ppxscal/embedding_network huggingface dataset:
State-Space Model for Gene Regulatory Networks with Time Delays
Authors: Fang-Xiang Wu, Wen-Jun Zhang, Anthony J. Kusalik
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

This work proposes a state-space model to account for time delays in gene regulatory network. This model views genes as the observation variables, whose expression values depend on the current internal state variables and any external inputs. The Bayesian information criterion (BIC) and probabilistic principal component analysis (PPCA) are used to estimate the number of internal state variables and their expression profiles from gene expression data. By constructing dynamic equations with time delays for the internal state variables and the relationships between them and the observation variables (gene expression profiles), state-space models for gene regulatory networks with time delays are realized. The parameters of the proposed model may be unambiguously identified from time-course gene expression data with low computational cost. The method is applied to one time-course gene expression dataset, and the modes constructed. The results show that not only is the model (almost) stable, but also it has better prediction accuracy than a model without incorporating time delay.
Lattice Boltzmann Simulation and Its Concurrent Visualization on the SX-6 Supercomputer
Authors: T. Takei, J. Bernsdorf, N. Masuda, H. Takahara
Venue: Proceedings of the High Performance Computing and Grid in Asia Pacific Region, Seventh International Conference (2004)

An emerging numerical method for simulating reactive flows in complex geometries, called the lattice Boltzmann method, is presented in combination with a concurrent visualization system. This combination enables an efficient simulation and visualization of time dependent transport and reaction processes such as the pollutant transport in porous media and the chemical processes in fixed bed reactors. The sustained computational performance of this lattice Boltzmann code on the NEC SX-6 supercomputer is 73% with respect to the theoretical maximum performance of its vector processors. An extension to the standard lattice Boltzmann model for adsorption processes is given together with simulation results and visualization examples for adsorption in porous media.
A Grand Challenge: Optimum Curriculum Design
Authors: Tak-Wai Chan
Venue: Proceedings of the Second International Conference on Creating, Connecting and Collaborating through Computing (2004)

It is obvious that in ten years, more and morestudents, whether teachers want it or not, will bringsome computing devices equipped with wirelesscommunication capabilities into the classrooms. Thiswill remarkably change the way of teaching andlearning. This paper discusses a framework fororchestrating global collaborative activities towardssome common goal that represents a grand challengeand beneficial both on local and global levels. Thisframework consists of some common goals, a group ofleading researchers, some international industries, aforum, websites for resource sharing, and acollaboration-model. A prominent common goal isoptimum curriculum design. How people learn withtechnology is a scientific inquiry, and by its own hasbeen the aim of such endeavors. But, from theapplication point of view, one can say that all theseendeavors are for accumulating knowledge in the hopethat one day such knowledge can lead to optimumcurriculum design. This paper presents somearguments of this challenge.
Implantation Guide for Collaborative Web-Based Systems (IGCWS)
Authors: V. M. Ruiz Penichet, J. A. Gallud, M. L. Gonzalez, P. Gonzalez
Venue: Proceedings of the Database and Expert Systems Applications, 15th International Workshop (2004)

Nowadays the traditional idea about information systems has changed due to the fact that communication technologies are better. An information system is not a simple program which resolves a particular problem. Now it is a coordination, cooperation and/or communication oriented application. Applications which are sometimes used by a high number of space and time distributed users. The newest applications are Web collaborative systems which use communication across the Internet. In this way, they improve their potential. Developing collaborative systems is a difficult task. To do this in the best way, efficient methodologies must been used. Lots of methodologies resolve the software life cycle. In this paper, we describe a new specialized, collaborative systems implantation oriented methodology called IGCWS.
Gridding and Compression of Microarray Images
Authors: Stefano Lonardi, Yu Luo
Venue: Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference (2004)

With the recent explosion of interest in microarray technology, massive amounts of microarray images are currently being produced. The storage and the transmission of this type of data are becoming increasingly challenging. Here we propose lossless and lossy compression algorithms for microarray images originally digitized at 16 bpp (bits per pixels) that achieve an average of 9.5 - 11.5 bpp (lossless) and 4.6 - 6.7 bpp (lossy, with a PSNR of 63 dB). The lossy compression is applied only on the background of the image, thereby preserving the regions of interest. The methods are based on a completely automatic gridding procedure of the image.
Structural analysis of network traffic flows
Authors: Anukool Lakhina, Konstantina Papagiannaki, Mark Crovella, Christophe Diot, Eric D. Kolaczyk, Nina Taft
Venue: ACM SIGMETRICS Performance Evaluation Review (2004)

Network traffic arises from the superposition of Origin-Destination (OD) flows. Hence, a thorough understanding of OD flows is essential for modeling network traffic, and for addressing a wide variety of problems including traffic engineering, traffic matrix estimation, capacity planning, forecasting and anomaly detection. However, to date, OD flows have not been closely studied, and there is very little known about their properties.We present the first analysis of complete sets of OD flow time-series, taken from two different backbone networks (Abilene and Sprint-Europe). Using Principal Component Analysis (PCA), we find that the set of OD flows has small intrinsic dimension. In fact, even in a network with over a hundred OD flows, these flows can be accurately modeled in time using a small number (10 or less) of independent components or dimensions.We also show how to use PCA to systematically decompose the structure of OD flow timeseries into three main constituents: common periodic trends, short-lived bursts, and noise. We provide insight into how the various constitutents contribute to the overall structure of OD flows and explore the extent to which this decomposition varies over time.
Display time as implicit feedback: understanding task effects
Authors: Diane Kelly, Nicholas J. Belkin
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

Recent research has had some success using the length of time a user displays a document in their web browser as implicit feedback for document preference. However, most studies have been confined to specific search domains, such as news, and have not considered the effects of task on display time, and the potential impact of this relationship on the effectiveness of display time as implicit feedback. We describe the results of an intensive naturalistic study of the online information-seeking behaviors of seven subjects during a fourteen-week period. Throughout the study, subjects' online information-seeking activities were monitored with various pieces of logging and evaluation software. Subjects were asked to identify the tasks with which they were working, classify the documents that they viewed according to these tasks, and evaluate the usefulness of the documents. Results of a user-centered analysis demonstrate no general, direct relationship between display time and usefulness, and that display times differ significantly according to specific task, and according to specific user.
Guides on the side? Tasks and challenges for teachers in telecollaborative projects
Authors: Robert O'Dowd, Katrin Eberbach
Venue: ReCALL (2004)

This paper reports on research carried out on an intercultural telecollaborative exchange between language learners in Germany and Ireland and focuses particularly on what was required of the teachers in the development of the project. The review of the literature looks at the role of telecollaboration within the field of network-based language learning and also offers an overview of the different types of interaction which have been identified on on-line message boards. Following that, the different tasks of the teachers in the German-Irish exchange are explored. These include developing learners&rsquo; understanding of intercultural learning, improving learners&rsquo; ability to make effective contributions to the on-line interaction, increasing their awareness of the difference between on-line monologues and dialogues and finally, establishing a good working relationship with the partner teacher. Based on these findings, recommendations are outlined on how to prepare teachers for telecollaborative projects.
On teaching theoretical foundations of Computer Science
Authors: Dino Mandrioli
Venue: ACM SIGACT News (1982)

Theoretical foundations of Computer Science (Automata Theory, Complexity, Formal Languages . . .) are taught almost everywhere within Computer Science curricula. However little effort is usually done to present this material in an integrated and motivated way, that is in such a way that its application and use in the solution of practical problems appears to any student.A proposal is developed in order to overcome this inadequacy and to emphasize the basic aspects of theoretical Computer Science.
Considering altruism in peer-to-peer internet streaming broadcast
Authors: Yang-hua Chu, Hui Zhang
Venue: Proceedings of the 14th international workshop on Network and operating systems support for digital audio and video (2004)

In peer-to-peer overlay or video broadcast, peers contribute a portion of the bandwidth to the overlay in return or the service. In the presence of network heterogeneity, it is not well understood how much bandwidth peers should contribute and receive in return. Existing protocols implicitly assume peers are either completely altruistic (which leads to airness concerns) or completely selfish (which leads to sub-optimal performance). In this paper, we argue that altruism should be explicitly considered. We propose a policy framework in which a wide range of altruism can be modeled and parameterized. The key findings are (i) the level of altruism has significant implication on the overall performance of the receivers; even a small degree of altruism goes a long way in improving their performance, and (ii) a wide range of altruism policy can be implemented efficiently in a distributed fashion. We validate these claims using simulation, with traces from real Internet broadcast events.
Network games
Authors: Éva Tardos
Venue: Proceedings of the thirty-sixth annual ACM symposium on Theory of computing (2004)

Network games approach some of the traditional algorithmic questions in networks from the perspective of game theory, which gives rise of a wide range of interesting issues. In this talk we will give an overview of recent progress in many of these areas, and show strong ties to certain algorithmic techniques.
Evaluation of filtering current news search results
Authors: Steven M. Beitzel, Eric C. Jensen, Abdur Chowdhury, David Grossman, Ophir Frieder
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

We describe an evaluation of result set filtering techniques for providing ultra-high precision in the task of presenting related news for general web queries. In this task, the negative user experience generated by retrieving non-relevant documents has a much worse impact than not retrieving relevant ones. We adapt cost-based metrics from the document filtering domain to this result filtering problem in order to explicitly examine the tradeoff between missing relevant documents and retrieving non-relevant ones. A large manual evaluation of three simple threshold filters shows that the basic approach of counting matching title terms outperforms also incorporating selected abstract terms based on part-of-speech or higher-level linguistic structures. Simultaneously, leveraging these cost-based metrics allows us to explicitly determine what other tasks would benefit from these alternative techniques.
A Characterization of Domination Reducible Graphs
Authors: Igor Ed. Zverovich
Venue: Graphs and Combinatorics (2004)

We introduce a hereditary class of domination reducible graphs where the minimum dominating set problem is polynomially solvable, and characterize this class in terms of forbidden induced subgraphs.
A Balanced Capacitive Threshold-Logic Gate
Authors: Javier López-García, José Fernández-Ramos, Alfonso Gago-Bohórquez
Venue: Analog Integrated Circuits and Signal Processing (2004)

In this paper a new threshold gate is proposed. Its main characteristics are high fan-in (128-inputs), low delay time (8.35 ns), low power consumption (<400 &mu;W) and optimal implementation of any threshold function. The gate can evaluate multiple input vectors in the same evaluation phase with only one clock signal. Synchronous (pipe-line) and asynchronous operations are possible, which makes it very suitable to implement logic designs with reduced depth. HSPICE simulations and simulation with files extracted from a layout in 0.6 &mu;m double-poly CMOS technology are presented, showing the validity of the proposed gate.
Configurable indexing and ranking for XML information retrieval
Authors: Shaorong Liu, Qinghua Zou, Wesley W. Chu
Venue: Proceedings of the 27th annual international ACM SIGIR conference on Research and development in information retrieval (2004)

Indexing and ranking are two key factors for efficient and effective XML information retrieval. Inappropriate indexing may result in false negatives and false positives, and improper ranking may lead to low precisions. In this paper, we propose a configurable XML information retrieval system, in which users can configure appropriate index types for XML tags and text contents. Based on users' index configurations, the system transforms XML structures into a compact tree representation, Ctree, and indexes XML text contents. To support XML ranking, we propose the concepts of "weighted term frequency" and "inverted element frequency," where the weight of a term depends on its frequency and location within an XML element as well as its popularity among similar elements in an XML dataset. We evaluate the effectiveness of our system through extensive experiments on the INEX 03 dataset and 30 content and structure (CAS) topics. The experimental results reveal that our system has significantly high precision at low recall regions and achieves the highest average precision (0.3309) as compared with 38 official INEX 03 submissions using the strict evaluation metric.
A greedy Delaunay-based surface reconstruction algorithm
Authors: David Cohen-Steiner, Frank Da
Venue: The Visual Computer: International Journal of Computer Graphics (2004)

In this paper, we present a new greedy algorithm for surface reconstruction from unorganized point sets. Starting from a seed facet, a piecewise linear surface is grown by adding Delaunay triangles one by one. The most plausible triangles are added first and in such a way as to prevent the appearance of topological singularities. The output is thus guaranteed to be a piecewise linear orientable manifold, possibly with boundary. Experiments show that this method is very fast and achieves topologically correct reconstruction in most cases. Moreover, it can handle surfaces with complex topology, boundaries, and nonuniform sampling.
Letter to the editor: an inhomogeneous eigenvalue problem
Authors: Ferdinand F. Cap
Venue: Journal of Computational and Applied Mathematics (2004)

In this paper it is shown that the general solution of an inhomogeneous boundary value problem may only consist of the general solution and that it is not necessary to superpose a partial solution. The eigenfrequencies of a membrane subject to inhomogeneous boundary conditions are calculated using the program Mathematica.
Scale models and rapid prototyping
Authors: Mark Weiser
Venue: Proceedings of the workshop on Rapid prototyping (1982)

A prototype of a system is a model of that system which sacrifices accuracy in some areas (such as ease of change) for a quick check of the system's function. A prototype is therefore one kind of <u>scale model--</u> a model accurate in some ways but inaccurate in others. Three different ways to build scale models of software correspond to the accurate modeling of the following three aspects of a software system: user interface, functionality, and performance. A prototype accurate in one of these areas will usually deliberately ignore accuracy in the other two. Specific scaling of results in a software scale model will be necessary depending upon what aspect has been ignored.
Statistical Verification of Power Grids Considering Process-Induced Leakage Current Variations
Authors: Imad A. Ferzli, Farid N. Najm
Venue: Proceedings of the 2003 IEEE/ACM international conference on Computer-aided design (2003)

Transistor threshold voltages (V{th}) have been reduced as partof on-going technology scaling. The smaller V{th} values featureincreased variations due to underlying process variations, witha strong within-die component. Correspondingly, given the exponential dependence of leakage on V{th}, circuit leakage currentsare increasing significantly and have strong within-die statistical variations.With these leakage currents loading the powergrid, the grid develops correspondingly large statistical voltagedrops. This leakage-induced voltage drop is an unavoidable background level of noise on the grid. Any additional non-leakagecurrents due to circuit activity will lead to voltage drop which isto be added to this background noise. We propose a techniquefor checking whether the statistical voltage drop on every node iswithin user-specified bounds, given user-specified statistics of theleakage currents.
Digital filter design using multiple pareto fronts
Authors: T. Schnier, X. Yao, P. Liu
Venue: Soft Computing - A Fusion of Foundations, Methodologies and Applications (2004)

Evolutionary approaches have been used in a large variety of design domains, from aircraft engineering to the designs of analog filters. Many of these approaches use measures to improve the variety of solutions in the population. One such measure is clustering. In this paper, clustering and Pareto optimisation are combined into a single evolutionary design algorithm. The population is split into a number of clusters, and parent and offspring selection, as well as fitness calculation, are performed on a per-cluster basis. The objective of this is to prevent the system from converging prematurely to a local minimum and to encourage a number of different designs that fulfil the design criteria. Our approach is demonstrated in the domain of digital filter design. Using a polar coordinate based pole-zero representation, two different lowpass filter design problems are explored. The results are compared to designs created by a human expert. They demonstrate that the evolutionary process is able to create designs that are competitive with those created using a conventional design process by a human expert. They also demonstrate that each evolutionary run can produce a number of different designs with similar fitness values, but very different characteristics.
Mimicking video: real-time morphable 3D model fitting
Authors: Kazuhiro Hiwada, Atsuto Maki, Akiko Nakashima
Venue: Proceedings of the ACM symposium on Virtual reality software and technology (2003)

This paper presents a new automatic scheme for tracking a 3D non-rigid object surface such as a human face in a real-time video sequence. We introduce a coordinate-oriented error minimization method for estimating the tracking parameters, whereas we base our algorithm on a morphable 3D model consisting of a combination of 3D linear bases, and show that it is extremely well suited to the task of fitting the 3D model to the target object in real time. The algorithm is straightforward, allowing the parameters of an object's pose and non-rigid motion to be computed in an integrated manner. Also, it is found that the illumination variability on the object surface, for instance due to the target motion, can be handled easily. Through the experiments we not only show that on-line tracking is indeed possible, but also demonstrate the effect of our technique of video mimicking.
Privacy-preserving data integration and sharing
Authors: Chris Clifton, Murat Kantarcioǧlu, AnHai Doan, Gunther Schadow, Jaideep Vaidya, Ahmed Elmagarmid, Dan Suciu
Venue: Proceedings of the 9th ACM SIGMOD workshop on Research issues in data mining and knowledge discovery (2004)

Integrating data from multiple sources has been a longstanding challenge in the database community. Techniques such as privacy-preserving data mining promises privacy, but assume data has integration has been accomplished. Data integration methods are seriously hampered by inability to share the data to be integrated. This paper lays out a privacy framework for data integration. Challenges for data integration in the context of this framework are discussed, in the context of existing accomplishments in data integration. Many of these challenges are opportunities for the data mining community.
An empirical study of profiling strategies for released software and their impact on testing activities
Authors: Sebastian Elbaum, Madeline Hardojo
Venue: Proceedings of the 2004 ACM SIGSOFT international symposium on Software testing and analysis (2004)

An understanding of how software is employed in the field can yield many opportunities for quality improvements. Profiling released software can provide such an understanding. However, profiling released software is diffcult due to the potentially large number of deployed sites that must be profiled, the extreme transparency expectations, and the remote data collection and deployment management process. Researchers have recently proposed various approaches to tap into the opportunities and overcome those challenges. Initial studies have illustrated the application of these approaches and have shown their feasibility. Still, the promising proposed approaches, and the tradeoffs between overhead, accuracy, and potential benefits for the testing activity have been barely quantified. This paper aims to over-come those limitations. Our analysis of 1200 user sessions on a 155 KLOC system substantiates the ability of field data to support test suite improvements, quantifies different approaches previously introduced in isolation, and assesses the efficiency of profiling techniques for released software and the effectiveness of their associated testing efforts.