Data Mining-based Fragmentation of XML Data Warehouses

With the multiplication of XML data sources, many XML data warehouse models have been proposed to handle data heterogeneity and complexity in a way relational data warehouses fail to achieve. However, XML-native database systems currently suffer from limited performances, both in terms of manageable data volume and response time. Fragmentation helps address both these issues. Derived horizontal fragmentation is typically used in relational data warehouses and can definitely be adapted to the XML context. However, the number of fragments produced by classical algorithms is difficult to control. In this paper, we propose the use of a k-means-based fragmentation approach that allows to master the number of fragments through its $k$ parameter. We experimentally compare its efficiency to classical derived horizontal fragmentation algorithms adapted to XML data warehouses and show its superiority

A unified view of data-intensive flows in business intelligence systems : a survey

Data-intensive flows are central processes in today’s business intelligence (BI) systems, deploying different technologies to deliver data, from a multitude of data sources, in user-preferred and analysis-ready formats. To meet complex requirements of next generation BI systems, we often need an effective combination of the traditionally batched extract-transform-load (ETL) processes that populate a data warehouse (DW) from integrated data sources, and more real-time and operational data flows that integrate source data at runtime. Both academia and industry thus must have a clear understanding of the foundations of data-intensive flows and the challenges of moving towards next generation BI environments. In this paper we present a survey of today’s research on data-intensive flows and the related fundamental fields of database theory. The study is based on a proposed set of dimensions describing the important challenges of data-intensive flows in the next generation BI setting. As a result of this survey, we envision an architecture of a system for managing the lifecycle of data-intensive flows. The results further provide a comprehensive understanding of data-intensive flows, recognizing challenges that still are to be addressed, and how the current solutions can be applied for addressing these challenges.Peer ReviewedPostprint (author's final draft

Automated data acquisition and analysis for high-resolution Fourier transform mass spectrometry of proteins and peptides

This thesis details the progress made in automating the data acquisition and data processing of MS and MS/MS data from Fourier transform ion cyclotron resonance mass spectrometers. These instruments have made great strides in the past few years, moving from labor-intensive, largely manual systems to the current flagship of the Kelleher group ??? a 12 tesla hybrid LTQ FT capable of analyzing hundreds of proteins per week with minimal user intervention. In early automation work centered around an 8.5 tesla hybrid quadrupole FT-ICR mass spectrometer, three strategies for automated operation of the instrument were developed. In one method, a charge state deconvolution algorithm was used to identify species of interest for isolation using a SWIFT waveform, which were then fragmented in the ICR cell using IRMPD. In another method, broad 20-60 m/z wide sections of the mass spectrum of a complex mixture were fragmented in parallel and this multiplexed fragment data was analyzed using an iterative algorithm. In the third method, samples were analyzed using a THRASH-based "quad march" method where data were acquired using consecutive, wide (20-60 m/z) isolation windows, analyzed using the THRASH algorithm, and then selected species were selected for MS/MS fragmentation. Results from the application of this platform to a survey of the Methanosarcina acetivorans proteome are presented. Later work focused on a commercial 12 tesla hybrid linear ion trap FT-ICR mass spectrometer. This automation scheme used hybrid online/offline data acquisition to take advantages of the features of both online LC-MS (efficient separation and rapid data collection) and offline direct infusion MS/MS (project-wide target selection, better MS/MS data). The workflow for the online portion of this scheme is a modified form of the THRASH-based "quad march" data acquisition scheme from the earlier 8.5 T automation work. The centerpiece of this - iii - platform is a database known as the Automation Warehouse, which acts as a repository for the intact mass data observed in a proteome project and stores the overall state of the project. Custom software binds together the raw data, the data stored in the warehouse and ProSight. Results from the application of this platform to a survey of proteins from HeLa cell nuclei are presented. In an attempt to begin applying the above platforms to membrane proteins, MS analysis of a putative cross-link in the active site of the C-type heme-copper oxygen reductase from Vibrio cholera was performed. Though the sequences in the region differed, other members of the HCO superfamily contained a similar cross-link (confirmed by mass spectrometry and crystal structures) that is important in the catalytic cycle of the enzyme. Computer modeling of the C-type oxidase suggested that the cross-link would be present, though the key amino acid would be located on a different helix. MS/MS analysis of a tryptic digest confirmed the presence of the cross-link and the evolutionary migration of the key amino acid

Data replication and update propagation in XML P2P data management systems

XML P2P data management systems are P2P systems that use XML as the underlying data format shared between peers in the network. These systems aim to bring the benefits of XML and P2P systems to the distributed data management field. However, P2P systems are known for their lack of central control and high degree of autonomy. Peers may leave the network at any time at will, increasing the risk of data loss. Despite this, most research in XML P2P systems focus on novel and efficient XML indexing and retrieval techniques. Mechanisms for ensuring data availability in XML P2P systems has received comparatively little attention. This project attempts to address this issue. We design an XML P2P data management framework to improve data availability. This framework includes mechanisms for wide-spread data replication, replica location and update propagation. It allows XML documents to be broken down into fragments. By doing so, we aim to reduce the cost of replicating data by distributing smaller XML fragments throughout the network rather than entire documents. To tackle the data replication problem, we propose a suite of selection and placement algorithms that may be interchanged to form a particular replication strategy. To support the placement of replicas anywhere in the network, we use a Fragment Location Catalogue, a global index that maintains the locations of replicas. We also propose a lazy update propagation algorithm to propagate updates to replicas. Experiments show that the data replication algorithms improve data availability in our experimental network environment. We also find that breaking XML documents into smaller pieces and replicating those instead of whole XML documents considerably reduces the replication cost, but at the price of some loss in data availability. For the update propagation tests, we find that the probability that queries return up-to-date results increases, but improvements to the algorithm are necessary to handle environments with high update rates

Cloud engineering is search based software engineering too

Many of the problems posed by the migration of computation to cloud platforms can be formulated and solved using techniques associated with Search Based Software Engineering (SBSE). Much of cloud software engineering involves problems of optimisation: performance, allocation, assignment and the dynamic balancing of resources to achieve pragmatic trade-offs between many competing technical and business objectives. SBSE is concerned with the application of computational search and optimisation to solve precisely these kinds of software engineering challenges. Interest in both cloud computing and SBSE has grown rapidly in the past five years, yet there has been little work on SBSE as a means of addressing cloud computing challenges. Like many computationally demanding activities, SBSE has the potential to benefit from the cloud; ‘SBSE in the cloud’. However, this paper focuses, instead, of the ways in which SBSE can benefit cloud computing. It thus develops the theme of ‘SBSE for the cloud’, formulating cloud computing challenges in ways that can be addressed using SBSE

The Family of MapReduce and Large Scale Data Processing Systems

In the last two decades, the continuous increase of computational power has produced an overwhelming flow of data which has called for a paradigm shift in the computing architecture and large scale data processing mechanisms. MapReduce is a simple and powerful programming model that enables easy development of scalable parallel applications to process vast amounts of data on large clusters of commodity machines. It isolates the application from the details of running a distributed program such as issues on data distribution, scheduling and fault tolerance. However, the original implementation of the MapReduce framework had some limitations that have been tackled by many research efforts in several followup works after its introduction. This article provides a comprehensive survey for a family of approaches and mechanisms of large scale data processing mechanisms that have been implemented based on the original idea of the MapReduce framework and are currently gaining a lot of momentum in both research and industrial communities. We also cover a set of introduced systems that have been implemented to provide declarative programming interfaces on top of the MapReduce framework. In addition, we review several large scale data processing systems that resemble some of the ideas of the MapReduce framework for different purposes and application scenarios. Finally, we discuss some of the future research directions for implementing the next generation of MapReduce-like solutions.Comment: arXiv admin note: text overlap with arXiv:1105.4252 by other author

A semantic and agent-based approach to support information retrieval, interoperability and multi-lateral viewpoints for heterogeneous environmental databases

PhDData stored in individual autonomous databases often needs to be combined and interrelated. For example, in the Inland Water (IW) environment monitoring domain, the spatial and temporal variation of measurements of different water quality indicators stored in different databases are of interest. Data from multiple data sources is more complex to combine when there is a lack of metadata in a computation forin and when the syntax and semantics of the stored data models are heterogeneous. The main types of information retrieval (IR) requirements are query transparency and data harmonisation for data interoperability and support for multiple user views. A combined Semantic Web based and Agent based distributed system framework has been developed to support the above IR requirements. It has been implemented using the Jena ontology and JADE agent toolkits. The semantic part supports the interoperability of autonomous data sources by merging their intensional data, using a Global-As-View or GAV approach, into a global semantic model, represented in DAML+OIL and in OWL. This is used to mediate between different local database views. The agent part provides the semantic services to import, align and parse semantic metadata instances, to support data mediation and to reason about data mappings during alignment. The framework has applied to support information retrieval, interoperability and multi-lateral viewpoints for four European environmental agency databases. An extended GAV approach has been developed and applied to handle queries that can be reformulated over multiple user views of the stored data. This allows users to retrieve data in a conceptualisation that is better suited to them rather than to have to understand the entire detailed global view conceptualisation. User viewpoints are derived from the global ontology or existing viewpoints of it. This has the advantage that it reduces the number of potential conceptualisations and their associated mappings to be more computationally manageable. Whereas an ad hoc framework based upon conventional distributed programming language and a rule framework could be used to support user views and adaptation to user views, a more formal framework has the benefit in that it can support reasoning about the consistency, equivalence, containment and conflict resolution when traversing data models. A preliminary formulation of the formal model has been undertaken and is based upon extending a Datalog type algebra with hierarchical, attribute and instance value operators. These operators can be applied to support compositional mapping and consistency checking of data views. The multiple viewpoint system was implemented as a Java-based application consisting of two sub-systems, one for viewpoint adaptation and management, the other for query processing and query result adjustment

LEAN DATA ENGINEERING. COMBINING STATE OF THE ART PRINCIPLES TO PROCESS DATA EFFICIENTLYS

The present work was developed during an internship, under Erasmus+ Traineeship program, in Fieldwork Robotics, a Cambridge based company that develops robots to operate in agricultural fields. They collect data from commercial greenhouses with sensors and real sense cameras, as well as with gripper cameras placed in the robotic arms. This data is recorded mainly in bag files, consisting of unstructured data, such as images and semi-structured data, such as metadata associated with both the conditions where the images were taken and information about the robot itself. Data was uploaded, extracted, cleaned and labelled manually before being used to train Artificial Intelligence (AI) algorithms to identify raspberries during the harvesting process. The amount of available data quickly escalates with every trip to the fields, which creates an ever-growing need for an automated process. This problem was addressed via the creation of a data engineering platform encom- passing a data lake, data warehouse and its needed processing capabilities. This platform was created following a series of principles entitled Lean Data Engineering Principles (LDEP), and the systems that follows them are called Lean Data Engineering Systems (LDES). These principles urge to start with the end in mind: process incoming batch or real-time data with no resource wasting, limiting the costs to the absolutely necessary for the job completion, in other words to be as lean as possible. The LDEP principles are a combination of state-of-the-art ideas stemming from several fields, such as data engineering, software engineering and DevOps, leveraging cloud technologies at its core. The proposed custom-made solution enabled the company to scale its data operations, being able to label images almost ten times faster while reducing over 99.9% of its associated costs in comparison to the previous process. In addition, the data lifecycle time has been reduced from weeks to hours while maintaining coherent data quality results, being able, for instance, to correctly identify 94% of the labels in comparison to a human counterpart.Este trabalho foi desenvolvido durante um estágio no âmbito do programa Erasmus+ Traineeship, na Fieldwork Robotics, uma empresa sediada em Cambridge que desenvolve robôs agrícolas. Estes robôs recolhem dados no terreno com sensores e câmeras real- sense, localizados na estrutura de alumínio e nos pulsos dos braços robóticos. Os dados recolhidos são ficheiros contendo dados não estruturados, tais como imagens, e dados semi- -estruturados, associados às condições em que as imagens foram recolhidas. Originalmente, o processo de tratamento dos dados recolhidos (upload, extração, limpeza e etiquetagem) era feito de forma manual, sendo depois utilizados para treinar algoritmos de Inteligência Artificial (IA) para identificar framboesas durante o processo de colheita. Como a quantidade de dados aumentava substancialmente com cada ida ao terreno, verificou-se uma necessidade crescente de um processo automatizado. Este problema foi endereçado com a criação de uma plataforma de engenharia de dados, composta por um data lake, uma data warehouse e o respetivo processamento, para movimentar os dados nas diferentes etapas do processo. Esta plataforma foi criada seguindo uma série de princípios intitulados Lean Data Engineering Principles (LDEP), sendo os sistemas que os seguem intitulados de Lean Data Engineering Systems (LDES). Estes princípios incitam a começar com o fim em mente: processar dados em batch ou em tempo real, sem desperdício de recursos, limitando os custos ao absolutamente necessário para a concluir o trabalho, ou seja, tornando-os o mais lean possível. Os LDEP combinam vertentes do estado da arte em diversas áreas, tais como engenharia de dados, engenharia de software, DevOps, tendo no seu cerne as tecnologias na cloud. O novo processo permitiu à empresa escalar as suas operações de dados, tornando-se capaz de etiquetar imagens quase 10× mais rápido e reduzindo em mais de 99,9% os custos associados, quando comparado com o processo anterior. Adicionalmente, o ciclo de vida dos dados foi reduzido de semanas para horas, mantendo uma qualidade equiparável, ao ser capaz de identificar corretamente 94% das etiquetas em comparação com um homólogo humano