ppxscal/embedding_network huggingface dataset:
MS2DB: An Algorithmic Approach to Determine Disulfide Linkage Patterns
Authors: Timothy Lee, Rahul Singh, Ten-Yang Yen, Bruce Macher
Venue: Proceedings of the 19th IEEE Symposium on Computer-Based Medical Systems (2006)

Determining the number and location of disulfide bonds within a protein provide valuable insight into the protein's three-dimensional structure. Purely computational methods that predict the bonded cysteine pairings given a protein's primary structure have limitations in both prediction correctness and the number of bonds that can be predicted. Our approach utilizes tandem mass spectrometric (MS/MS) experimental procedures that produce spectra of protein fragments joined by a disulfide bond. This allows the limitations in correctness and scaling to be overcome. The algorithmic problem then becomes how to match a theoretical mass space of all possible bonded fragments against the MS/MS data. In our algorithm, which we call the Indexed approach, the regions of the mass space that contain masses comparable to the MS/MS spectrum masses are located before the match is determined. We have developed a software package, MS2DB, which implements this approach. A performance study shows that the Indexed approach determines disulfide bond linkage patterns both correctly and efficiently.
Solving Markov Random Fields using Second Order Cone Programming Relaxations
Authors: M. Pawan Kumar, P. H. S. Torr, A. Zisserman
Venue: Proceedings of the 2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition - Volume 1 (2006)

This paper presents a generic method for solvingMarkov random fields (MRF) by formulating the problem of MAP estimation as 0-1 quadratic programming (QP). Though in general solving MRFs is NP-hard, we propose a second order cone programming relaxation scheme which solves a closely related (convex) approximation. In terms of computational efficiency, our method significantly outperforms the semidefinite relaxations previously used whilst providing equally (or even more) accurate results. Unlike popular inference schemes such as Belief Propagation and Graph Cuts, convergence is guaranteed within a small number of iterations. Furthermore, we also present a method for greatly reducing the runtime and increasing the accuracy of our approach for a large and useful class of MRFs. We compare our approach with the state-of-the-art methods for subgraph matching and object recognition and demonstrate significant improvements.
Easy-SC: a supply chain simulation tool
Authors: Juqi Liu, Wei Wang, Yueting Chai, Yi Liu
Venue: Proceedings of the 36th conference on Winter simulation (2004)

To assist the decision makers, we develop a new supply chain simulation software: Easy-SC, a Java-based tool that simplifies the supply chain simulation. In its current state of development, Easy-SC is a modeling tool for assessing the pros and cons of new facility locations, resource allocations and different combinations of policies. It can be used in the modeling of small projects such as single inventory units to large-scale projects such as world wide supply chains. This paper introduces Easy-SC by an examination of its current software module architecture, modeling elements, basic features and simulation processes.
An Intensity-augmented Ordinal Measure for Visual Correspondence
Authors: Anurag Mittal, Visvanathan Ramesh
Venue: Proceedings of the 2006 IEEE Computer Society Conference on Computer Vision and Pattern Recognition - Volume 1 (2006)

Determining the correspondence of image patches is one of the most important problems in Computer Vision. When the intensity space is variant due to several factors such as the camera gain or gamma correction, one needs methods that are robust to such transformations. While the most common assumption is that of a linear transformation, a more general assumption is that the change is monotonic. Therefore, methods have been developed previously that work on the rankings between different pixels as opposed to the intensities themselves. In this paper, we develop a new matching method that improves upon existing methods by using a combination of intensity and rank information. The method considers the difference in the intensities of the changed pixels in order to achieve greater robustness to Gaussian noise. Furthermore, only uncorrelated order changes are considered, which makes the method robust to changes in a single or a few pixels. These properties make the algorithm quite robust to different types of noise and other artifacts such as camera shake or image compression. Experiments illustrate the potential of the approach in several different applications such as change detection and feature matching.
Motorola SpecNL: A Hybrid System to Generate NL Descriptions from Test Case Specifications
Authors: Dante Torres, Daniel Leitao, Flavia Barros
Venue: Proceedings of the Sixth International Conference on Hybrid Intelligent Systems (2006)

SpecNL is a tool that generates software test cases descriptions in natural language from test case specifications. The main aim is to help test engineers to execute the manual tests. This tool is part of a project to automate software test for mobile phone applications. SpecNL is a hybrid system (from the Natural Language Generation viewpoint), since it combines linguistic information and output templates in the generation task. Experiments with the implemented prototype revealed satisfactory results. This is an original and innovative application of NLG in the Software Engineering area.
IBM's pragmatic embrace of open source
Authors: Pamela Samuelson
Venue: Communications of the ACM (2006)

Open source has changed the intellectual property landscape of the software industry.
Test/Repair Area Overhead Reduction for Small Embedded SRAMs
Authors: Baosheng Wang, Qiang Xu
Venue: Proceedings of the 15th Asian Test Symposium (2006)

For current highly-integrated and memory-dominant System-ona- Chips (SoCs), especially for graphics and networking SoCs, the test/repair area overhead of embedded SRAMs (e-SRAMs) is a big concern. This paper presents various approaches to tackle this problem from a practical point of view. Without sacrificing at-speed testability, diagnosis capability and repairability, the proposed approaches consider partly sharing wrapper for identical memories, sharing memory BIST controllers for e- SRAMs embedded in different functional blocks, test responses compression for wide memories, and various repair strategies for e-SRAMs with different configurations. By combining the above approaches, the test/repair area overhead for e-SRAMs can be significantly reduced. For example, for one benchmark SoC used in our experiments, it can be reduced as much as 10% of the entire memory array.
Multimodal interaction on mobile phones: development and evaluation using ACICARE
Authors: Marcos Serrano, Laurence Nigay, Rachel Demumieux, Jérôme Descos, Patrick Losquin
Venue: Proceedings of the 8th conference on Human-computer interaction with mobile devices and services (2006)

The development and the evaluation of multimodal interactive systems on mobile phones remains a difficult task. In this paper we address this problem by describing a component-based approach, called ACICARE, for developing and evaluating multimodal interfaces on mobile phones. ACICARE is dedicated to the overall iterative design process of mobile multimodal interfaces, which consists of cycles of designing, prototyping and evaluation. ACICARE is based on two complementary tools that are combined: ICARE and ACIDU. ICARE is a component-based platform for rapidly developing multimodal interfaces. We adapted the ICARE components to run on mobile phones and we connected them to ACIDU, a probe that gathers customer's usage on mobile phones. By reusing and assembling components, ACICARE enables the rapid development of multimodal interfaces as well as the automatic capture of multimodal usage for in-field evaluations. We illustrate ACICARE using our contact manager system, a multimodal system running on the SPV c500 mobile phone.
Distributing a large-scale, complex FAB simulation using HLA and Java: issues and lessons
Authors: Leon F. McGinnis
Venue: Proceedings of the 36th conference on Winter simulation (2004)

Distributed simulation promises a range of benefits and opportunities, especially for modeling large-scale complex systems, such as wafer fabs. However, as with many promising technologies, the devil is in the details. This paper describes some experiences in distributing a high-fidelity, full fab simulation model with federates implemented in Java representing manufacturing processes, automated material handling systems, and control systems. Some informal comparisons with AutoMod/ASAP are included.
Towards Adaptive Occlusion Culling Using Camera Coherence
Authors: I. Mansa, A. Amundarain, E. Elizalde, A. Garcia-Alonso, L. Matey
Venue: Proceedings of the conference on Information Visualization (2006)

Occlusion culling proves to be useful for the interactive visualization of environments that are not densely occluded. Those which are built up by dense geometric sets like aerospace engines composed of thousands of components and millions of polygons. In first place the convenience of using occlusion culling is studied with a simple scheme. Then improvements are analyzed. The key points to obtain frame rate speed-ups are: a convenient occlusion query scheduling provides the performance required; depth sorting is performed only when camera orientation changes more than a given threshold; coherence reduces the number of occlusion queries posted per frame. It is possible to select the percentage of occlusion queries that will be performed in each frame, from non-conservative schemes up to a conservative one. Furthermore, we propose a small addition to the GPU occlusion queries to perform faster renderings.
The role of people knowledge in learning narrative and domain content
Authors: Joan Davis, Tiffany Lee, Nancy Vye, John Bransford, Daniel L. Schwartz
Venue: Proceedings of the 7th international conference on Learning sciences (2006)

We argue that the addition of people knowledge to curricula has the potential---still largely unrecognized---to improve classroom learning. We describe the results of two studies on people knowledge and learning. Study 1 indicates that narrative information organized around familiar, as contrasted with unfamiliar, people is better remembered and judged to be more interesting and concrete by learners. Study 2 focuses on people knowledge and learning and transfer of pedagogical content knowledge.
Using Talking Heads for Real-Time Virtual Videophone in Wireless Networks
Authors: Yang Xiao, Max H. Garzon, Michael Nolan
Venue: IEEE MultiMedia (2006)

Low bandwidth makes real-time video over wireless and mobile networks expensive and limits transmission length. An architecture that substitutes a person's face with a text-based facial vector description transmitted over a network in tandem with a voice stream requires minimal bandwidth, enabling real-time videophony over various wireless networks.
Frequency-Domain Algorithms for Visual Analysis on Genomic Structures in Prokaryotes
Authors: Lee Sing Cheong, Feng Lin, Hock Soon Seah
Venue: Proceedings of the International Conference on Computer Graphics, Imaging and Visualisation (2006)

Frequency-domain algorithms are studied to provide the composition of each nucleic acid base simultaneously across numerous frequencies and along the base-positions, through Fourier transformation and color mapping of the bases. And also, composite colored scalograms are constructed by continuous wavelet transformation to provide their individual localized time and periodic energy content in a single figure. The visualization of three-dimensional information in the forms of bases, frequencies and base-positions allows visual analysis of correlated structural and genomic information, which can hardly be obtained from the conventional character string analysis. Significant features of the studied prokaryotic genomes were revealed by the use of the programs developed.
The re-definition of low power design for HPC: a paradigm shift
Authors: Reiner Hartenstein
Venue: Proceedings of the 19th annual symposium on Integrated circuits and systems design (2006)

Low Power Digital System Design has to be re-defined. Clever circuit level concepts to reduce leakage current effects etc. and to get along with a tiny battery have become lower-ranking. Slashing the electricity bill by up to millions of dollars has become the key issue - not only in High Performance Computing (HPC), e. g. also for server farms (for instance, Google's electricity bill amounts to about 50 million US-$/year).Increasing the clock frequency of single-core microprocessors has come to an end. Multi-core microprocessor chips are not really the promising way to go for very high performance (vHPC). This lesson we have learnt from the supercomputing crisis, where the electric power bill is the most important obstacle on the way to obtain Petaflops by monstrous architectures having followed the wrong road map for decades. This problem can be solved only by a paradigm shift instead of circuit level issues. For the solution we have to take a second look onto the Reconfigurable Computing Paradox. Although FPGAs have a substantially lower clock frequency, are power-hungry, are expensive, and their effective integration density is by 4 orders of magnitude behind Moore's law, the new road map is FPGA-based, it is based on the Reconfigurable Computing Paradigm. Software-to-Configware migration is the silver bullet to escape from the von Neumann paradigm trap for getting rid of the exponentially growing massive bottleneck problems coming along with traditional forms of increasing parallelism. Slashing the electricity bill is just a side effect of speedup factors having been published with up to 4 orders of magnitude.The talk also explains the fundamental issues and bashes educational deficits cemented by newest CS- related ACM/IEEE-CS/AIS curriculum recommendations.
A Heuristic Algorithm for the Offline One-Dimensional Bin Packing Problem Inspired by the Point Jacobi Matrix Iterative Method
Authors: Carlos D. Toledo Suarez Ernesto Palma Gonzlez Manuel Valenzuela Rendon
Venue: Proceedings of the Fifth Mexican International Conference on Artificial Intelligence (2006)

The bin packing problem is a well known NP-hard problem that consists in placing a set of items of different sizes in a mimimum number of bins. An iterative algorithm for the one-dimensional offline bin packing problem is presented whose number of iterations needed to reach an unchanging partition when faced to a particular instance is bounded by the performance of the point Jacobi method on the problem taken as a matrix relaxation one. The algorithm was tested on a large widely used benchmark instances from the literature and behaved very successfully on a class considered as very difficult.
Minimizing Sum of Completion Times and Makespan in Master-Slave Systems
Authors: Joseph Y. -T. Leung, Hairong Zhao
Venue: IEEE Transactions on Computers (2006)

We consider scheduling problems in the master-slave model. In this model, each job has to be processed sequentially in three stages. In the first stage, a preprocessing task runs on a master machine, in the second stage, a slave task runs on a dedicated slave machine, and, in the last stage, a postprocessing task again runs on a master machine, possibly different from the master machine in the first stage. It has been shown that the problem of minimizing the makespan or the sum of completion times is NP-hard in the strong sense even if preemption is allowed. In this paper, we design efficient approximation algorithms to minimize the sum of completion times in various settings. These are the first general results for the minsum problem in the master-slave model. We also show that these algorithms generate schedules with small makespan as well.
Design and Application of a Scalable Embedded Systems' Architecture with an FPGA Based Operating Infrastucture
Authors: Fritz Mayer-Lindenberg
Venue: Proceedings of the 9th EUROMICRO Conference on Digital System Design (2006)

Embedded systems may be designed from a few, properly chosen types of processing components equipped with interfaces for their networking to meet almost arbitrary performance requirements. In this work we describe a particular scalable architecture of this kind using both standard processor and FPGA processing components. It supports multiple FPGA applications through standard FPGA functions implementing the net-working support, and also provides standard CPU functions on the FPGA for the sequential control of application circuits and for their interfacing to the network. On standard von-Neumann machines, a set of such standard functions implemented with the resources of the machine but not directly available from it, and providing a higher level runtime environment for applications would be called an operating system. After defining the scalable architecture and the runtime support, system design and programming (in particular, of FPGA networks) can be automated. We demonstrate this through a simple algorithm to determine the required mix of components for a given application. The architecture is further supported by a system-level, compiled coordination language for functions compiled with the standard processor and FPGA tools.
Sojourn time approximations in queueing networks with feedback
Authors: B. M. M. Gijsen, R. D. van der Mei, P. Engelberts, J. L. van den Berg, K. M. C. van Wingerden
Venue: Performance Evaluation (2006)

This paper is motivated by the response-time analysis of distributed information systems, where transactions are handled by a sequence of front-end server and back-end server actions. We study sojourn times in an open queueing network with a single Processor Sharing (PS) node and an arbitrary number of M multi-server First-Come-First-Served (FCFS) nodes. Customers arrive at the PS according to a Poisson process. After departing from the PS node a customer jumps to FCFS node k with probability pk, and departs from the system with probability 1 - p, where p = Σk-1M pk (0 < p < 1). After receiving service at a FCFS node, a customer jumps back to the PS node. For this model, we focus on the mean and the variability of the sojourn time of an arbitrary customer in the system. The model is a product-form network, which immediately leads to a closed-form expression for the mean sojourn times. The variance of the sojourn times, however, does not admit an exact expression; the complexity is caused by the possibility of overtaking. To this end, we propose a new methodology for deriving closed-form approximations for the variance of sojourn times in queueing networks with feedback. Numerical results from extensive experimentation with simulations demonstrates that the approximations are highly accurate for a wide range of parameter values.
Resource Selection for Autonomic Database Tuning
Authors: Jeong Seok Oh, Sang Ho Lee
Venue: Proceedings of the 21st International Conference on Data Engineering Workshops (2005)

Database administrators should be aware of resource usages to maintain database system performance. As database applications become more complex and diverse, managing database systems becomes too costly and prone to error. Autonomic database tuning becomes more important than ever. This paper starts with an analysis on how resource usages respond by changing resource sizes in database systems. Then, we present a simple method that automatically selects resources that affect the system performance. An experiment using the TPC-C and TPC-W workloads has been carried out with a commercial database system. A preliminary analysis shows that our method works.
Blind indentifiability of a band-limited nonminimum phase system from its output autocorrelation
Authors: Y. Chen, C. L. Nikias
Venue: Proceedings of the Acoustics, Speech, and Signal Processing, 1993. ICASSP-93 Vol 4., 1993 IEEE International Conference on - Volume 04 (1993)

The authors address the problem of blind identification of a band-limited nonminimum-phase channel from its output autocorrelation when the input is a discrete-time white noise sequence. It has been well established in the literature that when the input to a linear-time-invariant (LTI) channel (system) is a continuous-time white noise, the identification of the phase of the channel from its output autocorrelation is impossible. To make the channel identification from its output autocorrelation unique, it is necessary to know a priori the whole phase response of the channel. It is shown that when the input is a discrete-time white noise sequence, what is needed to make the channel identification from its output autocorrelation unique is reduced to the phase response in the frequency range of -1/2T
Towards Information and Goal Based Agent Negotiation
Authors: Paul Bogg
Venue: Proceedings of the IEEE/WIC/ACM international conference on Intelligent Agent Technology (2006)

Negotiation is typically the way in which real world multi-issue commercial contracts are resolved and signed. The automation of negotiation in the B2B context has the potential to revolutionise trade. Intelligent agents have been proposed as the software architecture for automating negotiation. Goals are important based on the notion from [4] that an agent which focuses on negotiating by interests or goals rather than positions may increase the quality of agreement, and the speed of reaching the agreement. This paper will be presenting work towards goal based negotiation which extends an information theoretical framework for automating negotiation.
Developing a Learning Management System Based on the IMS Learning Design Specification
Authors: Kim Hagen, Diana Hibbert, Prof. Kinshuk
Venue: Proceedings of the Sixth IEEE International Conference on Advanced Learning Technologies (2006)

The IMS Learning Design Specification creates a standard XML format for modeling units of learning, which allows sharing of learning plans between educators using different learning management systems. This paper describes the implementation and formative evaluation of a prototype learning management system Voyager, which implements the data model and workflow of the IMS Learning Design Specification as closely as possible. Perceived benefits of such a system include the pedagogical benefit of a focus on learner activities rather than knowledge transfer, the ability for interaction between multiple learners and educators, and the flexibility of the IMS Learning Design model for different pedagogical approaches and differing levels of use. Problems encountered include the lack of specification and difficulty designing runtime functionality, the increased cognitive load of the unfamiliar theatre model for both educators and learners, and the complexity of the data model which lead to data redundancy and large amounts of data being created for even simple learning designs.
Exploring agent-supported simulation brokering on the semantic web: foundations for a dynamic composability approach
Authors: Levent Yilmaz, Tuncer I. Ören
Venue: Proceedings of the 36th conference on Winter simulation (2004)

Federated simulations address the need for interoperability, as well as the improvement of reuse and composability. The focal goal in a federated simulation is to facilitate composable simulations by standardizing interfaces to assure technical interoperability among disparate simulations. Yet, existing federated simulation infrastructures neither facilitate substantive interoperability nor are dynamically extensible. Emergent web services technologies hold out the potential to significantly improve the development of interoperable, extensible, and dynamically composable federations. As such, recent initiatives (i.e., XMSF) are urging the use of open standards that can be applied within an extensible framework for next generation modeling and simulation applications. We discuss how the realization of multimodel and multisimulation formalisms in terms of semantic web and agent technologies may bring new vistas to demonstrate runtime model discovery, instantiation, composition, and interoperation.