Large-scale Data Analysis and Deep Learning Using Distributed Cyberinfrastructures and High Performance Computing

Data in many research fields continues to grow in both size and complexity. For instance, recent technological advances have caused an increased throughput in data in various biological-related endeavors, such as DNA sequencing, molecular simulations, and medical imaging. In addition, the variance in the types of data (textual, signal, image, etc.) adds an additional complexity in analyzing the data. As such, there is a need for uniquely developed applications that cater towards the type of data. Several considerations must be made when attempting to create a tool for a particular dataset. First, we must consider the type of algorithm required for analyzing the data. Next, since the size and complexity of the data imposes high computation and memory requirements, it is important to select a proper hardware environment on which to build the application. By carefully both developing the algorithm and selecting the hardware, we can provide an effective environment in which to analyze huge amounts of highly complex data in a large-scale manner. In this dissertation, I go into detail regarding my applications using big data and deep learning techniques to analyze complex and large data. I investigate how big data frameworks, such as Hadoop, can be applied to problems such as large-scale molecular dynamics simulations. Following this, many popular deep learning frameworks are evaluated and compared to find those that suit certain hardware setups and deep learning models. Then, we explore an application of deep learning to a biomedical problem, namely ADHD diagnosis from fMRI data. Lastly, I demonstrate a framework for real-time and fine-grained vehicle detection and classification. With each of these works in this dissertation, a unique large-scale analysis algorithm or deep learning model is implemented that caters towards the problem and leverages specialized computing resources

Need for speed:Achieving fast image processing in acute stroke care

This thesis aims to investigate the use of high-performance computing (HPC) techniques in developing imaging biomarkers to support the clinical workflow of acute stroke patients. In the first part of this thesis, we evaluate different HPC technologies and how such technologies can be leveraged by different image analysis applications used in the context of acute stroke care. More specifically, we evaluated how computers with multiple computing devices can be used to accelerate medical imaging applications in Chapter 2. Chapter 3 proposes a novel data compression technique that efficiently processes CT perfusion (CTP) images in GPUs. Unfortunately, the size of CTP datasets makes data transfers to computing devices time-consuming and, therefore, unsuitable in acute situations. Chapter 4 further evaluates the algorithm's usefulness proposed in Chapter 3 with two different applications: a double threshold segmentation and a time-intensity profile similarity (TIPS) bilateral filter to reduce noise in CTP scans. Finally, Chapter 5 presents a cloud platform for deploying high-performance medical applications for acute stroke patients. In Part 2 of this thesis, Chapter 6 presents a convolutional neural network (CNN) for detecting and volumetric segmentation of subarachnoid hemorrhages (SAH) in non-contrast CT scans. Chapter 7 proposed another method based on CNNs to quantify the final infarct volumes in follow-up non-contrast CT scans from ischemic stroke patients

Helmholtz Portfolio Theme Large-Scale Data Management and Analysis (LSDMA)

The Helmholtz Association funded the "Large-Scale Data Management and Analysis" portfolio theme from 2012-2016. Four Helmholtz centres, six universities and another research institution in Germany joined to enable data-intensive science by optimising data life cycles in selected scientific communities. In our Data Life cycle Labs, data experts performed joint R&D together with scientific communities. The Data Services Integration Team focused on generic solutions applied by several communities

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

High-Performance Modelling and Simulation for Big Data Applications

This open access book was prepared as a Final Publication of the COST Action IC1406 “High-Performance Modelling and Simulation for Big Data Applications (cHiPSet)“ project. Long considered important pillars of the scientific method, Modelling and Simulation have evolved from traditional discrete numerical methods to complex data-intensive continuous analytical optimisations. Resolution, scale, and accuracy have become essential to predict and analyse natural and complex systems in science and engineering. When their level of abstraction raises to have a better discernment of the domain at hand, their representation gets increasingly demanding for computational and data resources. On the other hand, High Performance Computing typically entails the effective use of parallel and distributed processing units coupled with efficient storage, communication and visualisation systems to underpin complex data-intensive applications in distinct scientific and technical domains. It is then arguably required to have a seamless interaction of High Performance Computing with Modelling and Simulation in order to store, compute, analyse, and visualise large data sets in science and engineering. Funded by the European Commission, cHiPSet has provided a dynamic trans-European forum for their members and distinguished guests to openly discuss novel perspectives and topics of interests for these two communities. This cHiPSet compendium presents a set of selected case studies related to healthcare, biological data, computational advertising, multimedia, finance, bioinformatics, and telecommunications

Pathway and biomarker discovery in a posttraumatic stress disorder mouse model

Posttraumatic stress disorder (PTSD), a prevalent psychiatric disorder, is caused by exposure to a traumatic event. Individuals diagnosed for PTSD not only experience significant functional impairments but also have higher rates of physical morbidity and mortality. Despite intense research efforts, the neurobiological pathways affecting fear circuit brain regions in PTSD remain obscure and most of the previous studies were limited to characterization of specific markers in periphery or defined brain regions. In my PhD study, I employed proteomics, metabolomics and transcriptomcis technologies interrogating a foot shock induced PTSD mouse model. In addition, I studied the effects of early intervention of chronic fluoxetine treatment. By in silico analyses, altered cellular pathways associated with PTSD were identified in stress-vulnerable brain regions, including prelimbic cortex (PrL), anterior cingulate cortex (ACC), basolateral amygdala (BLA), central nucleus of amygdala(CeA), nucleus accumbens (NAc) and CA1 of the dorsal hippocampus. With RNA sequencing, I compared the brain transcriptome between shocked and control mice, with and without fluoxetine treatment. Differentially expressed genes were identified and clustered, and I observed increased inflammation in ACC and decreased neurotransmitter signaling in both ACC and CA1. I applied in vivo 15N metabolic labeling combined with mass spectrometry to study alterations at proteome level in the brain. By integrating proteomics and metabolomics profiling analyses, I found decreased Citric Acid Cycle pathway in both NAc and ACC, and dysregulated cytoskeleton assembly and myelination pathways in BLA, CeA and CA1. In addition, chronic fluoxetine treatment 12 hours after foot shock prevented altered inflammatory gene expression in ACC, and Citric Acid Cycle in NAc and ACC, and ameliorated conditioned fear response in shocked mice. These results shed light on the role of immune response and energy metabolism in PTSD pathogenesis. Furthermore, I performed microdialysis in medial prefrontal cortex and hippocampus to measure the changes in extracellular norepinephrine and free corticosterone (CORT) in the shocked mouse and related them to PTSD-like symptoms, including hyperaroual and contextual fear response. I found that increased free CORT was related to immediate stress response, whereas norepinephrine level, in a brain region specific manner, predicted arousal and contextual fear response one month after trauma. I also applied metabolomics analysis to investigate molecular changes in prefrontal microdialysates of shocked mice. Citric Acid Cycle, Glyoxylate and Dicarboxylate metabolism and Alanine, Aspartate and Glutamate metabolism pathways were found to be involved in foot shock induced hyperarousal. Taken together, my study provides novel insights into PTSD pathogenesis and suggests potential therapeutic applications targeting dysregulated pathways