A survey of cloud-based service computing solutions for mammalian genomics

Cloud-based service computing has started to change the way how research in science, in particular biology, medicine, and engineering, is being carried out. Researchers in the area of mammalian genomics have taken advantage of cloud computing technology to cost-effectively process large amounts of data and speed up discovery. Mammalian genomics is limited by the cost and complexity of analysis, which require large amounts of computational resources to analyse huge amount of data and biology specialists to interpret results. On the other hand the application of this technology requires computing knowledge, in particular programming and operations management skills to develop high performance computing (HPC) applications and deploy them on HPC clouds. We carried out a survey of cloud-based service computing solutions, as the most recent and promising instantiations of distributed computing systems, in the context their use in research of mammalian genomic analysis. We describe our most recent research and development effort which focuses on building Software as a Service (SaaS) clouds to simplify the use of HPC clouds for carrying out mammalian genomic analysis.

A block-aware hybrid data dissemination with hotspot elimination in wireless sensor network

As a significant milestone in the data dissemination of wireless sensor networks (WSNs), the comb-needle (CN) model was developed to dynamically balance the sensor data pushing and pulling during hybrid data dissemination. Unfortunately, the hybrid push-pull data dissemination strategy may overload some sensor nodes and form the hotspots that consume energy significantly. This usually leads to the collapse of the network at a very early stage. In the past decade, although many energy-aware dynamic data dissemination methods have been proposed to alleviate the hotspots issue, the block characteristic of sensor nodes has been overlooked and how to offload traffic from hot blocks with low energy through long-distance hybrid dissemination remains an open problem. In this paper, we developed a block-aware data dissemination model to balance the inter-block energy and eliminate the spreading of intra-block hotspots. Through the clustering mechanism based on geography and energy, "similar" large-scale sensor nodes can be efficiently grouped into specific blocks to form the global block information (GBI). Based on GBI, the long-distance block-cross hybrid algorithms are further developed by effectively aggregating inter-block and intra-block data disseminations. Extensive experimental results demonstrate the capability and the efficiency of the proposed approach. © 2014 Elsevier Ltd.

Control flow-based malware variant detection

Static detection of malware variants plays an important role in system security and control flow has been shown as an effective characteristic that represents polymorphic malware. In our research, we propose a similarity search of malware to detect these variants using novel distance metrics. We describe a malware signature by the set of control flowgraphs the malware contains. We use a distance metric based on the distance between feature vectors of string-based signatures. The feature vector is a decomposition of the set of graphs into either fixed size k-subgraphs, or q-gram strings of the high-level source after decompilation. We use this distance metric to perform pre-filtering. We also propose a more effective but less computationally efficient distance metric based on the minimum matching distance. The minimum matching distance uses the string edit distances between programs' decompiled flowgraphs, and the linear sum assignment problem to construct a minimum sum weight matching between two sets of graphs. We implement the distance metrics in a complete malware variant detection system. The evaluation shows that our approach is highly effective in terms of a limited false positive rate and our system detects more malware variants when compared to the detection rates of other algorithms. © 2013 IEEE.

Robust multi-factor authentication for fragile communications

In large-scale systems, user authentication usually needs the assistance from a remote central authentication server via networks. The authentication service however could be slow or unavailable due to natural disasters or various cyber attacks on communication channels. This has raised serious concerns in systems which need robust authentication in emergency situations. The contribution of this paper is two-fold. In a slow connection situation, we present a secure generic multi-factor authentication protocol to speed up the whole authentication process. Compared with another generic protocol in the literature, the new proposal provides the same function with significant improvements in computation and communication. Another authentication mechanism, which we name stand-alone authentication, can authenticate users when the connection to the central server is down. We investigate several issues in stand-alone authentication and show how to add it on multi-factor authentication protocols in an efficient and generic way.

Effect of mood, social connectivity and age in online depression community via topic and linguistic analysis

Depression afflicts one in four people during their lives. Several studies have shown that for the isolated and mentally ill, the Web and social media provide effective platforms for supports and treatments as well as to acquire scientific, clinical understanding of this mental condition. More and more individuals affected by depression join online communities to seek for information, express themselves, share their concerns and look for supports [12]. For the first time, we collect and study a large online depression community of more than 12,000 active members from Live Journal. We examine the effect of mood, social connectivity and age on the online messages authored by members in an online depression community. The posts are considered in two aspects: what is written (topic) and how it is written (language style). We use statistical and machine learning methods to discriminate the posts made by bloggers in low versus high valence mood, in different age categories and in different degrees of social connectivity. Using statistical tests, language styles are found to be significantly different between low and high valence cohorts, whilst topics are significantly different between people whose different degrees of social connectivity. High performance is achieved for low versus high valence post classification using writing style as features. The finding suggests the potential of using social media in depression screening, especially in online setting.

Modeling and analysis on the propagation dynamics of modern email malware

Due to the critical security threats imposed by email-based malware in recent years, modeling the propagation dynamics of email malware becomes a fundamental technique for predicting its potential damages and developing effective countermeasures. Compared to earlier versions of email malware, modern email malware exhibits two new features, reinfection and self-start. Reinfection refers to the malware behavior that modern email malware sends out malware copies whenever any healthy or infected recipients open the malicious attachment. Self-start refers to the behavior that malware starts to spread whenever compromised computers restart or certain files are visited. In the literature, several models are proposed for email malware propagation, but they did not take into account the above two features and cannot accurately model the propagation dynamics of modern email malware. To address this problem, we derive a novel difference equation based analytical model by introducing a new concept of virtual infected user. The proposed model can precisely present the repetitious spreading process caused by reinfection and self-start and effectively overcome the associated computational challenges. We perform comprehensive empirical and theoretical study to validate the proposed analytical model. The results show our model greatly outperforms previous models in terms of estimation accuracy. © 2013 IEEE.

Ipoll: Automatic polling using online search

For years, opinion polls rely on data collected through telephone or person-to-person surveys. The process is costly, inconvenient, and slow. Recently online search data has emerged as potential proxies for the survey data. However considerable human involvement is still needed for the selection of search indices, a task that requires knowledge of both the target issue and how search terms are used by the online community. The robustness of such manually selected search indices can be questionable. In this paper, we propose an automatic polling system through a novel application of machine learning. In this system, the needs for examining, comparing, and selecting search indices have been eliminated through automatic generation of candidate search indices and intelligent combination of the indices. The results include a publicly accessible web application that provides real-time, robust, and accurate measurements of public opinions on several subjects of general interest.

Simulation-based baggage handling system merge analysis

This paper details the investigation into the design and control of merging bottlenecks of conveyor-based baggage handling systems, encompassing the merging control algorithm and the impact of the merge's physical layout. A methodology for the analysis of simulation model results is presented. Results show that the layout of the merge influences bag throughput and when the physical configuration is in a preferred position, input variance has no effect on bag throughput performance. These results have potential application to other material handling systems, such as those used in manufacturing and warehousing.

Dynamic cloud service selection using an adaptive learning mechanism in multi-cloud computing

Cloud service selection in a multi-cloud computing environment is receiving more and more attentions. There is an abundance of emerging cloud service resources that makes it hard for users to select the better services for their applications in a changing multi-cloud environment, especially for online real time applications. To assist users to efficiently select their preferred cloud services, a cloud service selection model adopting the cloud service brokers is given, and based on this model, a dynamic cloud service selection strategy named DCS is put forward. In the process of selecting services, each cloud service broker manages some clustered cloud services, and performs the DCS strategy whose core is an adaptive learning mechanism that comprises the incentive, forgetting and degenerate functions. The mechanism is devised to dynamically optimize the cloud service selection and to return the best service result to the user. Correspondingly, a set of dynamic cloud service selection algorithms are presented in this paper to implement our mechanism. The results of the simulation experiments show that our strategy has better overall performance and efficiency in acquiring high quality service solutions at a lower computing cost than existing relevant approaches.

A suite of visual languages for model-driven development of statistical surveys and services

Objective: To provide statistician end users with a visual language environment for complex statistical survey design and implementation. Methods: We have developed, in conjunction with professional statisticians, the Statistical Design Language (SDL), an integrated suite of visual languages aimed at supporting the process of designing statistical surveys, and its support environment, SDLTool. SDL comprises five diagrammatic notations: survey diagrams, data diagrams, technique diagrams, task diagrams and process diagrams. SDLTool provides an integrated environment supporting design, coordination, execution, sharing and publication of complex statistical survey techniques as web services. SDLTool allows association of model components with survey artefacts, including data sets, metadata, and statistical package analysis scripts, with the ability to execute elements of the survey design model to implement survey analysis. Results: We describe three evaluations of SDL and SDLTool: use of the notation by expert statistician to design and execute surveys; useability evaluation of the environment; and assessment of several generated statistical analysis web services. Conclusion: We have shown the effectiveness of SDLTool for supporting statistical survey design and implementation. Practice implications: We have developed a more effective approach to supporting statisticians in their survey design work.

Specifying model transformations by direct manipulation using concrete visual notations and interactive recommendations

Model transformations are a crucial part of Model-Driven Engineering (MDE) technologies but are usually hard to specify and maintain for many engineers. Most current approaches use meta-model-driven transformation specification via textual scripting languages. These are often hard to specify, understand and maintain. We present a novel approach that instead allows domain experts to discover and specify transformation correspondences using concrete visualizations of example source and target models. From these example model correspondences, complex model transformation implementations are automatically generated. We also introduce a recommender system that helps domain experts and novice users find possible correspondences between large source and target model visualization elements. Correspondences are then specified by directly interacting with suggested recommendations or drag and drop of visual notational elements of source and target visualizations. We have implemented this approach in our prototype tool-set, CONVErT, and applied it to a variety of model transformation examples. Our evaluation of this approach includes a detailed user study of our tool and a quantitative analysis of the recommender system.

Generating reusable visual notations using model transformation

Visual notations are a key aspect of visual languages. They provide a direct mapping between the intended information and set of graphical symbols. Visual notations are most often implemented using the low level syntax of programming languages which is time consuming, error prone, difficult to maintain and hardly human-centric. In this paper we describe an alternative approach to generating visual notations using by-example model transformations. In our new approach, a semantic mapping between model and view is implemented using model transformations. The notations resulting from this approach can be reused by mapping varieties of input data to their model and can be composed into different visualizations. Our approach is implemented in the CONVErT framework and has been applied to many visualization examples. Three case studies for visualizing statistical charts, visualization of traffic data, and reuse of a Minard's map visualization's components, are presented in this paper. A detailed user study of our approach for reusing notations and generating visualizations has been provided. 80% of the participants in this user study agreed that the novel approach to visualization was easy and 87% stated that they quickly learned to use the tool support.

A visual language and environment for enterprise system modelling and automation

Objective: We want to support enterprise service modelling and generation using a more end user-friendly metaphor than current approaches, which fail to scale to large organisations with key issues of "cobweb" and "labyrinth" problems and large numbers of hidden dependencies. Method: We present and evaluate an integrated visual approach for business process modelling using a novel tree-based overlay structure that effectively mitigate complexity problems. A tree-overlay based visual notation (EML) and its integrated support environment (MaramaEML) supplement and integrate with existing solutions. Complex business architectures are represented as service trees and business processes are modelled as process overlay sequences on the service trees. Results: MaramaEML integrates EML and BPMN to provide complementary, high-level business service modelling and supports automatic BPEL code generation from the graphical representations to realise web services implementing the specified processes. It facilitates generated service validation using an integrated LTSA checker and provides a distortion-based fisheye and zooming function to enhance complex diagram navigation. Evaluations of EML show its effectiveness. Conclusions: We have successfully developed and evaluated a novel tree-based metaphor for business process modelling and enterprise service generation. Practice implications: a more user-friendly modelling approach and support tool for business end users.