ppxscal/embedding_network huggingface dataset:
Peak bagging for peptide mass fingerprinting
Authors: Zengyou He, Can Yang, Weichuan Yu
Venue: Bioinformatics (2008)

Motivation: Mass Spectrometry (MS)-based protein identification via peptide mass fingerprinting (PMF) is a key component in high-throughput proteome research. While PMF was the first commonly used protein identification method, provided higher throughput than the tandem MS-based method, its accuracy is lower than that of the tandem MS method. Thus, it is desirable to develop PMF-based algorithm with higher protein identification accuracy to facilitate proteome research. Results: We propose a peak bagging method for single MS-based protein identification. It combines results from multiple PMF algorithms, where each PMF algorithm takes a random peak subset as input. Evaluation with a set of real MALDI-TOF MS spectra shows that the new peak bagging method provides consistent improvements over the single PMF algorithm. Contact: eezyhe@ust.hk
PECOLE: P2P multimedia collaborative environment
Authors: Abdulmotaleb Saddik, Abdur Rahman, Souhail Abdala, Bogdan Solomon
Venue: Multimedia Tools and Applications (2008)

PECOLE (Peer-to-pEer COLlaborative Environment) is a fully decentralized multimedia collaborative environment that supports a wide range of collaborative multimedia applications, including chat, shared browsing, shared telepointer, multipoint-to-multipoint audio/video conferencing and multilingual collaboration. PECOLE can intelligently run on very constrained resources, is highly resilient, scalable and does not rely on dedicated servers. Instead, PECOLE is built upon a Peer-to-Peer (P2P) overlay network, using SUN's JXTA framework and SWT technology. In this paper, we present the architecture and implementation of PECOLE with the performance results of the tests we conducted.
A generic grid interface for parallel and adaptive scientific computing. Part II: implementation and tests in DUNE
Authors: P. Bastian, M. Blatt, A. Dedner, C. Engwer, R. Kl&#x00f6;fkorn, R. Kornhuber, M. Ohlberger, O. Sander
Venue: Computing (2008)

In a companion paper (Bastian et al. 2007, this issue) we introduced an abstract definition of a parallel and adaptive hierarchical grid for scientific computing. Based on this definition we derive an efficient interface specification as a set of C++ classes. This interface separates the applications from the grid data structures. Thus, user implementations become independent of the underlying grid implementation. Modern C++ template techniques are used to provide an interface implementation without big performance losses. The implementation is realized as part of the software environment DUNE (http://dune-project.org/). Numerical tests demonstrate the flexibility and the efficiency of our approach.
A projection pursuit algorithm for anomaly detection in hyperspectral imagery
Authors: José A. Malpica, Juan G. Rejas, María C. Alonso
Venue: Pattern Recognition (2008)

The main goal of this paper is to propose an innovative technique for anomaly detection in hyperspectral imageries. This technique allows anomalies to be identified whose signatures are spectrally distinct from their surroundings, without any a priori knowledge of the target spectral signature. It is based on an one-dimensional projection pursuit with the Legendre index as the measure of interest. The index optimization is performed with a simulated annealing over a simplex in order to bypass local optima which could be sub-optimal in certain cases. It is argued that the proposed technique could be considered as seeking a projection to depart from the normal distribution, and unfolding the outliers as a consequence. The algorithm is tested with AHS and HYDICE hyperspectral imageries, where the results show the benefits of the approach in detecting a great variety of objects whose spectral signatures have sufficient deviation from the background. The technique proves to be automatic in the sense that there is no need for parameter tuning, giving meaningful results in all cases. Even objects of sub-pixel size, which cannot be made out by the human naked eye in the original image, can be detected as anomalies. Furthermore, a comparison between the proposed approach and the popular RX technique is given. The former outperforms the latter demonstrating its ability to reduce the proportion of false alarms.
Applying a finite-horizon numerical optimization method to a periodic optimal control problem
Authors: Jeffrey Azzato, Jacek B. Krawczyk
Venue: Automatica (Journal of IFAC) (2008)

Computing a numerical solution to a periodic optimal control problem can be difficult, especially when the period is unknown. A method of approximating a solution to a stochastic optimal control problem using Markov chains was developed in [Krawczyk, J. B. (2001). A Markovian approximated solution to a portfolio management problem. Information Technology for Economics and Management, 1, http://www.item.woiz.polsl.pl/issue/journal1.htm]. This paper describes the application of that method to a periodic optimal control problem formulated in [Gaitsgory, V. & Rossomakhine, S. (2006). Linear programming approach to deterministic long run average problems of optimal control. SIAM Journal on Control and Optimization, 44(6), 2006-2037]. As a result, approximately optimal feedback rules are computed that can control the system both on and off the optimal orbit.
Stability of iterative processes with errors for a system of nonlinear (A,η)-accretive variational inclusions in Banach spaces
Authors: Heng-you Lan
Venue: Computers Mathematics with Applications (2008)

In this paper, by using the concept of (A,@h)-accretive mappings and the new resolvent operator technique associated with (A,@h)-accretive mappings, we introduce and study a system of general mixed quasivariational inclusions involving (A,@h)-accretive mappings in Banach spaces, and construct a new perturbed iterative algorithm with mixed errors for this system of nonlinear (A,@h)-accretive variational inclusions in q-uniformly smooth Banach spaces. Our results improve and generalize the corresponding results of recent works.
Neural nets method for estimation of the software retesting necessity
Authors: Viktor Mikolaiyovich Lokasyuk, Oksana Viktorivna Pomorova, Tatiana Olexandrivna Govorushchenko
Venue: Proceedings of the 2008 international workshop on Software Engineering in east and south europe (2008)

The new software retesting concept which bases on the idea of the hidden program errors detection was described in this paper. Purpose of this concept is the program hidden errors identification after basic testing. As a result, the software life cycle was supplemented, because customer realizes retesting at incoming inspection stage. We use special architecture of artificial neural net for estimation of the software retesting necessity. It is a multi-layer-perceptron, which is composed with a simple Rosenblatt perceptron. The most effective training algorithms for this architecture are CGB on base conjugate-gradient method, one-step algorithm of secant method, algorithm SCG and threshold back-propagation error algorithm. The trained neural net gives information about total quantity and importance of the different levels errors in program.
A Price-Based Task Scheduling for Grid Computing
Authors: Marcelo Massocco Cendron, Carlos Becker Westphall
Venue: Proceedings of the Seventh International Conference on Networking (2008)

In this paper, we present some principles of grid economy, why it’s useful to scheduling task and what is involved in aGrid computing. And we present some results obtained with a framework that use the two model of economy to form a price of a service based, in a macroeconomic way is attributed a initial price for a resource based in your computation characteristics, this is a commodities market, and the microeconomic way, with the node varying your local price based on the demand/supply economic model.
Secure multi-hop network programming with multiple one-way key chains
Authors: Hailun Tan, Sanjay Jha, Diet Ostry, John Zic, Vijay Sivaraman
Venue: Proceedings of the first ACM conference on Wireless network security (2008)

Current network programming protocols provide an efficient way to update the program image running on sensor nodes without physical access to them. However, given the open environment in which sensor nodes are deployed, securing network programming is a challenging task. Existing work addressing this issue either lack consideration of securing multi-hop network programming protocols, or are not cost-efficient. To our knowledge, none of them have evaluated the power consumption. In this paper, we propose a novel scheme to secure multi-hop network programming protocols using multiple one-way hash chains. This scheme is resilient to malicious program image injection by the compromised nodes and it secures multi-hop propagation of program images for sensor nodes. Based on the most popular network programming protocol, Deluge, an overhead analysis on this schemes is given. In addition, our scheme is implemented in TinyOS and a performance evaluation in terms of latency and energy consumption is presented.
A closed-loop fuzzy traffic controller for fair bandwidth sharing
Authors: Dario Pompili, Francesco Delli Priscoli
Venue: ACM SIGBED Review (2008)

This paper introduces an innovative closed-loop traffic controller to efficiently and fairly share a single common resource, e.g., the available bit rate in a wireless link, among a set of traffic flows characterized by different Quality of Service (QoS) requirements. The proposed traffic controller relies on a control-based approach that exploits a closed-loop feedback architecture including Proportional-Integral-Derivative (PID) controllers that are dynamically tuned using fuzzy logic. The traffic controller is able to react to different scenarios and traffic load conditions, while targeting the twofold objective of maximizing the resource utilization and respecting the flow QoS requirements. Simulation results demonstrate that the proposed closed-loop traffic controller outperforms a well-known open-loop traffic controller (based on Dual Leaky Buckets (DLBs) and Earliest Deadline First (EDF) scheduling algorithm.
A Study of the AADL Mode Change Protocol
Authors: Dominique Bertrand, Anne-Marie Déplanche, Sébastien Faucou, Olivier H. Roux
Venue: Proceedings of the 13th IEEE International Conference on on Engineering of Complex Computer Systems (2008)

This paper describes a contribution to the verification of AADL models. It focuses on the part of the language dealing with operating modes. An analysis of the AADL mode change protocol is provided. Then, a translation process is exposed, that takes as an input an AADL model and produces as an output a Time Petri Net. Lastly, it is explained how the resulting Time Petri Net model can be used to (formally) verify some real-time properties of the AADL model.
Approximating the pathway axis and the persistence diagram of a collection of balls in 3-space
Authors: Eitan Yaffe, Dan Halperin
Venue: Proceedings of the twenty-fourth annual symposium on Computational geometry (2008)

Given a collection β of balls in three-dimensional space, each having a radius of at least 1, we present an approximation scheme that constructs a collection Kε of unit balls that approximate β, such that the Hausdorff distance between ∪β and ∪Kε is at most ε. We define the pathway axis as the subset of the medial axis of the complement of ∪β for which the set of closest balls in β do not have a common intersection. It is the medial axis of the complement of ∪β without `dead-ends' and therefore it is a good starting point for finding pathways that lie outside ∪β. The recently introduced persistence diagram of the distance function from ∪β encodes topological characteristics of the function, giving a measure on the importance of topological features such as voids or tunnels during a uniform growth process of β. In this paper we introduce the pathway diagram as a useful subset of the Voronoi diagram of the centers of the unit balls in Kε, which can be easily and efficiently computed. We show that the pathway diagram contains an approximation of the pathway axis of β. We prove a bound on the ratio |Kε|/|β|, namely the ratio between the number of unit balls in Kε and the number of balls in β. We employ this bound to show how we efficiently approximate the persistence diagram of ∪β. Finally, we show that our approach is superior to the standard point-sample approaches for the two problems that we address in this paper: Approximating the medial axis of the complement of ∪β, and approximating the persistence diagram of ∪β. In a companion paper we introduce MolAxis, a tool for the identification of channels in macromolecules, that demonstrates how the pathway diagram and the persistence diagram are used to identify pathways in the complement of molecules.
Analysis of the geographical accessibility of neurosurgical emergency hospitals in Sapporo city using GIS and AHP
Authors: K. Ohta, G. Kobashi, S. Takano, S. Kagaya, H. Yamada, H. Minakami, E. Yamamura
Venue: International Journal of Geographical Information Science (2007)

To improve the geographical accessibility of neurosurgical emergency hospitals for elderly people, we developed several alternative site plans for a new neurosurgical emergency hospital in Sapporo, Japan. Hospitals, population data, routes, and the numerical information for the Analytic Hierarchy Process computations were input into a Geographical Information System. Pairwise comparison revealed the following weights which were assigned to each of the four criteria: 0.674 for availability of hospital beds; 0.169 for the maximum road distance of the shortest routes; 0.101 for the elderly population within a 3-km radius; and 0.056 for the median road distance of the shortest routes. The alternative proposed could cover 4000 more elderly people in the 3-km radius of the hospitals. The integration of Geographical Information Systems and the Analytic Hierarchy Process constitutes a powerful tool for analysing traffic conditions in mid-sized cities and for suggesting city planning to improve prognosis of stroke.
Comparing the Accuracy of End-to-End Network Performance Measurement Testbed and Simulation Model for Data Transfers in Heterogeneous Environment
Authors: Mohd Nazri Ismail, Abdullah Mohd Zin
Venue: Proceedings of the 2008 Second Asia International Conference on Modelling & Simulation (AMS) (2008)

We present a novel approach for the measurement of one-way delays and throughput between network nodes in heterogeneous environment. This research investigates performance evaluation of remote data transfers on heterogeneous services and technologies environment. We propose an enhanced equation to evaluate the performance of network traffic management via Little Law and Queuing theory to improve the evaluation algorithm. To get accuracy results on the performance of simulation model, we measure (verify and validate) data from lab experiment. We use network management tool to capture those data and Ping Plotter application (network analyzer) to generate traffic. As a result, this simulation model can provide a good approximation of the real traffic (one-way delays and throughput) observed in the real network environment.
Weighted fair sharing for dynamic virtual clusters
Authors: Laura E. Grit, Jeffrey S. Chase
Venue: Proceedings of the 2008 ACM SIGMETRICS international conference on Measurement and modeling of computer systems (2008)

In a shared server infrastructure, a scheduler controls how quantities of resources are shared over time in a fair manner across multiple, competing consumers. It should support wide (parallel) requests for variable-sized pool of resources, provide assurance of minimum resource allotment on demand, and give predictable assignments. Our approach integrates a fair queuing algorithm with a calendar scheduler. We present WINKS, a proportional share allocation policy that addresses the needs of shared server environments. It extends start-time fair queuing to support wide requests with backfill, advance reservations, dynamic cluster sizing, dynamic request sizing, and intra-flow request prioritization. It also preserves fairness properties across queue transformations and calendar operations needed to implement these extensions.
Spatial aspects of MRSA epidemiology: a case study using stochastic simulation, kernel estimation and SaTScan
Authors: L. Bastin, J. Rollason, A. Hilton, D. Pillay, C. Corcoran, J. Elgy, P. Lambert, P. De, T. Worthington, K. Burrows
Venue: International Journal of Geographical Information Science (2007)

The identification of disease clusters in space or space-time is of vital importance for public health policy and action. In the case of methicillin-resistant Staphylococcus aureus (MRSA), it is particularly important to distinguish between community and health care-associated infections, and to identify reservoirs of infection. 832 cases of MRSA in the West Midlands (UK) were tested for clustering and evidence of community transmission, after being geo-located to the centroids of UK unit postcodes (postal areas roughly equivalent to Zip+4 zip code areas). An age-stratified analysis was also carried out at the coarser spatial resolution of UK Census Output Areas. Stochastic simulation and kernel density estimation were combined to identify significant local clusters of MRSA (p
Fractal coding of color images using earth mover's distance
Authors: Daniele D. Giusto, Maurizio Murroni, Giulio Soro
Venue: Proceedings of the 2nd international conference on Mobile multimedia communications (2006)

Fractal theory gained attention by mathematicians and engineers during the last two decades as a promising technique to obtain compression of signals. Fractals also provides interesting interpolation features that can be used to zoom images or to achieve slow motions of video sequences. This paper proposes a fractal coding technique based on Iterated Function Systems (IFS) to encode color image signals. IFS aim to exploit the redundancy given by the self-similarity always contained in natural images. The novelty of this work is on the use of Earth Mover's Distance (EMD) measure to identify similarities within color images. The results obtained show that the proposed approach allows achieving better quality in the decoded images than a classic fractal coding based on Root Mean Square Error (RMS) measure.
Self-arranging preservation networks
Authors: Charles L. Cartledge, Michael L. Nelson
Venue: Proceedings of the 8th ACM/IEEE-CS joint conference on Digital libraries (2008)

We pose the question: what if digital library objects could self-arrange without intervention from repositories and minimal intervention from administrators? We present background information about networks, techniques on how networks can be created based on locally discovered information, and how a small set of controlling policies can profoundly affect network configuration. This poster reflects a work in progress, providing information about the project's genesis, current status and future efforts.
Audiovisual integration with Segment Models for tennis video parsing
Authors: Manolis Delakis, Guillaume Gravier, Patrick Gros
Venue: Computer Vision and Image Understanding (2008)

Automatic video content analysis is an emerging research subject with numerous applications to large video databases and personal video recording systems. The aim of this study is to fuse multimodal information in order to automatically parse the underlying structure of tennis broadcasts. The frame-based observation distributions of Hidden Markov Models are too strict in modeling heterogeneous audiovisual data. We propose instead the use of segmental features, of the framework of Segment Models, to overcome this limitation and extend the synchronization points to the segment boundaries. Considering each segment as a video scene, auditory and visual features collected inside the scene boundaries can thus be sampled and modeled with their native sampling rates and models. Experimental results on a corpus of 15-h tennis video demonstrated a performance superiority of Segment Models with synchronous audiovisual fusion over Hidden Markov Models. Results though with asynchronous fusion are less optimistic.
New monitoring concepts for optical access networks
Authors: Jörg Hehmann, Thomas Pfeiffer
Venue: Bell Labs Technical Journal (2008)

New integrated monitoring concepts for physical layer supervision of optical access networks are presented. Network faults and outage times are mainly originated by drifts and degradations of parameters on the physical layer. Simple remotely controlled integrated measurement systems will help network operators improve network quality and reliability and save operational costs. In addition to supervision under the performance parameters of active network components, the optical fiber plant itself will be supervised by an embedded fiber monitoring system in future. We present the functionality of a demarcation point monitor as a new network element which provides information about network availability up to the home network. The operation and the performance parameters of the new monitoring systems are described, and the compatibility with the transmission system is shown in detail. Finally, the additional expenditures and the benefits for the operator are discussed. &copy; 2008 Alcatel-Lucent.
The Impact of Packet Type on Signal Strength in WLANs
Authors: Tanja Lang, Geoff Fellows, John Louis
Venue: Proceedings of the 22nd International Conference on Advanced Information Networking and Applications (2008)

In this paper we present our investigation on the impact that different packet types (data, management, control) have on the signal strength values observed by access points. Signal strength is often used as the major indicator for client location in WLAN location determination systems. It is vital for accurate prediction that the signal strength distribution and its variations is understood and modeled as closely as possible. We show that different packet types result in significantly different signal strength distributions and that a location determination system should therefore distinguish between the packet types and use the appropriate distribution for each packet type.
Detection Network Anomalies Based on Packet and Flow Analysis
Authors: Hong Wang, Zhenghu Gong, Qing Guan, Baosheng Wang
Venue: Proceedings of the Seventh International Conference on Networking (2008)

Anomalies generate vast amounts of bogus traffic, which can overwhelm the network and any attached hosts. Identifying Traffic anomalies rapidly and accurately is critical to network stability and usefulness. Most papers focus on analyzing the volume of data or packets on the network. However, legitimate network traffic may be bursty or highly variable, rendering such naive approaches ineffective[7]. We propose a novel method called MultiA to solve this problem. Rather than just looking at volumes of packets, MultiA intelligently adopted Multistage Filter and information entropy take into account the behavior of the network. The MultiA is scalable, automated and self-training. We find this technique effectively identifies network traffic anomalies while avoiding the high false alarms rate.