ppxscal/embedding_network huggingface dataset:
Parallel Extreme Pathway Computation for Metabolic Networks
Authors: Lie-Quan Lee, Jeff Varner, Kwok Ko
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

We parallelized the serial extreme pathways algorithm presented by Schilling et al., in J. Theor. Biol. 203 (2000) using the Message Passing Interface (MPI). The parallel algorithm exhibits super-linear scalability because the number of independence tests performed decreases as the number of MPI nodes increases. A subsystem of the metabolic network of Escherichia coli with 140 reactions and 96 metabolites (without preprocessing) is used as a benchmark. The extreme pathways of this system are computed in under 280 seconds using 70 2.4 GHz Intel Pentium-IV CPUs with Myrinet interconnection among the dual-CPU nodes of the Linux cluster.
Design guidelines for a Content-Based Image Retrieval color-selection interface
Authors: Egon L. van den Broek, Peter M. F. Kisters, Louis G. Vuurpijl
Venue: Proceedings of the conference on Dutch directions in HCI (2004)

In Content-Based Image Retrieval (CBIR) two query-methods exist: query-by-example and query-by-memory. The user either selects an example image or selects image features retrieved from memory (such as color, texture, spatial attributes, and shape) to define his query. Hitherto, research on CBIR interfaces was absent. Hence, a usability evaluation of existing (CBIR) interfaces was done. Additionally, a study concerning human color cognition was conducted. Based on the resulting findings, a prototype color selection interface was developed. In a theoretical experiment, using Fitts' law, was proven that the prototype interface is highly efficient for CBIR purposes. This all resulted in a first set of design guidelines for CBIR color selection interfaces.
Array Composition and Decomposition for Optimizing Embedded Applications
Authors: G. Chen, M. Kandemir, A. Nadgir, U. Sezer
Venue: Proceedings of the 2003 IEEE/ACM international conference on Computer-aided design (2003)

Optimizing array accesses is extremely critical in embedded computingas many embedded applications make use of arrays (in formof images, video frames, etc). Previous research considered bothloop and data transformations for improving array accesses. However,data transformations considered were mostly limited to lineardata transformations and array interleaving. In this paper, we introducetwo data transformations: array decomposition (breaking upa large array into multiple smaller arrays) and array composition(combining multiple small arrays into a single large array). Thispaper discusses that it is feasible to implement these optimizationswithin an optimizing compiler.
Population set-based global optimization algorithms: some modifications and numerical studies
Authors: M. M. Ali, A. Törn
Venue: Computers and Operations Research (2004)

This paper studies the efficiency and robustness of some recent and well known population set-based direct search global optimization methods such as Controlled Random Search, Differential Evolution and the Genetic Algorithm. Some modifications are made to Differential Evolution and to the Genetic Algorithm to improve their efficiency and robustness. All methods are tested on two sets of test problems, one composed of easy but commonly used problems and the other of a number of relatively difficult problems.
Programming with small blocks
Authors: Mark K. Joseph
Venue: ACM SIGSOFT Software Engineering Notes (1984)

Programming style is a highly personalized characteristic of programs. Modular and block structured programming techniques provide many standards for good programming. These techniques are used to develop well designed but only marginally readable code. Similar organizational techniques are not typically applied to code inside subroutines, which is either too small or too specific to be further broken down into subroutines. The result is often obscure subroutine code that makes the maintenance programmer's job extremely difficult. Presented here is a styling technique for intra-subroutine code that groups program statements into "small BLOCKS" of function or conditional constraints. It is shown that this style of formating subroutine code can greatly improve the readability of the average program. The technique is demonstrated in Pascal, C, and Lisp.
Access to Community Pharmacies by the Elderly in Illinois: A Geographic Information Systems Analysis
Authors: Swu-Jane Lin
Venue: Journal of Medical Systems (2004)

Community pharmacies play an important role in maintaining population health in the United States. They are large in number, distribute widely across geographic areas, and operate for long hours. Because the elderly population tends to use more medications and have more frequent interaction with pharmacies and pharmacists, this study was carried out to understand the geographic access to community pharmacies by the elderly in Illinois and to estimate the disparity in the access between rural and urban areas. The addresses of all community pharmacies operating in 2001 were geocoded to identify their locations. The Census 2000 data on demographics at the census block group level was used to estimate the geographic distribution of the Illinois population by age group. Using the centroid of each census block group and the locations of community pharmacies, the distance to a nearest pharmacy for each census block group was calculated. The distance was then weighted to compute the aggregated distance required for the elderly to access a pharmacy. There were 1373 community pharmacies operating in Illinois in 2001. Most pharmacies (93.8%) were located in urban areas. On average, there were 1.27 and 0.38 pharmacies per 10,000 people in urban and rural areas, respectively. The average distance for an elderly person in Illinois to locate a community pharmacy was 0.9 miles in urban areas, but it was six times more (5.9 miles) in rural areas. At least 10% of the rural elderly had to travel more than 11.8 miles to find a community pharmacy, but only 0.1% had to travel more than 20 miles. The geographic access to community pharmacies appears to be appropriate in Illinois. However, a small portion of rural elderly who do not have a pharmacy in their nearby areas may warrant special attention.
OXYGENE: A Platform for the Development of Interoperable Geographic Applications and Web Services
Authors: Thierry Badard, Arnaud Braun
Venue: Proceedings of the Database and Expert Systems Applications, 15th International Workshop (2004)

This paper presents the OXYGENE platform, implemented at the COGIT laboratory of IGN (the French NMA). It allows for the development of interoperable geographic applications based on ISO/OGC specifications and aims at deploying researches undertaken at the IGN as "true" processing web services.
Bert
Venue: ACM SIGGRAPH 2003 video review on Animation theater program: part 1 - Volume 145 (2003)

A tale of a young vegetable's search for family. "Bert" is Lee's first film and senior project at Academy of Art College, San Francisco. Copyright held by creator. 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
The number of k-intersections of an intersecting family of r-sets
Authors: John Talbot
Venue: Journal of Combinatorial Theory Series A (2004)

The Erdös-Ko-Rado theorem tells us how large an intersecting family of r-sets from an n-set can be, while results due to Lovász and Tuza give bounds on the number of singletons that can occur as pairwise intersections of sets from such a family.We consider a natural common generalization of these problems. Given an intersecting family of r-sets from an n-set and 1 ≤ k ≤ r, how many k-sets can occur as pairwise intersections of sets from the family? For k = r and 1 this reduces to the problems described above. We answer this question exactly for all values of k and r, when n is sufficiently large. Our result is in the form of a structure theorem characterizing the extremal families in terms of extremal families for the Lovász-Tuza problem.
SaveCCM - A Component Model for Safety-Critical Real-Time Systems
Authors: Hans Hansson, Mikael Akerholm, Ivica Crnkovic, Martin Torngren
Venue: Proceedings of the 30th EUROMICRO Conference (2004)

Component-based development has proven effective in many engineering domains, and several general component technologies are available. Most of these are focused on providing an efficient software-engineering process. However for the majority of embedded systems, run-time efficiency andprediction of system behaviour are as important as process efficiency. This calls for specialized technologies. There is even a need for further specialized technologies adapted to different types of embedded systems, due to the heterogeneity of the domain and the close relation between the software and the often very application specific system. This paper presents the SaveCCM component model, intended for embedded control applications in vehicular systems. SaveCCM is a simple model in which flexibility is limited to facilitate analysis of real-time and dependability. We present and motivate the model, and provide examples of its use.
Two-level processor-sharing scheduling disciplines: mean delay analysis
Authors: Samuli Aalto, Urtzi Ayesta, Eeva Nyberg-Oksanen
Venue: ACM SIGMETRICS Performance Evaluation Review (2004)

Inspired by several recent papers that focus on scheduling disciplines for network flows, we present a mean delay analysis of Multilevel Processor Sharing (MLPS) scheduling disciplines in the context of M/G/1 queues. Such disciplines have been proposed to model the effect of the differentiation between short and long TCP flows in the Internet. Under MLPS, jobs are classified into classes depending on their attained service. We consider scheduling disciplines where jobs within the same class are served either with Processor Sharing (PS) or Foreground Background (FB) policy, and the class that contains jobs with the smallest attained service is served first. It is known that the FB policy minimizes (maximizes) the mean delay when the hazard rate of the job size distribution is decreasing (increasing). Our analysis, based on pathwise and meanwise arguments of the unfinished truncated work, shows that Two-Level Processor Sharing (TLPS) disciplines, e.g., FB+PS and PS+PS, are better than PS scheduling when the hazard rate of the job size distribution is decreasing. If the hazard rate is increasing and bounded, we show that PS outperforms PS+PS and FB+PS. We further extend our analysis to study local optimality within a level of an MLPS scheduling discipline.
Trench filling characteristics of low stress TEOS/ozone oxide deposited by PECVD and SACVD
Authors: C. Chang, T. Abe, M. Esashi
Venue: Microsystem Technologies (2004)

In this paper low stress silicon oxide was deposited with tetraethylorthosilicate (TEOS, Si(OC2H5)4)/ozone by plasma enhanced chemical vapor deposition (PECVD) and sub-atmospheric chemical vapor deposition (SACVD) for deep trench filling. Two kinds of PECVD oxide were fabricated: Coil antenna inductively coupled plasma (ICP) oxide and parallel plates capacitive coupled plasma (CCP) oxide. Adding ozone into the deposition process enhances the trench filling capability. Oxide filling in a deep trench (5 &#x03bc;m wide, 52 &#x03bc;m deep) was carried out using the SACVD process, which gave excellent conformal step coverage. However, the coil antenna ICP oxide was suitable as a sealing material. The effects of argon ion sputtering and magnetic field in the PECVD for the trench filling are discussed in this paper. Because the low temperature processes of PECVD and SACVD, the thermal residual stress was reduced and a low stress film of 85 MPa compression is available.
An Application using Pinwheel Scheduling Model
Authors: Shun-hung Yu, Hsin-hung Lin, Chih-wen Hsueh
Venue: Proceedings of the Parallel and Distributed Systems, Tenth International Conference (2004)

Real-time systems, ranging from small portable devices or embedded systems to more complex general-purpose computers, are designed to satisfy various ofreal-time computation. It is the most important toguarantee all the requests will be satisfied correctly intime. Rate monotonic algorithm is the most well-known real-time scheduling algorithm in the periodic task model. It not only has high schedulability, but alsohas a tight utilization bound to easily check whetherthe task set is feasible. In rate monotonic algorithm,a task will be executed once in each period, but thestart time of execution might be different in each period.On the contrary, for tasks scheduled using pinwheelmodel, the execution schedule in each period will be always the same. Therefore, pinwheel scheduling model is very suitable for real-time systems which need high predictability. The pinwheel scheduling model transforms the task periods into harmonic numbers shorter thanor equal to the original periods and provides many advantageous scheduling features. However, not all tasks allow to do the transformation and some would like tobe executed according to their original periods. In thispaper, we discuss how to solve the problem and give anapplication in power-aware real-time scheduling, wherewe can see the pinwheel model is very important in current embedded system design with power-aware requirement.
Efficient Response-Time Analysis for Tasks with Offsets
Venue: Proceedings of the 10th IEEE Real-Time and Embedded Technology and Applications Symposium (2004)

We present a method that enables an efficient implementationof the approximative response-time analysis (RTA)for tasks with offsets presented by Tindell [Using Offset Information to Analyse Static Priority Pre-emptively Scheduled Task Sets] and PalenciaGutierrez et al. [Schedulability Analysis for Tasks with Static and Dynamic Offsets].The method allows for significantly faster implementationsof schedulability tools using RTA. Furthermore, reducingcomputation time, from tens of milliseconds to just afraction of a millisecond, as we will show, is a step towardson-line RTA in for example admission control systems.We formally prove that our reformulation of earlier presentedequations is correct and allow us to statically representparts of the equation, reducing the calculations duringfix-point iteration. We show by simulations that the speed-upwhen using our method is substantial. When task setsgrow beyond a trivial number of tasks and/or transactionsa speed-up of more than 100 times (10 transactions and 10tasks/transaction) compared to the original analysis can beobtained.
VPC3: a fast and effective trace-compression algorithm
Authors: Martin Burtscher
Venue: Proceedings of the joint international conference on Measurement and modeling of computer systems (2004)

Trace files are widely used in research and academia to study the behavior of programs. They are simple to process and guarantee repeatability. Unfortunately, they tend to be very large. This paper describes vpc3, a fundamentally new approach to compressing program traces. Vpc3 employs value predictors to bring out and amplify patterns in the traces so that conventional compressors can compress them more effectively. In fact, our approach not only results in much higher compression rates but also provides faster compression and decompression. For example, compared to bzip2, vpc3's geometric mean compression rate on SPECcpu2000 store address traces is 18.4 times higher, compression is ten times faster, and decompression is three times faster.
On-the-fly maintenance of series-parallel relationships in fork-join multithreaded programs
Authors: Michael A. Bender, Jeremy T. Fineman, Seth Gilbert, Charles E. Leiserson
Venue: Proceedings of the sixteenth annual ACM symposium on Parallelism in algorithms and architectures (2004)

A key capability of data-race detectors is to determine whether one thread executes logically in parallel with another or whether the threads must operate in series. This paper provides two algorithms, one serial and one parallel, to maintain series-parallel (SP) relationships "on the fly" for fork-join multithreaded programs. The serial SP-order algorithm runs in O(1) amortized time per operation. In contrast, the previously best algorithm requires a time per operation that is proportional to Tarjan's functional inverse of Ackermann's function. SP-order employs an order-maintenance data structure that allows us to implement a more efficient "English-Hebrew" labeling scheme than was used in earlier race detectors, which immediately yields an improved determinacy-race detector. In particular, any fork-join program running in T1 time on a single processor can be checked on the fly for determinacy races in O(T1) time. Corresponding improved bounds can also be obtained for more sophisticated data-race detectors, for example, those that use locks.By combining SP-order with Feng and Leiserson's serial SP-bags algorithm, we obtain a parallel SP-maintenance algorithm, called SP-hybrid. Suppose that a fork-join program has n threads, T1 work, and a critical-path length of T∞. When executed on P processors, we prove that SP-hybrid runs in O((T1/P +PT,/i>∞)lg <i.n) expected time. To understand this bound, consider that the original program obtains linear speed-up over a 1-processor execution when P=O(T1T∞). In contrast, SP-hybrid obtains linear speed-up when P=O(√T1T∞), but the work is increased by a factor of O(lg n).
An Improved Mutual Authentication Scheme for Smart Card Secure Messaging
Authors: Lanjun Dang, Weidong Kou, Yuxia Xiao
Venue: Proceedings of the E-Commerce Technology for Dynamic E-Business, IEEE International Conference (2004)

Encryption of the card/card reader communications link is an important issue of smart card security, and a fundamental problem of all cryptological procedures is the secure distribution of the secret key. To overcome the problem of session key generation and distribution, in this paper, two improved mutual symmetric authentication schemes are proposed. The schemes include session key exchange for secure messaging. Security analyses to the new schemes are provided.
A Proxy Signature Scheme with Proxy Signer's Privacy Anonymity
Authors: Xiaotong Fu, Weidong Kou, Guozhen Xiao
Venue: Proceedings of the E-Commerce Technology for Dynamic E-Business, IEEE International Conference (2004)

A proxy signature scheme is proposed with the property that the proxy signers can sign messages on behalf of the original signer while providing anonymity to protect their privacy. The anonymity can be revoked when it is needed to identify the proxy signer who actually generated the proxy signature. Moreover, the proxy signing power can be recalled according to original signer's need in the scheme.
Frameworks: putting design patterns into perspective
Authors: Henrik Bærbak Christensen
Venue: Proceedings of the 9th annual SIGCSE conference on Innovation and technology in computer science education (2004)

Design patterns have made a strong impact on how object-oriented software is designed, implemented, and communicated in industrial projects. Teaching patterns is therefore of great importance. Patterns, however, have a natural catalogue-like nature, that easily misleads us into to lecturing them one at a time. This leaves an impression of patterns as isolated solutions to independent problems. We present our experience with trying to counteract this problem by using a well-engineered framework, JHotDraw, as a case study in how patterns work together to define a flexible and compositional software system of high quality.
On Universality of General Reversible Multiple-Valued Logic Gates
Venue: Proceedings of the 34th International Symposium on Multiple-Valued Logic (2004)

A set of p-valued logic gates (primitives) is calleduniversal if an arbitrary p-valued logic function can berealized by a logic circuit built up from a finite numberof gates belonging to this set. In the paper, we considerthe problem of determining the number of universalsingle-gate libraries of p-valued reversible logic gateswith two inputs and two outputs under the assumptionthat constant signals can be applied to arbitrary numberof inputs. We have proved some properties of such gatesand established that over 97% of ternary gates areuniversal.
User centred interfaces in co-operative distributed systems
Authors: Fulko van Westrenen
Venue: Proceedings of the conference on Dutch directions in HCI (2004)

This paper describes new developments in co-operative decision making in aviation and maritime navigation. Essential is the free exchange of state information between all participants, and the use of a common rule-set. Such a system lacks the need for central control.
Chains of smarandache semifields
Authors: A. S. Muktibodh, V. M. Wagh
Venue: Smarandache Notions Journal (2004)

In this paper we have constructed two chains of semifields. All semifieids in the chains are Smarandache semifields. Every member of the chain is an extension semifield of Ordered equilateral Integral triangles with Zero triangle such that it is a semivector space over RIeΔ
Effective Meshing and Form Factor Calculation for Accurate Progressive Radiosity
Venue: Proceedings of the Theory and Practice of Computer Graphics 2004 (TPCG'04) (2004)

In this paper, two effective methods are proposed to addresstwo inaccuracies, deficient meshing and error-proneform factors, respectively, in the context of progressive radiosity.The first one addresses the meshing problem usingan automatic adaptive subdivision that takes the radiositydifference, the radiosity residual, and the visibility informationas error estimates. The second method employs a hybridform-factor evaluation recursively combining an approximationto the analytic point-to-disk form factor andan accurate form factor from a differential area to a convexpolygon. Finally, we demonstrate the effectiveness andpracticability of the proposed methods by testing with a setof global illumination test scenes to show the experimentalresults qualitatively and quantitatively.
Playing with sounds as playing video games
Authors: Myriam Desainte-Catherine, Gyorgy Kurtag, Sylvain Marchand, Catherine Semal, Pierre Hanna
Venue: Computers in Entertainment (CIE) (2004)

In this article we propose a musical instrument that provides young children with a way to play in a virtual sound space by means of a joystick. We present the work of a multidiscipline team working on various aspects of this project. Sound models that are close to perception are used to define the sound spaces. Pedagogical experiments in public schools are done on the basis of cognitive pedagogy. Ethological and psychoacoustic experiments are carried out to improve the ergonomics of the instruments.
Monte Carlo Simulation of Complex Radiotherapy Treatments
Authors: Antonio Leal, Franciso Sanchez-Doblado, Maria Perucha, Ester Carrasco, Magnolia Rincon, Rafael Arrans, Carlos Bernal
Venue: Computing in Science and Engineering (2004)

Monte Carlo simulation is an accurate way of assessing radiotherapy dose distribution in nonhomogeneous volumes, but it requires long processing times. A new distribution model simulates radiotherapy treatments and runs on a PC network, which reduces the processing time and makes for a powerful treatment-verification tool.
An O(T log T) Algorithm for the Dynamic Lot Size Problem with Limited Storage and Linear Costs
Authors: A. Sedeño-Noda, J. Gutiérrez, B. Abdul-Jalbar, J. Sicilia
Venue: Computational Optimization and Applications (2004)

In this paper the dynamic lot size problem with time varying storage capacities and linear costs is addressed. Like in the uncapacitated version, this problem can be formulated as a network flow problem. Considering the properties of the underlying network, we devise an O(T log T) greedy algorithm to obtain optimal policies and we report computational results for randomly generated problems.