ppxscal/embedding_network huggingface dataset:
Shaping biological knowledge: applications in proteomics: Conference Reviews
Authors: F. Lisacek, C. Chichester, P. Gonnet, O. Jaillet, S. Kappus, F. Nikitin, P. Roland, G. Rossier, L. Truong, R. Appel
Venue: Comparative and Functional Genomics (2004)

The central dogma of molecular biology has provided a meaningful principle for data integration in the field of genomics. In this context, integration reflects the known transitions from a chromosome to a protein sequence: transcription, intron splicing, exon assembly and translation. There is no such clear principle for integrating proteomics data, since the laws governing protein folding and interactivity are not quite understood. In our effort to bring together independent pieces of information relative to proteins in a biologically meaningful way, we assess the bias of bioinformatics resources and consequent approximations in the framework of small-scale studies. We analyse proteomics data while following both a data-driven (focus on proteins smaller than 10 kDa) and a hypothesis-driven (focus on whole bacterial proteomes) approach. These applications are potentially the source of specialized complements to classical biological ontologies. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Algorithms for Countable State Markov Decision Models with an Absorbing Set
Authors: K. Hinderer, K.-H. Waldmann
Venue: SIAM Journal on Control and Optimization (2005)

We consider a countable state Markov decision process with bounded reward function and an absorbing set. At first we generalize known properties and derive new properties of the critical discount factor, which is roughly defined as the maximal discount factor under which for V, the maximal expected infinite-stage discounted reward, there is guaranteed existence, boundedness, and computability by the successive approximation method. The emphasis of the paper is on algorithms for computing V exactly (recursion in state space and policy iteration) or approximately (value iteration combined with an extrapolation and finite state approximation). Our extrapolation method is motivated by and based on the Perron--Frobenius theory for nonlinear operators. As a by-product we obtain an efficient algorithm for determining the distribution of the entrance time of a Markov chain into an absorbing set. Further results concern asymptotically $\epsilon$-optimal policies and a new turnpike theorem. Some of the results need tightness of the transition law, which turns out to be equivalent to compactness of a nonlinear operator, which is crucial for our study.
Managing structural genomic workflows using web services
Authors: Maria Cláudia Cavalcanti, Rafael Targino, Fernanda Baião, Shaila C. Rössle, Paulo M. Bisch, Paulo F. Pires, Maria Luiza M. Campos, Marta Mattoso
Venue: Data Knowledge Engineering (2005)

In silico scientific experiments encompass multiple combinations of program and data resources. Each resource combination in an execution flow is called a scientific workflow. In bioinformatics environments, program composition is a frequent operation, requiring complex management. A scientist faces many challenges when building an experiment: finding the right program to use, the adequate parameters to tune, managing input/output data, building and reusing workflows. Typically, these workflows are implemented using script languages because of their simplicity, despite their specificity and difficulty of reuse. In contrast, Web service technology was specially conceived to encapsulate and combine programs and data, providing interoperation between applications from different platforms. The Web services approach is superior to scripts with regard to interoperability, scalability and flexibility issues. We have combined metadata support with Web services within a framework that supports scientific workflows. While most works are focused on metadata issues to manage and integrate heterogeneous scientific data sources, in this work we concentrate on metadata support to program management within workflows. We have used this framework with a real structural genomic workflow, showing its viability and evidencing its advantages.
Steganography may increase learning everywhere
Authors: James Ryder
Venue: Journal of Computing Sciences in Colleges (2004)

In this paper, we describe an interesting and contemporary topic called steganography and ways that it can easily be included in computer science courses. Today, steganography is used in many ways. By discussing and demonstrating steganography, an instructor can show interesting examples, ranging from simple to complex, of how computer science is found in commercial, military, and private software applications. Our results, although strictly casual, suggest that steganography, and its applications, naturally stimulate interest in most computer science students. Any time a person is interested in a topic, he or she tends to focus more and better on it. In this case, the topics are computer science courses.
Fixed point analysis of single cell IEEE 802.11e WLANs: uniqueness, multistability and throughput differentiation
Authors: Venkatesh Ramaiyan, Anurag Kumar, Eitan Altman
Venue: Proceedings of the 2005 ACM SIGMETRICS international conference on Measurement and modeling of computer systems (2005)

We consider the vector fixed point equations arising out of the analysis of the saturation throughput of a single cell IEEE 802.11e wireless local area network with nodes that have different back-off parameters, including different Arbitration InterFrame Space (AIFS) values. We consider balanced and unbalanced solutions of the fixed point equations arising in homogeneous and nonhomogeneous networks. We are concerned, in particular, with (i) whether the fixed point is balanced within a class, and (ii) whether the fixed point is unique. Our simulations show that when multiple unbalanced fixed points exist in a homogeneous system then the time behaviour of the system demonstrates severe short term unfairness (or multistability). Implications for the use of the fixed point formulation for performance analysis are also discussed. We provide a condition for the fixed point solution to be balanced within a class, and also a condition for uniqueness. We then provide an extension of our general fixed point analysis to capture AIFS based differentiation; again a condition for uniqueness is established. An asymptotic analysis of the fixed point is provided for the case in which packets are never abandoned, and the number of nodes goes to ∞. Finally the fixed point equations are used to obtain insights into the throughput differentiation provided by different initial back-offs, persistence factors, and AIFS, for finite number of nodes, and for differentiation parameter values similar to those in the standard.
Bouncing Ball Modes and Quantum Chaos
Authors: Nicolas Burq
Venue: SIAM Review (2005)

Quantum ergodicity for classically chaotic systems has been studied extensively both theoretically and experimentally in mathematics and physics. Despite this long tradition we are able to prove a new rigorous result using only elementary calculus. In the case of the famous Bunimovich stadium shown in Figure 1, we prove that the wave functions have to spread to any neighborhood of the wings.
Predicting Cache Space Contention in Utility Computing Servers
Authors: Yan Solihin, Fei Guo, Seongbeom Kim
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 10 - Volume 11 (2005)

The need to provide performance guarantee in high performance servers has long been neglected. Providing performance guarantee in current and future servers is difficult because fine-grain resources, such as on-chip caches, are shared by multiple processors or thread contexts. Although inter-thread cache sharing generally improves the overall throughput of the system, the impact of cache contention on the threads that share it is highly non-uniform: some threads may be slowed down significantly, while others are not. This may cause severe performance problems such as sub-optimal throughput, cache thrashing, and thread starvation for threads that fail to occupy sufficient cache space to make good progress. Clearly, this situation is not desirable when performance guarantee needs to be provided, such as in utility computing servers. Unfortunately, there is no existing model that allows extensive investigation of the impact of cache sharing. To allow such a study, we propose an inductive probability model to predict the impact of cache sharing on co-scheduled threads. The input to the model is the isolated L2 circular sequence profile of each thread, which can be easily obtained on-line or off-line. The output of the model is the number of extra L2 cache misses for each thread due to cache sharing. We validate the model against a cycle-accurate simulation that implements a dual-core Chip Multi-Processor (CMP architecture), on fourteen pairs of mostly SPEC benchmarks. The model achieves an average error of only 3.9%.
Artistic Mosaic Generation
Authors: Xuelong Li, Yuan Yuan
Venue: Proceedings of the Third International Conference on Image and Graphics (2004)

In this paper, a new approach to image processing in arts is presented in the domain of generating a series of artistic mosaic pictures. The mosaic pictures consist of the same elements as each other, but might be extremely different from the semantic contents. Some preliminary experimental results are given to show the impact of the proposed special techniques.
Global Control of Robotic Highway Safety Markers: A Real-time Solution
Authors: Jiazheng Shi, Steve Goddard, Anagh Lal, Jason Dumpert, Shane Farritor
Venue: Real-Time Systems (2005)

This paper presents the design and implementation of a real-time solution for the global control of robotic highway safety markers. Problems addressed in the system are: (1) poor scalability and predictability as the number of markers increases, (2) jerky movement of markers, and (3) misidentification of safety markers caused by objects in the environment.An extensive analysis of the system and two solutions are offered: a basic solution and an enhanced solution. They are built respectively upon two task models: the periodic task model and the variable rate execution (VRE) task model. The former is characterized by four static parameters: phase, period, worst case execution time and relative deadline. The latter has similar parameters, but the parameter values are allowed to change at arbitrary times.The use of real-time tasks and scheduling techniques solve the first two problems. The third problem is solved using a refined Hough transform algorithm and a horizon scanning window. The approach decreases the time complexity of traditional implementations of the Hough transform with only slightly increased storage requirements.
Dynamic Resource Management Algorithm for a Distributed Real-time System
Authors: Charles Cavanaugh, Radhika Ari
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 2 - Volume 03 (2005)

In this paper we propose a framework and algorithm for dynamic resource management in a distributed real-time system. Our assumptions are as follows: first, multiple real-time & non real-time processes are active throughout the system. Those processes in the critical path fora given task, i.e., autopilot, fire control (as in firing weapons), surveillance, collaborative planning, are RT for the duration of the task and may or may not be party to multiple tasks in either critical or ancillary capacities. For instance, the radar may be part of the critical path during surveillance, but have uses other thaan that, say to take a snampshot during a collaborative planning sessiong that may serve an ancillary use (as a supplementary illusatration for discussion, e.g., "this is the depot we will go after tomorrow during a flyover") But then, if you can fly over it, why not go after it then? Another example: during a coordinated maneuver, plane-to-plane communications are in the critical path but during fire control they are not. Second, the operating system or run-time environment has task migration capabilities. Third, storage is cheap-can store images of multiple processes in different states on each computing device for purpose of instantiating one or more in any combination on that device and across devices for reconfigurable distributed computing. This paper presents a software architecture and an algorithm for resource management in such systems.
Optimal selection of ARQ parameters in QAM channels: Research Articles
Authors: Vlad Mitlin
Venue: Wireless Communications Mobile Computing (2005)

For a quadrature amplitude modulation (QAM) communication channel with forward error correction (FEC) and automatic repeat request (ARQ), the bit error rate (BER) is estimated as a function of the channel signal-to-noise ratio (SNR). A method is presented for trading off the number of allowed transmissions and the level of margin (or the line ARQ gain) applied to the channel SNR. The line ARQ gain maximizing the channel throughput is shown to be a sum of the channel SNR and some function of the bit load and FEC parameters. Using this result, we formulate a fast method of determining the optimum ARQ parameters at the actual channel conditions, based on their values at some reference conditions, the latter being either stored in the modem memory or pre-calculated prior to channel initialization. The derivations are presented both for AWGN and slowly fading channel conditions. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Software engineering education in the era of outsourcing, distributed development, and open source software: challenges and opportunities
Authors: Matthew J. Hawthorne, Dewayne E. Perry
Venue: Proceedings of the 27th international conference on Software engineering (2005)

As software development becomes increasingly globally distributed, and more software functions are delegated to common open source software (OSS) and commercial off-the-shelf (COTS) components, practicing software engineers face significant challenges for which current software engineering curricula may leave them inadequately prepared. A new multi-faceted distributed development model is emerging that effectively commoditizes many development activities once considered integral to software engineering, while simultaneously requiring practitioners to apply engineering principles in new and often unfamiliar contexts. We discuss the challenges that software engineers face as a direct result of outsourcing and other distributed development approaches that are increasingly being utilized by industry, and some of the key ways we need to evolve software engineering curricula to address these challenges.
Continuations and Web Servers
Authors: Christian Queinnec
Venue: Higher-Order and Symbolic Computation (2004)

Programming web applications in direct style with the help of continuations is a much simpler, safer, modular and better-performing technology than the current dominating "page-centric" technology combining CGI scripts, active pages or servlets. This paper discusses the use of continuations in the context of web applications, the problems they solve as well as some new problems they introduce.
Balanced matching of buyers and sellers in e-marketplaces: the barter trade exchange model
Authors: Peter Haddawy, Namthip Rujikeadkumjorn, Khaimook Dhananaiyapergse, Christine Cheng
Venue: Proceedings of the 6th international conference on Electronic commerce (2004)

In this paper, we describe the operation of barter trade exchanges by identifying key techniques used by trade brokers to stimulate trade and satisfy member needs, and present algorithms to automate some of these techniques. In particular, we develop algorithms that emulate the practice of trade brokers by matching buyers and sellers in such a way that trade volume is maximized while the balance of trade is maintained as much as possible. We show that the buyer/seller matching and trade balance problems can be decoupled, permitting efficient solution as well as numerous options for matching strategies.We model the trade balance problem as a minimum cost circulation problem (MCC) on a network. When the products have uniform cost or when the products can be traded in fractional units, we solve the problem exactly. Otherwise, we present a novel stochastic rounding algorithm that takes the fractional optimal solution to the trade balance problem and produces a valid integer solution. We then make use of a greedy heuristic that attempts to match buyers and sellers so that the average number of suppliers that a buyer must use to satisfy a given product need is minimized.We present results on the empirical evaluation of our algorithms on test problems and simulations. Experiments show that our algorithm (MCC + stochastic rounding) runs in a fraction of the time of a commercial mixed integer programming (MIP) package while producing solutions that are always within 0.7% of the MIP solution. We evaluate the effectiveness of our algorithm on maintaining balance and on stimulating trade using two different simulation techniques, both based on transaction history data from a trade exchange. The simulation results support the barter trade exchange rule of thumb that maximizing single-period trade volume while maintaining balance of trade helps to maximize trade volume over the long run.
Project BAR-S: monitoring and updating work standards systems
Authors: Gerardo A. Orellano, Cara J. Berry
Venue: Journal of Computing Sciences in Colleges (2004)

This project deals with the review of Work Standards and the development of a paperless management information system to monitor and update these standards. The Work Standards database will interface with the Worker Wages Computation system to determine workers wages. Some of the tasks we are undertaking are observing the operations in the warehouse and product dispatch sections and documenting the Standard Method for each operation; developing new Work Standards based on our observations and updating the existing database of work standards. We will also be creating a computerized database of the work standards and developing/implementing the procedures for keeping the database current and in line with the policies of BAR-S. We will then write the code for interfacing the Work Standards database system with the Workers Wage Computation system, test the system then implement the interface. We would also like to thank Dr. Harpal S. Dhillon for his guidance.
What's in your wallet?: implications for global e-wallet design
Authors: Scott D. Mainwaring, Ken Anderson, Michele F. Chang
Venue: CHI '05 extended abstracts on Human factors in computing systems (2005)

As part of a comparative ethnographic study of everyday life of young professionals in London, Los Angeles, and Tokyo, we conducted a detailed survey of wallets and their contents, through photographs, interviews, diary studies, and observation. Despite prominent differences in culture and lifestyle, there were remarkable similarities across all three sites in terms of what wallets contained and how they were used. Individuals arrived at similar (if imperfect) solutions to common problems of temptation management and access control, identity management and partitioning, and collecting tokens of affiliation and history. Our findings suggest that future electronic wallets (e-wallets), whether physical devices or distributed functionalities, will be able to capitalize on these existing patterns, solve some of the existing problems, and encounter new challenges. Furthermore, they frame the potential value of e-wallets in a broader context than traditional concerns over privacy, security, and efficiency.
Software test program: a software residency experience
Authors: Augusto Sampaio, Carlos Albuquerque, Joåo Vasconcelos, Luckerson Cruz, Luis Figueiredo, Sergio Cavalcante
Venue: Proceedings of the 27th international conference on Software engineering (2005)

The Software Test Program (STP) is a cooperation between Motorola and the Center for Informatics of the Federal University of Pernambuco. It has been conceived with inspiration on the Medical Residency, adjusted to the software development practice. A Software Residency includes the formal teaching of the relevant concepts and deep practice, with specialization on some specific subject; here the focus is on software testing. The STP has been of great benefit to all parties involved.
Minimum Energy Transmission Scheduling Subject to Deadline Constraints
Authors: Alessandro Tarello, Jun Sun, Murtaza Zafer, Eytan Modiano
Venue: Proceedings of the Third International Symposium on Modeling and Optimization in Mobile, Ad Hoc, and Wireless Networks (2005)

We consider the problem of transmission scheduling of data over a wireless fading channel with hard deadline constraints. Our system consists of N users, each with a fixed amount of data that must be served by a common deadline. Given that, for each user, the channel fade state determines the throughput per unit of energy expended, our objective is to minimize the overall expected energy consumption while satisfying the deadline constraint. We consider both a linear and a strictly convex rate-power curve and obtain optimal solutions, based on dynamic programming (DP), and tractable approximate heuristics in both cases. For the special non-fading channel case with convex rate-power curve, an optimal solution is obtained based on the Shortest Path formulation. In the case of a linear rate-power curve, our DP solution has a nice "threshold" form; while for the convex rate-power curve we are able to obtain a heuristic algorithm with comparable performance with that of the optimal scheduling scheme.
The Perception of Ecological Textures by Touch: Does the Perceptual Space Change under Bimodal Visual and Haptic Exploration?
Authors: Soledad Ballesteros, Jose M. Reales, Laura Ponce de Leon, Beatriz Garcia
Venue: Proceedings of the First Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (2005)

In 2 experiments, we investigated the dimensionality of 20 ecological surface textures explored haptically (Exp.1) and by vision and touch (Exp.2). The goal was to find out how haptic texture perception is integrated with visual information and whether the dimensionality of the perceptual space changes with multimodal perception. In each experiment, human participants performed a spatial arrangement task, a free classification task, and a hedonic rating task. The results suggested that two dimensions interpreted as roughness/smoothness and slippery/adherent explain most of the data not only in touch but also in bimodal surface texture exploration.