ppxscal/embedding_network huggingface dataset:
Detecting Regulator-Target Gene Pairs from Expression Profile of Microarray
Authors: Hee-Jeong Jin, Ji-Yeon Lee, Hwan-Gue Cho
Venue: Proceedings of the 2007 Frontiers in the Convergence of Bioscience and Information Technologies (2007)

Generally time-series microarrays are widely used to detect the regulation structure because they contain useful information about the relationship among a few thousand genes. Lots of different approaches have been introduced to detect regulator-target pairs using whole expression data. In this paper, we present a simple, but efficient method for detecting the regulator-target pairs based on an alignment method. Comparing to previous work based on event-string comparison approach, the basic idea of our algorithm is different in that we have applied a parametric optimization for alignment scoring matrix by using a simple machine learning procedure. As a result, we get a sensitivity and a specificity that is 10 % higher than the recent work by Kwon[1].
Design of PDC fuzzy controllers under persistent disturbances and application in mechanical systems
Authors: J. V. Salcedo, M. Martínez
Venue: Advances in Engineering Software (2008)

This article proposes a method for designing parallel-distributed compensation fuzzy state-feedback controllers for nonlinear systems affected by persistent disturbances. Firstly, some methods proposed in the literature are analyzed and their weak points are discussed. A design scheme based on minimizing the 1-norm between the disturbance signal input and output is then proposed. Specifically, an upper bound on this norm, the *-norm, is minimized, which, unlike the 1-norm, can be formulated in terms of linear and bilinear matrix inequalities. Finally, this method is applied to a nonlinear mechanical system.
Fingerprint Verification Based on Absolute Distance and Intelligent BPNN
Authors: JuCheng Yang, ByoungJun Min, DongSun Park
Venue: Proceedings of the 2007 Frontiers in the Convergence of Bioscience and Information Technologies (2007)

A fingerprint verification system based on absolute distance and intelligent BPNN is proposed. An image-based method with invariant moment features for fingerprint matching is to overcome the demerits of the traditional minutiae-based method and Gabor feature-based method. The fingerprint verification system contains two stages: the off-line stage and the on-line stage. Each stage has a feature extraction model. A total of four sets of seven invariant moment features are extracted from four partition sub-images of a Region of Interest (ROI). Measuring the similarity between the feature vectors of test fingerprint and those of template fingerprint in the database is implemented by two methods, the absolute distance and the Back Propagation Neural Network (BPNN). The experimental results show that the proposed method with BPNN matching has a higher matching accuracy, while with absolute distance matching has a faster matching speed. Comparing with a traditional method, the proposed method performs better with a higher recognition rate, too. Keywords: fingerprint verification, matching invariant moments, absolute distance, BPNN
Log-det approximation based on uniformly distributed seeds and its application to Gaussian process regression
Authors: Yunong Zhang, W. E. Leithead, D. J. Leith, L. Walshe
Venue: Journal of Computational and Applied Mathematics (2008)

Maximum likelihood estimation (MLE) of hyperparameters in Gaussian process regression as well as other computational models usually and frequently requires the evaluation of the logarithm of the determinant of a positive-definite matrix (denoted by C hereafter). In general, the exact computation of logdetC is of O(N^3) operations where N is the matrix dimension. The approximation of logdetC could be developed with O(N^2) operations based on power-series expansion and randomized trace estimator. In this paper, the accuracy and effectiveness of using uniformly distributed seeds for logdetC approximation are investigated. The research shows that uniform-seed based approximation is an equally good alternative to Gaussian-seed based approximation, having slightly better approximation accuracy and smaller variance. Gaussian process regression examples also substantiate the effectiveness of such a uniform-seed based log-det approximation scheme.
Introducing privacy in a hospital information system
Authors: Stefano Braghin, Alberto Coen-Porisini, Pietro Colombo, Sabrina Sicari, Alberto Trombetta
Venue: Proceedings of the fourth international workshop on Software engineering for secure systems (2008)

Security and privacy issues in healthcare data management play a fundamental role in the widespread adoption of medical information systems. As a consequence, it is very important to define the right means for expressing and managing policies in order to comply with privacy-related standards and regulations. In this work, we extend an open source hospital information system in order to provide support for expressing and enforcing privacy-related policies, using as a starting point a conceptual model the authors developed in a previous work.
Estimation of stochastic volatility with LRD
Authors: Isabel Casas
Venue: Mathematics and Computers in Simulation (2008)

Understanding the behaviour of market prices is not simple. Stock market prices tend to have complicated distributions with strong skewness and fat tails. One important step in forecasting tomorrow's price is to estimate the volatility, i.e. how much tomorrow's price is expected to differ from today's price. In this paper the volatility is assumed to be a lognormal random process and in addition, it may display long-range dependence (LRD). The aim is to obtain the estimates of the mean, standard deviation and LRD parameter of the volatility process of the S&P 500.
Efficient cryptographic schemes provably as secure as subset sum
Authors: R. Impagliazzo, M. Naor
Venue: Proceedings of the 30th Annual Symposium on Foundations of Computer Science (1989)

Very efficient constructions, based on the intractability of the subset sum problem for certain dimensions, are shown for a pseudorandom generator and for a universal one-way hash function. (Pseudorandom generators can be used for private key encryption, and universal one-way hash functions for signature schemes). The increase in efficiency in the construction is due to the fact that many bits can be generated/hashed with one application of the assumed one-way function. All the constructions can be implemented in NC using an optimal number of processors.
Understanding the Universal Turing Machine: an implementation in JFLAP
Authors: Jonathan Jarvis, Joan M. Lucas
Venue: Journal of Computing Sciences in Colleges (2008)

We describe the implementation of a Universal Turing Machine for the JFLAP platform. JFLAP is most successful and widely used tool for visualizing and simulating automata such as finite state machines, pushdown automata, and Turing Machines. By executing our Universal Turing Machine in JFLAP, students get a direct and interactive experience of how this Turing Machine is capable of emulating other Turing Machines.
Practical Multicast Security Architecture Using Sleep State
Authors: Hoyoung Lee, Jing Liu, Sunyoung Han
Venue: Proceedings of the 22nd International Conference on Advanced Information Networking and Applications - Workshops (2008)

Multicast security researches have been going on for a decades. In representative, some standard documents have been submitted by IETF Working Group (WG) MSEC. The reason that multicast group security is more difficult than one-to-one security is because all group members must share single group key at the same time. Whenever members join and leave, the group key must be updated and distributed to all members to keep forward and backward secrecy. At this time, ‘1 affects n’ problem occurs. For a practical multicast security service in an actual world, it is not sufficient that membership state is divided into only two parts: join and leave. This paper describes different features between multicast and multicast security, and suggests the SLEEP state for the practical multicast security service.
Fast Computation of Hyper-exponential Approximations of the Response Time Distribution of MMPP/M/1 Queues
Authors: Paolo Romano, Bruno Ciciani, Andrea Santoro, Francesco Quaglia
Venue: Proceedings of the 41st Annual Simulation Symposium (anss-41 2008) (2008)

Input characterization to describe the flow of incoming traffic in network systems, such as the GRID and the WWW, is often performed by using Markov Modulated Poisson Processes (MMPP). Therefore, to enact capacity planning and Quality-of-Service (QoS) oriented design, the model of the servers that receive the incoming traffic is often described as a $MMPP/M/1$ queue. In a recent work we have provided an approximate solution for the response time distribution of the $MMPP/M/1$ queue, which is based on a hyper-exponential process obtained via a weighted superposition of the response time distributions of $M/M/1$ queues. Compared to exact solution methods, or simulative techniques, the aim of this approximation is to provide the potential for more efficient model solution, so to enable, e.g., real-time what-if analysis in system reconfiguration scenarios. In this paper, we show how fast the computation can be supported in practical settings by ad-hoc techniques allowing the hyper-exponential model to be solved with no iterative or numerical costly steps, which would otherwise be required in order to compute the length of transient phases due to state switches in the MMPP arrival process. An application to the context of performance analysis of a GRID system is also shown, supporting the efficiency of our proposal.
Kinematics Modeling of Human Motion Using System Identification Technique
Authors: R. Ahmad, M. S. Yaacob, M. B. Che Omar
Venue: Proceedings of the 2008 Second Asia International Conference on Modelling & Simulation (AMS) (2008)

Image processing techniques from motion captured images are accurate and cost effective method to give aset of data that defines the location of specified limb at every sequence of human motion. From this set of data, system identification was done to model the human motion. This project is a study on how performance of a model is influenced by the type of model whether it is a linear model or non-linear model and a single variable model or multi variable model. Two types of parameter estimator was used which were the least square estimate and recursive least square estimate. The study also was conducted to see how the number of lags can give effects to the model. The objective is to formulate a predictive model to analyze human motion. Simulation was done through the model to see the result and performance of model whether it can be a model for human motion representation.
Hypergraph partitioning for document clustering: a unified clique perspective
Authors: Tianming Hu, Hui Xiong, Wenjun Zhou, Sam Yuan Sung, Hangzai Luo
Venue: Proceedings of the 31st annual international ACM SIGIR conference on Research and development in information retrieval (2008)

Hypergraph partitioning has been considered as a promising method to address the challenges of high dimensionality in document clustering. With documents modeled as vertices and the relationship among documents captured by the hyperedges, the goal of graph partitioning is to minimize the edge cut. Therefore, the definition of hyperedges is vital to the clustering performance. While several definitions of hyperedges have been proposed, a systematic understanding of desired characteristics of hyperedges is still missing. To that end, in this paper, we first provide a unified clique perspective of the definition of hyperedges, which serves as a guide to define hyperedges. With this perspective, based on the concepts of hypercliques and shared (reverse) nearest neighbors, we propose three new types of clique hyperedges and analyze their properties regarding purity and size issues. Finally, we present an extensive evaluation using real-world document datasets. The experimental results show that, with shared (reverse) nearest neighbor based hyperedges, the clustering performance can be improved significantly in terms of various external validation measures without the need for fine tuning of parameters.
Multistreamed web transport for developing regions
Authors: Preethi Natarajan, Paul D. Amer, Randall Stewart
Venue: Proceedings of the second ACM SIGCOMM workshop on Networked systems for developing regions (2008)

A multistreamed web transport has the potential to reduce head-of-line (HOL) blocking, and improve response times in high latency Internet browsing environments, typical of developing regions. In our position paper [13], we proposed a design for HTTP over the multistreamed Stream Control Transmission Protocol (SCTP), and implemented the design for non-pipelined (HTTP 1.0) transactions in the Apache web server and Firefox web browser. We have since adapted Apache and Firefox to handle HTTP 1.1 persistent, pipelined transfers over SCTP streams. Initial emulation results over high latency paths reveal that HTTP over SCTP streams benefits from faster page downloads, and achieves visually perceivable improvements to pipelined objects' response times. Movies comparing page downloads of HTTP/TCP vs. HTTP/SCTP streams can be found on the author's website [12]. The promising results have motivated us to propose a low cost, easily realizable, gateway-based HTTP over SCTP deployment solution to enhance users' browsing experience in developing regions.
Dynamic aspect weaving using a planning-based adaptation middleware
Authors: Romain Rouvoy, Mikaël Beauvois, Frank Eliassen
Venue: Proceedings of the 2nd workshop on Middleware-application interaction: affiliated with the DisCoTec federated conferences 2008 (2008)

The growing complexity of applications has enforced the need for separation concern and modularity. These requirements become critical when considering self-adaptive mobile applications, which are capable of optimizing their behavior depending on their context of execution. In our context, the crosscutting concerns of a component-based application are managed by an adaptation middleware. This planning-based adaptation middleware tries to maximize the user satisfaction while minimizing the adaptation cost and the resource consumption. However, the integration of crosscutting concerns (e.g., logging, security) usually leads to a combinatorial explosion of the alternative implementations. Therefore, we propose to integrate aspect-oriented programming principles in our planning-based adaptation middleware to leverage the development and the integration of crosscutting concerns. Thanks to a uniform modeling approach, our adaptation middleware is able to automatically select and configure the aspect(s) to weave into a base component for improving its quality of service.
Search effectiveness with a breadth-first crawl
Authors: Dennis Fetterly, Nick Craswell, Vishwa Vinay
Venue: Proceedings of the 31st annual international ACM SIGIR conference on Research and development in information retrieval (2008)

Previous scalability experiments found that early precision improves as collection size increases. However, that was under the assumption that a collection's documents are all sampled with uniform probability from the same population. We contrast this to a large breadth-first web crawl, an important scenario in real-world Web search, where the early documents have quite different characteristics from the later documents.
Prediction of Interacting Motif Pairs Using Stochastic Boosting
Authors: Jisu Kim, Byungkyu Park, Kyungsook Han
Venue: Proceedings of the 2007 Frontiers in the Convergence of Bioscience and Information Technologies (2007)

The recent development of high-throughput experimental methods has generated a large amount of protein interaction data, which is becoming the foundation for new biological discoveries. There are several methods developed for motif discovery, but these methods focus on detecting individual motifs rather than interacting motif pairs. The primary focus of this study is to predict reliable interacting motif pairs from combinations of protein features using a stochastic method. This paper describes an improved boosting algorithm for predicting interacting motif pairs of proteins and a method for generating negative interaction data for the algorithm.
Using semantics in XML query processing
Authors: Zhifeng Bao, Huayu Wu, Bo Chen, Tok Wang Ling
Venue: Proceedings of the 2nd international conference on Ubiquitous information management and communication (2008)

Efficient query processing in XML database has attracted extensive research efforts. However, majority of existing approaches for XML query processing do not exploit semantic information in the underlying database. In this paper, we address the importance of using semantics for XML query processing. In particular, we consider two common types of queries in XML, twig pattern query and keyword search query. We discuss how semantics can be used for optimizing twig pattern queries. Then, we discuss the usage of semantics to interpret keyword queries in order to retrieve and rank the most relevant results to users.
Numerical solutions of the generalized Kuramoto-Sivashinsky equation by Chebyshev spectral collocation methods
Authors: A. H. Khater, R. S. Temsah
Venue: Computers Mathematics with Applications (2008)

Chebyshev spectral collocation methods (known as El-Gendi method [S.E. El-Gendi, Chebyshev solution of differential integral and integro-differential equations, Comput. J. 12 (1969) 282-287; B. Mihaila, I. Mihaila, Numerical approximation using Chebyshev polynomial expansions: El-gendi's method revisited, J. Phys. A 35 (2002) 731-746]) are extended to deal with the generalized Kuramoto-Sivashinsky equation. The problem is reduced to a system of ordinary differential equations that are solved by combinations of backward differential formula and appropriate explicit schemes (implicit-explicit BDF methods [G. Akrivis, Y.S. Smyrlis, Implicit-explicit BDF methods for the Kuramoto-Sivashinsky equation, Appl. Numer. Math. 51 (2004) 151-169]). Good numerical results have been obtained and compared with the exact solutions.
An integrated web-based system for assignment creation, management, and peer evaluation
Authors: Vishal Monpara, Dulal C. Kar
Venue: Journal of Computing Sciences in Colleges (2008)

Many public domain and commercial course management systems that are available these days meet some general requirements for managing courses of an institution. Unfortunately, none of them offer the capability of assignment creation, management, and peer evaluation integrated into a single system that can save time and effort for students and instructors as well as offer convenience. In this work, we propose an integrated, multipurpose assignment management system that assists instructors to create and maintain assignment problems and allows students to view assignments, submit their solutions, and do online evaluation of assignments of peer students from a Web-based interface. The system supports multiple courses and has a common question bank that holds static questions as well as templates of questions that can be used by instructors to dynamically generate specific questions through substitution of parameters during assignment creation. In order to guide students in peer evaluation of an assignment, an instructor can create and publish a rubric-a scoring tool with a list of criteria to evaluate a peer's work. The system provides an excellent environment for students to do peer-evaluation anonymously and learn from each other in the process.
Accelerated VB 2008 (Accelerated)
Authors: Guy Fouch, Trey Nash
Venue:  (2008)

Visual Basic 2008 offers powerful new features, and Accelerated VB 2008 is the fastest path to mastering them, and the rest of Visual Basic, for both experienced Visual Basic programmers moving to VB 2008 and programmers moving to Visual Basic from another objectoriented language. Many books introduce VB, but very few also explain how to use it optimally with the .NET common language runtime (CLR). This book teaches both core Visual Basic language concepts and how to wisely employ VB idioms and objectoriented design patterns to exploit the power of VB and the CLR. Accelerated VB 2008 is both a rapid tutorial and a permanent reference. Youll quickly master VB syntax while learning how the CLR simplifies many programming tasks. Youll also learn best practices that ensure your code will be efficient, reusable, and robust. Why spend months or years discovering the best ways to design and code VB when this book will show you how to do things the right way, right from the start? Comprehensively and concisely explains both Visual Basic 2005 and Visual Basic 2008 features Focuses on the language itself and on how to use Visual Basic 2008 proficiently for all .NET application development Concentrates on how VB features work and how to best use them for robust, highperformance code What youll learn How VB works with and exploits the CLR How to use arrays and collections How to handle events with delegates How to design and use generic types and methods How to thread efficiently and robustly How the new VB 2008 anonymous types, lamba expressions, and extension methods work and how to use them Who is this book for? If youre an experienced VB programmer, you need to understand how VB has changed with VB 2008. If youre an experienced objectoriented programmer moving to VB, you want to ramp up quickly in the language while learning the latest features and techniques. In either case, this book is for you. The first three chapters succinctly present VB fundamentals for those new to or reviewing VB. The rest of the book covers all the major VB features in great detail, explaining how they work and how best to use them. Whatever your background or need, youll treasure this book for as long as you code in VB 2008. Related Titles Beginning ASP.NET 3.5 in VB 2008: From Novice to Professional Visual Basic 2008 Recipes: A Problem-Solution Approach Pro WPF in VB 2008: Windows Presentation Foundation in .NET 3.5 Pro VB 2008 and the .NET 3.5 Platform, Third Edition
Irredundance in inflated graphs
Authors: Odile Favaron
Venue: Journal of Graph Theory (1998)

The inflation GI of a graph G with n(G) vertices and m(G) edges is obtained by replacing every vertex of degree d of G by a clique Kd. We study the lower and upper irredundance parameters ir and IR of an inflation. We prove in particular that if &gamma; denotes the domination number of a graph, &gamma;(GI) - ir(GI) can be arbitrarily large, IR(GI) &le; m(G) and IR(GI) &le; n2(G)-4. These results disprove a conjecture of Dunbar and Haynes (Congr. Num. 118 (1996), 143154) and answer another open question. &copy; 1998 John Wiley Sons, Inc. J Graph Theory 28: 97104, 1998
Techniques and tools for the automatic generation of optimal test data at code, model and interface level
Authors: Florin Pinte, Norbert Oster, Francesca Saglietti
Venue: Companion of the 30th international conference on Software engineering (2008)

This article presents two different tools automating the generation of optimized test data for unit, model-based and integration testing by maximizing the coverage and minimizing the number of test cases required. To cope with these conflicting goals, hybrid self-adaptive and multi-objective evolutionary algorithms were applied. The efficiency was demonstrated by evaluating fault detection capability by mutation testing. Thanks to the effort reduction offered, the approach is particularly suitable for the verification of complex, safety-relevant software systems.