ppxscal/embedding_network huggingface dataset:
Bioinformatics: searching for primers
Authors: Ryan Menzer
Venue: Journal of Computing Sciences in Colleges (2004)

In order to help predict the way proteins will act in an organism, biologists cross-examine sequences of amino acids from many proteins. There are a total of 20 amino acids in existence and proteins often consist of 300 or more amino acids. Amino acids are categorized into groups by degree of biological similarity. The sequences are collected in a tabular format with one row per sequence and each sequence beginning at the leftmost column. A "multiple alignment" is performed on the collection of sequences to maximize the areas where the amino acids belong to the same group. The process involves inserting "wild cards" in each sequence to shift the columns and thus altering the alignment. Online websites presently are available to accomplish the task. 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
Elements of prescribed order, prescribed traces and systems of rational functions over finite fields
Authors: Ferruh Özbudak
Venue: Designs, Codes and Cryptography (2005)

Let k ≥ 1 and f1 .... , fr ∈ Fqk (x) be a system of rational functions forming a strongly linearly independent set over a finite field Fq. Let γ1 ..... γr ∈ Fq be arbitrarily prescribed elements. We prove that for all sufficiently large extensions Fqkm, there is an element ξ ∈ Fqkm of prescribed order such that TrFqkm/Fq (fi (ξ))= γi for i = 1, ..., r, where TrFqkm/Fq is the relative trace map from Fqkm onto Fq. We give some applications to BCH codes, finite field arithmetic and ordered orthogonal arrays. We also solve a question of Helleseth et al. (Hypercubic 4 and 5-designs from Double-Error-Correcting codes, Des. Codes. Cryptgr. 28(2003). pp. 265-282) completely.
An efficient genetic algorithm for a fixed frequency assignment problem with limited bandwidth constraint
Authors: Shouichi Matsui, Isamu Watanabe, Ken-Ichi Tokoro
Venue: Systems and Computers in Japan (2004)

In this paper, we propose an efficient genetic algorithm (GA) for a fixed frequency assignment problem with limited bandwidth constraint. We propose a new GA-based algorithm for the problem of minimizing the weighted sum of damage due to interference and damage due to blocked call, which was formulated by Jin and colleagues. The proposed algorithm, which uses a steady-state GA that adaptively controls the mutation rate to search for an appropriate instruction sequence for a virtual machine performing the frequency assignment work, introduces a solution improvement algorithm based on a local search. The results of applying the proposed algorithm to benchmark problems, which show better performance than the existing GAs, indicate that this is an efficient algorithm. &copy; 2004 Wiley Periodicals, Inc. Syst Comp Jpn, 35(10): 32&ndash;39, 2004; Published online in Wiley InterScience (). DOI 10.1002&sol;scj.10677
Clustering for probabilistic model estimation for CF
Authors: Qing Li, Byeong Man Kim, Sung Hyon Myaeng
Venue: Special interest tracks and posters of the 14th international conference on World Wide Web (2005)

Based on the type of collaborative objects, a collaborative filtering (CF) system falls into one of two categories: item-based CF and user-based CF. Clustering is the basic idea in both cases, where users or items are classified into user groups where users share similar preference or item groups where items have similar attributes or characteristics. Observing the fact that in user-based CF each user community is characterized by a Gaussian distribution on the ratings for each item and the fact that in item-based CF the ratings of each user in item community satisfy a Gaussian distribution, we propose a method of probabilistic model estimation for CF, where objects (user or items) are classified into groups based on the content information and ratings at the same time and predictions are made considering the Gaussian distribution of ratings. Experiments on a real-world data set illustrate that our approach is favorable.
Data Cache Prefetching Using a Global History Buffer
Authors: Kyle J. Nesbit, James E. Smith
Venue: IEEE Micro (2005)

By organizing data cache prefetch information in a new way, a GHB supports existing prefetch algorithms more effectively than conventional prefetch tables. It reduces stale table data, improving accuracy and reducing memory traffic. It contains a more complete picture of cache miss history and is smaller than conventional tables
Video-Based Framework for Face Recognition in Video
Authors: Dmitry O. Gorodnichy
Venue: Proceedings of the 2nd Canadian conference on Computer and Robot Vision (2005)

This paper presents a number of new views and techniques claimed to be very important for the problem of face recognition in video (FRiV). First, a clear differentiation is made between photographic facial data and video-acquired facial data as being two different modalities: one providing hard biometrics, the other providing softer biometrics. Second, faces which have the resolution of at least 12 pixels between the eyes are shown to be recognizable by computers just as they are by humans. As a way to deal with low resolution and quality of each individual video frame, the paper offers to use the neuro-associative principle employed by human brain, according to which both memorization and recognition of data are done based on a flow of frames rather than on one frame: synaptic plasticity provides a way to memorize from a sequence, while the collective decision making over time is very suitable for recognition of a sequence. As a benchmark for FRiV approaches, the paper introduces the IIT-NRC video-based database of faces which consists of pairs of low-resolution video clips of unconstrained facial motions. The recognition rate of over 95%, which we achieve on this database, as well as the results obtained on real-time annotation of people on TV allow us to believe that the proposed framework brings us closer to the ultimate benchmark for the FRiV approaches, which is "if you are able to recognize a person, so should the computer".
Hardware-Software Interaction: Preliminary Observations
Authors: Neil Steiner, Peter Athanas
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Workshop 3 - Volume 04 (2005)

As computational devices continue to advance, there are reasons to examine their foundations a little more deeply, and to ask whether there may not be something more to be found. The fundamental manner in which hardware and software interact is poorly understood, and yet there is little indication in the literature that this is being discussed or explored. In spite of our technological achievements, we are at a loss to precisely define the boundaries between hardware and software, and to describe the nature of their interface. This paper aims to raise some of the major issues and questions, to propose a hardware-information duality, and to suggest directions in which further research might be pursued.
An on-line purchasing and decision support system for distributed retail chain stores
Authors: Azwina M. Yusof
Venue: Proceedings of the 6th international conference on Electronic commerce (2004)

This paper looks into how integrating on-line purchasing with inventory management system for distributed retail chain stores can automate and aid the process of decision-making in relation to on-line product sales and distribution. It extends the work done in [1], to include not only on-demand and automatic communication between the retail chain store's head office and point-of-sale (POS) outlets, but also to include on-line purchasing capabilities for home users. The application uses distributed databases to store information relevant to customers, products and product transactions at different geographical locations. The system is designed to facilitate the management process between the head office and the POS outlets: it aids top-level management to make the right business decisions in terms of the right products being distributed at the right location and at the right time, and also products ordered by home users to be sent by the right POS outlet, and it aids low-level employees to manage the daily business transactions of each POS outlet efficiently.
Dynamic channel management in MIMO OFDM cellular systems: Research Articles
Authors: Ben Lu, Xiaodong Wang, Richard D. Gitlin, Mohammad Madihian
Venue: Wireless Communications Mobile Computing (2004)

We consider dynamic channel management (DCM), more specifically power control and channel allocation, in multi-carrier multi-antenna wireless cellular systems. A quasi-static channel model is assumed such that the channels remain approximately time-invariant within each packet. On a packet-by-packet basis, the mobile station (MS) receivers feed back the DCM parameters to the corresponding base station (BS) transmitters in order to minimize the transmission power and strive to satisfy every individual user's data-rate request. While optimum, centralized DCM for all active cells typically requires solution of a non-convex optimization problem (which is subject to local minima) and requires intense channel feedback to a central controller. We instead consider sub-optimal distributed DCM, where each individual cell locally optimizes its own performance based on the local channel information. In particular, we compare three distributed DCM schemes, namely the two-dimensional DCM, which jointly adjusts both spatial and frequency sub-channels of each BS&ndash;MS link, the one-dimensional DCM, which adjusts only the frequency sub-channels and the scalar DCM, which adjusts each BS&ndash;MS link by one scalar power coefficient. These DCM schemes are investigated in multi-cell environments with realistic parameters; and it is seen that due to the multiple antennas, the maximum supportable rate (i.e. the rate supported by practically finite transmission power) is significantly increased, for example by a factor of two for users using four antennas and close to cell boundary. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Stochastic resonance in the brain
Authors: Toshio Mori, Shoichi Kai
Venue: Systems and Computers in Japan (2004)

This paper investigates the existence of stochastic resonance (SR) in the human brain, based on the noise effect of the &alpha;-wave. In order to show clear evidence of the SR phenomenon in the central nervous system, the measurement was carried out under the following conditions; the periodic and noisy light stimuli are respectively applied to the right and left eye of a subject separately. When the periodic stimulus is applied with a subthreshold condition and the amplitude of noise stimulus of which the frequency bandwidth ranges from 15 to 60 Hz is varied, strong entrainment occurs for a certain range of the noise amplitude. Then the curve for the amplitude of the peak versus the noise amplitude shows a bell-type shape, that is, the maximum signal amplitude at an optimum noise. Thus, the SR phenomenon occurs not on the retina but on the visual processing area after the optic chiasm&mdash;no mixing occurs before primary visual cortex in this manner, because the periodic and random stimuli are separately applied to the right and left eyes, respectively. This result suggests that the human brain may exploit internal and&sol;or external noise for the higher-order activities such as perception and cognition. &copy; 2004 Wiley Periodicals, Inc. Syst Comp Jpn, 35(11): 39&ndash;47, 2004; Published online in Wiley InterScience (). DOI 10.1002&sol;scj.10398
ConsDiff: an algorithm for the detection of conserved differences between protein sequences
Authors: Saumil Mehta, Deendayal Dinakarpandian
Venue: Data Knowledge Engineering (2005)

Proteins have been classified into families based on metrics of similarity such as sequence or structural similarity. However, there are significant differences in function even within families. Mapping these differences to individual amino-acid residues is typically done by an expert. This is a subjective and nonscalable approach. ConsDiff is an algorithm that automates this process. It is based on a set of parametric rules using amino-acid substitution matrices and a multiple sequence alignment. This allows the automated discovery of candidate residues that may be responsible for critical differences in function, which may then be experimentally verified.
Switch Design to Enable Predictive Multiplexed Switching in Multiprocessor Networks
Authors: Z. Ding, R. Hoare, A. Jones, D. Li, S. Shao, S. Tung, J. Zheng, R. Melhem
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Papers - Volume 01 (2005)

Predictive multiplexed switching is a new approach for building interconnection switches for high performance parallel systems. This approach advocates sacrificing some link bandwidth in return for more efficient network control and simpler connection management. The main idea is to depart from the traditional packet and wormhole switching in favor of row data communication over established communication pipes (connections). The overhead of this circuit switching approach can be justified when established connections are repeatedly used before they are torn down. For this, we use multiplexing to allow multiple connections to share the same resources (links and switches), thus avoiding tearing down connections prematurely. The connection establishment overhead is further reduced by exploring communication locality and predictability in applications that exhibit these properties. We present the design of an interconnection system which is based on multiplexed switching and which establishes connections either reactively, in response to dynamically generated requests, or proactively, in response to compiler or application directives. A communication prediction component may be supported to reduce the network control overhead in applications that exhibit communication locality and predictability. The design is evaluated using hardware design, synthesis, and cycle-accurate simulation. Comparison with more traditional switching paradigms shows the potential of our predictive multiplexed switching approach.
Engineering agent-based software systems
Authors: Sajjan G. Shiva, Linda Sherrell, Sarah Lee, Andrew Olney
Venue: Journal of Computing Sciences in Colleges (2005)

Building software systems with using modules has been a popular trend. The concept of the 'module' has changed from a subroutine, to object, to component (DCOM, JavaBean) and now to an 'agent'. Various definitions of the agent have been used over the past few years. In general, a software agent is a component that can exhibit both proactive and reactive behaviors. It works in an autonomous mode and possibly has a capability to learn to improve its performance. Several agent-based systems have been built. Several methodologies and tools exist to aid the development of such systems. Several conferences dealing with the software engineering of agent-based systems have been held. But, the software engineering aspects seem to have taken a back seat, although some recent efforts have addressed this issue. The panel will concentrate on looking at the state-of-the-art in software engineering of agent-based systems and the directions needed. The panel will also address the issues involved in teaching this paradigm in computer science curricula. In particular, we will address the question: Do we need to do anything different in software engineering courses to accommodate this paradigm?
One project, four schema languages: medley or melee?
Authors: Makoto Murata
Venue: Special interest tracks and posters of the 14th international conference on World Wide Web (2005)

This talk first gives an overview of an XML project for e-Local Governments, which is under the auspices of MIAC (Ministry of Internal Affairs and Communications) of Japan. This talk then focuses on schema authoring and user interfaces. In particular, the use of four schema languages, namely RELAX NG, W3C XML Schema, DTD, and Schematron, is highlighted. 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
Appearance-Guided Particle Filtering for Articulated Hand Tracking
Authors: Wen-Yan Chang, Chu-Song Chen, Yi-Ping Hung
Venue: Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05) - Volume 1 - Volume 01 (2005)

We propose a model-based tracking method, called appearance-guided particle filtering (AGPF), which integrates both sequential motion transition information and appearance information. A probability propagation model is derived from a Bayesian formulation for this framework, and a sequential Monte Carlo method is introduced for its realization. We apply the proposed method to articulated hand tracking, and show that it performs better than methods that only use either sequential motion transition information or only use appearance information.
Matching Stochastic Algorithms to Objective Function Landscapes
Authors: W. P. Baritompa, M. Dür, E. M. Hendrix, L. Noakes, W. J. Pullan, G. R. Wood
Venue: Journal of Global Optimization (2005)

Large scale optimisation problems are frequently solved using stochastic methods. Such methods often generate points randomly in a search region in a neighbourhood of the current point, backtrack to get past barriers and employ a local optimiser. The aim of this paper is to explore how these algorithmic components should be used, given a particular objective function landscape. In a nutshell, we begin to provide rules for efficient travel, if we have some knowledge of the large or small scale geometry.
SOAR: A Second-order Arnoldi Method for the Solution of the Quadratic Eigenvalue Problem
Authors: Zhaojun Bai, Yangfeng Su
Venue: SIAM Journal on Matrix Analysis and Applications (2005)

We first introduce a second-order Krylov subspace $\mathcal{G}_n$(A,B;u) based on a pair of square matrices A and B and a vector u. The subspace is spanned by a sequence of vectors defined via a second-order linear homogeneous recurrence relation with coefficient matrices A and B and an initial vector u. It generalizes the well-known Krylov subspace $\mathcal{K}_n$(A;v), which is spanned by a sequence of vectors defined via a first-order linear homogeneous recurrence relation with a single coefficient matrix A and an initial vector v. Then we present a second-order Arnoldi (SOAR) procedure for generating an orthonormal basis of $\mathcal{G}_n$(A,B;u). By applying the standard Rayleigh--Ritz orthogonal projection technique, we derive an SOAR method for solving a large-scale quadratic eigenvalue problem (QEP). This method is applied to the QEP directly. Hence it preserves essential structures and properties of the QEP. Numerical examples demonstrate that the SOAR method outperforms convergence behaviors of the Krylov subspace--based Arnoldi method applied to the linearized QEP.
Come_IN: using computers to foster the integration of migrant communities
Authors: Gunnar Stevens, Michael Veith, Volker Wulf
Venue: ACM SIGGROUP Bulletin (2003)

Modern western societies are facing the challenges of immigration and integration. The main criterion for social participation and democratic collaboration is the successful integration of immigrants. A lack of social as well as cultural integration, especially among young immigrants, seems to be the consequence of a low level of education and unequal opportunities. Immigrant children who are enrolled at primary schools, for instance, show significant deficits in tests of German language acquisition in comparison to German pupils on the one hand, and even to other immigrant pupils of their parent's generation, on the other.
Controlling fluid animation with geometric potential: Research Articles
Authors: Jeong-Mo Hong, Chang-Hun Kim
Venue: Computer Animation and Virtual Worlds (2004)

We propose a new fluid control technique that uses a geometrically induced potential field. Instead of optimizing the control forces exerted at each frame, as was done in previous work, a potential is added as an extra dimension to the simulation space which coerces the fluid inside this space to form the target shape. This type of shape control requires practically no additional computing by the Navier-Stokes solver at run-time, and adds little overhead to implementation. The confinement potentials are induced from geometric information given by animators, and so the control forces that take fluids to a lower potential can be decided in a preprocessing step. We show that a slightly generalized Navier-Stokes equation for fluids in potential fields can be simulated without changing the solver itself. A harmonic potential function can be quickly found with the Poisson solver which is already implemented as a part of the Navier-Stokes solver. 2 and 3 dimensional flows designed by common methods such as hand drawing, traditional shape modeling and key-framing, can be animated efficiently with our control technique. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Converting dependency structures to phrase structures
Authors: Fei Xia, Martha Palmer
Venue: Proceedings of the first international conference on Human language technology research (2001)

Treebanks are of two types according to their annotation schemata: phrase-structure Treebanks such as the English Penn Treebank [8] and dependency Treebanks such as the Czech dependency Treebank [6]. Long before Treebanks were developed and widely used for natural language processing, there had been much discussion of comparison between dependency grammars and context-free phrase-structure grammars [5]. In this paper, we address the relationship between dependency structures and phrase structures from a practical perspective; namely, the exploration of different algorithms that convert dependency structures to phrase structures and the evaluation of their performance against an existing Treebank. This work not only provides ways to convert Treebanks from one type of representation to the other, but also clarifies the differences in representational coverage of the two approaches.
Connectivity with Static Transmission Range in Vehicular Ad Hoc Networks
Authors: Maen M. Artimy, William J. Phillips, William Robertson
Venue: Proceedings of the 3rd Annual Communication Networks and Services Research Conference (2005)

Connectivity in mobile wireless ad-hoc networks is maintained by setting the transmission range so that a node can establish a link to any other node in the network either directly or over multiple hops. Many analytical and experimental studies have focused on determining the minimum transmission range (MTR) that provides connectivity while minimizing transceiver power for various levels of node densities. In this paper, we determine, using simulations, the MTR in vehicular ad hoc networks (VANET) of various road configurations. We show that in 1-lane,2-lane, and 2-way roads, MTR values confirm the analytical relations developed in the literature for1-dimensional networks until density increases beyond a critical vehicle density. Moreover, where traffic jams are forming at intersections, MTR values are not affected by the change in vehicle density. Therefore, a large static transmission range must be chosen in order to keep the network connected in all traffic scenarios.
Research at the Artificial Intelligence corp.
Authors: Larry R. Harris
Venue: Issue 79 (January 1982) (1982)

The Artificial Intelligence Corporation was formed in 1975 to develop and market a commercial natural language database query product. The company currently employs 30 people to enhance, support and market its product known as INTELLECT, which is the productization of the earlier prototype system known as ROBOT.