ppxscal/embedding_network huggingface dataset:
Feature Extraction from Protein Sequences and Classification of Enzyme Function
Authors: Bum Ju Lee, Keun Ho Ryu
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

Enzymes are biological catalysts that mediate almost all chemical reactions and are found in all tissues and fluids of the body. These enzymes play a central role in metabolic pathways, and in the prediction of metabolic pathways. Our goals in the present study were to identify new features for reliable enzyme functional classification and prediction that do not rely on sequence alignment, and to improve the accuracy or lower the error rate using the attribute selection method. In this study, we designed novel features, including PPR, NNR, PNPR, PPRDist(x, y), NNRDist(x, y), and PNPRDist(x, y), extracted from each protein sequence. Using only protein sequences, we compiled a set of 84 attributes that characterize proteins, and obtained accuracy of 72.13% through identification of optimal attributes in a given dataset. Our experiment results demonstrate that these attributes, as novel features, are useful for enzyme functional classification. In addition, we identify and analyze the biologically meaningful features of a given dataset.
Fibonacci Heaps And Their Uses In Improved Network Optimization Algorithms
Authors: M. L. Fredman
Venue: Proceedings of the 25th Annual Symposium onFoundations of Computer Science, 1984 (1984)

In this paper we develop a new data structure for implementing heaps (priority queues). Our structure, Fibonacci heaps (abbreviated F-heaps), extends the binomial queues proposed by Vuillemin and studied further by Brown. F-heaps support arbitrary deletion from an n-item heap in 0(log n) amortized time and all other standard heap operations in 0(1) amortized time. Using F-heaps we are able to obtain improved running times for several network optimization algorithms.
Orthogonal space-time block coding with adaptive transmit diversity for correlated MIMO channels
Authors: Kevin H. Lin, Zahir M. Hussain, Richard Harris
Venue: Proceedings of the 2nd WSEAS International Conference on Electronics, Control and Signal Processing (2003)

In this paper we introduce a technique of eigenbeamforming based on the channel correlation matrix and paired with orthogonal space-time code (O-STBC) at the transmitter side of the link. This structure combines the spatial signal paths decorrelation with the diversity gain provided by the space-time code, which results in performance improvement. The probability distributions for both bit-error-rate (BER) and symbol-error-rate (SER) are presented based on the received signal-to-noise ratio (SNR) for this system. The system has been simulated using four transmit antennas in both uncorrelated and correlated channels. Results showed that the proposed scheme provides a significant improvement in the error rate performance of spatially correlated channels.
Closed Sets for Labeled Data
Authors: Gemma C. Garriga, Petra Kralj, Nada Lavrač
Venue: The Journal of Machine Learning Research (2008)

Closed sets have been proven successful in the context of compacted data representation for association rule learning. However, their use is mainly descriptive, dealing only with unlabeled data. This paper shows that when considering labeled data, closed sets can be adapted for classification and discrimination purposes by conveniently contrasting covering properties on positive and negative examples. We formally prove that these sets characterize the space of relevant combinations of features for discriminating the target class. In practice, identifying relevant/irrelevant combinations of features through closed sets is useful in many applications: to compact emerging patterns of typical descriptive mining applications, to reduce the number of essential rules in classification, and to efficiently learn subgroup descriptions, as demonstrated in real-life subgroup discovery experiments on a high dimensional microarray data set.
Using space windowing for a preliminary analysis of complex time data in human component system studies. Examples with eye-tracking in advertising and car/head movements in driving
Authors: P. Loslever, P. Simon, F. Rousseau, J. C. Popieul
Venue: Information Sciences: an International Journal (2008)

Empirical studies of human systems often involve recording multidimensional signals because the system components may require physical measurements (e.g., temperature, pressure, body movements and/or movements in the environment) and physiological measurements (e.g., electromyography or electrocardiography). Analysis of such data becomes complex if both the multifactor aspect and the multivariate aspect are retained. Three examples are used to illustrate the role of fuzzy space windowing and the large number of data analysis paths. The first example is a classic simulated data set found in the literature, which we use to compare several data analysis paths generated with principal component analysis and multiple correspondence analysis with crisp and fuzzy windowing. The second example involves eye-tracking data based on advertising, with a focus on the case of one category variable, but with the possibility of several space windowing models and time entities. The third example concerns car and head movement data from a driving vigilance study, with a focus on the case involving several quantitative variables. The notions of analysis path multiplicity and information are discussed both from a general perspective and in terms of our two real examples.
A Survey of Opportunistic Networks
Authors: Chung-Ming Huang, Kun-chan Lan, Chang-Zhou Tsai
Venue: Proceedings of the 22nd International Conference on Advanced Information Networking and Applications - Workshops (2008)

We define an opportunistic network as one type of challenged networks where network contacts are intermittent or where link performance is highly variable or extreme. In such a network, there does not exist a complete path from source to destination for most of the time. In addition, the path can be highly unstable and may change or break quickly. Therefore, in order to make communication possible in an opportunistic network, the intermediate nodes may take custody of data during the blackout and forward it when the connectivity resumes. In this paper, we discuss some research challenges in an opportunistic network.
Predicting contact map using Radial Basis Function Neural Network with Conformational Energy Function
Authors: Peng Chen, De-Shuang Huang, Xing-Ming Zhao, Xueling Li
Venue: International Journal of Bioinformatics Research and Applications (2008)

Contact map, which is important to understand and reconstruct protein's three-dimensional (3D) structure, may be helpful to solve the protein's 3D structure. This paper presents a novel approach to predict the contact map using Radial Basis Function Neural Network (RBFNN) optimised by Conformational Energy Function (CEF) based on chemico-physical knowledge of amino acids. Finally, the results are trimmed by Short-Range Contact Function (SRCF). Consequently, it can be found that our proposed method is better than the existing methods such as PROFcon and the PE-based method. Particularly, this method can accurately predict 35% of contacts at a distance cutoff of 8 Å.
Learning Agents in an Artificial Power Exchange: Tacit Collusion, Market Power and Efficiency of Two Double-auction Mechanisms
Authors: Eric Guerci, Stefano Ivaldi, Silvano Cincotti
Venue: Computational Economics (2008)

This paper investigates the relative efficiency of two double-auction mechanisms for power exchanges, using agent-based modeling. Two standard pricing rules are considered and compared (i.e., "discriminatory" and "uniform") and computational experiments, characterized by different inelastic demand level, explore oligopolistic competitions on both quantity and price between learning sellers/producers. Two reinforcement learning algorithms are considered as well--"Marimon and McGrattan" and "Q-learning"--in an attempt to simulate different behavioral types. In particular, greedy sellers (optimizing their instantaneous rewards on a tick-by-tick basis) and inter-temporal optimizing sellers are simulated. Results are interpreted relative to game-theoretical solutions and performance metrics. Nash equilibria in pure strategies and sellers' joint profit maximization are employed to analyze the convergence behavior of the learning algorithms. Furthermore, the difference between payments to suppliers and total generation costs are estimated so as to measure the degree of market inefficiency. Results point out that collusive behaviors are penalized by the discriminatory auction mechanism in low demand scenarios, whereas in a high demand scenario the difference appears to be negligible.
Vector extrapolation methods with applications to solution of large systems of equations and to PageRank computations
Authors: Avram Sidi
Venue: Computers Mathematics with Applications (2008)

An important problem that arises in different areas of science and engineering is that of computing the limits of sequences of vectors {x"n}, where x"n@?C^N with N very large. Such sequences arise, for example, in the solution of systems of linear or nonlinear equations by fixed-point iterative methods, and lim"n"->"~x"n are simply the required solutions. In most cases of interest, however, these sequences converge to their limits extremely slowly. One practical way to make the sequences {x"n} converge more quickly is to apply to them vector extrapolation methods. In this work, we review two polynomial-type vector extrapolation methods that have proved to be very efficient convergence accelerators; namely, the minimal polynomial extrapolation (MPE) and the reduced rank extrapolation (RRE). We discuss the derivation of these methods, describe the most accurate and stable algorithms for their implementation along with the effective modes of usage in solving systems of equations, nonlinear as well as linear, and present their convergence and stability theory. We also discuss their close connection with the method of Arnoldi and with GMRES, two well-known Krylov subspace methods for linear systems. We show that they can be used very effectively to obtain the dominant eigenvectors of large sparse matrices when the corresponding eigenvalues are known, and provide the relevant theory as well. One such problem is that of computing the PageRank of the Google matrix, which we discuss in detail. In addition, we show that a recent extrapolation method of Kamvar et al. that was proposed for computing the PageRank is very closely related to MPE. We present a generalization of the method of Kamvar et al. along with a very economical algorithm for this generalization. We also provide the missing convergence theory for it.
Optimal control problem of development of an electric power system
Authors: I. V. Karaulova, E. V. Markova
Venue: Automation and Remote Control (2008)

A problem is considered for the definition of long-term strategies of the placing in service and disassembly of electric powers of an electric power system, which is described with the aid of nonclassical Volterra integral equations of the 1st kind. A problem is stated of the search for optimal terms of service of generating powers that afford the prescribed requirement for electric energy at the minimum of total expenditures, for the placing in service (input) and operation of generating powers. Results are given of the calculation for the United electric power system of Russia.
A two-step etching method to fabricate nanopores in silicon
Authors: Gou-Jen Wang, Wei-Zheng Chen, Kang J. Chang
Venue: Microsystem Technologies (2008)

A cost effective method to fabricate nanopores in silicon by only using the conventional wet-etching technique is developed in this research. The main concept of the proposed method is a two-step etching process, including a premier double-sided wet etching and a succeeding track-etching. A special fixture is designed to hold the pre-etched silicon wafer inside it such that the track-etching can be effectively carried out. An electrochemical system is employed to detect and record the ion diffusion current once the pre-etched cavities are etched into a through nanopore. Experimental results indicate that the proposed method can cost effectively fabricate nanopores in silicon. A through pore with pore size being around 14&#x00a0;nm can be fabricated.
Embedding of graphs in two-irregular graphs
Authors: M. Axenovich, Z. Füredi
Venue: Journal of Graph Theory (2001)

A graph G on n vertices is called two-irregular if there are at most two vertices having the same degree for all possible degrees. We show that every graph with maximal degree at most n-8&thinsp;-&thinsp;O(n3-4) can be embedded into a two-irregular graph. We obtain it as a corollary of an algorithmic proof of a result about packing the graphs. This improves the bound of O(n1-4) given by Faudree et al. &copy; 2001 John Wiley & Sons, Inc. J Graph Theory 36: 75&ndash;83, 2001
A service-curve framework for packet scheduling with switch configuration delays
Authors: R. L. Cruz, Saleh Al-Harthi
Venue: IEEE/ACM Transactions on Networking (TON) (2008)

In modern packet switches, technology limitations may introduce switch configuration delays that are nonnegligible compared with the time required to transmit a single packet. In this paper, we propose a methodology for scheduling of packets, in the context of these technology limitations. If the total tolerable delay through a packet switch is at least on the order of the switch configuration delay, we show that a near 100% utilization of the communication links is possible, while providing strict quality of service guarantees. The main idea is to increase the quantum with which data is scheduled and switched to beyond that of a single packet. This also decreases the rate at which scheduling need to be made, and hence decreases the implementation complexity. The quality of service guarantees we consider are in terms of a service curve. Specifically, we present a framework for the provision of service curves while coping with non-negligible switch configuration delays.
Delay-bounded routing in vehicular ad-hoc networks
Authors: Antonios Skordylis, Niki Trigoni
Venue: Proceedings of the 9th ACM international symposium on Mobile ad hoc networking and computing (2008)

Ad hoc networks formed by traveling vehicles are envisaged to become a common platform that will support a wide variety of applications, ranging from road safety to advertising and entertainment. The multitude of vehicular applications calls for routing schemes that satisfy user-defined delay requirements while at the same time maintaining a low level of channel utilization to allow their coexistence. This paper focuses on the development of carry-and-forward schemes that attempt to deliver data from vehicles to fixed infrastructure nodes in an urban setting. The proposed algorithms leverage local or global knowledge of traffic statistics to carefully alternate between the Data Muling and Multihop Forwarding strategies, in order to minimize communication overhead while adhering to delay constraints imposed by the application. We provide an extensive evaluation of our schemes using realistic vehicular traces on a real city map.
Inferring locks for atomic sections
Authors: Sigmund Cherem, Trishul Chilimbi, Sumit Gulwani
Venue: ACM SIGPLAN Notices (2008)

Atomic sections are a recent and popular idiom to support the development of concurrent programs. Updates performed within an atomic section should not be visible to other threads until the atomic section has been executed entirely. Traditionally, atomic sections are supported through the use of optimistic concurrency, either using a transactional memory hardware, or an equivalent software emulation (STM). This paper explores automatically supporting atomic sections using pessimistic concurrency. We present a system that combines compiler and runtime techniques to automatically transform programs written with atomic sections into programs that only use locking primitives. To minimize contention in the transformed programs, our compiler chooses from several lock granularities, using fine-grain locks whenever it is possible. This paper formally presents our framework, shows that our compiler is sound (i.e., it protects all shared locations accessed within atomic sections), and reports experimental results.
Simulators of the Direction Channel of the Passive Optoelectronic Rangefinder
Authors: Vladimir Cech, Jiri Jevicky
Venue: Proceedings of the Tenth International Conference on Computer Modeling and Simulation (2008)

The contribution includes characterizations of basic properties of two physically realized devices – simulators. It is the simulator of random kinematics excitation (the RKE Simulator) and the simulator of direction channel (the DCh Simulator). These simulators serve to probe for properties of the operator as an element of special man-machine system, which is the subsystem of the sensory system on the base of a passive optoelectronic rangefinder.
Memory hierarchy performance measurement of commercial dual-core desktop processors
Authors: Lu Peng, Jih-Kwon Peir, Tribuvan K. Prakash, Carl Staelin, Yen-Kuang Chen, David Koppelman
Venue: Journal of Systems Architecture: the EUROMICRO Journal (2008)

As chip multiprocessor (CMP) has become the mainstream in processor architectures, Intel and AMD have introduced their dual-core processors. In this paper, performance measurement on an Intel Core 2 Duo, an Intel Pentium D and an AMD Athlon 64x2 processor are reported. According to the design specifications, key derivations exist in the critical memory hierarchy architecture among these dual-core processors. In addition to the overall execution time and throughput measurement using both multi-program-med and multi-threaded workloads, this paper provides detailed analysis on the memory hierarchy performance and on the performance scalability between single and dual cores. Our results indicate that for better performance and scalability, it is important to have (1) fast cache-to-cache communication, (2) large L2 or shared capacity, (3) fast L2 to core latency, and (4) fair cache resource sharing. Three dual-core processors that we studied have shown benefits of some of these factors, but not all of them. Core 2 Duo has the best performance for most of the workloads because of its microarchitecture features such as the shared L2 cache. Pentium D shows the worst performance in many aspects due to its technology-remap of Pentium 4 without taking the advantage of on-chip communication.
Binding skolem clauses in theorem prover resolution for automated hypothetical question answering
Authors: A. K. Rabiah, T. M. T. Sembok, B. Z. Halimah
Venue: Proceedings of the 5th WSEAS International Conference on Computational Intelligence, Man-Machine Systems and Cybernetics (2006)

This paper described a new approach of adapting an existing theorem prover to the hypothetical question in generating an automated answer to a restricted domain such as reading comprehension. The adaptation of this theorem prover involves the modification of some components from our experiment such as: Knowledge Representation and Answer Extraction Agent. Question answering systems employing Skolemized Clauses Binding as the basic reasoning technique have been used to provide hypothetical answers to questions by considering a theorem to be proven as question. Hypothetical answer is an answer which comes from the text and logical thinking that is not explicitly stated in the text. It can be shown in general form X ⇒ Y, where X cannot be proven based on the information in the knowledge base. The notion of what constitutes an answer can be expanded so that the skolemized clauses binding, added as an intermediate approach generated while finding the hypothetical answer, may be regarded as answer. When there is not enough information in a knowledge base to provide a hypothetical answer, an approach such as answer generation requires an external resource similar to world knowledge in order to obtain relevant answer for the question given.
The Practical System Architecture for the Wireless Sensor Networks
Authors: Hyun-Jin Kim, Junmo Yang
Venue: Proceedings of the 2008 International Conference on Multimedia and Ubiquitous Engineering (2008)

In Wireless Sensor Networks (WSNs) and Wireless Personal Area Networks (WPANs), IEEE 802.15.4 [1] has emerged to be one of promising radio specifications at the view of physical layer and medium access control. Without any help of infrastructure, the low rate and low power communication should be guaranteed. To utilize the collected information under WSNs, the data typically pass through gateways or sinks. Simultaneously, the control messages for sensor networks reach to each sensor node via gateways. However, both multi-destinations of sensing data and multi-devices of each sensor node make the design of gateways and application servers be challenging issues. In this paper, the practical system architecture of WSNs has been proposed with the respect to the gateways and service broker. Additionally, the real deployment of proposed WSN system architecture will be discussed in this paper.
New architecture and algorithms for fast construction of hose-model VPNs
Authors: Jian Chu, Chin-Tau Lea
Venue: IEEE/ACM Transactions on Networking (TON) (2008)

Hose-model virtual private networks (VPNs) provide customers with more flexibility in specifying bandwidth requirements than pipe-model VPNs. Many hose-model VPN provisioning algorithms have been proposed, and they focus on the bandwidth efficiency in the construction of a single hose-model VPN. In practice, however, VPNs come and go and the dynamics will affect the performance of these VPN provisioning algorithms. If the frequency of adding and deleting VPNs is high, these algorithms will have a scalability problem. We propose in this paper a new network architecture for dynamic VPN construction. In the proposed architecture, adding a new VPN is much simpler and faster, and all that is required is to check if the edge routers have enough bandwidth. There is no need to check the bandwidth left on each internal link because the architecture guarantees that as long as the edge routers have enough capacities to accept the VPN, the internal links will never experience overflow caused by adding the new VPN. We present a linear programming formulation for finding the optimal routing that maximizes the amount of admissible VPN traffic in the network. We then exploit the underlying network flow structure and convert the linear programming problem into a subgradient iterative search problem. The resulting solution is significantly faster than the linear programming approach.
Abstract State Spaces for Time Petri Nets Analysis
Authors: Bernard Berthomieu, Florent Peres, François Vernadat
Venue: Proceedings of the 2008 11th IEEE Symposium on Object Oriented Real-Time Distributed Computing (2008)

Since their introduction by Merlin in 1974, Time Petri nets have been widely used for the specification and verification of time constrained systems. The state spaces of Time Petri nets are typically infinite. Model checking them first requires to produce finite abstractions for their state spaces preserving the properties of interest. The paper overviews the essential available abstractions.
Proposed Design Notation for Model Transformation
Authors: Lukman Ab. Rahim, Sharifah Bahiyah Rahayu Syed Mansoor
Venue: Proceedings of the 19th Australian Conference on Software Engineering (2008)

In developing software using model-driven approach, the key technique used is model transformation. Model transformation requires the development of transformation rules. Design of the transformation rules will allow the rules to be understood by people without the need to know the language to write the rules. This paper proposes a notation for designing the transformation rules. The abstract syntax, concrete syntax, semantics and well-formedness of the proposed notation are explained here. Examples and experience in using the notation are also given.