ppxscal/embedding_network huggingface dataset:
A web service for biomedical term look-up: Conference Papers
Authors: Henk Harkema, Ian Roberts, Rob Gaizauskas, Mark Hepple
Venue: Comparative and Functional Genomics (2005)

Recent years have seen a huge increase in the amount of biomedical information that is available in electronic format. Consequently, for biomedical researchers wishing to relate their experimental results to relevant data lurking somewhere within this expanding universe of on-line information, the ability to access and navigate biomedical information sources in an efficient manner has become increasingly important. Natural language and text processing techniques can facilitate this task by making the information contained in textual resources such as MEDLINE more readily accessible and amenable to computational processing. Names of biological entities such as genes and proteins provide critical links between different biomedical information sources and researchers' experimental data. Therefore, automatic identification and classification of these terms in text is an essential capability of any natural language processing system aimed at managing the wealth of biomedical information that is available electronically. To support term recognition in the biomedical domain, we have developed Termino, a large-scale terminological resource for text processing applications, which has two main components: first, a database into which very large numbers of terms can be loaded from resources such as UMLS, and stored together with various kinds of relevant information; second, a finite state recognizer, for fast and efficient identification and mark-up of terms within text. Since many biomedical applications require this functionality, we have made Termino available to the community as a web service, which allows for its integration into larger applications as a remotely located component, accessed through a standardized interface over the web. Copyright &copy; 2005 John Wiley & Sons, Ltd.
Dynamics modeling and analysis of a biped walking robot actuated by a closed-chain mechanism
Authors: Hyeung-Sik Choi, Changyul Baek
Venue: Journal of Robotic Systems (2004)

We developed a new type of human-sized biped walking robot (BWR) driven by the closed-chain type of joint actuator. Each leg of the robot is composed of three pitch joints and one roll joint. In all, a 15 degree-of-freedom robot including four arm joints and three joints for the head was developed. The BWR was developed to walk autonomously such that all leg joints are actuated by small 90 W dc motors&sol;drivers and dc batteries and controllers which are boarded. The joint actuator for the BWR is composed of the four-bar-link mechanism driven by the ball screw which has high strength and high gear ratio. A dynamics modeling of the developed BWR for forward walking is presented in which the revolute joint dynamics are transformed into the prismatic joint dynamics of the ball screw. Also, an analysis on the four-bar-link mechanism applied to the joint actuator and on the structure of the BWR is shown. The design specification of the actuating motor for the BWR is analyzed through the torque analysis of the four-bar-link actuator. Through walking experiments of the BWR, the walking performance and trajectory tracking ability is shown. &copy; 2004 Wiley Periodicals, Inc.
Quantitative genome-wide analysis of yeast deletion strain sensitivities to oxidative and chemical stress: Research Articles
Authors: Chandra L. Tucker, Stanley Fields
Venue: Comparative and Functional Genomics (2004)

Understanding the actions of drugs and toxins in a cell is of critical importance to medicine, yet many of the molecular events involved in chemical resistance are relatively uncharacterized. In order to identify the cellular processes and pathways targeted by chemicals, we took advantage of the haploid Saccharomyces cerevisiae deletion strains (Winzeler et al., [1999];. Although &sim;4800 of the strains are viable, the loss of a gene in a pathway affected by a drug can lead to a synthetic lethal effect in which the combination of a deletion and a normally sublethal dose of a chemical results in loss of viability. We carried out genome-wide screens to determine quantitative sensitivities of the deletion set to four chemicals: hydrogen peroxide, menadione, ibuprofen and mefloquine. Hydrogen peroxide and menadione induce oxidative stress in the cell, whereas ibuprofen and mefloquine are toxic to yeast by unknown mechanisms. Here we report the sensitivities of 659 deletion strains that are sensitive to one or more of these four compounds, including 163 multichemical-sensitive strains, 394 strains specific to hydrogen peroxide and&#x002F;or menadione, 47 specific to ibuprofen and 55 specific to mefloquine. We correlate these results with data from other large-scale studies to yield novel insights into cellular function. Copyright &copy; 2004 John Wiley & Sons, Ltd.
Us, ourselves, and we: thoughts about social (self-) categorization
Authors: Markus Rohde, David Williamson Shaffer
Venue: ACM SIGGROUP Bulletin (2003)

In a recent Workshop on community-based learning at the 6th International Conference on Learning Sciences (ICLS 2004), one persistent theme was the variety of terms used to describe collections of people (group, community, network, collective) and components of interaction (culture, identity, collaboration, cooperation) in group learning activities. Here, we describe some of the thinking that emerged in those discussions, not as a comprehensive literature review or completely elaborated socio-cultural theory, but rather as an invitation to further discussion. We suggest that a group is the most generic and general social category: all of the analytical units in the literature on collective learning - teams, social networks, and communities - are groups. We argue that these other terms have additional structural characteristics that make them distinct subsets of the generic term group. For example, a team is a group with a common task, a network is a group with strong social ties, and a community is a group with a shared culture. We propose a two-dimensional space of social organizations characterized by shared culture and shared interaction, and suggest both individuals and collectives show a developmental history through the space of collectives, moving from loose group affiliation to increasing identification with, development of, and participation in shared interactions within a shared culture. This analysis suggests, we argue, that: (a) tools to support "collaboration" may need different affordances for different kinds of collectives; (b) understanding different kinds of collectives requires different methodologies; and (c) culture plays a prominent role in the space of collectives we describe, and thus, we argue, should play a significant role in the analysis of any community. We hope that this brief discussion will lead to further work on the social entities within which group learning takes place, on the processes of learning in such settings, and on the technologies that can support such processes.
Efficient mining of sequential patterns with time constraints by delimited pattern growth
Authors: Ming-Yen Lin, Suh-Yin Lee
Venue: Knowledge and Information Systems (2005)

An active research topic in data mining is the discovery of sequential patterns, which finds all frequent subsequences in a sequence database. The generalized sequential pattern (GSP) algorithm was proposed to solve the mining of sequential patterns with time constraints, such as time gaps and sliding time windows. Recent studies indicate that the pattern-growth methodology could speed up sequence mining. However, the capabilities to mine sequential patterns with time constraints were previously available only within the Apriori framework. Therefore, we propose the DELISP (delimited sequential pattern) approach to provide the capabilities within the pattern-growth methodology. DELISP features in reducing the size of projected databases by bounded and windowed projection techniques. Bounded projection keeps only time-gap valid subsequences and windowed projection saves nonredundant subsequences satisfying the sliding time-window constraint. Furthermore, the delimited growth technique directly generates constraint-satisfactory patterns and speeds up the pattern growing process. The comprehensive experiments conducted show that DELISP has good scalability and outperforms the well-known GSP algorithm in the discovery of sequential patterns with time constraints.
An experimental card game for teaching software engineering processes
Authors: Alex Baker, Emily Oh Navarro, André van der Hoek
Venue: Journal of Systems and Software (2005)

The typical software engineering course consists of lectures in which concepts and theories are conveyed, along with a small "toy" software engineering project which attempts to give students the opportunity to put this knowledge into practice. Although both of these components are essential, neither one provides students with adequate practical knowledge regarding the process of software engineering. Namely, lectures allow only passive learning and projects are so constrained by the time and scope requirements of the academic environment that they cannot be large enough to exhibit many of the phenomena occurring in real-world software engineering processes. To address this problem, we have developed Problems and Programmers, an educational card game that simulates the software engineering process and is designed to teach those process issues that are not sufficiently highlighted by lectures and projects. We describe how the game is designed, the mechanics of its game play, and the results of an experiment we conducted involving students playing the game.
Some remarks on Hajós' conjecture
Authors: Carsten Thomassen
Venue: Journal of Combinatorial Theory Series B (2005)

Hajós' conjecture is false for almost all graphs but only few explicit counterexamples have appeared in the literature. We relate Hajós' conjecture to Ramsey theory, perfect graphs, and the maximum cut problem and obtain thereby new classes of explicit counterexamples. On the other hand, we show that some of the graphs which Catlin conjectured to be counterexamples to Hajós' conjecture satisfy the conjecture, and we characterize completely the graphs which satisfy Catlin's conjecture.
Learning with Constrained and Unlabelled Data
Authors: Tilman Lange, Martin H. C. Law, Anil K. Jain, Joachim M. Buhmann
Venue: Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05) - Volume 1 - Volume 01 (2005)

Classification problems abundantly arise in many computer vision tasks ¿ being of supervised, semi-supervised or unsupervised nature. Even when class labels are not available, a user still might favor certain grouping solutions over others. This bias can be expressed either by providing a clustering criterion or cost function and, in addition to that, by specifying pairwise constraints on the assignment of objects to classes. In this work, we discuss a unifying formulation for labelled and unlabelled data that can incorporate constrained data for model fitting. Our approach models the constraint information by the maximum entropy principle. This modeling strategy allows us (i) to handle constraint violations and soft constraints, and, at the same time, (ii) to speed up the optimization process. Experimental results on face classification and image segmentation indicates that the proposed algorithm is computationallyefficient and generates superior groupings when compared with alternative techniques.
Improved Flicker Removal through Motion Vectors Compensation
Authors: K. K. Wong, A. Das, M. N. Chong
Venue: Proceedings of the Third International Conference on Image and Graphics (2004)

Image flicker, the unnatural temporal fluctuations in perceived image intensity, is an annoying artifact existing in many old film sequences and its removal is an integral part in any old film restoration process. In this paper, we propose an improved flicker removal method based on flicker parameters estimation with the aide of motion vectors compensation. We tested the proposed method on sequences with artificially added global and local flicker, as well as on natural real flicker film material. Test results obtained showed the proposed method produced much better flicker correction quality than an established flicker removal method known as the "Roosmalen method".
Runtime Compression of MPI Messanes to Improve the Performance and Scalability of Parallel Applications
Authors: Jian Ke, Martin Burtscher, Evan Speight
Venue: Proceedings of the 2004 ACM/IEEE conference on Supercomputing (2004)

Communication-intensive parallel applications spend a significant amount of their total execution time exchanging data between processes, which leads to poor performance in many cases. In this paper, we investigate message compression in the context of large-scale parallel message-passing systems to reduce the communication time of individual messages and to improve the bandwidth of the overall system. We implement and evaluate the cMPImessage-passing library, which quickly compresses messages on-the-fly with a low enough overhead that a net execution time reduction is obtained. Our results on six large-scale benchmark applications show that their execution speed improves by up to 98% when message compression is enabled.
Automatic predicate argument analysis of the Penn TreeBank
Authors: Martha Palmer, Joseph Rosenzweig, Scott Cotton
Venue: Proceedings of the first international conference on Human language technology research (2001)

One of the primary tasks of Information Extraction is recognizing all of the different guises in which a particular type of event can appear. For instance, a meeting between two dignitaries can be referred to as A meets B or A and B meet, or a meeting between A and B took place/was held/opened/convened/finished/dragged on or A had/presided over a meeting/conference with B
Adobe Illustrator Revealed
Authors: Chris Botello
Venue:  (2005)

Coverage includes- Targets towards beginner-to-intermediate level students and professionals who want to learn how to use the latest version of Illustrator, Adobe's essential design software. Illustrates concepts and skills clearly with a visually-stimulating graphics and a unique tutorial-based pedagogy. Allows readers to build their portfolio with multiple projects throughout the text like creating advertisements, brochures, and flyers. Covers introductory through more advanced features of the latest release of Adobe Illustrator, including how to prepare illustrations for print production. Provides instruction on how to work in the latest release of Illustrator using either Mac or PC platforms.
Using Tropos to Model Agent Based Architectures for Adaptive Systems: A Case Study in Ambient Intelligence
Authors: Loris Penserini, Paolo Bresciani, Tsvi Kuflik, Paolo Busetta
Venue: Proceedings of the IEEE International Conference on Software - Science, Technology & Engineering (2005)

The realization of complex distributed applications required in areas such as e-Business, e-Government, and ambient intelligence calls for new software development paradigms, such as the Service Oriented Computing approach, which accommodates for dynamic and adaptive interaction schemata, carried on at a peer-to-peer level. Multi Agent Systems promise to offer the natural architectural solutions to several requirements imposed by such an adaptive approach. Nevertheless, architectural design patterns commonly adopted to model agent interaction schemata do not totally fit the needs implied by highly adaptable service oriented computing scenarios. In this paper, the agent oriented software engineering methodology Tropos is adopted to discuss common architectural agent patterns, and propose architectural improvements to better deal with high degrees of dynamic system adaptability. The novel architectures are illustrated through a case study in the field of ambient intelligence, namely a real Multi Agent System application implementing a pervasive museum visitors guide.
Multilayer neural network with back propagation: hardware solution to learning XOR
Authors: Richard Zbeda, Pramod Nathan
Venue: Journal of Computing Sciences in Colleges (2005)

In this paper we present our current work on a hardware implementation of Artificial Neural Networks (ANNs). In specific, we are working to create a multilayer neural network with back propagation that can learn the XOR training input. The larger agenda of this project is to make progress in intelligent robot controllers. This is a difficult issue because microcontrollers used as onboard controllers for the robot must be capable of dealing with a changing environment. ANNs are particularly suitable candidates for a control system; they can deal effectively with the micro-structure of the robot's sensors and motors, they are robust in affecting behavior, can adjust to an environment, have tolerance to noise, and are well structured for producing the appropriate behavior [1]. To compute the best neural network, genetic algorithms (GAs) are often used. Since they can be computationally expensive, GAs are usually carried out in a simulation, where the best neural network control program is evolved. Parker and Lee (2002) used a genetic algorithm in a simulation to learn the best neural network for an individual leg controller on a hexapod robot [2]. Floreano and Mondada (1994) allowed a neural-network driven robot to completely evolve on its own by directing its genetic evolution to a workstation through a wire while the robot was moving [1]. Despite this autonomy, the robot was still not completely autonomous because it relied on the workstation to perform the genetic algorithm. In addition, the ANN on the microcontroller was executed through a sequence of serial instructions, unlike the parallel method of a biological neural network.
An Improved Pseudo-Random Generator Based on the Discrete Logarithm Problem
Authors: Rosario Gennaro
Venue: Journal of Cryptology (2005)

Under the assumption that solving the discrete logarithm problem modulo an n-bit safe prime p is hard even when the exponent is a small c-bit number, we construct a new pseudo-random bit generator. This new generator outputs n &#x2013; c &#x2013; 1 bits per exponentiation with a c-bit exponent and is among the fastest generators based on hard number-theoretic problems.
A Self-Organizing Flock of Condors
Authors: Ali Raza Butt, Rongmei Zhang, Y. Charlie Hu
Venue: Proceedings of the 2003 ACM/IEEE conference on Supercomputing (2003)

Condor provides high throughput computing by leveraging idle-cycles on off-the-shelf desktop machines. It also supports flocking, a mechanism for sharing resources among Condor pools. Since Condor pools distributed over a wide area can have dynamically changing availability and sharing preferences, the current flocking mechanism based on static configurations can limit the potential of sharing resources across Condor pools. This paper presents a technique for resource discovery in distributed Condor pools using peer-to-peer mechanisms that are self-organizing, fault-tolerant, scalable, and locality-aware. Locality-awareness guarantees that applications are not shipped across long distances when nearby resources are available. Measurements using a synthetic job trace show that self-organized flocking reduces the maximum job wait time in queue for a heavily loaded pool by a factor of 10 compared to without flocking. Simulations of 1000 Condor pools are also presented and the results confirm that our technique discovers and utilizes nearby resources in the physical network.
Risk management for electronic commerce between Japan and China
Authors: Masamitsu Moriyama, Kentaro Takemoto, Takio Shimosakon
Venue: Proceedings of the 6th international conference on Electronic commerce (2004)

This study aims at realization of electronic commerce (EC hereunder) through the Internet between Japan and China which have different systems. For this purpose, we have established the China Hosho Network (CHN hereunder) consortium which consists of universities and private research organizations. The consortium operates with an information disclosure policy, and is conducting a study on the credit guarantee system which will play a key role in facilitating the growth of EC between Japan and China [1].In EC, business is basically conducted on a credit basis; therefore many cases of failure are expected to occur in trade between Japan and China due to the difference in social and commercial systems and customs. Since the current civil codes of China do not provide regulations on international trade, there is a great demand among traders in Japan for establishment of credit guarantee systems for EC similar to damage insurance for international trade [2].This paper will discuss the development of the risk management system for EC between Japan and China, which functions as a credit guarantee system. The risk management system operates for its members who fulfil the terms of the membership agreement. It has a two-tire structure, consisting of risk control (preventive measures) and risk finance (financial arrangements including insurance coverage and/or other financial measures for possible trade failures). The risk control is a quality assurance system which can be realized by inspection before shipment. The risk finance is a guarantee insurance system which was developed incorporating conventional marine and fire insurance for trade. This paper also presents the results of a demonstrative application of the risk management system in order to prove its validity.
Image Representation for Stereo: Stripes and Stripe Adjacency Graph
Authors: Changchang Wu, Zengfu Wang
Venue: Proceedings of the Third International Conference on Image and Graphics (2004)

A new algorithm for stereo correspondence and surface reconstruction is presented in this paper. We advances stripe as the matching primitive. The stripe is a special kind of region composed of some adjacent similar scanline segments. Each input image is segmented into stripes and then converted to a stripe adjacency graph. Our method matches stripes and stripe adjacencies globally and adaptively, with stripes being merged or split according to the disparity estimates. A pair of matched stripes constructs a surface patch, and, correspondingly, a pair of matched subgraph presents a smooth surface. Experimental results show that our algorithm is fast and effective.
Efficient FORTRAN subprograms for the solution of elliptic partial differential equations (abstract)
Authors: Paul Swarztrauber, Roland Sweet
Venue: ACM SIGNUM Newsletter (1975)

The purpose of this paper is to describe technical note, NCAR TN/IA-109, which is intended to provide scientists with a package of computer programs which make use of current methods for solving elliptic partial differential equations. Computer models of geophysical processes often require the numerical solution of elliptic partial differential equations. This is particularly true for models which make use of stream functions, velocity potentials, or vorticity equations, or in which the pressure of an incompressible fluid is computed. The numerical solution of elliptic equations can be a formidable programming task. Also, the equations are often time-dependent, requiring repeated solutions and, hence, considerable computing resources. Efficient, reliable, and well-documented computer subroutines for solving such equations are needed. With recent advances in computing methods, it became apparent to the authors that a very large class of elliptic equations (separable) could be solved rapidly and with minimal storage. Of particular importance was the fact that, as a result of work on singular problems, this class was free of special cases for which solutions could not be obtained numerically.