Big tranSMART for clinical decision making

Molecular profiling data based patient stratification plays a key role in clinical decision making, such as identification of disease subgroups and prediction of treatment responses of individual subjects. Many existing knowledge management systems like tranSMART enable scientists to do such analysis. But in the big data era, molecular profiling data size increases sharply due to new biological techniques, such as next generation sequencing. None of the existing storage systems work well while considering the three ”V” features of big data (Volume, Variety, and Velocity). New Key Value data stores like Apache HBase and Google Bigtable can provide high speed queries by the Key. These databases can be modeled as Distributed Ordered Table (DOT), which horizontally partitions a table into regions and distributes regions to region servers by the Key. However, none of existing data models work well for DOT. A Collaborative Genomic Data Model (CGDM) has been designed to solve all these is- sues. CGDM creates three Collaborative Global Clustering Index Tables to improve the data query velocity. Microarray implementation of CGDM on HBase performed up to 246, 7 and 20 times faster than the relational data model on HBase, MySQL Cluster and MongoDB. Single nucleotide polymorphism implementation of CGDM on HBase outperformed the relational model on HBase and MySQL Cluster by up to 351 and 9 times. Raw sequence implementation of CGDM on HBase gains up to 440-fold and 22-fold speedup, compared to the sequence alignment map format implemented in HBase and a binary alignment map server. The integration into tranSMART shows up to 7-fold speedup in the data export function. In addition, a popular hierarchical clustering algorithm in tranSMART has been used as an application to indicate how CGDM can influence the velocity of the algorithm. The optimized method using CGDM performs more than 7 times faster than the same method using the relational model implemented in MySQL Cluster.Open Acces

Enhancing the Programmability of Cloud Object Storage

En un món que depèn cada vegada més de la tecnologia, les dades digitals es generen a una escala sense precedents. Això fa que empreses que requereixen d'un gran espai d'emmagatzematge, com Netflix o Dropbox, utilitzin solucions d'emmagatzematge al núvol. Mes concretament, l'emmagatzematge d'objectes, donada la seva simplicitat, escalabilitat i alta disponibilitat. No obstant això, aquests magatzems s'enfronten a tres desafiaments principals: 1) Gestió flexible de càrregues de treball de múltiples usuaris. Normalment, els magatzems d'objectes són sistemes multi-usuari, la qual cosa significa que tots ells comparteixen els mateixos recursos, el que podria ocasionar problemes d'interferència. A més, és complex administrar polítiques d'emmagatzematge heterogènies a gran escala en ells. 2) Autogestió de dades. Els magatzems d'objectes no ofereixen molta flexibilitat pel que fa a l'autogestió de dades per part dels usuaris. Típicament, són sistemes rígids, la qual cosa impedeix gestionar els requisits específics dels objectes. 3) Còmput elàstic prop de les dades. Situar els càlculs prop de les dades pot ser útil per reduir la transferència de dades. Però, el desafiament aquí és com aconseguir la seva elasticitat sense provocar contenció de recursos i interferències en la capa d'emmagatzematge. En aquesta tesi presentem tres contribucions innovadores que resolen aquests desafiaments. En primer lloc, presentem la primera arquitectura d'emmagatzematge definida per programari (SDS) per a magatzems d'objectes que separa les capes de control i de dades. Això permet gestionar les càrregues de treball de múltiples usuaris d'una manera flexible i dinàmica. En segon lloc, hem dissenyat una nova abstracció de polítiques anomenada "microcontrolador" que transforma els objectes comuns en objectes intel·ligents, permetent als usuaris programar el seu comportament. Finalment, presentem la primera plataforma informàtica "serverless" guiada per dades i elàstica, que mitiga els problemes de col·locar el càlcul prop de les dades.En un mundo que depende cada vez más de la tecnología, los datos digitales se generan a una escala sin precedentes. Esto hace que empresas que requieren de un gran espacio de almacenamiento, como Netflix o Dropbox, usen soluciones de almacenamiento en la nube. Mas concretamente, el almacenamiento de objectos, dada su escalabilidad y alta disponibilidad. Sin embargo, estos almacenes se enfrentan a tres desafíos principales: 1) Gestión flexible de cargas de trabajo de múltiples usuarios. Normalmente, los almacenes de objetos son sistemas multi-usuario, lo que significa que todos ellos comparten los mismos recursos, lo que podría ocasionar problemas de interferencia. Además, es complejo administrar políticas de almacenamiento heterogéneas a gran escala en ellos. 2) Autogestión de datos. Los almacenes de objetos no ofrecen mucha flexibilidad con respecto a la autogestión de datos por parte de los usuarios. Típicamente, son sistemas rígidos, lo que impide gestionar los requisitos específicos de los objetos. 3) Cómputo elástico cerca de los datos. Situar los cálculos cerca de los datos puede ser útil para reducir la transferencia de datos. Pero, el desafío aquí es cómo lograr su elasticidad sin provocar contención de recursos e interferencias en la capa de almacenamiento. En esta tesis presentamos tres contribuciones que resuelven estos desafíos. En primer lugar, presentamos la primera arquitectura de almacenamiento definida por software (SDS) para almacenes de objetos que separa las capas de control y de datos. Esto permite gestionar las cargas de trabajo de múltiples usuarios de una manera flexible y dinámica. En segundo lugar, hemos diseñado una nueva abstracción de políticas llamada "microcontrolador" que transforma los objetos comunes en objetos inteligentes, permitiendo a los usuarios programar su comportamiento. Finalmente, presentamos la primera plataforma informática "serverless" guiada por datos y elástica, que mitiga los problemas de colocar el cálculo cerca de los datos.In a world that is increasingly dependent on technology, digital data is generated in an unprecedented way. This makes companies that require large storage space, such as Netflix or Dropbox, use cloud object storage solutions. This is mainly thanks to their built-in characteristics, such as simplicity, scalability and high-availability. However, cloud object stores face three main challenges: 1) Flexible management of multi-tenant workloads. Commonly, cloud object stores are multi-tenant systems, meaning that all tenants share the same system resources, which could lead to interference problems. Furthermore, it is now complex to manage heterogeneous storage policies in a massive scale. 2) Data self-management. Cloud object stores themselves do not offer much flexibility regarding data self-management by tenants. Typically, they are rigid, which prevent tenants to handle the specific requirements of their objects. 3) Elastic computation close to the data. Placing computations close to the data can be useful to reduce data transfers. But, the challenge here is how to achieve elasticity in those computations without provoking resource contention and interferences in the storage layer. In this thesis, we present three novel research contributions that solve the aforementioned challenges. Firstly, we introduce the first Software-defined Storage (SDS) architecture for cloud object stores that separates the control plane from the data plane, allowing to manage multi-tenant workloads in a flexible and dynamic way. For example, by applying different service levels of bandwidth to different tenants. Secondly, we designed a novel policy abstraction called microcontroller that transforms common objects into smart objects, enabling tenants to programmatically manage their behavior. For example, a content-level access control microcontroller attached to an specific object to filter its content depending on who is accessing it. Finally, we present the first elastic data-driven serverless computing platform that mitigates the resource contention problem of placing computation close to the data

Big Data and Large-scale Data Analytics: Efficiency of Sustainable Scalability and Security of Centralized Clouds and Edge Deployment Architectures

One of the significant shifts of the next-generation computing technologies will certainly be in the development of Big Data (BD) deployment architectures. Apache Hadoop, the BD landmark, evolved as a widely deployed BD operating system. Its new features include federation structure and many associated frameworks, which provide Hadoop 3.x with the maturity to serve different markets. This dissertation addresses two leading issues involved in exploiting BD and large-scale data analytics realm using the Hadoop platform. Namely, (i)Scalability that directly affects the system performance and overall throughput using portable Docker containers. (ii) Security that spread the adoption of data protection practices among practitioners using access controls. An Enhanced Mapreduce Environment (EME), OPportunistic and Elastic Resource Allocation (OPERA) scheduler, BD Federation Access Broker (BDFAB), and a Secure Intelligent Transportation System (SITS) of multi-tiers architecture for data streaming to the cloud computing are the main contribution of this thesis study

An Effective Approach to Predicting Large Dataset in Spatial Data Mining Area

Due to enormous quantities of spatial satellite images, telecommunication images, health related tools etc., it is often impractical for users to have detailed and thorough examination of spatial data (S). Large dataset is very common and pervasive in a number of application areas. Discovering or predicting patterns from these datasets is very vital. This research focused on developing new methods, models and techniques for accomplishing advanced spatial data mining (ASDM) tasks. The algorithms were designed to challenge state-of-the-art data technologies and they are tested with randomly generated and actual real-world data. Two main approaches were adopted to achieve the objectives (1) identifying the actual data types (DTs), data structures and spatial content of a given dataset (to make our model versatile and robust) and (2) integrating these data types into an appropriate database management system (DBMS) framework, for easy management and manipulation. These two approaches helped to discover the general and varying types of patterns that exist within any given dataset non-spatial, spatial or even temporal (because spatial data are always influenced by temporal agents) datasets. An iterative method was adopted for system development methodology in this study. The method was adopted as a strategy to combat the irregularity that often exists within spatial datasets. In the course of this study, some of the challenges we encountered which also doubled as current challenges facing spatial data mining includes: (a) time complexity in availing useful data for analysis, (b) time complexity in loading data to storage and (c) difficulties in discovering spatial, non-spatial and temporal correlations between different data objects. However, despite the above challenges, there are some opportunities that spatial data can benefit from including: Cloud computing, Spark technology, Parallelisation, and Bulk-loading methods. Techniques and application areas of spatial data mining (SDM) were identified and their strength and limitations were equally documented. Finally, new methods and algorithms for mining very large data of spatial/non-spatial bias were created. The proposed models/systems are documented in the sections as follows: (a) Development of a new technique for parallel indexing of large dataset (PaX-DBSCAN), (b) Development of new techniques for clustering (X-DBSCAN) in a learning process, (c) Development of a new technique for detecting human skin in an image, (d) Development of a new technique for finding face in an image, (e) Development of a novel technique for management of large spatial and non-spatial datasets (aX-tree). The most prominent among our methods is the new structure used in (c) above -- packed maintained k-dimensional tree (Pmkd-tree), for fast spatial indexing and querying. The structure is a combination system that combines all the proposed algorithms to produce one solid, standard, useful and quality system. The intention of the new final algorithm (system) is to combine the entire initial proposed algorithms to come up with one strong generic effective tool for predicting large dataset SDM area, which it is capable of finding patterns that exist among spatial or non-spatial objects in a DBMS. In addition to Pmkd-tree, we also implemented a novel spatial structure, packed quad-tree (Pquad-Tree), to balance and speed up the performance of the regular quad-tree. Our systems so far have shown a manifestation of efficiency in terms of performance, storage and speed. The final Systems (Pmkd-tree and Pquad-Tree) are generic systems that are flexible, robust, light and stable. They are explicit spatial models for analysing any given problem and for predicting objects as spatially distributed events, using basic SDM algorithms. They can be applied to pattern matching, image processing, computer vision, bioinformatics, information retrieval, machine learning (classification and clustering) and many other computational tasks

Enabling Hyperscale Web Services

Modern web services such as social media, online messaging, web search, video streaming, and online banking often support billions of users, requiring data centers that scale to hundreds of thousands of servers, i.e., hyperscale. In fact, the world continues to expect hyperscale computing to drive more futuristic applications such as virtual reality, self-driving cars, conversational AI, and the Internet of Things. This dissertation presents technologies that will enable tomorrow’s web services to meet the world’s expectations. The key challenge in enabling hyperscale web services arises from two important trends. First, over the past few years, there has been a radical shift in hyperscale computing due to an unprecedented growth in data, users, and web service software functionality. Second, modern hardware can no longer support this growth in hyperscale trends due to a decline in hardware performance scaling. To enable this new hyperscale era, hardware architects must become more aware of hyperscale software needs and software researchers can no longer expect unlimited hardware performance scaling. In short, systems researchers can no longer follow the traditional approach of building each layer of the systems stack separately. Instead, they must rethink the synergy between the software and hardware worlds from the ground up. This dissertation establishes such a synergy to enable futuristic hyperscale web services. This dissertation bridges the software and hardware worlds, demonstrating the importance of that bridge in realizing efficient hyperscale web services via solutions that span the systems stack. The specific goal is to design software that is aware of new hardware constraints and architect hardware that efficiently supports new hyperscale software requirements. This dissertation spans two broad thrusts: (1) a software and (2) a hardware thrust to analyze the complex hyperscale design space and use insights from these analyses to design efficient cross-stack solutions for hyperscale computation. In the software thrust, this dissertation contributes uSuite, the first open-source benchmark suite of web services built with a new hyperscale software paradigm, that is used in academia and industry to study hyperscale behaviors. Next, this dissertation uses uSuite to study software threading implications in light of today’s hardware reality, identifying new insights in the age-old research area of software threading. Driven by these insights, this dissertation demonstrates how threading models must be redesigned at hyperscale by presenting an automated approach and tool, uTune, that makes intelligent run-time threading decisions. In the hardware thrust, this dissertation architects both commodity and custom hardware to efficiently support hyperscale software requirements. First, this dissertation characterizes commodity hardware’s shortcomings, revealing insights that influenced commercial CPU designs. Based on these insights, this dissertation presents an approach and tool, SoftSKU, that enables cheap commodity hardware to efficiently support new hyperscale software paradigms, improving the efficiency of real-world web services that serve billions of users, saving millions of dollars, and meaningfully reducing the global carbon footprint. This dissertation also presents a hardware-software co-design, uNotify, that redesigns commodity hardware with minimal modifications by using existing hardware mechanisms more intelligently to overcome new hyperscale overheads. Next, this dissertation characterizes how custom hardware must be designed at hyperscale, resulting in industry-academia benchmarking efforts, commercial hardware changes, and improved software development. Based on this characterization’s insights, this dissertation presents Accelerometer, an analytical model that estimates gains from hardware customization. Multiple hyperscale enterprises and hardware vendors use Accelerometer to make well-informed hardware decisions.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/169802/1/akshitha_1.pd

The twofold role of Cloud Computing in Digital Forensics: target of investigations and helping hand to evidence analysis

This PhD thesis discusses the impact of Cloud Computing infrastructures on Digital Forensics in the twofold role of target of investigations and as a helping hand to investigators. The Cloud offers a cheap and almost limitless computing power and storage space for data which can be leveraged to commit either new or old crimes and host related traces. Conversely, the Cloud can help forensic examiners to find clues better and earlier than traditional analysis applications, thanks to its dramatically improved evidence processing capabilities. In both cases, a new arsenal of software tools needs to be made available. The development of this novel weaponry and its technical and legal implications from the point of view of repeatability of technical assessments is discussed throughout the following pages and constitutes the unprecedented contribution of this wor

WICC 2017 : XIX Workshop de Investigadores en Ciencias de la Computación

Actas del XIX Workshop de Investigadores en Ciencias de la Computación (WICC 2017), realizado en el Instituto Tecnológico de Buenos Aires (ITBA), el 27 y 28 de abril de 2017.Red de Universidades con Carreras en Informática (RedUNCI