ppxscal/embedding_network huggingface dataset:
An FPGA-Based, Multi-model Simulation Method for Biochemical Systems
Authors: Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Yow Iwaoka, Yuichiro Shibata, Hiroaki Kitano, Akira Funahashi, Noriko Hiroi, Hideharu Amano
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 3 - Volume 04 (2005)

Modeling and simulation of a cellular system on computers are now becoming an essential process in biological researches. However, modern PCs can't provide enough performance to simulate large-scale biochemical networks. ReCSiP is the alternative FPGA-based solution for biochemical simulations. In this paper, the novel method of biochemical simulation with multiple reaction models on an FPGA is proposed. The method generates optimal circuit and its optimal schedule for each simulation models written in SBML, the standard markup language in systems biology. ReCSiP has a Xilinx's XC2VP70 and achieved over 20-fold speedup compared to Intelýs PentiumIII 1.13GHz.
Flexible access for a space communications network with IP functionality
Authors: Michael Hadjitheodosiou, Hui Zeng, Alex Nguyen, Brenda L. Ellis
Venue: Computer Networks and ISDN Systems (2005)

The vision for the future space network involves a scenario where all scientific spacecraft form a distributed network to provide real-time information transfer to users on the ground. This scenario will require sensors and instruments on spacecraft to become addressable nodes in a communication network. To enable this vision, there is critical need for advanced communications and dynamic network connectivity to provide broad coverage and intelligent-based real-time data delivery to scientists. These new missions will introduce a number of complex routing, network control, scheduling, data management and communication problems that need to be studied in detail. We describe the potential advantages of a dynamic mission's operations concept and the need to develop a dynamic bandwidth allocation enabling more efficient use of the space resources. In this scenario, a number of spacecraft, each with several instruments on-board, are sending data to ground stations through the NASA relay system. Our objective is to provide an optimal or near-optimal t utilization and fair allocation of bandwidth of the downlink channel while guaranteeing specific QoS requirements for different service classes. We try to understand the traffic profiles that need to be supported and propose a suitable hybrid Time Division Multiple Access (TDMA)-based protocol. We formulate and study an assignment problem for optimal timeslot scheduling. By using simulation, the protocol performance is analyzed and compared with that of the existing static fixed-assignment scheme. We also address the benefits of increasing spacecraft availability using a Direct-to-Ground communications option that can be enabled in an IP-based network. By addressing these issues we try to contribute in the development of the next generation space network infrastructure that will serve as an enabler for better space exploration.
Estimating the maximum
Authors: Ben Gum, Richard J. Lipton, Andrea LaPaugh, Faith Fich
Venue: Journal of Algorithms (2005)

Estimating the maximum of a sampled dataset is an important and daunting task. We give a sampling algorithm for general datasets which gives estimates strictly better than the largest sample for an infinite family of datasets. Our algorithm overshoots the true maximum of the worst case dataset with probability at most (1/e) + O( 1/k), where k is the size of our sample, which is much smaller than the size of the dataset. Our proof is the result of a new extremal graph coloring theorem: given any red/green coloring of the edges of a complete graph of n vertices, the probability that the edges among k randomly sampled vertices have a certain property is at most (1/e) + O(1/k). In addition, we show that if an algorithm gives an estimate strictly better than the largest sample for some dataset, then the algorithm overshoots the maximum on some other dataset with probability at least (1/e) - O(1/k).
A computer checked algebraic verification of a distributed summation algorithm
Authors: Jan Friso Groote, Fran&#x00e7;ois Monin, Jan Springintveld
Venue: Formal Aspects of Computing (2005)

We present an algebraic verification of Segall&#x2019;s propagation of information with feedback algorithm and we report on the verification of the proof using the PVS system. This algorithm serves as a nice benchmark for verification exercises (see [2, 8, 17]). The verification is based on the methodology presented in [7] and demonstrates its suitability to deliver mechanically verifiable correctness proofs of highly nondeterministic distributed algorithms.
Comparing inverted files and signature files for searching a large lexicon
Authors: Ben Carterette, Fazli Can
Venue: Information Processing and Management: an International Journal (2005)

Signature files and inverted files are well-known index structures. In this paper we undertake a direct comparision of the two for searching for partially-specified queries in a large lexicon stored in main memory. Using n-grams to index lexicon terms, a bit-sliced signature file can be compressed to a smaller size than an inverted file if each n-gram sets only one bit in the term signature. With a signature width less than half the number of unique n-grams in the lexicon, the signature file method is about as fast as the inverted file method, and significantly smaller. Greater flexibility in memory usage and faster index generation time make signature files appropriate for searching large lexicons or other collections in an environment where memory is at a premium.
On the Finite Element Solution of the Pure Neumann Problem
Authors: Pavel Bochev, R. B. Lehoucq
Venue: SIAM Review (2005)

This paper considers the finite element approximation and algebraic solution of the pure Neumann problem. Our goal is to present a concise variational framework for the finite element solution of the Neumann problem that focuses on the interplay between the algebraic and variational problems. While many of the results that stem from our analysis are known by some experts, they are seldom derived in a rigorous fashion and remain part of numerical folklore. As a result, this knowledge is not accessible (or appreciated) by many practitioners---both novices and experts---in one source. Our paper contributes a simple, yet insightful link between the continuous and algebraic variational forms that will prove useful.
A transformation strategy for multi-device menus and toolbars
Authors: Kai Richter
Venue: CHI '05 extended abstracts on Human factors in computing systems (2005)

The increasing variety of different devices with different screen size, interaction paradigms and application areas raises the need for new technologies of cross-device development. Automatic transformation of user interfaces between devices of different screen size and interaction devices can increase the speed of multi-device software development and decrease the costs for testing and maintenance while providing inter- and intra-device consistency. Therefore transformation strategies have to be developed and evaluated. In this article we introduce a classification scheme for such transformation strategies. An example transformation strategy for menus and toolbars supporting the migration between desktop PCs an palm-sized devices has been developed and evaluated.
Quintic Spline Based Computational Scheme for Singularly Perturbed Convection-Diffusion Problems
Authors: Rajesh K. Bawa, S. Natesan
Venue: Proceedings of the 19th International Symposium on High Performance Computing Systems and Applications (2005)

In this article, we propose a fourth-order difference scheme using quintic spline for singularly perturbed convection ¿ diffusion Dirichlet boundary ¿ value problems. Theoretical error estimates are derived for the method. Computational efficiency and accuracy are verified through numerical examples.
An Efficient Algorithm for Computing the Fitness Function of a Hydrophobic-Hydrophilic Model
Authors: Tamjidul Hoque, Madhu Chetty, Laurence S. Dooley
Venue: Proceedings of the Fourth International Conference on Hybrid Intelligent Systems (2004)

The protein folding problem is a minimization problem in which the energy function is often regarded as the fitness function. There are several models for protein folding prediction including the Hydrophobic-Hydrophilic (HP) model. Though thismodel is an elementary one, it is widely used as a test-bed for faster execution of new algorithms. Fitness computation is one of the major computational parts of the HP model. This paper proposes an efficient search (ES) approach for computing the fitness value requiring only O(n) complexity in contrast to the full search (FS) approach that requires O(n^2 ) complexity. The efficiency of the proposed ES approach results due to its utilization of some inherent properties of the HP model. The ES approach represents residues in a cartesian coordinate framework and then uses relative distance and coordinate polarity to reduce complexity.
VISUAL INTERACTION DESIGN SPECIAL INTEREST AREA: INTERDISCIPLINARY DESIGN
Authors: Maria G. Wadlow
Venue: ACM SIGCHI Bulletin (1993)

Most of us have worked in design teams at one time or another. As visual interaction designers, we're accustomed to being the one graphic designer, or the one typographer, or the one human factors specialist in a team that is otherwise constructed entirely of computer scientists, or of engineers, or of psychologists. It's easy to think of ourselves as outsiders, foreigners who don't quite speak the language and aren't familiar with the customs of the rest of the team.
Book review: Inside Autosketch (Ver. 3.0), 2nd Ed. by Frank Lenk (New Riders Publishing, 1990)
Venue: ACM SIGSMALL/PC Notes (1992)

"Inside Autosketch" is a supplementary how-to manual for the beginning user of the excellent program Autosketch by Autodesk, Inc.. The book would be as well suited for the experienced Autosketch user, as I have been for several years, and is a very good main manual covering all features of the software. It does so in a more complete and readable manner than the documentation supplied with the program. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Multiple embedding using robust watermarks for wireless medical images
Authors: Dominic Osborne, Derek Abbott, Matthew Sorell, Derek Rogers
Venue: Proceedings of the 3rd international conference on Mobile and ubiquitous multimedia (2004)

Within the expanding paradigm of medical imaging and wireless communications there is increasing demand for transmitting diagnostic medical imagery over error-prone wireless communication channels such as those encountered in cellular phone technology. Medical images must be compressed with minimal file size to minimize transmission time and robustly coded to withstand these wireless environments. It has been reinforced through extensive research that the most crucial regions of medical images must not be degraded and compressed by a lossless or near lossless algorithm. This type of area is called the Region of Interest (ROI). Conversely, the Region of Backgrounds (ROB) may be compressed with some loss of information to achieve a higher compression level. This type of hybrid coding scheme is most useful for wireless communication where the 'bit-budget' is devoted to the ROI. This paper also develops a way for this system to operate externally to the Joint Picture Experts Group (JPEG) still image compression standard without the use of hybrid coding. A multiple watermarking technique is developed to verify the integrity of the ROI after transmission and in the situation where there may be incidental degradation that is hard to perceive or unexpected levels of compression that may degrade ROI content beyond an acceptable level. The most useful contribution in this work is assurance of ROI image content integrity after image files are subject to incidental degradation in these environments. This is made possible with extraction of DCT signature coefficients from the ROI and embedding multiply in the ROB. Strong focus is placed on the robustness to JPEG compression and the mobile channel as well as minimizing the image file size while maintaining its integrity with the use of semi-fragile, robust watermarking.
Weak feature size and persistent homology: computing homology of solids in Rn from noisy data samples
Authors: Frédéric Chazal, André Lieutier
Venue: Proceedings of the twenty-first annual symposium on Computational geometry (2005)

In this work, one proves that under quite general assumptions one can deduce the topology of a bounded open set in Rn from a Hausdorff distance approximation of it. For this, one introduces the weak feature size (wfs) that generalizes the notion of local feature size. Our results apply to open sets with positive wfs, which include many sets whose boundaries are not smooth and even nowhere smooth. This class includes also the piecewise analytic open sets which cover many cases encountered in practical applications. The proofs are based on the study of distance functions to closed sets and their critical points. As an application, one gives an algorithmic way, thanks to persistent homology techniques, to compute the homology groups of open sets from noisy samples of points on their boundary.
Teaching software engineering using a traceability-based development methodology
Authors: Sandeep Mitra, T. M. Rao, Thomas A. Bullinger
Venue: Journal of Computing Sciences in Colleges (2005)

Instructors of Software Engineering (SE) classes in small Computer Science programs face the challenge of selecting a coherent set of SE concepts that can be taught in a one-semester course. This challenge is more significant when the students' background lacks significant exposure to Object-Oriented (OO) design. A second challenge is the design of "right-sized" case studies that rigorously illustrate the application of the selected SE concepts, can be comprehensively presented in the classroom and assigned as term projects. In this paper, we address the first challenge by proposing the use of a traceability-based methodology for SE instruction. We address the second challenge by advocating the use of a particular type of problem -- namely, "GUI-based workflow applications". We present an ATM case study in class and focus on how the issues inherent in this problem can be tackled by choosing appropriate OOSE concepts. We have found that this approach allows us to teach concepts such as design patterns and coding idioms as they naturally arise in the problem. Our experience with a small group of students indicates that, with this approach, they were able to better understand the SE process itself and come up with high-quality software designs in a similar term project.
Generating Configuration Files: The Director's Cut
Authors: Jon Finke
Venue: Proceedings of the 17th USENIX conference on System administration (2003)

The generation of system configuration files and other documents directly from a database has proven to be a very powerful technique. However, there were some limitations to this approach. With the introduction of Oracle 8i, and more specifically, the addition of support for XML, we have been able to eliminate many of these limitations and take the file generation and maintenance to a new level.
UMM: an operational memory model specification framework with integrated model checking capability: Research Articles
Authors: Yue Yang, Ganesh Gopalakrishnan, Gary Lindstrom
Venue: Concurrency and Computation: Practice Experience (2005)

Given the complicated nature of modern shared memory systems, it is vital to have a systematic approach to specifying and analyzing memory consistency requirements. In this paper, we present the UMM specification framework, which integrates two key features to support memory model verification: (i) it employs a simple and generic memory abstraction that can capture a large collection of memory models as guarded commands with a uniform notation, and (ii) it provides built-in model checking capability to enable formal reasoning about thread behaviors. Using this framework, memory models can be specified in a parameterized style&mdash;designers can simply redefine a few bypassing rules and visibility ordering rules to obtain an executable specification of another memory model. We formalize several classical memory models, including Sequential Consistency, Coherence, and PRAM, to illustrate the general techniques of applying this framework. We then provide an alternative specification of the Java memory model, based on a proposal from Manson and Pugh, and demonstrate how to analyze Java thread semantics using model checking. We also compare our operational specification style with axiomatic specification styles and explore a mechanism that converts a memory model definition from one style to the other. Copyright &copy; 2005 John Wiley & Sons, Ltd.
Analog LSI neuron model inspired by biological excitable membrane
Authors: Shin'Ichiro Kanoh, Makoto Imai, Nozomu Hoshimiya
Venue: Systems and Computers in Japan (2005)

An analog hardware neuron model having biological neuron characteristics is proposed and its basic characteristics are reported. The proposed circuit model is constructed from a membrane capacitance part, negative resistance circuit part, and reactance circuit part, and realizes the membrane excitability observed in biological neurons by voltage-controlled negative resistance characteristics. This model exhibits an action potential generation mechanism similar to that of biological neurons. HSPICE simulation reveals that this model can reproduce both the well-known responses to excitatory inputs and the postinhibitory rebound (PIR) firing which is a neuronal activity occurring by the release from an inhibitory input discharge, and that the characteristics of the input pulse amplitude-latency and entrained response to the periodic input are similar to those of biological neurons. In addition, this model is developed by considering compatibility with integrated circuit processes, and design results of LSI implementation of the model are also presented in this article. PIR firing cannot be reproduced by the simple neuronal model used in conventional neurochips, but it plays an important role in information processing in the brain. The functionality of neurochips is expected to be improved by simulating biological neurons by such a biologically inspired hardware neuron model. &copy; 2005 Wiley Periodicals, Inc. Syst Comp Jpn, 36(6): 84&ndash;91, 2005; Published online in Wiley InterScience (). DOI 10.1002&sol;scj.10676
Reducing Pattern Delay Variations for Screening Frequency Dependent Defects
Authors: Benjamin N. Lee, Li-C. Wang, Magdy S. Abadir
Venue: Proceedings of the 23rd IEEE VLSI Test Symposium (2005)

The delay variations of a pattern set can come from two sources: (1) Different patterns sensitize different parts of the circuit and result in different delays. (2) The same pattern, applied on different chips, results in different delays because of process variations. For structural delay testing, these pattern variations may result in difficulty for finding an optimal test clock setting, which may significantly impact the defect screening effectiveness. This paper investigates the possibility of applying statistical timing analysis techniques to reduce pattern variations for structural delay testing. We develop an efficient statistical pattern-based timing simulator and devise pattern selection algorithms for reducing such variations. By constructing pattern sets with smaller variations, we show that higher screening effectiveness can be achieved. We present experimental results to demonstrate the advantages of our techniques based on benchmark circuits.
Adaptive page ranking with neural networks
Authors: Franco Scarselli, Sweah Liang Yong, Markus Hagenbuchner, Ah Chung Tsoi
Venue: Special interest tracks and posters of the 14th international conference on World Wide Web (2005)

Recent developments in the area of neural networks provided new models which are capable of processing general types of graph structures. Neural networks are well-known for their generalization capabilities. This paper explores the idea of applying a novel neural network model to a web graph to compute an adaptive ranking of pages. Some early experimental results indicate that the new neural network models generalize exceptionally well when trained on a relatively small number of pages.
Analysis of [H-1,L2,L2] first-order system least squares for the incompressible Oseen type equations
Authors: Sang Dong Kim, Yong Hun Lee, Suh-Yuh Yang
Venue: Applied Numerical Mathematics (2005)

This paper is devoted to the error analysis of least-squares finite element approximations to the stationary incompressible Oseen type equations with the homogeneous velocity boundary condition. With the vorticity as a new dependent variable, we consider two first-order system problems for the Oseen type equations in the velocity-vorticity-pressure and the velocity-vorticity-Bernoulli pressure formulations. The least-squares functional is defined in terms of the sum of the squared H-1 and L2 norms of the residual equations over a suitable product function space. The well-posedness of the proposed least-squares variational problem is shown. We then analyze the case where the H-1 norm in the least-squares functional is replaced by a discrete functional to make the computation feasible. Optimal error estimates for all unknowns are derived.
Memetic approach to the dissemination of e-learning objects
Authors: Yuzuru Tanaka
Venue: Proceedings of the 4th international symposium on Information and communication technologies (2005)

Recently e-learning systems have become interested in using Web technologies for the following reasons; (1) easy and standard authoring of learning contents in HTML, (2) publication and sharing of learning contents and their components, (3) ease of forming user- and/or author- communities, (4) easy delivery of learning contents, and (5) easy development of distributed e-learning environments.The Web publication however has no support for us to extract any portion of published intellectual resources such as learning contents, to combine them together for their local reuse, nor to publish the newly defined composite object as a new Web content. The composition here means not only layout combination but also functional federation of embedded tools and services. We need some support to reedit and to redistribute Web contents for their further reuse. Meme media technologies proposed by our group solve this problem. Meme media technologies provide Web-based e-learning systems with the following additional features; (1) easy reuse of existing Web contents, tools and services for e-learning systems, (2) easy customization and combination of Web-published e-learning systems and components, and (3) acceleration of the memetic cultural evolution of e-learning contents.