Constructing distributed time-critical applications using cognitive enabled services

Time-critical analytics applications are increasingly making use of distributed service interfaces (e.g., micro-services) that support the rapid construction of new applications by dynamically linking the services into different workflow configurations. Traditional service-based applications, in fixed networks, are typically constructed and managed centrally and assume stable service endpoints and adequate network connectivity. Constructing and maintaining such applications in dynamic heterogeneous wireless networked environments, where limited bandwidth and transient connectivity are commonplace, presents significant challenges and makes centralized application construction and management impossible. In this paper we present an architecture which is capable of providing an adaptable and resilient method for on-demand decentralized construction and management of complex time-critical applications in such environments. The approach uses a Vector Symbolic Architecture (VSA) to compactly represent an application as a single semantic vector that encodes the service interfaces, workflow, and the time-critical constraints required. By extending existing services interfaces, with a simple cognitive layer that can interpret and exchange the vectors, we show how the required services can be dynamically discovered and interconnected in a completely decentralized manner. We demonstrate the viability of this approach by using a VSA to encode various time-critical data analytics workflows. We show that these vectors can be used to dynamically construct and run applications using services that are distributed across an emulated Mobile Ad-Hoc Wireless Network (MANET). Scalability is demonstrated via an empirical evaluation

Preface

DAMSS-2018 is the jubilee 10th international workshop on data analysis methods for software systems, organized in Druskininkai, Lithuania, at the end of the year. The same place and the same time every year. Ten years passed from the first workshop. History of the workshop starts from 2009 with 16 presentations. The idea of such workshop came up at the Institute of Mathematics and Informatics. Lithuanian Academy of Sciences and the Lithuanian Computer Society supported this idea. This idea got approval both in the Lithuanian research community and abroad. The number of this year presentations is 81. The number of registered participants is 113 from 13 countries. In 2010, the Institute of Mathematics and Informatics became a member of Vilnius University, the largest university of Lithuania. In 2017, the institute changes its name into the Institute of Data Science and Digital Technologies. This name reflects recent activities of the institute. The renewed institute has eight research groups: Cognitive Computing, Image and Signal Analysis, Cyber-Social Systems Engineering, Statistics and Probability, Global Optimization, Intelligent Technologies, Education Systems, Blockchain Technologies. The main goal of the workshop is to introduce the research undertaken at Lithuanian and foreign universities in the fields of data science and software engineering. Annual organization of the workshop allows the fast interchanging of new ideas among the research community. Even 11 companies supported the workshop this year. This means that the topics of the workshop are actual for business, too. Topics of the workshop cover big data, bioinformatics, data science, blockchain technologies, deep learning, digital technologies, high-performance computing, visualization methods for multidimensional data, machine learning, medical informatics, ontological engineering, optimization in data science, business rules, and software engineering. Seeking to facilitate relations between science and business, a special session and panel discussion is organized this year about topical business problems that may be solved together with the research community. This book gives an overview of all presentations of DAMSS-2018.DAMSS-2018 is the jubilee 10th international workshop on data analysis methods for software systems, organized in Druskininkai, Lithuania, at the end of the year. The same place and the same time every year. Ten years passed from the first workshop. History of the workshop starts from 2009 with 16 presentations. The idea of such workshop came up at the Institute of Mathematics and Informatics. Lithuanian Academy of Sciences and the Lithuanian Computer Society supported this idea. This idea got approval both in the Lithuanian research community and abroad. The number of this year presentations is 81. The number of registered participants is 113 from 13 countries. In 2010, the Institute of Mathematics and Informatics became a member of Vilnius University, the largest university of Lithuania. In 2017, the institute changes its name into the Institute of Data Science and Digital Technologies. This name reflects recent activities of the institute. The renewed institute has eight research groups: Cognitive Computing, Image and Signal Analysis, Cyber-Social Systems Engineering, Statistics and Probability, Global Optimization, Intelligent Technologies, Education Systems, Blockchain Technologies. The main goal of the workshop is to introduce the research undertaken at Lithuanian and foreign universities in the fields of data science and software engineering. Annual organization of the workshop allows the fast interchanging of new ideas among the research community. Even 11 companies supported the workshop this year. This means that the topics of the workshop are actual for business, too. Topics of the workshop cover big data, bioinformatics, data science, blockchain technologies, deep learning, digital technologies, high-performance computing, visualization methods for multidimensional data, machine learning, medical informatics, ontological engineering, optimization in data science, business rules, and software engineering. Seeking to facilitate relations between science and business, a special session and panel discussion is organized this year about topical business problems that may be solved together with the research community. This book gives an overview of all presentations of DAMSS-2018

A Study of Scalability and Cost-effectiveness of Large-scale Scientific Applications over Heterogeneous Computing Environment

Recent advances in large-scale experimental facilities ushered in an era of data-driven science. These large-scale data increase the opportunity to answer many fundamental questions in basic science. However, these data pose new challenges to the scientific community in terms of their optimal processing and transfer. Consequently, scientists are in dire need of robust high performance computing (HPC) solutions that can scale with terabytes of data. In this thesis, I address the challenges in three major aspects of scientific big data processing as follows: 1) Developing scalable software and algorithms for data- and compute-intensive scientific applications. 2) Proposing new cluster architectures that these software tools need for good performance. 3) Transferring the big scientific dataset among clusters situated at geographically disparate locations. In the first part, I develop scalable algorithms to process huge amounts of scientific big data using the power of recent analytic tools such as, Hadoop, Giraph, NoSQL, etc. At a broader level, these algorithms take the advantage of locality-based computing that can scale with increasing amount of data. The thesis mainly addresses the challenges involved in large-scale genome analysis applications such as, genomic error correction and genome assembly which made their way to the forefront of big data challenges recently. In the second part of the thesis, I perform a systematic benchmark study using the above-mentioned algorithms on different distributed cyberinfrastructures to pinpoint the limitations in a traditional HPC cluster to process big data. Then I propose the solution to those limitations by balancing the I/O bandwidth of the solid state drive (SSD) with the computational speed of high-performance CPUs. A theoretical model has been also proposed to help the HPC system designers who are striving for system balance. In the third part of the thesis, I develop a high throughput architecture for transferring these big scientific datasets among geographically disparate clusters. The architecture leverages the power of Ethereum\u27s Blockchain technology and Swarm\u27s peer-to-peer (P2P) storage technology to transfer the data in secure, tamper-proof fashion. Instead of optimizing the computation in a single cluster, in this part, my major motivation is to foster translational research and data interoperability in collaboration with multiple institutions

Link Prediction in Complex Networks: A Survey

Link prediction in complex networks has attracted increasing attention from both physical and computer science communities. The algorithms can be used to extract missing information, identify spurious interactions, evaluate network evolving mechanisms, and so on. This article summaries recent progress about link prediction algorithms, emphasizing on the contributions from physical perspectives and approaches, such as the random-walk-based methods and the maximum likelihood methods. We also introduce three typical applications: reconstruction of networks, evaluation of network evolving mechanism and classification of partially labelled networks. Finally, we introduce some applications and outline future challenges of link prediction algorithms.Comment: 44 pages, 5 figure

An Efficient Holistic Data Distribution and Storage Solution for Online Social Networks

In the past few years, Online Social Networks (OSNs) have dramatically spread over the world. Facebook [4], one of the largest worldwide OSNs, has 1.35 billion users, 82.2% of whom are outside the US [36]. The browsing and posting interactions (text content) between OSN users lead to user data reads (visits) and writes (updates) in OSN datacenters, and Facebook now serves a billion reads and tens of millions of writes per second [37]. Besides that, Facebook has become one of the top Internet traffic sources [36] by sharing tremendous number of large multimedia files including photos and videos. The servers in datacenters have limited resources (e.g. bandwidth) to supply latency efficient service for multimedia file sharing among the rapid growing users worldwide. Most online applications operate under soft real-time constraints (e.g., ≤ 300 ms latency) for good user experience, and its service latency is negatively proportional to its income. Thus, the service latency is a very important requirement for Quality of Service (QoS) to the OSN as a web service, since it is relevant to the OSN’s revenue and user experience. Also, to increase OSN revenue, OSN service providers need to constrain capital investment, operation costs, and the resource (bandwidth) usage costs. Therefore, it is critical for the OSN to supply a guaranteed QoS for both text and multimedia contents to users while minimizing its costs. To achieve this goal, in this dissertation, we address three problems. i) Data distribution among datacenters: how to allocate data (text contents) among data servers with low service latency and minimized inter-datacenter network load; ii) Efficient multimedia file sharing: how to facilitate the servers in datacenters to efficiently share multimedia files among users; iii) Cost minimized data allocation among cloud storages: how to save the infrastructure (datacenters) capital investment and operation costs by leveraging commercial cloud storage services. Data distribution among datacenters. To serve the text content, the new OSN model, which deploys datacenters globally, helps reduce service latency to worldwide distributed users and release the load of the existing datacenters. However, it causes higher inter-datacenter communica-tion load. In the OSN, each datacenter has a full copy of all data, and the master datacenter updates all other datacenters, generating tremendous load in this new model. The distributed data storage, which only stores a user’s data to his/her geographically closest datacenters, simply mitigates the problem. However, frequent interactions between distant users lead to frequent inter-datacenter com-munication and hence long service latencies. Therefore, the OSNs need a data allocation algorithm among datacenters with minimized network load and low service latency. Efficient multimedia file sharing. To serve multimedia file sharing with rapid growing user population, the file distribution method should be scalable and cost efficient, e.g. minimiza-tion of bandwidth usage of the centralized servers. The P2P networks have been widely used for file sharing among a large amount of users [58, 131], and meet both scalable and cost efficient re-quirements. However, without fully utilizing the altruism and trust among friends in the OSNs, current P2P assisted file sharing systems depend on strangers or anonymous users to distribute files that degrades their performance due to user selfish and malicious behaviors. Therefore, the OSNs need a cost efficient and trustworthy P2P-assisted file sharing system to serve multimedia content distribution. Cost minimized data allocation among cloud storages. The new trend of OSNs needs to build worldwide datacenters, which introduce a large amount of capital investment and maintenance costs. In order to save the capital expenditures to build and maintain the hardware infrastructures, the OSNs can leverage the storage services from multiple Cloud Service Providers (CSPs) with existing worldwide distributed datacenters [30, 125, 126]. These datacenters provide different Get/Put latencies and unit prices for resource utilization and reservation. Thus, when se-lecting different CSPs’ datacenters, an OSN as a cloud customer of a globally distributed application faces two challenges: i) how to allocate data to worldwide datacenters to satisfy application SLA (service level agreement) requirements including both data retrieval latency and availability, and ii) how to allocate data and reserve resources in datacenters belonging to different CSPs to minimize the payment cost. Therefore, the OSNs need a data allocation system distributing data among CSPs’ datacenters with cost minimization and SLA guarantee. In all, the OSN needs an efficient holistic data distribution and storage solution to minimize its network load and cost to supply a guaranteed QoS for both text and multimedia contents. In this dissertation, we propose methods to solve each of the aforementioned challenges in OSNs. Firstly, we verify the benefits of the new trend of OSNs and present OSN typical properties that lay the basis of our design. We then propose Selective Data replication mechanism in Distributed Datacenters (SD3) to allocate user data among geographical distributed datacenters. In SD3,a datacenter jointly considers update rate and visit rate to select user data for replication, and further atomizes a user’s different types of data (e.g., status update, friend post) for replication, making sure that a replica always reduces inter-datacenter communication. Secondly, we analyze a BitTorrent file sharing trace, which proves the necessity of proximity-and interest-aware clustering. Based on the trace study and OSN properties, to address the second problem, we propose a SoCial Network integrated P2P file sharing system for enhanced Efficiency and Trustworthiness (SOCNET) to fully and cooperatively leverage the common-interest, geographically-close and trust properties of OSN friends. SOCNET uses a hierarchical distributed hash table (DHT) to cluster common-interest nodes, and then further clusters geographically close nodes into a subcluster, and connects the nodes in a subcluster with social links. Thus, when queries travel along trustable social links, they also gain higher probability of being successfully resolved by proximity-close nodes, simultaneously enhancing efficiency and trustworthiness. Thirdly, to handle the third problem, we model the cost minimization problem under the SLA constraints using integer programming. According to the system model, we propose an Eco-nomical and SLA-guaranteed cloud Storage Service (ES3), which finds a data allocation and resource reservation schedule with cost minimization and SLA guarantee. ES3 incorporates (1) a data al-location and reservation algorithm, which allocates each data item to a datacenter and determines the reservation amount on datacenters by leveraging all the pricing policies; (2) a genetic algorithm based data allocation adjustment approach, which makes data Get/Put rates stable in each data-center to maximize the reservation benefit; and (3) a dynamic request redirection algorithm, which dynamically redirects a data request from an over-utilized datacenter to an under-utilized datacenter with sufficient reserved resource when the request rate varies greatly to further reduce the payment. Finally, we conducted trace driven experiments on a distributed testbed, PlanetLab, and real commercial cloud storage (Amazon S3, Windows Azure Storage and Google Cloud Storage) to demonstrate the efficiency and effectiveness of our proposed systems in comparison with other systems. The results show that our systems outperform others in the network savings and data distribution efficiency

Metagenomics - a guide from sampling to data analysis

Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared

Who wrote this scientific text?

The IEEE bibliographic database contains a number of proven duplications with indication of the original paper(s) copied. This corpus is used to test a method for the detection of hidden intertextuality (commonly named "plagiarism"). The intertextual distance, combined with the sliding window and with various classification techniques, identifies these duplications with a very low risk of error. These experiments also show that several factors blur the identity of the scientific author, including variable group authorship and the high levels of intertextuality accepted, and sometimes desired, in scientific papers on the same topic

L'intertextualité dans les publications scientifiques

La base de données bibliographiques de l'IEEE contient un certain nombre de duplications avérées avec indication des originaux copiés. Ce corpus est utilisé pour tester une méthode d'attribution d'auteur. La combinaison de la distance intertextuelle avec la fenêtre glissante et diverses techniques de classification permet d'identifier ces duplications avec un risque d'erreur très faible. Cette expérience montre également que plusieurs facteurs brouillent l'identité de l'auteur scientifique, notamment des collectifs de chercheurs à géométrie variable et une forte dose d'intertextualité acceptée voire recherchée

BIRCH: A user-oriented, locally-customizable, bioinformatics system

BACKGROUND: Molecular biologists need sophisticated analytical tools which often demand extensive computational resources. While finding, installing, and using these tools can be challenging, pipelining data from one program to the next is particularly awkward, especially when using web-based programs. At the same time, system administrators tasked with maintaining these tools do not always appreciate the needs of research biologists. RESULTS: BIRCH (Biological Research Computing Hierarchy) is an organizational framework for delivering bioinformatics resources to a user group, scaling from a single lab to a large institution. The BIRCH core distribution includes many popular bioinformatics programs, unified within the GDE (Genetic Data Environment) graphic interface. Of equal importance, BIRCH provides the system administrator with tools that simplify the job of managing a multiuser bioinformatics system across different platforms and operating systems. These include tools for integrating locally-installed programs and databases into BIRCH, and for customizing the local BIRCH system to meet the needs of the user base. BIRCH can also act as a front end to provide a unified view of already-existing collections of bioinformatics software. Documentation for the BIRCH and locally-added programs is merged in a hierarchical set of web pages. In addition to manual pages for individual programs, BIRCH tutorials employ step by step examples, with screen shots and sample files, to illustrate both the important theoretical and practical considerations behind complex analytical tasks. CONCLUSION: BIRCH provides a versatile organizational framework for managing software and databases, and making these accessible to a user base. Because of its network-centric design, BIRCH makes it possible for any user to do any task from anywhere