupervised-learning-focused method often achieves significantly better outcomes than existing classification-focused methods

Classification of Carpiodes Using Fourier Descriptors: A Content Based Image Retrieval Approach

Taxonomic classification has always been important to the study of any biological system. Many biological species will go unclassified and become lost forever at the current rate of classification. The current state of computer technology makes image storage and retrieval possible on a global level. As a result, computer-aided taxonomy is now possible. Content based image retrieval techniques utilize visual features of the image for classification. By utilizing image content and computer technology, the gap between taxonomic classification and species destruction is shrinking. This content based study utilizes the Fourier Descriptors of fifteen known landmark features on three Carpiodes species: C.carpio, C.velifer, and C.cyprinus. Classification analysis involves both unsupervised and supervised machine learning algorithms. Fourier Descriptors of the fifteen known landmarks provide for strong classification power on image data. Feature reduction analysis indicates feature reduction is possible. This proves useful for increasing generalization power of classification