ppxscal/embedding_network huggingface dataset:
Finding the Next Computational Model: Experience with the UCSC Kestrel
Authors: Richard Hughey, Andrea Blas
Venue: Journal of Signal Processing Systems (2008)

Architects and industry have been searching for the next durable computational model, the next step beyond the standard CPU. Graphics co-processors, though ubiquitous and powerful, can only be effectively used on a limited range of stream-based applications. The UCSC Kestrel parallel processor is part of a continuum of parallel processing architectures, stretching from the application-specific through the application-specialized to the application-unspecific. Kestrel combines an ALU, multiplier, and local memory, with Systolic Shared Registers for seamless merging of communication and computation, and an innovative condition stack for rapid conditionals. The result has been a readily programmable and efficient co-processor for a wide range of applications, including biological sequence analysis, image processing, and irregular problems. Experience with Kestrel indicates that programmable systolic processing, and its natural combination with the Single Instruction-Multiple Data (SIMD) parallel architecture, is the most powerful, flexible, and power-efficient computational model available for a large group of applications. Unlike other approaches that try to displace or replace the standard serial processor, our model recognizes that the expansion in the application landscape and performance requirements simply imply that the most efficient solution is the combination of more than one type of processor. We propose a model in which the CPU and the GPU are complemented by "the third big chip," a massively-parallel SIMD processor.
Simulation studies on router buffer sizing for short-lived and pacing TCP flows
Authors: Go Hasegawa, Takeshi Tomioka, Kentarou Tada, Masayuki Murata
Venue: Computer Communications (2008)

Traditionally, the size of router buffers is determined by the bandwidth-delay product discipline (normal discipline), which is the product of the link bandwidth and average round-trip time (RTT) of flows passing through the router. However, recent research results have revealed that when the number of flows is sufficiently large, the buffer size can be decreased to the bandwidth-delay product divided by the square-root of the number of flows (sqrtN discipline), without introducing under-utilization of the link bandwidth. This assertion has been verified primarily for long-lived flows. In contrast, there has not been a thorough verification of short-lived flows, which make up the majority of Internet flows. Furthermore, the effects of network parameters, such as the link bandwidth and propagation delay, have not yet been investigated. In the present paper, we compare the performance of the above two disciplines by simulation experiments. We focus on the performance of both long-lived and short-lived TCP connections traversing the router under various network environments. We show that sqrtN discipline would degrade the TCP performance in terms of the packet loss ratio and file transmission delay, and it may be useful only when the size of the file being transferred is approximately 50-100Kbytes or when the propagation delay between the sender and the receiver hosts is significantly small. In addition, we demonstrate that using pacing TCP cannot improve the network performance in many situations and that sqrtN discipline is not suitable for situations in which pacing and non-pacing TCP flows co-exist in the network.
DQML: A Modeling Language for Configuring Distributed Publish/Subscribe Quality of Service Policies
Authors: Joe Hoffert, Douglas Schmidt, Aniruddha Gokhale
Venue: Proceedings of the OTM 2008 Confederated International Conferences, CoopIS, DOA, GADA, IS, and ODBASE 2008. Part I on On the Move to Meaningful Internet Systems: (2008)

Many publish/subscribe (pub/sub) middleware platforms provide flexibility in configuring policies that affect end-to-end quality of service (QoS). While the functionality and tunability of pub/sub middleware has increased, so has the complexity of creating semantically compatible QoS policy configurations. This paper makes two contributions to addressing these challenges. First, it describes how a domain-specific modeling language (DSML) can automate the analysis and synthesis of semantically compatible QoS policy configurations. Second, it empirically evaluates how this DSML increases productivity when generating valid QoS policy configurations. Our experimental results show a 54% reduction in development effort using DQML over manual methods.
Evaluating retina image fusion based on quantitative approaches
Authors: Zhengmao Ye, Hua Cao, Sitharama Iyengar, Habib Mohamadian
Venue: WSEAS Transactions on Computers (2008)

Image registration and fusion are conducted using an automated approach, which applies the automatic adaptation from frame to frame with the threshold parameters. Rather than qualitative approach, quantitative measures have been proposed to evaluate outcomes of retina image fusion. Concepts of the discrete entropy, discrete energy, relative entropy, mutual information, uncertainty coefficient and information redundancy have been introduced. Both the Canny edge detector and control point identification are employed to extract retinal vasculature using the adaptive exploratory algorithms. The shape similarity criteria have been selected for control point matching. The Mutual-Pixel-Count maximization based optimal procedure has also been developed to adjust the control points at the subpixel level. Then the global maxima equivalent result has been derived by calculating Mutual-Pixel-Count local maxima. For two cases of image fusion practices, the testing results are evaluated on a basis of information theories where the satisfactory outcomes have been made.
Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
Authors: Markus W. Covert, Nan Xiao, Tiffany J. Chen, Jonathan R. Karr
Venue: Bioinformatics (2008)

Motivation: The effort to build a whole-cell model requires the development of new modeling approaches, and in particular, the integration of models for different types of processes, each of which may be best described using different representation. Flux-balance analysis (FBA) has been useful for large-scale analysis of metabolic networks, and methods have been developed to incorporate transcriptional regulation (regulatory FBA, or rFBA). Of current interest is the integration of these approaches with detailed models based on ordinary differential equations (ODEs). Results: We developed an approach to modeling the dynamic behavior of metabolic, regulatory and signaling networks by combining FBA with regulatory Boolean logic, and ordinary differential equations. We use this approach (called integrated FBA, or iFBA) to create an integrated model of Escherichia coli which combines a flux-balance-based, central carbon metabolic and transcriptional regulatory model with an ODE-based, detailed model of carbohydrate uptake control. We compare the predicted Escherichia coli wild-type and single gene perturbation phenotypes for diauxic growth on glucose/lactose and glucose/glucose-6-phosphate with that of the individual models. We find that iFBA encapsulates the dynamics of three internal metabolites and three transporters inadequately predicted by rFBA. Furthermore, we find that iFBA predicts different and more accurate phenotypes than the ODE model for 85 of 334 single gene perturbation simulations, as well for the wild-type simulations. We conclude that iFBA is a significant improvement over the individual rFBA and ODE modeling paradigms. Availability: All MATLAB files used in this study are available at http://www.simtk.org/home/ifba/. Contact: covert@stanford.edu Supplementary information:Supplementary data are available at Bioinformatics online.
Dynamic Objective and Advance Scheduling in Federated Grids
Authors: Katia Leal, Eduardo Huedo, Ignacio M. Llorente
Venue: Proceedings of the OTM 2008 Confederated International Conferences, CoopIS, DOA, GADA, IS, and ODBASE 2008. Part I on On the Move to Meaningful Internet Systems: (2008)

In this paper we present a dynamic mapping strategy for scheduling independent tasks in Federated Grids. This strategy is performed in two steps: first we calculate a new objective, and then we apply advance scheduling to meet the new objective. The results obtained by simulation show that the combination of these two steps reduces the makespan and increases the throughput. Thus, the mapping strategy proposed meets two of the most common objective functions of tasks scheduling problems: makespan and performance of the resources. The presented algorithm is easy to implement, unlike Genetic Algorithms is fast enough to be used in a realistic scheduling, and is efficient. In addition, the information the strategy needs can be provided by any Grid Information Service, and its does not require the deployment of complex prediction services or service level agreement: it can work in any Grid.
Using Parallelization to Solve a Macroeconomic Model: A Parallel Parameterized Expectations Algorithm
Authors: Michael Creel
Venue: Computational Economics (2008)

Solving nonlinear macroeconomic models with rational expectations can be time-consuming. This paper shows how the parameterized expectations algorithm (PEA) can be parallelized to reduce the time needed to solve a simple model by more than 80%. The general idea of using parallelization applies naturally to other algorithms, as well. This paper is illustrative of the speedup that can be obtained, and it provides computer code that may serve as an example for parallelization of other algorithms. For those who would like to use the parallelized PEA, the implementation does not confront end users with the details of parallelization. To solve a model, it is only necessary to provide ordinary serial code that simulates data from the model. All needed code is available, on a standalone basis, or pre-installed on ParallelKnoppix (Creel, J Appl Economet 22:215---223, 2007).
Design Patterns Applied in a User Interface Design (UID) Process for Safety Critical Environments (SCEs)
Authors: Thomas Grill, Margit Blauhut
Venue: Proceedings of the 4th Symposium of the Workgroup Human-Computer Interaction and Usability Engineering of the Austrian Computer Society on HCI and Usability for Education and Work (2008)

When designing applications and interfaces within the area of safety critical environments the user plays an important role. During the design phase of such applications and their interfaces, companies argue that they regard the user and comply with their needs when defining user interfaces for safety critical systems. Nevertheless the usual process that is went through in this domain is that users are rarely consulted during the requirements engineering and design process. Usability requirements are often defined by the customer himself without consulting the user and defining the user's and usage requirements. When regarding the whole spectrum of safety critical applications that are used in safety critical environments it is not possible to simply define safety critical parameters and requirements that are taken in general into account when defining such user interfaces. In order to accomplish with this we use the approach of using and reusing patterns that serve as already proven examples for design problems to address the issue of regarding the user within a user interface design process. Having the threat for people's life in focus the appropriate design solutions are evaluated against this problem and requirement. Through building a pattern repository that reflects the design issues for user interfaces within such areas we address the manifold issues of safety critical environments and propose a solution-oriented approach of addressing the user and his requirements within safety critical environments.
An algebraic analysis of conchoids to algebraic curves
Authors: J. R. Sendra, J. Sendra
Venue: Applicable Algebra in Engineering, Communication and Computing (2008)

We study the conchoid to an algebraic affine plane curve $${\mathcal C}$$from the perspective of algebraic geometry, analyzing their main algebraic properties. Beside $${\mathcal C}$$, the notion of conchoid involves a point A in the affine plane (the focus) and a non-zero field element d (the distance). We introduce the formal definition of conchoid by means of incidence diagrams. We prove that the conchoid is a 1-dimensional algebraic set having at most two irreducible components. Moreover, with the exception of circles centered at the focus A and taking d as its radius, all components of the corresponding conchoid have dimension 1. In addition, we introduce the notions of special and simple components of a conchoid. Furthermore we state that, with the exception of lines passing through A, the conchoid always has at least one simple component and that, for almost every distance, all the components of the conchoid are simple. We state that, in the reducible case, simple conchoid components are birationally equivalent to $${\mathcal C}$$, and we show how special components can be used to decide whether a given algebraic curve is the conchoid of another curve.
Tied boltzmann machines for cold start recommendations
Authors: Asela Gunawardana, Christopher Meek
Venue: Proceedings of the 2008 ACM conference on Recommender systems (2008)

We describe a novel statistical model, the tied Boltzmann machine, for combining collaborative and content information for recommendations. In our model, pairwise interactions between items are captured through a Boltzmann machine, whose parameters are constrained according to the content associated with the items. This allows the model to use content information to recommend items that are not seen during training. We describe a tractable algorithm for training the model, and give experimental results evaluating the model in two cold start recommendation tasks on the MovieLens data set.
The business knowledge for customer relationship management: an ontological perspective
Authors: Diego Magro, Anna Goy
Venue: Proceedings of the first international workshop on Ontology-supported business intelligence (2008)

This paper presents some results of an ongoing ontological analysis of the CRM field. In particular, it describes a fragment of O-CREAM, an ontology for CRM based on DOLCE and on other three DOLCE-based modules, i.e. DnS (for the representation of roles and for handling reification), OIO (for modeling information objects, the key concept for representing business knowledge), and OoP (whose notions are used to express the derivation of new business knowledge). Since the business knowledge plays a major role within CRM activities, a significant fragment of O-CREAM is devoted to the formal characterization of notions related to business knowledge; such a fragment is the focus of this paper.
Context-aware clustering of DNS query traffic
Authors: David Plonka, Paul Barford
Venue: Proceedings of the 8th ACM SIGCOMM conference on Internet measurement (2008)

The Domain Name System (DNS) is a one of the most widely used services in the Internet. In this paper, we consider the question of how DNS traffic monitoring can provide an important and useful perspective on network traffic in an enterprise. We approach this problem by considering three classes of DNS traffic: canonical (i.e., RFC-intended behaviors), overloaded (e.g.,black-list services), and unwanted (i.e., queries that will never succeed). We describe a context-aware clustering methodology that is applied to DNS query-responses to generate the desired aggregates. Our method enables the analysis to be scaled to expose the desired level of detail of each traffic type, and to expose their time varying characteristics. We implement our method in a tool we call TreeTop, which can be used to analyze and visualize DNS traffic in real-time. We demonstrate the capabilities of our methodology and the utility of TreeTop using a set of DNS traces that we collected from our campus network over a period of three months. Our evaluation highlights both the coarse and fine level of detail that can be revealed by our method. Finally, we show preliminary results on how DNS analysis can be coupled with general network traffic monitoring to provide a useful perspective for network management and operations.
A User Interface for a Mathematical System that Allows Ambiguous Formulae
Authors: Claudio Sacerdoti Coen
Venue: Electronic Notes in Theoretical Computer Science (ENTCS) (2009)

Mathematical systems that understand the usual ambiguous mathematical notation need well thought out user interfaces 1) to provide feedback on the way formulae are automatically interpreted, when a single best interpretation exists; 2) to dialogue with the user when human intervention is required because multiple best interpretations exist; 3) to present sets of errors to the user when no correct interpretation exists. In this paper we discuss how we handle ambiguity in the user interfaces of the Matita interactive theorem prover and the Whelp search engine.
Temporal Changes in Connection Patterns of an Email-Based Social Network
Authors: Krzysztof Juszczyszyn, Przemyslaw Kazienko, Katarzyna Musial, Bogdan Gabrys
Venue: Proceedings of the 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology - Volume 03 (2008)

Network motifs are small subgraphs that reflect local network topology and were shown to be useful for creating profiles that reveal several properties of the network. Analysis of three-node motifs (triads) was used in this paper to track the temporal changes in the structure of large social network derived from email communication between the employees of Wroclaw University of Technology.
How Can Agents Know What to Assume When?
Authors: Georgios K. Giannikis, Aspassia Daskalopulu
Venue: Proceedings of the 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology - Volume 02 (2008)

The work in this paper is motivated from the need for assumption-based reasoning in normative systems, where, realistically, agents will have incomplete knowledge about their environment, and about other agents. The question we seek to address is whether it is possible for agents to identify appropriate assumptions dynamically, in order to fill in informational gaps. We discuss and illustrate our proposal with reference to an e-commerce example. In our previous work, we argued that e-contracts could be represented as Default Theories and proposed a theoretical way in which such theories could be constructed automatically from initial Event Calculus representations. That proposal relied on determining what information could be proved from the agent’s knowledge base, in order to decide whether it would serve as an assumption or not. In this paper we present an incremental technique that can be used for this construction that enables the dynamic and ad hoc identification of candidate assumptions, without resorting to proof.
How good is opportunistic routing?: a reality check under Rayleigh fading channels
Authors: Rong Zheng, Chengzhi Li
Venue: Proceedings of the 11th international symposium on Modeling, analysis and simulation of wireless and mobile systems (2008)

Considerations of realistic channel dynamics motivate the design of a new breed of opportunistic schemes, such as opportunistic transmission, scheduling and routing. Compared to their deterministic counter part, opportunistic schemes have been shown to increase network throughput, and/or reduce delay in limited experimental/simulation scenarios. In this paper, we propose analytical models that characterize the performance of routing protocols in lossy wireless networks with Rayleigh fading channels. We investigate the efficiency of a few representative deterministic and opportunistic routing protocols under both light-loaded and saturated traffic conditions. This work deviates from existing work that assumes idealistic packet reception, and is thus of practical relevance. Our study shows that opportunistic routing significantly outperforms its deterministic counterpart in average effective progresses made in single-hop transmissions. In deterministic routing schemes, tuning of parameters based on node density is critical to achieve optimal performance.
IS 2008 PC Co-chairs' Message
Authors: Jong Hyuk Park, Bart Preneel, Ravi Sandhu, André Zúquete
Venue: Proceedings of the OTM 2008 Confederated International Conferences, CoopIS, DOA, GADA, IS, and ODBASE 2008. Part II on On the Move to Meaningful Internet Systems (2008)

On behalf of the Program Committee of the Third International Symposium on Information Security (IS 2008), it was our great pleasure to welcome the participants to the IS 2008 conference, held in conjunction with OnTheMove Federated Conferences (OTM 2008), November 9---14, 2008, in Monterrey, Mexico. Information security is a challenging and rapidly evolving research area with an increasing impact on the overall ICT sector. The objective of the symposium was to stimulate research on information security and to encourage interaction between researchers from all over the world. In response to the call for papers, 33 submissions were received, from which 14 were carefully selected for presentation in five technical sessions. Each paper was peer reviewed by at least three members of the Program Committee or external reviewers. The symposium program covered a broad range of research topics: intrusion detection, information hiding, data and risk management, access control, and finally evaluation and implementation. We thank all the authors who submitted valuable papers to the symposium. We would like to express our gratitude to the members of the Program Committee and to the external reviewers for their constructive and insightful comments. We are also indebted to the many individuals and organizations that have contributed to this event, and we would like to thank in particular Springer. Last but not least, we are grateful to the OTM organizing committee and chairs for their help in all aspects of the organization of this symposium. We hope that you enjoyed the Third International Symposium on Information Security at Monterrey, Mexico, and that you found it a stimulating forum for the exchange of ideas, results and recent findings.
Invited review: A comparative analysis of several asymmetric traveling salesman problem formulations
Authors: Temel Öncan, İ. Kuban Altınel, Gilbert Laporte
Venue: Computers and Operations Research (2009)

In this survey, a classification of 24 asymmetric traveling salesman problem (ATSP) formulations is presented. The strength of their LP relaxations is discussed and known relationships from the literature are reviewed. Some new relationships are also introduced, and computational results are reported.