ppxscal/embedding_network huggingface dataset:
Searching for and beyond replication origins
Authors: Simon Tavare
Venue:  (2006)

Yeast DNA replication is a precisely controlled process that involves multiple replication origins. We are interested in mapping these origins and studying their replication dynamics. To map replication origins, we first characterized their "sandwich" structure, which is a two-block motif named EACS-B1 flanked by an A-rich region and a T-rich region. We built different classifiers using discriminant analysis methods based on this structure. All classifiers, when applied to genome scan, give too high a false discovery rate (&ge; 84%). To reduce false positive calls, we used tiling arrays to narrow down the region to scan. We developed a special hidden Markov model which is robust to probe failure to call binding sites. The 529 sites (&sim; 5% of yeast genome) called by the HMM reduced the false discovery rate for searching EACS-B1 to 18%. Therefore, this study provided a set of candidate origins with their exact binding sites identified with high accuracy. To study replication dynamics, we designed an oligonucleotide array with about one-third of the probes representing replication origins and about two-thirds of the probes tiling across chromosome 6. We went through the whole process of setting up an array platform, which included validation, quality control, data analysis, experiment design and optimization of experimental conditions. We further demonstrated the applicability of our array in studying replication dynamics using two time course experiments.
Signal modeling for speaker identification
Authors: Li Liu
Venue: Proceedings of the Acoustics, Speech, and Signal Processing, 1996. on Conference Proceedings., 1996 IEEE International Conference - Volume 02 (1996)

A large number of parameters, including pitch, LPCC, /spl Delta/LPCC, PARCOR, MFCC, /spl Delta/MFCC, and residual cepstrum (RCEP) were extracted from speech signals and their effectiveness for text-independent speaker identification was evaluated. In addition, the usefulness of two signal processing techniques, preemphasis and cepstral weighting, was also studied. The VQ-based speaker recognition method with codebooks fine-tuned by LVQ algorithm was used. It was shown that both LPCC and MFCC are effective representations, for smaller number of parameters, LPCC representation performs better but is surpassed by MFCC if the analysis order is larger. Pitch is an independent parameter so that it can be used jointly with other spectral features. In an evaluation experiment, the correct identification rate for 112 male speakers with test utterances of less than one second reached 98.2%.
A Multidimensional Scaling Analysis of Texture Gradient Perception via Haptic Exploration
Authors: Barry Hughes, Kirstin Shields
Venue: Proceedings of the Second Joint EuroHaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (2007)

More than one line of research has established roughness as the primary subjective attribute of textured surfaces explored by touch and to be a robust attribute largely unaffected by exploratory velocities or whether exploration is active or passive in nature. Roughness perception appears to be based on sensitivity to spatial distributions of texture elements. We investigated sensitivity to these spatial properties by using texture gradients of known form, explored by one or two fingers, and subjected to multidimensional scaling analysis. Our data suggest that irrespective finger use, perceivers are sensitive to direction and magnitudes of gradients, but not in strict conformance with these physical dimensions, and that a third (but unknown) dimension may also be involved.
Modeling Changes in Maintenance Activities through Fine-Tuning Markov Models of Ageing Equipment
Authors: Jaroslaw Sugier, George J. Anders
Venue: Proceedings of the 2nd International Conference on Dependability of Computer Systems (2007)

Markov models are well established technique used widely for modeling equipment deterioration. This work presents an approach where Markov models represent equipment ageing and also incorporate various maintenance activities. Having available some basic model representing both deterioration and maintenance processes it is possible to adjust its parameters so that it corresponds to some hypothetical new maintenance policy and then to examine impact that this new policy has on various reliability characteristics of the system. The paper presents a method of model adjustment and discusses implementation of three numerical algorithms solving the problem of parameter approximation. A practical example confirms validity of the approach and illustrates its efficiency.
Beamforming design with partially adaptive and minimum redundancy arrays
Authors: L. L. Presti
Venue: Proceedings of the Acoustics, Speech, and Signal Processing, 1996. on Conference Proceedings., 1996 IEEE International Conference - Volume 06 (1996)

This paper proposes a beamforming design method for interference cancellation using a special thinned array structure, termed minimum redundancy array (MRA). MRA is analyzed with partially adaptive beamforming design techniques and compared with corresponding uniform regular array (URA) over a set of likely interference scenarios. The partially adaptive beamformer design is subject to worst-case performance constraints. Extensive numerical simulations with several sets of interference scenarios show that MRA almost always outperforms URA, in both cases of fully adaptive beamformers and of partially adaptive beamformers. We also introduce a design criterion to take into account both the array geometry and partially adaptive beamforming methods.
Design fault directed test generation for microprocessor validation
Authors: Deepak A. Mathaikutty, Sandeep K. Shukla, Sreekumar V. Kodakara, David Lilja, Ajit Dingankar
Venue: Proceedings of the conference on Design, automation and test in Europe (2007)

Functional validation of modern microprocessors is an important and complex problem. One of the problems in functional validation is the generation of test cases that has higher potential to find faults in the design. We propose a model based test generation framework that generates tests for design fault classes inspired from software validation. There are two main contributions in this paper. Firstly, we propose a microprocessor modeling and test generation framework that generates test suites to satisfy Modified Condition Decision Coverage (MCDC), a structural coverage metric that detects most of the classified design faults as well as the remaining faults not covered by MCDC. Secondly, we show that there exists good correlation between types of design faults proposed by software validation and the errors/bugs reported in case studies on microprocessor validation. We demonstrate the framework by modeling and generating tests for the microarchitecture of VESPA, a 32-bit microprocessor. In the results section, we show that the tests generated using our framework's coverage directed approach detects the fault classes with 100% coverage, when compared to model-random test generation.
Sentence alignment using P-NNT and GMM
Authors: Mohamed Abdel Fattah, David B. Bracewell, Fuji Ren, Shingo Kuroiwa
Venue: Computer Speech and Language (2007)

Parallel corpora have become an essential resource for work in multilingual natural language processing. However, sentence aligned parallel corpora are more efficient than non-aligned parallel corpora for cross-language information retrieval and machine translation applications. In this paper, we present two new approaches to align English-Arabic sentences in bilingual parallel corpora based on probabilistic neural network (P-NNT) and Gaussian mixture model (GMM) classifiers. A feature vector is extracted from the text pair under consideration. This vector contains text features such as length, punctuation score, and cognate score values. A set of manually prepared training data was assigned to train the probabilistic neural network and Gaussian mixture model. Another set of data was used for testing. Using the probabilistic neural network and Gaussian mixture model approaches, we could achieve error reduction of 27% and 50%, respectively, over the length based approach when applied on a set of parallel English-Arabic documents. In addition, the results of (P-NNT) and (GMM) outperform the results of the combined model which exploits length, punctuation and cognates in a dynamic framework. The GMM approach outperforms Melamed and Moore's approaches too. Moreover these new approaches are valid for any languages pair and are quite flexible since the feature vector may contain more, less or different features, such as a lexical matching feature and Hanzi characters in Japanese-Chinese texts, than the ones used in the current research.
Parallel Scan-Like Testing and Fault Diagnosis Techniques for Digital Microfluidic Biochips
Authors: Tao Xu, Krishnendu Chakrabarty
Venue: Proceedings of the 12th IEEE European Test Symposium (2007)

Dependability is an important attribute for microfluidic biochips that are used for safety-critical applications such as point-of-care health assessment, air-quality monitoring, and food-safety testing. Therefore, these devices must be adequately tested after manufacture and during bioassay operations. Moreover, since disposable biochips are being targeted for a highly competitive and low-cost market segment, test and diagnosis methods should be inexpensive, quick, and effective. We propose a cost-effective testing methodology referred to as "parallel scan-like test", and a rapid diagnosis method based on test outcomes, for droplet-based microfluidic devices. The proposed method allows testing using parallel droplet pathways in both on-line and off-line scenarios. The diagnosis outcome can be used to reconfigure a droplet-based biochip such that faults can be easily avoided, thereby enhancing chip yield and defect tolerance. We evaluate the proposed test and diagnosis methods using complexity analysis as well as experiments using a fabricated biochip.
Detection of change in periodic, nonstationary data
Authors: C. M. Gruner
Venue: Proceedings of the Acoustics, Speech, and Signal Processing, 1996. on Conference Proceedings., 1996 IEEE International Conference - Volume 05 (1996)

Traditional change detection strategies are limited in cases where the data are nonstationary and the distributions are unknown. We present an algorithm for change detection problems in which we do not know the form of the distribution. Our algorithm uses distributed detection with a bank of type-based front end detectors that achieve asymptotically optimal type I error performance. Our simulations indicate that this algorithm performs much better than traditional methods.
Distributed link scheduling with constant overhead
Authors: Sujay Sanghavi, Loc Bui, R. Srikant
Venue: Proceedings of the 2007 ACM SIGMETRICS international conference on Measurement and modeling of computer systems (2007)

This paper proposes a new class of simple, distributed algorithms for scheduling in wireless networks. The algorithms generate new schedules in a distributed manner via simple local changes to existing schedules. The class is parameterized by integers k\geq 1. We show that algorithm k of our class achieves k/(k+2) of the capacity region, for every k\geq 1. . The algorithms have small and constant worst-case overheads: in particular, algorithm k generates a new schedule using (a) time less than 4k+2 round-trip times between neighboring nodes in the network, and (b) at most three control transmissions by any given node, for any k. The control signals are explicitly specified, and face the same interference effects as normal data transmissions. Our class of distributed wireless scheduling algorithms are the first ones guaranteed to achieve any fixed fraction of the capacity region while using small and constant overheads that do not scale with network size. The parameter k explicitly captures the tradeoff between control overhead and scheduler throughput performance and provides a tuning knob protocol designers can use to harness this trade-off in practice.
SOCOM: A Service-Oriented Collaboration Middleware for Multi-User Interaction with Web Services based Scientific Resources
Authors: Yongwang Zhao, Dianfu Ma, Chunyang Hu, Min Liu, Yonggang Huang
Venue: Proceedings of the Sixth International Symposium on Parallel and Distributed Computing (2007)

Scientific collaboration has become more and more important in current scientific research. A collaboration environment which simplifies integration and collaboration of heterogeneous scientific resources, for instance scientific computing software and scientific apparatuses, can accelerate progress of scientific research remarkably. We present a novel middleware to facilitate development of distributed and collaborative application for scientific research. A service-oriented collaboration bus is proposed to enable scientific resources to be plugged in and users to interact with these resources collaboratively and transparently. Collaboration bus engines in different organizations can interoperate with each other to support distributed collaboration. We also show our prototype implementation of this middleware and a demonstration of Collaborative Visualization System for Seismic Data in earth science.
MAPGrid: A New Architecture for Empowering Mobile Data Placement in Grid Environments
Authors: Yun Huang, Nalini Venkatasubramanian, Yang Wang
Venue: Proceedings of the Seventh IEEE International Symposium on Cluster Computing and the Grid (2007)

The rising popularity of mobile applications and devices has brought about an enhanced interest in infrastructure support for mobile computing. Our work focuses on the development of a mobile grid infrastructure called MAPGrid (Mobile Applications on Grids), where grid resources are exploited as proxies to enable advanced mobile applications. However, intermittent availability of grid resources presents challenges for data-intensive mobile applications. In this paper, we propose novel methodologies for placing mobile data on grid proxies. We introduce a notion of twotier architecture for MAPGrid, where the upper tier captures grid related features and the lower tier represents features associated with mobile environments. We further develop an intelligent mobile data placement mechanism that effectively balances tradeoffs between replication cost and data access cost by leveraging knowledge of grid availability and mobile data request patterns. Through extensive experimentation, we illustrate the superiority of the proposed techniques over several popular data placement strategies.
Application of DC Analyzer to Combinatorial Optimization Problems
Authors: Gaurav Trivedi, Sumit Punglia, H. Narayanan
Venue: Proceedings of the 20th International Conference on VLSI Design held jointly with 6th International Conference: Embedded Systems (2007)

Solution of many combinatorial optimization problems can be found by analyzing appropriate electrical networks made up of positive resistors, voltage sources, current sources and ideal diodes. This method is an alternative approach for the approximate solution of such problems. Two Graph method based fast simulator is a more suitable option for this purpose than Modified Nodal Analysis based conventional simulators. Using this approach we have made an attempt to solve min cost flow and single source shortest path problems. A planar min cost flow problem of size 200; 000 nodes and 600; 000 edges is solved by our simulator approximately within 0:1% of the optimum solution in about 11 mins. We have exactly solved a planar single source shortest path problem (having negative edge weights also) of size 100; 000 nodes and 600; 000 edges in about 2 mins. We have performed our experiments on a PIV processor having 1 GB RAM.
Discrete powers-of-two kernels for time-frequency distributions
Authors: G. T. Venkatesan
Venue: Proceedings of the Acoustics, Speech, and Signal Processing, 1996. on Conference Proceedings., 1996 IEEE International Conference - Volume 03 (1996)

We introduce a new class of powers-of-two (PFT) kernels for fast real time implementations of time-frequency distributions. In this class, the local autocorrelation function is computed using a series of shifting and addition operations. PFT filter design techniques are not limited to the design of fixed kernels. They can also be used to design data-dependent kernels suitable for specific operating environments. In the time-frequency context, where the task is to identify the signal autoterms in the time-frequency domain, a discretized powers-of-two kernel shows little or no difference in performance from its infinite precision counterpart. A simple modification of the PFT design technique that significantly improves the approximation when small register lengths are used, is also introduced.
A degree-constrained QoS-aware routing algorithm for application layer multicast
Authors: Baoliu Ye, Minyi Guo, Daoxu Chen, Sanglu Lu
Venue: Information Sciences: an International Journal (2007)

Application layer multicast (ALM) provides a low-cost solution for multicast over the Internet. It overcomes the deployment hurdle of IP multicast by moving all multicast related functions from network routers to end-hosts. However, since packet replication is performed on end-hosts, the system performance of an ALM is limited by the bandwidth of end-hosts. Therefore, degree-constrained QoS-aware multicast routing becomes one of the key concerns for implementing realtime multicast services, such as continuous streaming applications. In this paper, we claim that the QoS gained by most users will be better evaluated using the overall latency, and we explore the optimization of Degree-Constrained Minimum Overall Latency Spanning Tree (DCMOLST). The process for optimizing the overall latency is divided into two phases, i.e., the initialization phase and the dynamic adjustment phase. In the former phase, we present a heuristic DCMOLST algorithm which negotiates both transmission delay and node bandwidth simultaneously, so as to avoid QoS degradation caused by any single metrics. In the later phase, we define a set of distributed iterative optimizing operations to swap the position between nearby end-hosts for further optimization. Experimental results show that the proposed degree-constrained QoS-aware routing algorithm could improve the overall performance of application layer multicast services.
Microelectronics processing education using the Internet
Authors: K. Mitchell, G. Kerdoncuff, G. S. May
Venue: Proceedings of the Frontiers in Education Conference on 1995. Proceedings., 1995 vol 1. - Volume 01 (1995)

Integrated circuits (ICs) are fabricated by a sophisticated series of process steps. A complete education in the field of semiconductor processing requires a thorough understanding of the fabrication process. However, due to space, equipment, and budget constraints, hands-on microelectronics instruction is usually limited, despite high student demand. To alleviate these resource limitations and to enhance the educational experience, an environment which simulates IC fabrication instruction in a physical laboratory using interactive multimedia is currently being developed at the Georgia Institute of Technology Microelectronics Research Center. This Virtual Cleanroom will allow students to use a high-performance workstation (equipped with the necessary audio, video and graphics capability) to simulate the fabrication of an IC. Simulation modules for each of the unit process steps used in IC fabrication are being constructed on the X-Mosaic platform, thereby making the courseware accessible through Internet via the World-Wide Web. This has allowed the incorporation of a variety of other IC process simulators into the Virtual Cleanroom environment, enabling the student to visualize the results of performing a step while simultaneously learning the physical activities involved.
Research Opportunities in the IST Thematic Priority of the 7th Framework Program
Authors: Merce Griera i Fisa
Venue: Proceedings of the 19th Euromicro Conference on Real-Time Systems (2007)

This presentation will focus on the second call for Objective 3.7 on "Network Embedded and Control Systems", opening on June 2007, with a closing date on October 2007. Please find details at http://cordis.europa.eu/fp7/ict/
CGCExplorer: a semi-automated search procedure for provably correct concurrent collectors
Authors: Martin T. Vechev, Eran Yahav, David F. Bacon, Noam Rinetzky
Venue: Proceedings of the 2007 ACM SIGPLAN conference on Programming language design and implementation (2007)

Concurrent garbage collectors are notoriously hard to design, implement, and verify. We present a framework for the automatic exploration of a space of concurrent mark-and-sweep collectors. In our framework, the designer specifies a set of "building blocks" from which algorithms can be constructed. These blocks reflect the designer's insights about the coordination between the collector and the mutator. Given a set of building blocks, our framework automatically explores a space of algorithms, using model checking with abstraction to verify algorithms in the space. We capture the intuition behind some common mark-and-sweep algorithms using a set of building blocks. We utilize our framework to automatically explore a space of more than 1,600,000 algorithms built from these blocks, and derive over 100 correct fine-grained algorithms with various space, synchronization, and precision tradeoffs.
High Resolution Analysis of Impact Sounds and Forces
Authors: L-M Reissell, Dinesh K. Pai
Venue: Proceedings of the Second Joint EuroHaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems (2007)

Impact sounds and vibrations are an important source of information about contact interactions in haptics, robotics, and virtual reality. However, accurate estimation of their parameters for perceptually acceptable resynthesis is difficult with traditional methods. In this paper we describe the phase-constrained estimation algorithm for estimating modes and amplitudes from impact signals. It is based on ESPRIT and least squares estimation, and produces better resynthesis results than previously used methods.
Pastwatch: a distributed version control system
Authors: Alexander Yip, Benjie Chen, Robert Morris
Venue: Proceedings of the 3rd conference on Networked Systems Design & Implementation - Volume 3 (2006)

Pastwatch is a version control system that acts like a traditional client-server system when users are connected to the network; users can see each other's changes immediately after the changes are committed. When a user is not connected, Pastwatch also allows users to read revisions from the repository, commit new revisions and share modifications directly between users, all without access to the central repository. In contrast, most existing version control systems require connectivity to a centralized server in order to read or update the repository. Each Pastwatch user's host keeps its own writable replica of the repository, including historical revisions. Users can synchronize their local replicas with each other or with one or more servers. Synchronization must handle inconsistency between replicas because users may commit concurrent and conflicting changes to their local replicas. Pastwatch represents its repository as a "revtree" data structure which tracks the relationships among these conflicting changes, including any reconciliation. The revtree also ensures that the replicas eventually converge to identical images after sufficient synchronization. We have implemented Pastwatch and evaluate it in a setting distributed over North America. We have been using it actively for more than a year. We show that the system is scalable beyond 190 users per project and that commit and update operations only take 2-4 seconds. Currently, five users and six different projects regularly use the system; they find that the system is easy to use and that the system's replication has masked several network and storage failures.