ppxscal/embedding_network huggingface dataset:
Efficient Data Access for Parallel BLAST
Authors: Heshan Lin, Xiaosong Ma, Praveen Chandramohan, Al Geist, Nagiza Samatova
Venue: Proceedings of the 19th IEEE International Parallel and Distributed Processing Symposium (IPDPS'05) - Papers - Volume 01 (2005)

Searching biological sequence databases is one of the most routine tasks in computational biology. This task is significantly hampered by the exponential growth in sequence database sizes. Recent advances in parallelization of biological sequence search applications have enabled bioinformatics researchers to utilize high-performance computing platforms and, as a result, greatly reduce the execution time of their sequence database searches. However, existing parallel sequence search tools have been focusing mostly on parallelizing the sequence alignment engine. While the computation-intensive alignment tasks become cheaper with larger machines, data-intensive initial preparation and result merging tasks become more expensive. Inefficient handling of input and output data can easily create performance bottlenecks even on supercomputers. It also causes a considerable data management overhead. In this paper, we present a set of techniques for efficient and flexible data handling in parallel sequence search applications. We demonstrate our optimizations through improving mpiBLAST, an open-source parallel BLAST tool rapidly gaining popularity. These optimization techniques aim at enabling flexible database partitioning, reducing I/O by caching small auxiliary files and results, enabling parallel I/O on shared files, and performing scalable result processing protocols. As a result, we reduce mpiBLAST users' operational overhead by removing the requirement of prepartitioning databases. Meanwhile, our experiments show that these techniques can bring by an order of magnitude improvement to both the overall performance and scalability of mpiBLAST.
Fast Parallel Non-Contiguous File Access
Authors: Joachim Worringen, Jesper Larsson Traff, Hubert Ritzdorf
Venue: Proceedings of the 2003 ACM/IEEE conference on Supercomputing (2003)

Many applications of parallel I/O perform non-contiguous file accesses: instead of accessing a single (large) block of data in a file, a number of (smaller) blocks of data scattered throughout the file needs to be accessed in each logical I/O operation. However, only few file system interfaces directly support this kind of non-contiguous file access. In contrast, the most commonly used parallel programming interface, MPI, incorporates a exible model of parallel I/O through its MPI-IO interface. With MPI-IO, arbitrary non-contiguous file accesses are supported in a uniform fashion by the use of derived MPI datatypes set up by the user to re ect the desired I/O pattern. Despite a considerable amount of recent work in this area, current MPI-IO implementations suffer from low performance of such non-contiguous accesses when compared to the performance of the storage system for contiguous accesses. In this paper we analyze an important bottleneck in the efficient handling of non-contiguous access patterns in current implementations of MPI-IO. We present a new technique, termed listless I/O, that can be incorporated into MPI-IO implementations like the well-known ROMIO implementation, and completely eliminates this bottleneck. We have implemented the technique in MPI/SX, the MPI implementation for the NEC SX-series of parallel vector computers. Results with a synthetic benchmark and an application kernel show that listless I/O is able to increase the bandwidth for non-contiguous file access by sometimes more than a factor of 500 when compared to the traditional approach.
Dynamic Removal Algorithm for Constrained Delaunay Triangulations
Authors: Dong-Yu Xu, Guang-Rong Tang, Yu-Pin Luo
Venue: Proceedings of the Third International Conference on Image and Graphics (2004)

Delaunay Triangulations and Constrained Delaunay Triangulations are very popular tool used to analyze planar domain. An efficient removal algorithm is required when constructing the approximate skeleton of complicated dynamic planar domains. We present a fully dynamic algorithm for CDT. It inserts and removes constraints that maybe points or any kind of polygonal lines. Furthermore, the algorithm automatically detects and deals with the overlapping, self-intersections and duplicate of constraints.
Minimum Bayes Error Features for Visual Recognition by Sequential Feature Selection and Extraction
Authors: Gustavo Carneiro, Nuno Vasconcelos
Venue: Proceedings of the 2nd Canadian conference on Computer and Robot Vision (2005)

The extraction of optimal features, in a classification sense, is still quite challenging in the context of large-scale classification problems (such as visual recognition), involving a large number of classes and significant amounts of training data per class. We present an optimal, in the minimum Bayes error sense, algorithm for feature design that combines the most appealing properties of the two strategies that are currently dominant: feature extraction (FE) and feature selection (FS). The new algorithm proceeds by interleaving pairs of FS and FE steps, which amount to a sequential search for the most discriminant directions in a collection of two dimensional subspaces. It combines the fast convergence rate of FS with the ability of FE to uncover optimal features that are not part of the original basis functions, leading to solutions that are better than those achievable by either FE or FS alone, in a small number of iterations. Because the basic iteration has very low complexity, the new algorithm is scalable in the number of classes of the recognition problem, a property that is currently only available for feature extraction methods that are either sub-optimal or optimal under restrictive assumptions that do not hold for generic recognition. Experimental results show significant improvements over these methods, either through much greater robustness to local minima or by achieving significantly faster convergence.
A Lossless Medical Image Compression Scheme Using Modified S-Tree Structure
Authors: Chi-Shiang Chan, Chin-Chen Chang
Venue: Proceedings of the 19th International Conference on Advanced Information Networking and Applications - Volume 2 (2005)

The medical images have an important characteristic that the pixel-to-pixel correlation is very close. In order to preserve this characteristic, we propose a lossless medical image compression method in this paper. Our method builds the modified S-tree structure to make each block contain similar pixels. Therefore, our method can reduce the needed number of bits to record those pixels. The experimental results also show that our method is better than other methods in almost all cases.
Level-of-detail representation of bidirectional texture functions for real-time rendering
Authors: Wan-Chun Ma, Sung-Hsiang Chao, Yu-Ting Tseng, Yung-Yu Chuang, Chun-Fa Chang, Bing-Yu Chen, Ming Ouhyoung
Venue: Proceedings of the 2005 symposium on Interactive 3D graphics and games (2005)

This paper presents a new technique for rendering bidirectional texture functions (BTFs) at different levels of detail (LODs). Our method first decomposes each BTF image into multiple subbands with a Laplacian pyramid. Each vector of Laplacian coefficients of a texel at the same level is regarded as a Laplacian bidirectional reflectance distribution function (BRDF). These vectors are then further compressed by applying principal components analysis (PCA). At the rendering stage, the LOD parameter for each pixel is calculated according to the distance from the viewpoint to the surface. Our rendering algorithm uses this parameter to determine how many levels of BTF Laplacian pyramid are required for rendering. Under the same sampling resolution, a BTF gradually transits to a BRDF as the camera moves away from the surface. Our method precomputes this transition and uses it for multiresolution BTF rendering. Our Laplacian pyramid representation allows real-time anti-aliased rendering of BTFs using graphics hardware. In addition to provide visually satisfactory multiresolution rendering for BTFs, our method has a comparable compression rate to the available single-resolution BTF compression techniques.
PHR: A Parallel Hierarchical Radiosity System with Dynamic Load Balancing
Authors: Ali Kemal Sinop, Tolga Abaci, Ümit Akkuş, Attila Gürsoy, Ugur Güdükbay
Venue: The Journal of Supercomputing (2005)

In this paper, we present a parallel system called PHR for computing hierarchical radiosity solutions of complex scenes. The system is targeted for multi-processor architectures with distributed memory. The system evaluates and subdivides the interactions level by level in a breadth first fashion, and the interactions are redistributed at the end of each level to keep load balanced. In order to allow interactions freely travel across processors, all the patch data is replicated on all the processors. Hence, the system favors load balancing at the expense of increased communication volume. However, the results show that the overhead of communication is negligible compared with total execution time. We obtained a speed-up of 25 for 32 processors in our test scenes.
Business transaction assurance in business service networks
Authors: David Ching
Venue: Proceedings of the IEEE EEE05 international workshop on Business services networks (2005)

Business service networks provide a low cost, efficient way to transact business between multiple peer-to-peer partners across the Internet using web services. Many standards through the standards group OASIS are being adopted or proposed to assure that web services can be successfully orchestrated or choreographed including individual standards for web services orchestration and web services choreography. Regardless of the methods used, statistics need to be measured in operational environments that enable the partners participating to assure that business levels are being met. That could include performance and availability information as well as individual transaction delivery times in high value or high volume transaction environments. The purpose of this paper is to review various standards or proposed standards and how they can be used to expose proper measurement information across public and private processes in addition to providing an example of the application of these standards to a commercially available product that provides performance, availability and transaction measurement capabilities.
Qualitative simulation and related approaches for the analysis of dynamic systems
Authors: Hidde De Jong
Venue: The Knowledge Engineering Review (2004)

Methods for qualitative simulation allow predictions on the dynamics of a system to be made in the absence of quantitative information, by inferring the range of possible qualitative behaviors compatible with the structure of the system. This article reviews QSIM and other qualitative simulation methods. It discusses two problems that have seriously compromised the application of these methods to realistic problems in science and engineering: the occurrence of spurious behavior predictions and the combinatorial explosion of the number of behavior predictions. In response to these problems, related approaches for the qualitative analysis of dynamic systems have emerged: qualitative phase-space analysis and semi-quantitative simulation. The article argues for a synthesis of these approaches in order to obtain a computational framework for the qualitative analysis of dynamic systems. This should provide a solid basis for further upscaling and for the development of model-based reasoning applications of a wider scope.
Comparison of Non-Parametric Methods for Assessing Classifier Performance in Terms of ROC Parameters
Authors: Waleed A. Yousef, Robert F. Wagner, Murray H. Loew
Venue: Proceedings of the 33rd Applied Imagery Pattern Recognition Workshop (2004)

The most common metric to assess a classifier's performance is the classification error rate, or the probability of misclassification (PMC). Receiver Operating Characteristic (ROC) analysis isa more general way to measure the performance. Some metrics that summarize the ROC curve are the two normal-deviate-axes parameters, i.e., a and b, and the Area Under the Curve (AUC). The parameters "a" and "b" represent the intercept and slope, respectively, for the ROC curve if plotted on normal-deviate-axes scale. AUC represents the average of the classifier TPF over FPF resulting from considering different threshold values. In the present work, we used Monte-Carlo simulations to compare different bootstrap-based estimators, e.g., leave-one-out, .632, and .632+ bootstraps, to estimate the AUC. The results show the comparable performance of the different estimators in terms of RMS, while the .632+ is the least biased.
I/O performance of an RAID-10 style parallel file system
Authors: Dan Feng, Hong Jiang, Yi-Feng Zhu
Venue: Journal of Computer Science and Technology (2004)

Without any additional cost, all the disks on the nodes of a cluster can be connected together through CEFT-PVFS, an RAID-10 style parallel file system, to provide a multi-GB/s parallel I/O performance. I/O response time is one of the most important measures of quality of service for a client. When multiple clients submit data-intensive jobs at the same time, the response time experienced by the user is an indicator of the power of the cluster. In this paper, a queuing model is used to analyze in detail the average response time when multiple clients access CEFT-PVFS. The results reveal that response time is with a function of several operational parameters. The results show that I/O response time decreases with the increases in I/O buffer hit rate for read requests, write buffer size for write requests and the number of server nodes in the parallel file system, while the higher the I/O requests arrival rate, the longer the I/O response time. On the other hand, the collective power of a large cluster supported by CEFT-PVFS is shown to be able to sustain a steady and stable I/O response time for a relatively large range of the request arrival rate.
Nodes Localization through Data Fusion in Sensor Network
Authors: Ren C. Luo, Ogst Chen, L. C. Tu
Venue: Proceedings of the 19th International Conference on Advanced Information Networking and Applications - Volume 1 (2005)

The Location of nodes in sensor network is an important problem with application in resource allocation, location sensitive browsing, and emergency communications. A key problem in sensor network location is the creation of a method that is robust to measurement quantization and measurement noise and also has a reasonable implementation cost. The RSS and TDoA are the popular distance measurement methods, but can be easy affected by noise and not independent. This paper explores a Covariance Intersection (CI) that fuses together location estimations obtained from power propagation loss measurements and propagation time to obtain higher accuracy location estimate. The performances of Kalman filter type estimators are severely affected by the ignored cross covariance. CI algorithm provides a mechanism to fuse two or more random variables with unknown correlation such that the computed covariance of the new estimate is consistent; therefore CI method is quite suitable for sensor network application. In simulation result shows that position estimates are correct within small ranging distance with few initial master nodes of the system.
Measurement of heavy traffic in a tunnel from image sequences
Authors: Hideo Kuboyama, Shinji Ozawa
Venue: Systems and Computers in Japan (2004)

The measurement of traffic plays a major role in Intelligent Transport Systems (ITS) in providing beneficial information to the control center or drivers. In this paper, the authors propose a technique for counting the number of vehicles by detecting vehicles from images taken by cameras installed in tunnels. Since the camera height within a tunnel is low, the vehicles overlap when traffic is congested and it is difficult to separate them. As a result, the authors herein propose a powerful measurement technique for congested traffic based on vehicle edge information by using a horizontal edge and the left side of a vehicle to create a vehicle model and performing a cumulative evaluation according to settled frame tracking of this model. In addition, they applied the proposed algorithm to actual in-tunnel images and showed the results of a vehicle counting experiment. &copy; 2004 Wiley Periodicals, Inc. Syst Comp Jpn, 35(13): 52&ndash;62, 2004; Published online in Wiley InterScience (). DOI 10.1002&sol; scj.10287
The making of a software engineer challenges for the educator
Authors: Clemens Szyperski
Venue: Proceedings of the 27th international conference on Software engineering (2005)

Software engineering is foremost an engineering discipline. Engineering in general and software engineering specifically has to balance many factors to achieve viable tradeoffs - an understanding of the factors as well as the viability criteria is at the heart of the educational challenge. All engineering has one ultimate goal: the delivery of artifacts (products, commercial or not) that meet the needs of those using such artifacts. All engineering lives in the intersection of people, technology, domain, and opportunity aspects. Software engineering, however, is laden with its own specific difficulties. Software as an engineering medium fills a space between the fluidity of digital content, with which software shares the representation, and the nature of machines, with which software shares the flexible and repeatable application.
A framework for modeling and evaluating automatic semantic reconciliation
Authors: Avigdor Gal, Ateret Anaby-Tavor, Alberto Trombetta, Danilo Montesi
Venue: The VLDB Journal &mdash; The International Journal on Very Large Data Bases (2005)

The introduction of the Semantic Web vision and the shift toward machine understandable Web resources has unearthed the importance of automatic semantic reconciliation. Consequently, new tools for automating the process were proposed. In this work we present a formal model of semantic reconciliation and analyze in a systematic manner the properties of the process outcome, primarily the inherent uncertainty of the matching process and how it reflects on the resulting mappings. An important feature of this research is the identification and analysis of factors that impact the effectiveness of algorithms for automatic semantic reconciliation, leading, it is hoped, to the design of better algorithms by reducing the uncertainty of existing algorithms. Against this background we empirically study the aptitude of two algorithms to correctly match concepts. This research is both timely and practical in light of recent attempts to develop and utilize methods for automatic semantic reconciliation.
An Improved Interval Global Optimization Algorithm Using Higher-order Inclusion Function Forms
Authors: P. S. Nataraj, K. Kotecha
Venue: Journal of Global Optimization (2005)

We propose an improved algorithm for unconstrained global optimization in the framework of the Moore--Skelboe algorithm of interval analysis (H. Ratschek and J. Rokne, New computer methods for global optimization, Wiley, New York, 1988). The proposed algorithm is an improvement over the one recently proposed in P.S.V. Nataraj and K. Kotecha, (J. Global Optimization, 24 (2002) 417). A novel and powerful feature of the proposed algorithm is that it uses a variety of inclusion function forms for the objective function -- the simple natural inclusion, the Taylor model (M. Berz and G. Hoffstatter, Reliable Computing, 4 (1998) 83), and the combined Taylor--Bernstein form (P.S.V. Nataraj and K. Kotecha, Reliable Computing, in press). Several improvements are also proposed for the combined Taylor--Bernstein form. The performance of the proposed algorithm is numerically tested and compared with those of existing algorithms on 11 benchmark examples. The results of the tests show the proposed algorithm to be overall considerably superior to the rest, in terms of the various performance metrics chosen for comparison.
EMPIRICISM VERSUS JUDGEMENT: COMPARING USER INTERFACE EVALUATION METHODS ON A NEW TELEPHONE-BASED INTERFACE
Authors: Heather Desurvire, Debbie Lawrence, Michael Atwood
Venue: ACM SIGCHI Bulletin (1991)

In an attempt to reduce the time and cost of laboratory usability testing, new techniques for evaluating user interfaces are being developed by human factors researchers. In one such technique, heuristic evaluation (Nielsen and Molich, 1990), experts evaluate interfaces using pre-established usability guidelines. The current study attempts to test the heuristic method of evaluation under several conditions and user interface (UI) experts' "best guess" predictions, for comparing to laboratory performance testing results.
Perceptron-Based Branch Confidence Estimation
Authors: Haitham Akkary, Srikanth T. Srinivasan, Rajendar Koltur, Yogesh Patil, Wael Refaai
Venue: Proceedings of the 10th International Symposium on High Performance Computer Architecture (2004)

Pipeline gating has been proposed for reducing wasted speculative execution due to branch mispredictions. As processors become deeper or wider, pipeline gating becomes more important because the amount of wasted speculative execution increases. The quality of pipeline gating relies heavily on the branch confidence estimator used. Not much work has been done on branch confidence estimators since the initial work [6]. We show the accuracy and coverage characteristics of the initial proposals do not sufficiently reduce mis-speculative execution on future deep pipeline processors. In this paper, we present a new, perceptron-based, branch confidence estimator, which is twice as accurate as the current best-known method and achieves reasonable mispredicted branch coverage. Further, the output of our predictor is multi-valued, which enables us to classify branches further as "strongly low confident" and "weakly low confident". We reverse the predictions of "strongly low confident" branches and apply pipeline gating to the "weakly low confident" branches. This combination of pipeline gating and branch reversal provides a spectrum of interesting design options ranging from significantly reducing total execution for only a small performance loss, to lower but still significant reductions in total execution, without any performance loss.
Preventing Wheel Reinvention: The psgconf System Configuration Framework
Authors: Mark D. Roth
Venue: Proceedings of the 17th USENIX conference on System administration (2003)

Most existing Unix system configuration tools are designed monolithically. Each tool stores configuration data in its own way, has its own mechanism for enforcing policy, has a fixed repertoire of actions that can be performed to modify the system, and provides a specific strategy for configuration management. As a result, most tools are useful only in environments that very closely match the environment for which the tool was designed. This inflexibility results in a great deal of duplication of effort in the system administration community.In this paper, I present a new architecture for system configuration tools using a modular design. I explain how this architecture allows a single tool to use different strategies for configuration management, enforce different ideas of policy, and prevent duplication of effort. I also describe the implementation of this architecture at my site and identify some areas for future research.