ppxscal/embedding_network huggingface dataset:
A simple method for screening variables before clustering microarray data
Authors: Wojtek J. Krzanowski, David J. Hand
Venue: Computational Statistics Data Analysis (2009)

A simple and computationally fast procedure is proposed for screening a large number of variables prior to cluster analysis. Each variable is considered in turn, the sample is divided into the two groups that maximise the ratio of between-group to within-group sum of squares for that variable, and the achieved value of this ratio is tested to see if it is significantly greater than what would be expected when partitioning a sample from a single homogeneous population. Those variables that achieve significance are then used in the cluster analysis. It is suggested that significance levels be assessed using a Monte Carlo computational procedure; by assuming within-group normality an analytical approximation is derived, but caution in its use is advocated. Computational details are provided for both the partitioning and the testing. The procedure is applied to several microarray data sets, showing that it can often achieve good results both quickly and simply.
A predictor-corrector algorithm for the coupling of stiff ODEs to a particle population balance
Authors: Matthew Celnik, Robert Patterson, Markus Kraft, Wolfgang Wagner
Venue: Journal of Computational Physics (2009)

In this paper a novel predictor-corrector algorithm is presented for the solution of coupled gas-phase - particulate systems. The emphasis of this work is the study of soot formation, but the concepts can be applied to other systems. This algorithm couples a stiff ODE solver to a Monte Carlo population balance solver. Such coupling has been achieved previously for similar systems using a Strang operator splitting algorithm, however, that algorithm demonstrated several numerical issues which resulted in a high computational cost to acquire adequate precision. In particular a source-sink instability was identified whereby a large-magnitude source term present in the ODE system was competing with a similarly sized sink term in the population balance. This instability required that the splitting step size was very small in order to keep numerical error sufficiently low. A predictor-corrector algorithm has been formulated to negate this instability. An additional efficiency is gained with this algorithm as a principal computational cost of the Strang splitting algorithm is removed: the requirement to re-initialise the ODE solver every splitting step. The numerical convergence of the new algorithm is demonstrated, and its efficiency is compared to that of the Strang splitting algorithm. Substantial computation time savings are demonstrated, which allow a fixed error in three studied system functionals to be achieved with an order-of-magnitude reduction in computation time.
Physical optimization for FPGAs using post-placement topology rewriting
Authors: Val Pevzner, Andrew Kennings, Andy Fox
Venue: Proceedings of the 2009 international symposium on Physical design (2009)

Due to poor correlations between pre- and post-placement timing analysis, many post-placement optimization strategies have been proposed for the FPGA CAD flow to improve circuit performance. Typically, these methods depend on logic duplication or decomposition methods combine together with incremental placement. Circuit rewriting has proven to be a useful optimization strategy, but is typically applied during the technology mapping step of the FPGA CAD flow. While beneficial, rewriting either before or after technology mapping must rely on circuit depth rather than post-placement delays for timing optimization. In this paper, we show that circuit rewriting can also be used as a post-placement optimization for FPGAs. We present a post-placement optimization based on circuit rewriting which is guided by post-placement timing analysis. We replace, or rewrite, cones of logic on critical paths to improve the timing performance of a circuit. Our method is integrated with incremental placement to ensure valid placements and to guarantee that our timing analysis remains accurate throughout our proposed rewriting method. The key to our method is the ability to quickly determine if an alternative topology of LUTs is suitable for the replacement of a cone of logic on a critical path. We have implemented our proposed method in a commercial FPGA CAD flow. Experimental results demonstrate that the application of our rewriting algorithm can improve the routed timing performance of a design by 3.1% on average and by as much as 37.9% when applied to a set of 136 industrial designs.
Letter to the editor: A triple level finite element method for large eddy simulations
Authors: Weiming Liu
Venue: Journal of Computational Physics (2009)

Since large eddy simulation (LES) was introduced by Smagorinsky in 1963, it has been improved with various thoughts from many researchers. Unfortunately, despite that, the filtered approach that is widely used at present still suffers because quite empirical factors are used to determine non-closured subgrid Reynolds stresses. Based on a new definition of LES and multiscale finite element concepts, this work presents an attempt to remove such factors. Using direct sum decomposition of the solution space, we devised a hierarchical multi-level formulation of the Navier-Stokes equations for turbulence. The base-level, bearing the information of large eddies, is calculated by the conventional finite element method. The finer levels are for small scale eddies of turbulence. We address the solution methods for the small scale movements. In particular, a spectral element method is introduced for the finer level solutions. Thus large eddies and small eddies to some extent may be accurately obtained. The introduced approach offers not only access to calculate turbulence in complex geometries because of the nature of finite element method but also an effective tool for multiscale physical problems with turbulence, such as reaction flows. It is worth noting that the approach introduced here is similar to the implicit LES in finite volume and finite difference methods.
Invertible, Involutory and Permutation Matrix Generation Methods for Hill Cipher System
Authors: Bibhudendra Acharya, Debasish Jena, Sarat Kumar Patra, Ganapati Panda
Venue: Proceedings of the 2009 International Conference on Advanced Computer Control (2009)

Hill cipher's susceptibility to cryptanalysis has rendered it unusable in practice, it still serves an important pedagogical role in both cryptology and linear algebra. Hill cipher requires inverse of the key matrix while decryption. In fact that not all the matrices have an inverse and therefore they will not be eligible as key matrices in the Hill cipher scheme. Furthermore, due to its linear nature, the basic Hill cipher succumbs to known-plaintext attacks. In order to repair these flaws of the original Hill cipher, in this paper we proposed Invertible, Involutory and Permutation Matrix Generation Methods for Hill Cipher System.
Planning high-speed digital services in the Bell system
Authors: Gary J. Handler
Venue: Proceedings of the May 16-19, 1983, national computer conference (1983)

High-speed digital transport has been an integral part of the Bell Network since the introduction of T1 facilities in the early 1960s. Since that time a growing percentage of short- and long-haul digital facilities have been integrated into the network via various technologies such as digital radio, coax, and fiber. More recently, customer needs for data communications have required the extension of high-speed digital transport to the customer premises. This paper discusses the growth of high-speed digital services. We describe the customer applications that led to the requirement for such transport, the technological environment, and finally some near-term and longer-term plans for high-speed transport capabilities. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player
Transductive Component Analysis
Authors: Wei Liu, Dacheng Tao, Jianzhuang Liu
Venue: Proceedings of the 2008 Eighth IEEE International Conference on Data Mining (2008)

In this paper, we study semi-supervised linear dimensionality reduction. Beyond conventional supervised methods which merely consider labeled instances, the semi-supervised scheme allows to leverage abundant and ample unlabeled instances into learning so as to achieve better generalization performance. Under semi-supervised settings, our objective is to learn a smooth as well as discriminative subspace and linear dimensionality reduction is thus achieved by mapping all samples into the subspace. Specifically, we present the Transductive Component Analysis (TCA) algorithm to generate such a subspace founded on a graph-theoretic framework.Considering TCA is non-orthogonal, we further present the Orthogonal Transductive Component Analysis (OTCA) algorithm to iteratively produce a series of orthogonal basis vectors. OTCA has better discriminating power than TCA. Experiments carried out on synthetic and real-world datasets by OTCA show a clear improvement over the results of representative dimensionality reduction algorithms.
Mobile technology at the frontlines of patient care: Understanding fit and human drives in utilization decisions and performance
Authors: Iris Junglas, Chon Abraham, Blake Ives
Venue: Decision Support Systems (2009)

Mobile information communication technologies (MICTs) have considerable promise in patient care settings. But that promise can only be realized if the MICT applications are used by the medical staff. This paper reports on a study examining nurses' decisions to utilize MICTs. A mixed-methods approach is used, consisting of both qualitative and quantitative elements, that reveals and empirically tests the significance of novel constellations of fit (i.e., identification, information, patient interaction, physical, time criticality, user comfort, and workflow fit) and individual characteristics, presented as basic human drives (i.e., drive to acquire, bond, defend, and learn). Findings indicate that fit is a multi-faceted construct and that archetypical human drives have an influence on these various notions, which in turn, impact technology adoption in the healthcare context.
Evolutionary Clustering by Hierarchical Dirichlet Process with Hidden Markov State
Authors: Tianbing Xu, Zhongfei (Mark) Zhang, Philip S. Yu, Bo Long
Venue: Proceedings of the 2008 Eighth IEEE International Conference on Data Mining (2008)

This paper studies evolutionary clustering, which is a recently hot topic with many important applications, noticeably in social network analysis. In this paper, based on the recent literature on Hierarchical Dirichlet Process (HDP) and Hidden Markov Model (HMM), we have developed a statistical model HDP-HTM that combines HDP with a Hierarchical Transition Matrix (HTM) based on the proposed Infinite Hierarchical Hidden Markov State model (iH$^2$MS) as an effective solution to this problem. The HDP-HTM model substantially advances the literature on evolutionary clustering in the sense that not only it performs better than the existing literature, but more importantly it is capable of automatically learning the cluster numbers and structures and at the same time explicitly addresses the correspondence issue during the evolution. Extensive evaluations have demonstrated the effectiveness and promise of this solution against the state-of-the-art literature.
Make: Technology on Your Time Volume 09 technology on your time
Authors: Mark Frauenfelder
Venue:  (2007)

If you like to tweak, disassemble, re-create, and invent cool new uses for technology, you'll love MAKE our quarterly publication for the inquisitive do-it-yourselfer. Every issue is packed with projects to help you make the most of all the technology in your life. If there's a way to hack it, tweak it, bend it, or remix it, you will find out about it in MAKE. MAKE magazine leaves no stone unturned in its quest for the bizarre in Volume 09, the Fringe issue. Behold such wonders as the cosmic ray cloud chamber, high-voltage levitation, and the amazing vortex tube. Plus, learn how to make almost anything with carbon fiber, photograph the luminous auras around everything, and build a $5 guitar amp. Explore the fringes of technology with projects and articles that push the boundaries of physics and reason.
A Method for Evaluating Multimedia Learning Software
Authors: Stephane Crozat, Olivier Hu, Philippe Trigano
Venue: Proceedings of the IEEE International Conference on Multimedia Computing and Systems - Volume 2 (1999)

We submit a method (EMPI: Evaluation of Multimedia, Pedagogical and Interactive software) to evaluate multimedia software used in educational context. Our purpose is to help users (teachers or students) to decide in front of the large choice of software actually proposed. We structured a list of evaluation criteria, grouped through six approaches: the general feeling, the technical quality, the usability, the scenario, the multimedia documents, and the didactical aspects. A global questionnaire joins all this modules. We are also designing software that could make the method easier to use and more powerful. We present in this paper the list of the criteria we selected and organised, along with some examples of questions, and a brief description of the method and the linked software.
Visualisation of Personal Communication Patterns Using Mobile Phones
Authors: Bradley Tonder, Janet Wesson
Venue: Engineering Interactive Systems: EIS 2007 Joint Working Conferences, EHCI 2007, DSV-IS 2007, HCSE 2007, Salamanca, Spain, March 22-24, 2007. Selected Papers (2008)

Ambient displays are attractive, subtle visualisations of information. They are typically situated on the periphery of human perception, requiring minimal effort to be understood. The vast volume of communication facilitated by modern means of communication has led to research into methods of visualising this information to facilitate rapid understanding. These two research areas have, however, seldom been combined to include the use of ambient displays as visualisations of personal communication patterns. The research outlined in this paper addresses this issue by combining ambient displays and visualisation of personal communication patterns in a mobile context. This paper details the development of the AmbiMate system, analyses its usefulness and investigates the lessons which can be learned from its implementation in order to guide the future development of such systems.
Construction K-Dominating Set with Multiple Relaying Technique in Wireless Mobile Ad Hoc Networks
Authors: Yongsheng Fu, Xinyu Wang, Shanping Li
Venue: Proceedings of the 2009 WRI International Conference on Communications and Mobile Computing - Volume 02 (2009)

The (k, r)-dominating set problem, (k, r)-DS, is defined as the problem of selecting a minimum cardinality vertex set D (dominating nodes, also referred as cluster-heads) of a graph G=(V, E), such that every vertex u not in D is in r hops from at least k (multiple domination parameter) vertices in D. In mobile ad hoc networks (MANETs), computing dominating set should be distributed, because the topology may change frequently. In this paper, we present a distributed clustering algorithm based on MPR technique, named MPR-KD, to addressing redundancy of dominating nodes in 1-hop for MANETs. 1-CDS is still supported in MPR-KD and extensive simulations are conducted to compare this algorithm with another distributed algorithm DKR. Simulation results show that the new algorithm outperforms DKR in terms of number of dominating nodes, both in dense and sparse networks.
Statistical methods of background correction for Illumina BeadArray data
Authors: Yang Xie, Xinlei Wang, Michael Story
Venue: Bioinformatics (2009)

Motivation: Advances in technology have made different microarray platforms available. Among the many, Illumina BeadArrays are relatively new and have captured significant market share. With BeadArray technology, high data quality is generated from low sample input at reduced cost. However, the analysis methods for Illumina BeadArrays are far behind those for Affymetrix oligonucleotide arrays, and so need to be improved. Results: In this article, we consider the problem of background correction for BeadArray data. One distinct feature of BeadArrays is that for each array, the noise is controlled by over 1000 bead types conjugated with non-specific oligonucleotide sequences. We extend the robust multi-array analysis (RMA) background correction model to incorporate the information from negative control beads, and consider three commonly used approaches for parameter estimation, namely, non-parametric, maximum likelihood estimation (MLE) and Bayesian estimation. The proposed approaches, as well as the existing background correction methods, are compared through simulation studies and a data example. We find that the maximum likelihood and Bayes methods seem to be the most promising. Contact: yang.xie@utsouthwestern.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Logic analysis and its tools
Authors: R. S. Wang
Venue: Proceedings of the May 16-19, 1983, national computer conference (1983)

This article discusses the logic analysis of a program, points out problems with the logic analysis process in general use, and introduces an approach to logic analysis that is more effective and less time consuming. The new method generates logic paths out of programs and preanalyzes the paths in lieu of directly analyzing the program. Three preanalysis software tools are introduced: procedure logic path generator, program logic path generator, and logic path preanalyzer. Sample outputs are given to demonstrate the difference between program analysis and logic path analysis.
Highlights of a group effort in algorithmic development for packet-switched voice networks
Authors: J. D. Markel
Venue: Proceedings of the May 4-7, 1981, national computer conference (1981)

Since 1973 the Defense Advanced Research Project Agency (DARPA) has sponsored several research groups engaged in a program of developing new and improved algorithms for demonstrating low bit-rate speech transmission across a packet-switched network. The first real-time packet-switched voice system was demonstrated by this group in 1974.
Automatic database system conversion: schema revision, data translation, and source-to-source program transformation
Authors: Ben Shneiderman, Glenn Thomas
Venue: Proceedings of the June 7-10, 1982, national computer conference (1982)

Changing data requirements present database administrators with a difficult problem: the revision of the schema, the translation of the stored database, and the conversion of the numerous application programs. This paper describes an automatic database system conversion facility which provides one approach for coping with this problem. The Pure Definition Language and the Pure Manipulation Language have been designed to facilitate the conversions specified in the Pure Transformation Language. Two conversions and their effect on retrievals are demonstrated.
Developing a decision support system for sustainable cage aquaculture
Authors: Halmar Halide, A. Stigebrandt, M. Rehbein, A. D. McKinnon
Venue: Environmental Modelling Software (2009)

A decision support system to assist cage aquaculture managers is presented. The system enables managers to perform four essential tasks: (i) site classification, (ii) site selection, (iii) holding capacity determination, and (iv) economic appraisal of an aquaculture farm at a given site. Based on measurements of water and substrate qualities, hydrometeorology and socioeconomic factors, a cage aquaculture site is classified into three categories - poor, medium, and good. With this information, the AHP (analytical hierarchy process) tool is used to evaluate the best site from several alternatives. A simplified version of the Modelling-On growing-Monitoring (MOM), SMOM, is developed and applied to determine how much fish can be grown on site without harming the environment. The simplified model has been calibrated against MOM, compared with other carrying capacity models and validated with farm data. A break-even point-price and return on investment (ROI) are calculated using cage-holding density and volume, mean fish weight at harvest, feed conversion ratio (FCR), survival rate of seed, costs of feed, seed and cages, the interest rate on borrowed funds and the fish price. All model components are integrated seamlessly into a user-friendly interface implemented in Java^(R) called CADS_TOOL (Cage Aquaculture Decision Support Tool). The program with a user's guide is freely available.
Yard crane dispatching based on real time data driven simulation for container terminals
Authors: Xi Guo, Shell Ying Huang, Wen Jing Hsu, Malcolm Yoke Hean Low
Venue: Proceedings of the 40th Conference on Winter Simulation (2008)

This paper studies the problem of real time yard crane dispatching in container terminals. Many technologies, including transponders, RFID and GPS have been used in the container terminal setting for real-time tracking of terminal equipment. A judicious integration of real-time data into the yard crane management system will allow better utilization of terminal resources to improve overall terminal productivity. We propose a yard crane dispatching algorithm based on real time data driven simulation to solve the problem of yard crane job sequencing to minimize average vehicle waiting time. The algorithm will produce optimal operation sequence for each planning window. Several policies to select jobs to form the planning window are also proposed. Our simulation results show that dispatching yard crane based on real time data driven simulation is of great value in improving yard crane performance in 3 scenarios with different vehicle arriving patterns and our results are 10% worse off a loosely estimated overall optimal performance result.
The observable part of a network
Authors: Piet Van Mieghem, Huijuan Wang
Venue: IEEE/ACM Transactions on Networking (TON) (2009)

The union of all shortest path trees GUspt is the maximally observable part of a network when traffic follows shortest paths. Overlay networks such as peer to peer networks or virtual private networks can be regarded as a subgraph of GUspt. We investigate properties of GUspt in different underlying topologies with regular i.i.d. link weights. In particular, we show that the overlay GUspt in an Erdös-Rényi random graph Gp (N) is a connected GPc (N) where Pc ∼ log N/N is the critical link density, an observation with potential for ad-hoc networks. Shortest paths and, thus also the overlay GUspt, can be controlled by link weights. By tuning the power exponent α of polynomial link weights in different underlying graphs, the phase transitions in the structure of GUspt are shown by simulations to follow a same universal curve FT (α) = Pr[GUspt is a tree]. The existence of a controllable phase transition in networks may allow network operators to steer and balance flows in their network. The structure of GUspt in terms of the extreme value index α is further examined together with its spectrum, the eigenvalues of the corresponding adjacency matrix of GUspt.