ppxscal/embedding_network huggingface dataset:
Efficient automatic exact motif discovery algorithms for biological sequences
Authors: Ali Karci
Venue: Expert Systems with Applications: An International Journal (2009)

Objective: This paper presents an algorithm for the solution of the motif discovery problem (MDP). Methods and materials: Motif discovery problem can be considered in two cases: motifs with insertions/deletions, and motifs without insertions/deletions. The first group motifs can be found by stochastic and approximated methods. The second group can be found by using stochastic and approximated methods, but also deterministic method. We proved that the second group motifs can be found with a deterministic algorithm, and so, it can be said that the second motifs finding is a P-type problem as proved in this paper. Results and conclusions: An algorithm was proposed in this paper for motif discovery problem. The proposed algorithm finds all motifs which are occurred in the sequence at least two times, and it also finds motifs of various sizes. Due to this case, this algorithm is regarded as Automatic Exact Motif Discovery Algorithm. All motifs of different sizes can be found with this algorithm, and this case was proven in this paper. It shown that automatic exact motif discovery is a P-type problem in this paper. The application of the proposed algorithm has been shown that this algorithm is superior to MEME, MEME3, Motif Sampler, WEEDER, CONSENSUS, AlignACE.
Faster convergence and higher accuracy for the Dirichlet-Neumann map
Authors: Johan Helsing
Venue: Journal of Computational Physics (2009)

New techniques allow for more efficient boundary integral algorithms to compute the Dirichlet-Neumann map for Laplace's equation in two-dimensional exterior domains. Novelties include a new post-processor which reduces the need for discretization points with 50%, a new integral equation which reduces the error for resolved geometries with a factor equal to the system size, systematic use of regularization which reduces the error even further, and adaptive mesh generation based on kernel resolution.
The Optimal H∞ Norm of a Parametric System Achievable by an Output Feedback Controller
Authors: Takuya Kitamoto, Tetsu Yamaguchi
Venue: IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences (2008)

H∞ optimal control is one of the most successful achievements in the post modern control theory. In the H∞ optimal control, we design a controller that minimizes the H∞ norm of a given system. Although the algorithms to solve the problem have already been reported, they focus on numerical systems (systems without any unknown parameters) and, can not be applied for parametric systems (systems with unknown parameters). Given a parametric system, this paper presents an algorithm to compute the optimal H∞ norm of the system achieved by an output feedback controller. The optimal H∞ norm is expressed as 1/√Φ(k), where Φ(k) denotes a root of a bivariate polynomial. A numerical example is given to show the effectiveness of the algorithm.
An efficient ranking and selection procedure for a linear transient mean performance measure
Authors: Douglas J. Morrice, Mark W. Brantley, Chun-Hung Chen
Venue: Proceedings of the 40th Conference on Winter Simulation (2008)

We develop a Ranking and Selection procedure for selecting the best configuration based on a transient mean performance measure. The procedure extends the OCBA approach to systems whose means are a function of some other variable such as time. In particular, we characterize this as a prediction problem and imbed a regression model in the OCBA procedure. In this paper, we analyze the linear case and discuss a number of extensions. Additionally, we provide some motivating examples for this approach.
A two-way paraxial system for simulation of wave backscattering by a random medium
Authors: Josselin Garnier, Knut Sølna
Venue: Journal of Computational Physics (2009)

This paper presents a probabilistic analysis of an iterative two-way paraxial scheme for the simulation of wave propagation in anisotropic random media. This scheme has the computational cost of the standard one-way paraxial wave equation but has the accuracy of the full wave equation in a regime beyond the classical paraxial regime. More precisely, it accurately predicts the statistics of the reflected wave field. The accuracy depends on two parameters: the order of the iterative scheme and the ratio of the random backscattering intensity over the random forward-scattering intensity.
A case-based approach for coordinated action selection in robot soccer
Authors: Raquel Ros, Josep Lluís Arcos, Ramon Lopez de Mantaras, Manuela Veloso
Venue: Artificial Intelligence (2009)

Designing coordinated robot behaviors in uncertain, dynamic, real-time, adversarial environments, such as in robot soccer, is very challenging. In this work we present a case-based reasoning approach for cooperative action selection, which relies on the storage, retrieval, and adaptation of example cases. We focus on cases of coordinated attacking passes between robots in the presence of the defending opponent robots. We present the case representation explicitly distinguishing between controllable and uncontrollable indexing features, corresponding to the positions of the team members and opponent robots, respectively. We use the symmetric properties of the domain to automatically augment the case library. We introduce a retrieval technique that weights the similarity of a situation in terms of the continuous ball positional features, the uncontrollable features, and the cost of moving the robots from the current situation to match the case controllable features. The case adaptation includes a best match between the positions of the robots in the past case and in the new situation. The robots are assigned an adapted position to which they move to maximize the match to the retrieved case. Case retrieval and reuse are achieved within the distributed team of robots through communication and sharing of own internal states and actions. We evaluate our approach, both in simulation and with real robots, in laboratory scenarios with two attacking robots versus two defending robots as well as versus a defender and a goalie. We show that we achieve the desired coordinated passing behavior, and also outperform a reactive action selection approach.
Modeling and analysis of semiconductor manufacturing in a shrinking world: challenges and successes
Authors: Chen-Fu Chien, Stéphane Dauzère-Pérès, Hans Ehm, John W. Fowler, Zhibin Jiang, Shekar Krishnaswamy, Lars Mönch, Reha Uzsoy
Venue: Proceedings of the 40th Conference on Winter Simulation (2008)

A panel session on the role of modeling and analysis in semiconductor manufacturing in a shrinking world is presented. Therefore, two participants are from Asia, two from Europe, and two from US and there are two panel organizers/moderators (Fowler and M&ouml;nch). One panelist from each continent is from industry and one from academia. Only initial position statements are included in the proceedings. However, these initial statements form the basis for the panel discussion. The statements of the panelists from industry relate to modeling and analysis problems found in their own companies. The position statements of the panelists from academia describe the role that modeling and analysis is expected to play in their current and ongoing research in semiconductor manufacturing. Furthermore, their views on the challenges and successes of modeling and analysis in a globalized world are also included.
Frequency-aware PPV: a robust phase macromodel for accurate oscillator noise analysis
Authors: Xiaolue Lai
Venue: Proceedings of the 2008 IEEE/ACM International Conference on Computer-Aided Design (2008)

Perturbation Projection Vector (PPV) is an established technique for oscillator phase noise analysis; However, the PPV method significantly loses accuracy when circuits have large time constants, resulting in over-estimation of oscillator phase noise. In this paper, we show the problem of the PPV phase equation that it ignores the dynamics of oscillator frequency responses, and propose an improved PPV technique: Frequency-Aware PPV (FW-PPV). Using the FW-PPV technique, we derive analytical phase noise equations, which work accurately for all oscillators, especially for oscillators with large time constants. We apply the proposed technique on real oscillator circuits, and compare the results to Cadence Spectre RF. Simulation results show that our method has better accuracy than previous approaches.
Terminological cleansing for improved information retrieval based on ontological terms
Authors: Antonio Jimeno-Yepes, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann
Venue: Proceedings of the WSDM '09 Workshop on Exploiting Semantic Annotations in Information Retrieval (2009)

Ontologies are frequently used in information retrieval being their main applications the expansion of queries, semantic indexing of documents and the organization of search results. However, the optimization of an ontology to perform information retrieval tasks is still unclear. In this paper, we propose an ontology query model to analyze the usefulness of ontologies in effectively performing document searches. Moreover, we propose a series of heuristic techniques that optimize ontologies for information retrieval tasks. Preliminary results demonstrate that current domain ontologies provide enough information to support user requests and that ontologies might be improved with simple methods.
An improved variable tap-length LMS algorithm
Authors: Ning Li, Yonggang Zhang, Yuxin Zhao, Yanling Hao
Venue: Signal Processing (2009)

An improved variable tap-length LMS algorithm is proposed in this paper. As compared with the original fractional tap-length LMS (FT-LMS) algorithm, the proposed algorithm can obtain both a fast convergence rate and a small steady-state error of the tap-length. Algorithm analysis is given which also provides a guideline for the parameter choice of the proposed algorithm. Simulations are performed under low noise and high noise conditions with time varying impulse responses. All simulation results show the advantages of the proposed algorithm as compared with the FT-LMS algorithm, and confirm the algorithm analysis.
Estimation of the autoregression parameter with infinite dispersion of noise
Authors: A. S. Markov
Venue: Automation and Remote Control (2009)

To estimate the unknown autoregression parameter in the case when noise has an infinite dispersion, the weighted estimate by the least-squares method is suggested. The limit distribution of the error of estimation is obtained. It is shown that the weighted estimate is asymptotically more exact in comparison with the common estimate by the least-squares method.
National security, individual privacy and public access to government-held information: the need for changing perspectives in a global environment
Authors: Shannon Martin, Debbie Rabina
Venue: Information and Communications Technology Law (2009)

Governments are often the largest collectors of data within their jurisdiction, and often that data collection and storage is financially supported with public taxes. How governments manage and make available that information when requested by non-government parties varies by country. As the data-sharing world finds new and multi-platform ways to network, variations in legal access to government-held information create both opportunities and challenges. In this article, recent research is reviewed on problems faced by legal systems trying to navigate conflicts between individual privacy, public access and national state security.
Categorizing Social Norms in a Simulated Resource Gathering Society
Authors: Daniel Villatoro, Jordi Sabater-Mir
Venue: Coordination, Organizations, Institutions and Norms in Agent Systems IV: COIN 2008 International Workshops, COIN@AAMAS 2008, Estoril, Portugal, May 12, 2008. COIN@AAAI 2008, Chicago, USA, July 14, 2008. Revised Selected Papers (2009)

Our main interest research is focused on reaching a decentralized form of social order through the usage of social norms in virtual communities. In this paper, we analyze the effects of different sets of social norms within a society. The simulation scenario used for the experiments is a metaphor of a resource-gatherer prehistoric society. Finally, we obtain a qualitative ranking of all the possible sets of social norms in our scenario performing agent-based simulation.
Interaction manifolds: understanding behaviour around a shareable interface
Authors: Cecily Morrison
Venue: Proceedings of the 21st British HCI Group Annual Conference on HCI 2008: People and Computers XXI: HCI...but not as we know it - Volume 2 (2007)

This poster presents a suggestion for how ethnography of shareable interfaces might be used to inform subsequent design decisions by creating an analytical construct that we name the interaction manifold. We first describe and summarize results of our research to date in a medical intensive care unit. We then propose why and how an analytic construct might prove useful for design of shareable interfaces.
Design of DL-based certificateless digital signatures
Authors: Lein Harn, Jian Ren, Changlu Lin
Venue: Journal of Systems and Software (2009)

Public-key cryptosystems without requiring digital certificates are very attractive in wireless communications due to limitations imposed by communication bandwidth and computational resource of the mobile wireless communication devices. To eliminate public-key digital certificate, Shamir introduced the concept of the identity-based (ID-based) cryptosystem. The main advantage of the ID-based cryptosystem is that instead of using a random integer as each user's public key as in the traditional public-key systems, the user's real identity, such as user's name or email address, becomes the user's public key. However, all identity-based signature (IBS) schemes have the inherent key escrow problem, that is private key generator (PKG) knows the private key of each user. As a result, the PKG is able to sign any message on the users' behalf. This nature violates the ''non-repudiation'' requirement of digital signatures. To solve the key escrow problem of the IBS while still taking advantage of the benefits of the IBS, certificateless digital signature (CDS) was introduced. In this paper, we propose a generalized approach to construct CDS schemes. In our proposed CDS scheme, the user's private key is known only to the user himself, therefore, it can eliminate the key escrow problem from the PKG. The proposed construction can be applied to all Discrete Logarithm (DL)-based signature schemes to convert a digital signature scheme into a CDS scheme. The proposed CDS scheme is secure against adaptive chosen-message attack in the random oracle model. In addition, it is also efficient in signature generation and verification.
Ant Colony Optimization and Swarm Intelligence: 6th International Conference, ANTS 2008, Brussels, Belgium, September 22-24, 2008, Proceedings (Lecture ... Computer Science and General Issues), 1 edition
Authors: Marco Dorigo, Mauro Birattari, Christian Blum, Maurice Clerc, Thomas Sttzle, Alan Winfield
Venue:  (2008)

This book constitutes the refereed proceedings of the 6th International Workshop on Ant Colony Optimization and Swarm Intelligence, ANTS 2008, held in Brussels, Belgium, in September 2008. The 17 revised full papers, 24 revised short papers, and 10 extended abstracts presented were carefully reviewed and selected from 91 submissions. The papers cover theoretical and foundational aspects of computational intelligence and related disciplines with special focus on swarm intelligence and are devoted to behavioral models of social insects and new algorithmic approaches, empirical and theoretical research in swarm intelligence, applications such as ant colony optimization or particle swarm optimization, and theoretical and experimental research in swarm robotics systems.
An adaptive hierarchical sparse grid collocation algorithm for the solution of stochastic differential equations
Authors: Xiang Ma, Nicholas Zabaras
Venue: Journal of Computational Physics (2009)

In recent years, there has been a growing interest in analyzing and quantifying the effects of random inputs in the solution of ordinary/partial differential equations. To this end, the spectral stochastic finite element method (SSFEM) is the most popular method due to its fast convergence rate. Recently, the stochastic sparse grid collocation method has emerged as an attractive alternative to SSFEM. It approximates the solution in the stochastic space using Lagrange polynomial interpolation. The collocation method requires only repetitive calls to an existing deterministic solver, similar to the Monte Carlo method. However, both the SSFEM and current sparse grid collocation methods utilize global polynomials in the stochastic space. Thus when there are steep gradients or finite discontinuities in the stochastic space, these methods converge very slowly or even fail to converge. In this paper, we develop an adaptive sparse grid collocation strategy using piecewise multi-linear hierarchical basis functions. Hierarchical surplus is used as an error indicator to automatically detect the discontinuity region in the stochastic space and adaptively refine the collocation points in this region. Numerical examples, especially for problems related to long-term integration and stochastic discontinuity, are presented. Comparisons with Monte Carlo and multi-element based random domain decomposition methods are also given to show the efficiency and accuracy of the proposed method.
A reliable communications architecture for real-time IP mobile applications
Authors: J-Ch. Gregoire, Omneya Issa, Yacine Belala, James Wong
Venue: International Journal of Mobile Communications (2009)

While the availability of a variety of wireless access technologies already provides users with ubiquitous access to critical content and applications, ensuring a satisfactory Quality of Service (QoS) and high availability further requires reliable delivery schemes that optimally use the available bandwidth. This paper presents a novel architecture to support adaptive real-time IP applications. It includes a layer of abstraction to isolate the application from the actual transport channels. It also uses a message-based protocol to improve communications reliability. Adaptation mechanisms are introduced and validated using a healthcare application. Experimental results are reported that demonstrate the viability of the approach.
Broken arrows
Authors: Teddy Furon, Patrick Bas
Venue: EURASIP Journal on Information Security (2008)

This paper makes an account of the design and investigations done for the still image watermarking technique used in the 2nd edition of the BOWS challenge. This technique is named "broken arrows" for some reasons given later on, and abbreviated "BA." This zero-bit algorithm is an implementation of a recent theoretical result by Merhav and Sabbag (2008) with precautions taken with respect to robustness, security, and imperceptibility. A new robustness criterion, based on the nearest border point of a cone, is proposed. The security constraint is taken into account by increasing the diversity of the watermark, sculpturing and randomizing the shape of the detection regions. The imperceptibility and robustness are also provided by adopting proportional embedding in the wavelet domain. The algorithm has been benchmarked using a database of 2000 images. For a probability of false alarm below 3ċ10-6 and a PSNR of 43 dB, the overall robustness regarding various classical image processing seems a promising and strong basis for the challenge.
Egocentric affordance fields in pedestrian steering
Authors: Mubbasir Kapadia, Shawn Singh, William Hewlett, Petros Faloutsos
Venue: Proceedings of the 2009 symposium on Interactive 3D graphics and games (2009)

In this paper we propose a general framework for local path-planning and steering that can be easily extended to perform high-level behaviors. Our framework is based on the concept of affordances - the possible ways an agent can interact with its environment. Each agent perceives the environment through a set of vector and scalar fields that are represented in the agent's local space. This egocentric property allows us to efficiently compute a local space-time plan. We then use these perception fields to compute a fitness measure for every possible action, known as an affordance field. The action that has the optimal value in the affordance field is the agent's steering decision. Using our framework, we demonstrate autonomous virtual pedestrians that perform steering and path planning in unknown environments along with the emergence of high-level responses to never seen before situations.
Utilizing Web2.0 in Web Service Ranking
Authors: Ioan Toma, Ying Ding, Krissada Chalermsook, Elena Simperl, Dieter Fensel
Venue: Proceedings of the 2009 Third International Conference on Digital Society (2009)

The current shift in realizing distributed applications by applying service-oriented principles translates into more and more web services being published on the Web each day. This introduces a set of new challenges such as how to organize, search, rank and select services. For ranking especially the use of any external information to the service, such as social information coming from Web2.0 sources has the potential to improve the accuracy of this task. In this paper we explore the idea of using social annotations technology for ranking web services. We show how such approach can be implemented using information provided by one of the largest social networks - del.icio.us.
A coordinated approach to hedge the risks in stochastic inventory-routing problem
Authors: Yee Ming Chen, Chun-Ta Lin
Venue: Computers and Industrial Engineering (2009)

The inventory routing problem (IRP) studied in this research involves repeated delivery of products from a depot to a set of retailers that face stochastic demands over a long period. The main objective in the IRP is to design the set of routes and delivery quantities that minimize transportation cost while controlling inventory costs. Traditional IRP focuses on risk-neutral decision makers, i.e., characterizing replenishment policies that maximize expected total net present value, or equivalently, minimize expected total cost over a planning horizon. In this research, for incorporating risk aversion, a hedge-based stochastic inventory-routing system (HSIRS) integrated with Generalized Autoregressive Conditional Heteroskedasticity (GARCH) model and Forward Option Pricing (FOP)model based on Black-Scholes model, from hedge point of view, is proposed to solve the multi-product multi-period inventory routing problem with stochastic demand. Computational results demonstrate the importance of this approach not only to risk-averse decision makers, but also to maximize the net present value at an acceptable service level. As a result, an optimal portfolio (R, s, S) system of product group can be generated to maximize the net present value under an acceptable service level in a given planning horizon. Meanwhile, the target group needed to be served and the relative transportation policy also can be determined accordingly based on the time required to be served as a priori partition to minimize the average transportation costs; hence, the routing assignment problem can be successfully optimized through a Predicting Particle Swarm Optimization algorithm.