Broadcasting Automata and Patterns on Z^2

The Broadcasting Automata model draws inspiration from a variety of sources such as Ad-Hoc radio networks, cellular automata, neighbourhood se- quences and nature, employing many of the same pattern forming methods that can be seen in the superposition of waves and resonance. Algorithms for broad- casting automata model are in the same vain as those encountered in distributed algorithms using a simple notion of waves, messages passed from automata to au- tomata throughout the topology, to construct computations. The waves generated by activating processes in a digital environment can be used for designing a vari- ety of wave algorithms. In this chapter we aim to study the geometrical shapes of informational waves on integer grid generated in broadcasting automata model as well as their potential use for metric approximation in a discrete space. An explo- ration of the ability to vary the broadcasting radius of each node leads to results of categorisations of digital discs, their form, composition, encodings and gener- ation. Results pertaining to the nodal patterns generated by arbitrary transmission radii on the plane are explored with a connection to broadcasting sequences and ap- proximation of discrete metrics of which results are given for the approximation of astroids, a previously unachievable concave metric, through a novel application of the aggregation of waves via a number of explored functions

An Emergent Architecture for Scaling Decentralized Communication Systems (DCS)

With recent technological advancements now accelerating the mobile and wireless Internet solution space, a ubiquitous computing Internet is well within the research and industrial community's design reach - a decentralized system design, which is not solely driven by static physical models and sound engineering principals, but more dynamically, perhaps sub-optimally at initial deployment and socially-influenced in its evolution. To complement today's Internet system, this thesis proposes a Decentralized Communication System (DCS) architecture with the following characteristics: flat physical topologies with numerous compute oriented and communication intensive nodes in the network with many of these nodes operating in multiple functional roles; self-organizing virtual structures formed through alternative mobility scenarios and capable of serving ad hoc networking formations; emergent operations and control with limited dependency on centralized control and management administration. Today, decentralized systems are not commercially scalable or viable for broad adoption in the same way we have to come to rely on the Internet or telephony systems. The premise in this thesis is that DCS can reach high levels of resilience, usefulness, scale that the industry has come to experience with traditional centralized systems by exploiting the following properties: (i.) network density and topological diversity; (ii.) self-organization and emergent attributes; (iii.) cooperative and dynamic infrastructure; and (iv.) node role diversity. This thesis delivers key contributions towards advancing the current state of the art in decentralized systems. First, we present the vision and a conceptual framework for DCS. Second, the thesis demonstrates that such a framework and concept architecture is feasible by prototyping a DCS platform that exhibits the above properties or minimally, demonstrates that these properties are feasible through prototyped network services. Third, this work expands on an alternative approach to network clustering using hierarchical virtual clusters (HVC) to facilitate self-organizing network structures. With increasing network complexity, decentralized systems can generally lead to unreliable and irregular service quality, especially given unpredictable node mobility and traffic dynamics. The HVC framework is an architectural strategy to address organizational disorder associated with traditional decentralized systems. The proposed HVC architecture along with the associated promotional methodology organizes distributed control and management services by leveraging alternative organizational models (e.g., peer-to-peer (P2P), centralized or tiered) in hierarchical and virtual fashion. Through simulation and analytical modeling, we demonstrate HVC efficiencies in DCS structural scalability and resilience by comparing static and dynamic HVC node configurations against traditional physical configurations based on P2P, centralized or tiered structures. Next, an emergent management architecture for DCS exploiting HVC for self-organization, introduces emergence as an operational approach to scaling DCS services for state management and policy control. In this thesis, emergence scales in hierarchical fashion using virtual clustering to create multiple tiers of local and global separation for aggregation, distribution and network control. Emergence is an architectural objective, which HVC introduces into the proposed self-management design for scaling and stability purposes. Since HVC expands the clustering model hierarchically and virtually, a clusterhead (CH) node, positioned as a proxy for a specific cluster or grouped DCS nodes, can also operate in a micro-capacity as a peer member of an organized cluster in a higher tier. As the HVC promotional process continues through the hierarchy, each tier of the hierarchy exhibits emergent behavior. With HVC as the self-organizing structural framework, a multi-tiered, emergent architecture enables the decentralized management strategy to improve scaling objectives that traditionally challenge decentralized systems. The HVC organizational concept and the emergence properties align with and the view of the human brain's neocortex layering structure of sensory storage, prediction and intelligence. It is the position in this thesis, that for DCS to scale and maintain broad stability, network control and management must strive towards an emergent or natural approach. While today's models for network control and management have proven to lack scalability and responsiveness based on pure centralized models, it is unlikely that singular organizational models can withstand the operational complexities associated with DCS. In this work, we integrate emergence and learning-based methods in a cooperative computing manner towards realizing DCS self-management. However, unlike many existing work in these areas which break down with increased network complexity and dynamics, the proposed HVC framework is utilized to offset these issues through effective separation, aggregation and asynchronous processing of both distributed state and policy. Using modeling techniques, we demonstrate that such architecture is feasible and can improve the operational robustness of DCS. The modeling emphasis focuses on demonstrating the operational advantages of an HVC-based organizational strategy for emergent management services (i.e., reachability, availability or performance). By integrating the two approaches, the DCS architecture forms a scalable system to address the challenges associated with traditional decentralized systems. The hypothesis is that the emergent management system architecture will improve the operational scaling properties of DCS-based applications and services. Additionally, we demonstrate structural flexibility of HVC as an underlying service infrastructure to build and deploy DCS applications and layered services. The modeling results demonstrate that an HVC-based emergent management and control system operationally outperforms traditional structural organizational models. In summary, this thesis brings together the above contributions towards delivering a scalable, decentralized system for Internet mobile computing and communications

Multiple Biolgical Sequence Alignment: Scoring Functions, Algorithms, and Evaluations

Aligning multiple biological sequences such as protein sequences or DNA/RNA sequences is a fundamental task in bioinformatics and sequence analysis. These alignments may contain invaluable information that scientists need to predict the sequences\u27 structures, determine the evolutionary relationships between them, or discover drug-like compounds that can bind to the sequences. Unfortunately, multiple sequence alignment (MSA) is NP-Complete. In addition, the lack of a reliable scoring method makes it very hard to align the sequences reliably and to evaluate the alignment outcomes. In this dissertation, we have designed a new scoring method for use in multiple sequence alignment. Our scoring method encapsulates stereo-chemical properties of sequence residues and their substitution probabilities into a tree-structure scoring scheme. This new technique provides a reliable scoring scheme with low computational complexity. In addition to the new scoring scheme, we have designed an overlapping sequence clustering algorithm to use in our new three multiple sequence alignment algorithms. One of our alignment algorithms uses a dynamic weighted guidance tree to perform multiple sequence alignment in progressive fashion. The use of dynamic weighted tree allows errors in the early alignment stages to be corrected in the subsequence stages. Other two algorithms utilize sequence knowledge-bases and sequence consistency to produce biological meaningful sequence alignments. To improve the speed of the multiple sequence alignment, we have developed a parallel algorithm that can be deployed on reconfigurable computer models. Analytically, our parallel algorithm is the fastest progressive multiple sequence alignment algorithm

Language: A Bridge or Barrier to Social Groups

Language acts as either a bridge or a barrier to social groups dependent upon the individual’s effective use of a social group’s language. The individual uses the language of the group in order to join the group and to be understood by the group. This suggests that language is behavioral in part and can be treated as a form of social norms which delegate who is a part of the group and who is not. By utilizing the language of the group effectively, an individual is able to join the group. This group language may be temporary, and the dynamics of the group’s language can be held only within specific situations, such as with inside jokes, or can be more lasting, such as the language of a discourse. Examples of group language include the use of academic jargon in the academy, key terms specific to an academic field, and the standardization of the English language. To formulate an interdisciplinary study of social epistemic rhetoric, this thesis looks at the crossovers between two fields of study through a comparative analysis of social epistemic rhetorical theory and psychological research concerning language production and perception, the effect language has on understanding, and social mirroring processes that may be generalized to language production. This rhetorical theory now grounded in psychological science calls for experimental testing to find the limitations of group dynamics involving language

CHORUS Deliverable 2.2: Second report - identification of multi-disciplinary key issues for gap analysis toward EU multimedia search engines roadmap

After addressing the state-of-the-art during the first year of Chorus and establishing the existing landscape in multimedia search engines, we have identified and analyzed gaps within European research effort during our second year. In this period we focused on three directions, notably technological issues, user-centred issues and use-cases and socio- economic and legal aspects. These were assessed by two central studies: firstly, a concerted vision of functional breakdown of generic multimedia search engine, and secondly, a representative use-cases descriptions with the related discussion on requirement for technological challenges. Both studies have been carried out in cooperation and consultation with the community at large through EC concertation meetings (multimedia search engines cluster), several meetings with our Think-Tank, presentations in international conferences, and surveys addressed to EU projects coordinators as well as National initiatives coordinators. Based on the obtained feedback we identified two types of gaps, namely core technological gaps that involve research challenges, and “enablers”, which are not necessarily technical research challenges, but have impact on innovation progress. New socio-economic trends are presented as well as emerging legal challenges

Automated Injection of Curated Knowledge Into Real-Time Clinical Systems: CDS Architecture for the 21st Century

abstract: Clinical Decision Support (CDS) is primarily associated with alerts, reminders, order entry, rule-based invocation, diagnostic aids, and on-demand information retrieval. While valuable, these foci have been in production use for decades, and do not provide a broader, interoperable means of plugging structured clinical knowledge into live electronic health record (EHR) ecosystems for purposes of orchestrating the user experiences of patients and clinicians. To date, the gap between knowledge representation and user-facing EHR integration has been considered an “implementation concern” requiring unscalable manual human efforts and governance coordination. Drafting a questionnaire engineered to meet the specifications of the HL7 CDS Knowledge Artifact specification, for example, carries no reasonable expectation that it may be imported and deployed into a live system without significant burdens. Dramatic reduction of the time and effort gap in the research and application cycle could be revolutionary. Doing so, however, requires both a floor-to-ceiling precoordination of functional boundaries in the knowledge management lifecycle, as well as formalization of the human processes by which this occurs. This research introduces ARTAKA: Architecture for Real-Time Application of Knowledge Artifacts, as a concrete floor-to-ceiling technological blueprint for both provider heath IT (HIT) and vendor organizations to incrementally introduce value into existing systems dynamically. This is made possible by service-ization of curated knowledge artifacts, then injected into a highly scalable backend infrastructure by automated orchestration through public marketplaces. Supplementary examples of client app integration are also provided. Compilation of knowledge into platform-specific form has been left flexible, in so far as implementations comply with ARTAKA’s Context Event Service (CES) communication and Health Services Platform (HSP) Marketplace service packaging standards. Towards the goal of interoperable human processes, ARTAKA’s treatment of knowledge artifacts as a specialized form of software allows knowledge engineers to operate as a type of software engineering practice. Thus, nearly a century of software development processes, tools, policies, and lessons offer immediate benefit: in some cases, with remarkable parity. Analyses of experimentation is provided with guidelines in how choice aspects of software development life cycles (SDLCs) apply to knowledge artifact development in an ARTAKA environment. Portions of this culminating document have been further initiated with Standards Developing Organizations (SDOs) intended to ultimately produce normative standards, as have active relationships with other bodies.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

A decentralized framework for cross administrative domain data sharing

Federation of messaging and storage platforms located in remote datacenters is an essential functionality to share data among geographically distributed platforms. When systems are administered by the same owner data replication reduces data access latency bringing data closer to applications and enables fault tolerance to face disaster recovery of an entire location. When storage platforms are administered by different owners data replication across different administrative domains is essential for enterprise application data integration. Contents and services managed by different software platforms need to be integrated to provide richer contents and services. Clients may need to share subsets of data in order to enable collaborative analysis and service integration. Platforms usually include proprietary federation functionalities and specific APIs to let external software and platforms access their internal data. These different techniques may not be applicable to all environments and networks due to security and technological restrictions. Moreover the federation of dispersed nodes under a decentralized administration scheme is still a research issue. This thesis is a contribution along this research direction as it introduces and describes a framework, called \u201cWideGroups\u201d, directed towards the creation and the management of an automatic federation and integration of widely dispersed platform nodes. It is based on groups to exchange messages among distributed applications located in different remote datacenters. Groups are created and managed using client side programmatic configuration without touching servers. WideGroups enables the extension of the software platform services to nodes belonging to different administrative domains in a wide area network environment. It lets different nodes form ad-hoc overlay networks on-the-fly depending on message destinations located in distinct administrative domains. It supports multiple dynamic overlay networks based on message groups, dynamic discovery of nodes and automatic setup of overlay networks among nodes with no server-side configuration. I designed and implemented platform connectors to integrate the framework as the federation module of Message Oriented Middleware and Key Value Store platforms, which are among the most widespread paradigms supporting data sharing in distributed systems