ppxscal/embedding_network huggingface dataset:
Peptide Identification by Tandem Mass Spectra: An Efficient Parallel Searching
Authors: Jung Hun Oh, Jean Gao
Venue: Proceedings of the Fifth IEEE Symposium on Bioinformatics and Bioengineering (2005)

De novo peptide sequencing that determines the amino acid sequence of a peptide via tandem mass spectrometry (MS/MS) has been increasingly used nowadays in proteomics for protein identification. Current de novo methods generally employ a graph theory which usually produces a large number of candidate sequences and causes heavy computational cost while trying to determine a sequence with less ambiguity. We present a novel de novo sequencing algorithm which greatly reduces the number of candidate sequences. By utilizing certain properties of b- and y-ion series in MS/MS spectrum, we propose a reliable two-way parallel searching algorithm to filter out the peptide candidates which are further pruned by an intensity evidence based screening criterion. And we find an adjusted value required to determine the position of end node of b- and y-ion series for the charged +2 precursor in our graph. Results of our algorithm are compared with those of PEAKS, a well-known de novo sequencing software. Experimental results demonstrate the six sequences are identical with the correct sequences. And for the further pruning, rankings of our result remain unchanged even though the screening criterion changes. Therefore we can reduce the number of candidate sequences by adopting a proper screening criterion.
K-tai Campus: University-Sharing Campus Information System Applicable to Mobile Phone and PC
Authors: Yoshiaki Hada, Masanori Shinohara, Yasutaka Shimizu
Venue: Proceedings of the IEEE International Workshop on Wireless and Mobile Technologies in Education (2005)

Recently, mobile devices have functions that allow them to be used as tools for obtaining information from cell-phone websites. To support universities in Japan by providing communication between those universities and their students in classes or anywhere on campus, the National Institute of Multimedia Education, Japan has developed an online mobile phone campus information system called K-tai Campus. This development was conducted under our policy of providing system functions as an application service provider and that of providing open source systems. In this paper, we describe the design and functions of K-tai Campus, how they provide ease of operation, and we discuss the proper means of connecting both PCs and PC-websites. This paper also focuses on the communication functions provided for teachers and students to further support education.
Power-Aware Real-Time Scheduling Using Pinwheel Model and Profiling Technique
Authors: Hsin-hung Lin, Chih-Wen Hsueh
Venue: Proceedings of the 11th IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (2005)

Energy consumption is a critical design issue in embedded systems, especially in battery-operated systems. Maintaining high performance while extending the battery life is an interesting challenge for system designers. Dynamic voltage scaling and dynamic frequency scaling allow us to adjust supply voltage and processor frequency to adapt to the workload demand for better energy management. Because of the high complexity involved, most solutions depend on heuristics for online power-aware real-time scheduling or offline time-consuming scheduling. In this paper, we discuss how we can apply pinwheel model to power-aware real-time scheduling so that task information, including start times, finish times, preemption times, etc, can be efficiently derived using pinwheel model. System predictability is thus increased and under better control on power-awareness. However, job execution time may be only a small portion of its worst case execution time and can only be determined at runtime. We implement a profiling tool to insert codes for collecting runtime information of real-time tasks. Worst case execution time is updated on-line for scheduler to perform better rescheduling according to actual execution. Simulations have shown that at most 50% energy can be saved by the proposed scheduling algorithm. Moreover, at most additional 33% energy can be saved when the profiling technique is applied.
Optimizing simulated systems
Authors: Georg Ch. Pflug
Venue: ACM SIGSIM Simulation Digest (1984)

A major part of all simulation models contains a number of decision variables. For such models the problem of optimal decision arises in a natural way. The combination of simulation and optimization for probabilistic models with continuous decision variables is discussed in this paper. Several important techniques for solving the combined problem are presented. In particular the stochastic quasigradient method which is a well known technique in stochastic optimization may also successfully applied for simulation-optimization problems.
Sound science: Marking ten international conferences on auditory display
Authors: Gregory Kramer, Bruce N. Walker
Venue: ACM Transactions on Applied Perception (TAP) (2005)

This special issue of ACM Transactions on Applied Perception is intended to commemorate the tenth International Conference on Auditory Display (ICAD) and to serve as an introduction and overview of the field of auditory displays. This paper discusses the goals of the issue and describes the paper selection process. The selected papers are also introduced, with their connections to each other, their place in ICAD, and their relevance to other fields briefly highlighted.
A practical system for laser pointer interaction on large displays
Authors: Benjamin A. Ahlborn, David Thompson, Oliver Kreylos, Bernd Hamann, Oliver G. Staadt
Venue: Proceedings of the ACM symposium on Virtual reality software and technology (2005)

Much work has been done on the development of laser pointers as interaction devices. Typically a camera captures images of a display surface and extracts a laser pointer dot location. This location is processed and used as a cursor position. While the current literature well explains such a system, we feel that some important practical concerns have gone unaddressed. We discuss the design of such a tracking system, focusing on key practical implementation details. In particular we present a robust and efficient dot detection algorithm that allows us to use our system under a variety lighting conditions, and allows us to reduce the amount of image parsing required to find a laser position by an order of magnitude.
Vizster: Visualizing Online Social Networks
Authors: Jeffrey Heer, Danah Boyd
Venue: Proceedings of the Proceedings of the 2005 IEEE Symposium on Information Visualization (2005)

Recent years have witnessed the dramatic popularity of online social networking services, in which millions of members publicly articulate mutual "friendship" relations. Guided by ethnographic research of these online communities, we have designed and implemented a visualization system for playful end-user exploration and navigation of large-scale online social networks. Our design builds upon familiar node-link network layouts to contribute customized techniques for exploring connectivity in large graph structures, supporting visual search and analysis, and automatically identifying and visualizing community structures. Both public installation and controlled studies of the system provide evidence of the system's usability, capacity for facilitating discovery, and potential for fun and engaged social activity.
Toward securing untrusted storage without public-key operations
Authors: Dalit Naor, Amir Shenhav, Avishai Wool
Venue: Proceedings of the 2005 ACM workshop on Storage security and survivability (2005)

Adding security capabilities to shared, remote and untrusted storage file systems leads to performance degradation that limits their use. Public-key cryptographic primitives, widely used in such file systems, are known to have worse performance than their symmetric key counterparts. In this paper we examine design alternatives that avoid public-key cryptography operations to achieve better performance. We present the trade-offs and limitations that are introduced by these substitutions.
Energy management in wireless networks
Authors: Ding-Zhu Du, Jaideep Srivastava
Venue:  (2005)

Energy is a great concern in wireless networks. Therefore, when designing algorithms and protocols for wireless networks, energy must be considered and should be used efficiently. This dissertation studies how to efficiently conserve energy for different issues in wireless networks so that the network lifetime can be extended. Broadcast is a mainly used communication method in wireless networks. The broadcast problem is to decide a transmission power for each host so that the source can broadcast to all other hosts either directly or indirectly through the relay hosts. In this dissertation, we solve this problem by constructing a broadcast tree with the purpose to balance the energy consumptions of all the nodes. We also propose a method to construct a strongly connected broadcast tree with bounded total energy consumption while the transmission latencies between the source and all other hosts are also bounded. The topology control problem in wireless networks studies how to adjust the transmission power at each node in order to achieve a desired topological property. In this dissertation, we solve this problem by focusing on the network connectivity and try to find an energy-efficient way to maximize the network lifetime. With a limited number of hosts actively participating in the routing tasks, both the total energy consumption and the communication can be reduced greatly. A virtual backbone based routing mechanism is then stimulated. In this dissertation, we approximate a virtual backbone by a Connected Dominating Set (CDS). The problem to find a minimum CDS is NP-hard and we propose several approximation algorithms for this problem. Finally, we study the target coverage problem in sensor networks. It requires finding a small number of sensors that can cover some targets in the monitored area. In this dissertation, we study this problem by organizing the sensors into a maximal number of set covers that are activated successively to conserve energy and extend the network lifetime. Only the sensors from the current active set monitor the targets, all the other sensors are in a sleep mode.
Hybrid Learning Neuro-Fuzzy Approach for Complex Modeling Using Asymmetric Fuzzy Sets
Authors: Chunshien Li, Kuo-Hsiang Cheng, Jiann-Der Lee
Venue: Proceedings of the 17th IEEE International Conference on Tools with Artificial Intelligence (2005)

A hybrid learning neuro-fuzzy system with asymmetric fuzzy sets (HLNFS-A) is proposed in this paper. The learning methods of random optimization (RO) and least square estimation (LSE) are used in hybrid way to train the system parameters of HLNFS-A to achieve stable and fast convergence. In the HLNFSA, the premise and the consequent parameters are updated by RO and LSE, respectively. With the proposed asymmetric fuzzy sets (AFS), the neuro-fuzzy system can capture the essence of nonlinear property of dynamic system, when used in the application of modeling. To demonstrate the feasibility and the potential of the proposed approach, an example of chaotic time series for system identification and prediction is given to verify the nonlinear mapping capability of the HLNFS-A. The experimental results show that the proposed HLNFS-A can achieve excellent performance for system modeling.
Detection and Localization of Road Area in Traffic Video Sequences Using Motion Information and Fuzzy-Shadowed Sets
Authors: Do Lenh Hung Son, Truong Thien Dinh, Van Chi Nam, Tran Thi Bich Hanh, Ho Ngoc Lam
Venue: Proceedings of the Seventh IEEE International Symposium on Multimedia (2005)

The goal of this work is to accurately detect and localize the road area in traffic video sequences. A new approach is presented in which motion information and fuzzy-shadowed sets are used. A motion history image (MHI) is calculated from the video sequence, and then combined with background model to detect the candidate road image. The last task to get the final road image, the road localization step, is accomplished by applying a fuzzy-shadowed theoretic technique with the membership function based on both chromatic characteristics and spatial characteristics. The proposed approach was tested with recorded video under various traffic conditions and the testing results were shown to be precise in detecting and localizing the road area.
Matching service delivery to market requirements: process selection for online banking
Authors: Kathryn M. Zuckweiler
Venue:  (2005)

The growth of electronic commerce has forced firms to rethink how they deliver a service to their customers. Not only is the face-to-face human interaction lost, but the concept of neighborhood services has given way to business unconstrained by geographic boundaries. For services, the service delivery process would seem to be markedly altered by the lack of human interaction and geographic boundaries. This forces companies wishing to sell services in an electronic environment to reexamine the key elements of their service process and the relationships between service process and market requirements. Nowhere is the effect of electronic commerce more evident than in the banking industry. Traditionally, banks depended heavily on human interaction and a neighborhood presence for their business. Interestingly, this industry has also been quick to embrace electronic commerce, with some banks developing web sites as early as 1995. This research project investigated relationships among company factors, process selection and business performance for service delivery via electronic commerce, using online banking as an example of a nearly pure service delivered electronically. The study used a sample of Nebraska state-chartered banks that offer online banking. Managers of these banks were surveyed about the importance of cost savings motivation, likelihood of technology adoption, level of security control, and legal and regulatory compliance burden, and their banks' experiences with online banking usage. Survey responses were combined with publicly-available performance data to evaluate the hypothesized relationships through multiple regression. The results indicate that cost savings motivation and likelihood of technology adoption are important predictors of process selection. Additionally, process selection is an important predictor of business performance.
Advances in X3D multi-user virtual environments
Authors: Ch. Bouras, A. Panagopoulos, Th. Tsiatsos
Venue: Proceedings of the Seventh IEEE International Symposium on Multimedia (2005)

This paper presents the current state of the art in web3d multi-user technologies and more specifically networked virtual environment platforms that support the X3D standard, which are currently limited in number, and also the existing X3D browsers that enable these applications. Furthermore, this paper presents the architecture of a platform, called EVE, which was developed to support multi-user virtual environments and was initially based on VRML, as well as the implementation regarding the process of upgrading this platform in order to fully support the X3D standard, using the open-source Xj3D library. Finally, the benefits of shifting to the X3D standard are presented, and some of the problems that currently exist are discussed.
An FPGA-Based Floating-Point Jacobi Iterative Solver
Authors: Gerald R. Morris, Viktor K. Prasanna
Venue: Proceedings of the 8th International Symposium on Parallel Architectures,Algorithms and Networks (2005)

Within the parallel computing domain, field programmable gate arrays (FPGA) are no longer restricted to their traditional role as substitutes for application-specific integrated circuits as hardware "hidden" from the end user. Several high performance computing vendors offer parallel reconfigurable computers employing user-programmable FPGAs. These exciting new architectures allow end-users to, in effect, create reconfigurable coprocessors targeting the computationally intensive parts of each problem. The increased capability of contemporary FPGAs coupled with the embarrassingly parallel nature of the Jacobi iterative method make the Jacobi method an ideal candidate for hardware acceleration. This paper introduces a parameterized design for a deeply pipelined, highly parallelized IEEE 64-bit floating-point version of the Jacobi method. A Jacobi circuit is implemented using a Xilinx Virtex-II Pro as the target FPGA device. Implementation statistics and performance estimates are presented.
Software Defect Rediscoveries: A Discrete Lognormal Model
Authors: Robert E. Mullen, Swapna S. Gokhale
Venue: Proceedings of the 16th IEEE International Symposium on Software Reliability Engineering (2005)

Corrective software maintenance, which consists of fixing defects that escape detection and manifest as field failures, is expensive, yet vital to ensuring customer satisfaction. To allocate and use maintenance resources effectively, it is necessary to understand the defect occurrence phenomenon in the field. A preliminary analysis of the defect occurrence data suggests that software defects vary in rate from corner cases, which may occur only once, to the pervasive, which occur many times. This suggests that the distribution of occurrence counts is heavy-tailed. Theoretical reasons and mounting evidence indicate that the distribution of defect occurrence rates is lognormal. We hypothesize that the distribution of occurrence rates is lognormal, and further hypothesize that the distribution of the number of occurrence counts follows the Discrete-Lognormal,also known as the Poisson-Lognormal. We confirm that hypothesis, using a variety of data from widely used networking software. We also discuss how the Discrete-Lognormal applies to subsets of defects, where subsets are formed according to year of occurrence, products, Orthogonal Defect Classification (ODC) Age, and severities. We use straightforward interpretations of the parameters of the lognormal to understand how values differ for different types of defects and for different software characteristics.
ClickRemoval: interactive pinpoint image object removal
Authors: Frank Nielsen, Richard Nock
Venue: Proceedings of the 13th annual ACM international conference on Multimedia (2005)

In this paper, we explore the problem of deleting objects in still pictures. We present an interactive system based on an intuitive user-friendly interface for removing undesirable objects in digital pictures. To erase an object in an image, a user indicates which object is to be removed by simply pinpointing it with the mouse cursor. As the mouse cursor rolls over the image, the current implicit selected object's border is highlighted, providing a visual feedback. In case where the computer-segmented area does not match the users' perception of the object, users can further provide a few inside/outside object cues by clicking on a small number of object or nonobject pixels. A small number of such cues is generally enough to reach a correct matching, even for complex textured images. Afterwards, the user removes the object by clicking the left mouse button, and a hole-filling technique is initiated to generate a seamless background portion. Our image manipulation system consists of two components: (i) fully automatic or partially user-steered image segmentation based on an improved fast statistical region-growing segmentation, and (ii) texture synthesis or image inpainting of irregular shaped hole regions. Experiments on a variety of photographs display the ability of the system to handle complex scenes with highly textured objects.
First robotics as a model for experiential problem-based learning: a comparison of student attitudes and interests in science, mathematics, engineering, and technology
Authors: Clinton Howard Isbell
Venue:  (2005)

This research study was undertaken to examine potential relationships between high school students' attitudes and interests in science, mathematics, engineering, and technology, and their participation in the FIRST Robotics Competition six-week challenge to design, and build a robot. High school students' gender and race, in relationship to students' interest in the aforementioned topics was also examined in this study. A convenience sample of 727 South Carolina public high school students agreed to participate in the study. Data were collected using pre-and post-survey questionnaires. Student participants completed pre-survey questionnaires at the onset of the 2005 FIRST Robotics Competition Kick-off, concurrent with the beginning of the second semester of the 2004&ndash;2005 school year. Participants completed post-survey questionnaires after six-weeks, the period of time allocated for teams to design, build, and ship their 2005 FIRST Robotics Competition robot. Data analyzed was collected from the group of students participating in FIRST Robotics (treatment), the experimental group, and the group of students who are not participating in FIRST Robotics (control). Findings reported that the pre- and post-survey questionnaire responses regarding attitudinal change were not significantly different in either the experimental or control group. High pre-survey dependent variable scores provided by students in the FIRST group did not allow for significant gain in each of the seven-attitudinal categories. Findings also indicated that there were significant attitudinal differences between students in the experimental group (FIRST), and students the control group (SMET) pre- and post-survey responses. Students in the FIRST group had statistically significant higher attitude means than students in the SMET group on both pre- and post-surveys in the seven-attitudinal categories. The frequency for responses to each question in the three interest categories on the pre- and post-survey was calculated for the experimental and control group to evaluate differences. The results expressed in percentages indicated that there were significant differences in respondent scores for the pre-survey versus the post-survey in the FIRST group. The null hypothesis concerning interest differences of high school students that participate in the FIRST Robotics six-week challenge as compared to students that do not participate in the program was rejected.
A new approach to complex object distributed storage distribution and identification
Authors: Henry Nelson Jerez Morales
Venue:  (2005)

This work introduces a new architectural framework for distributed complex object storage that improves upon the monolithic approach that is now commonly used in P2P networks. The framework provides almost complete independence to the two main components of these architectures, the identification and resource storage mechanisms. This is accomplished by extrapolating indirection in a manner reminiscent of the model-view-controller software design pattern. The various trade-offs associated with the design of such a system are evaluated with respect to the optimization of message generation for identifier resolution, content retrieval, overall throughput, as well as query and retrieval times. A major feature of the proposed architecture is that it allows for the inclusion of new distribution and storage technologies, while maintaining the functionality and independence of the underlying components found in existing distributed content storage networks.
Changes to the TODS editorial board
Authors: Richard Snodgrass
Venue: ACM SIGMOD Record (2005)

The December issue should be out soon, if it isn't already. It is a special issue of papers invited from the SIGMOD'04 and PODS'04 conferences. I thank the authors, associate editors, and reviewers (some from the SIGMOD and PODS program committees) for writing, reviewing, revising, reviewing again, and then getting into final form these papers in the amazingly short time of eighteen months. This is a very nice issue, with seven substantive papers.