ppxscal/embedding_network huggingface dataset:
Analyzing gene expression data in terms of gene sets
Authors: Jelle J. Goeman, Peter Bühlmann
Venue: Bioinformatics (2007)

Motivation: Many statistical tests have been proposed in recent years for analyzing gene expression data in terms of gene sets, usually from Gene Ontology. These methods are based on widely different methodological assumptions. Some approaches test differential expression of each gene set against differential expression of the rest of the genes, whereas others test each gene set on its own. Also, some methods are based on a model in which the genes are the sampling units, whereas others treat the subjects as the sampling units. This article aims to clarify the assumptions behind different approaches and to indicate a preferential methodology of gene set testing. Results: We identify some crucial assumptions which are needed by the majority of methods. P-values derived from methods that use a model which takes the genes as the sampling unit are easily misinterpreted, as they are based on a statistical model that does not resemble the biological experiment actually performed. Furthermore, because these models are based on a crucial and unrealistic independence assumption between genes, the P-values derived from such methods can be wildly anti-conservative, as a simulation experiment shows. We also argue that methods that competitively test each gene set against the rest of the genes create an unnecessary rift between single gene testing and gene set testing. Contact: j.j.goeman@lumc.nl
Bandwidth Management for Supporting Differentiated Service Aware Traffic Engineering
Authors: Tong Shan, Oliver Yang
Venue: IEEE Transactions on Parallel and Distributed Systems (2007)

This paper presents a bandwidth management framework for the support of the differentiated service aware traffic engineering (DS-TE) in the multiprotocol label switching (MPLS) networks. Our bandwidth management framework contains both bandwidth allocation and preemption mechanisms, in which the link bandwidth is managed in two dimensions: class type and preemption priority. We put forward a Max- Min bandwidth constraint model, in which we propose a novel "use it or lend it" strategy. The new model is able to guarantee a minimum bandwidth for each class type without causing resource fragmentation. Furthermore, we design three new bandwidth preemption algorithms for three bandwidth constraint models, respectively. An extensive simulation study is carried out to evaluate the effectiveness of the bandwidth constraint models and preemption algorithms. Comparing with the existing constraint models and preemption rules, the proposed Max-Min constraint model and preemption algorithms improve not only bandwidth efficiency, but also robustness and fairness. They achieve significant performance improvement for the well-behaving traffic classes, in terms of bandwidth utilization, bandwidth blocking and preemption probability. We also provide guidelines for selecting different DS-TE bandwidth management mechanisms.
Interactive image registration tool for positioning verification in head and neck radiotherapy
Authors: Ching-Fen Jiang, Ti-Cheng Lu, Shuh-Ping Sun
Venue: Computers in Biology and Medicine (2008)

This paper presents the development of a computer-aided image management tool, named CAIMT, used for patient setup error measurement in radiation treatment planning. The CAIMT incorporates user interaction to facilitate contour detection from both portal film and simulation film. The detected contours were then used as features for image registration through application of the generalized Hough transform (GHT). Positioning error was measured when the optimal registration was achieved. The CAIMT has been applied to register the image pairs of a rando^T^M phantom and five real subjects, in order to evaluate its reliability and stability. The promising results suggest that the CAIMT can assist radiotherapists to align the simulation film and the portal film precisely and steadily and therefore adjust patient positioning to the optimum in a more efficient way.
Improving uml profile design practices by leveraging conceptual domain models
Authors: François Lagarde, Huáscar Espinoza, François Terrier, Sébastien Gérard
Venue: Proceedings of the twenty-second IEEE/ACM international conference on Automated software engineering (2007)

The profile extension mechanism has permitted a rapid growth of the use of UML as a domain-specific modeling language. However, designing profiles typically falls into ad-hoc processes that often rely on domain-inappropriate primitives. One of the fundamental reasons is that profiles are specified on the same level of abstraction as the UML abstract syntax and consequently they narrow down the design space to an implementation level. In order to improvethis situation, some profile designers start from a "conceptual domain model" that states the domain ontology, and only then deal with finding out the profile extensions to support it. In spite of this, building truthfulness conceptual domain models and maintaining traceable mapping with the profile view is a bit of an art. In this paper, we propose to systematize the design of UML profiles built-upon conceptual domain models, by adopting a minimal setof framing rules. As these rules are defined on the basis of regularly occurring design patterns, domain models can be afterward checked for self-consistency and interactively transformed in stereotypes, tags and constraints
An Authentication Method for Copy Areas of Images
Authors: Shenggen Ju, Jiliu Zhou, Kun He
Venue: Proceedings of the Fourth International Conference on Image and Graphics (2007)

This paper presents an effective automatic detection technique for copy areas of digital images. This technique adopts primary components analysis for small image blocks with fixed size, and generates the degraded dimensions representation. This representation is robust for small difference caused by noises or lossy compression. This technique detects the copy areas according to the ascending order of all image blocks. The effectiveness and robusticity for resisting authentic forgery, and the sensitivity for lossy compression or additive noises of this technique are analyzed in this paper. Some simulation results are also provided to show the advantages of this technique.
3D Brain Segmentation Based on Immune Genetic Algorithm
Authors: Wang Yi, Niu Yilong, Monika Lehmpfuhl, Tian Yun, Hao Chongyang
Venue: Proceedings of the Fourth International Conference on Image and Graphics (2007)

To solve large time-consumption subject of the complete search (CS), the instability and inaccurateness of the simple genetic algorithm (SGA), a 3D brain data segmentation procedure, utilizing optimal entropy multi-thresholding method, is proposed. Global maximum entropy for the segmentation is yielded fast by the immune genetic algorithm (IGA). Compared to the SGA, the IGA constructs a better selection scheme and ensures various individuals to be selected for preserving the diversity of the population. Meanwhile the general expressing form of this kind of selection probability is given. The proposed method also includes the elitist strategy and the adaptive crossover and mutation mechanism to enhance the convergence. Results of 50 simulations demonstrate that the 3D brain volume can be successfully classified into three parts: the white matter, the gray matter and the cerebrospinal fluid on the IDL platform. The stability and accuracy of our algorithm, compared with other methods, are all improved according to their performance contrasts.
Guest Editor's Introduction: The Embedded Systems Landscape
Authors: Wayne Wolf
Venue: Computer (2007)

What makes high-performance embedded computing so difficult is not just the performance levels but achieving that performance in the face of two major requirements: real time and low power.
An approach to mining call-usage patternswith syntactic context
Authors: Huzefa Kagdi, Michael L. Collard, Jonathan I. Maletic
Venue: Proceedings of the twenty-second IEEE/ACM international conference on Automated software engineering (2007)

An approach to mine frequently appearing ordered sets of function-call usages, taking into account their proximal control constructs (e.g., if-statements), in the source code is presented. These ordered sets are termed as call-usage patterns. Additionally, variant usages, such as those with missing or out of order calls, are automatically identified along with their specific contextual location. The approach uses lightweight source code analysis and frequent sequential pattern mining. The hypothesis is that these call-usage patterns embody latent programming rules that developers commonly reuse, for example standard usages of API calls. The variants are an indicator of future changes such as the elimination of non-standard usages and/or bugs
Probabilistic feature-based transformation for speaker verification over telephone networks
Authors: Man-Wai Mak, Kwok-Kwong Yiu, Sun-Yuan Kung
Venue: Neurocomputing (2007)

Feature transformation aims to reduce the effects of channel- and handset-distortion in telephone-based speaker verification. This paper compares several feature transformation techniques and evaluates their verification performance and computation time under the 2000 NIST speaker recognition evaluation protocol. Techniques compared include feature mapping (FM), stochastic feature transformation (SFT), blind stochastic feature transformation (BSFT), feature warping (FW), and short-time Gaussianization (STG). The paper proposes a probabilistic feature mapping (PFM) in which the mapped features depend not only on the top-1 decoded Gaussian but also on the posterior probabilities of other Gaussians in the root model. The paper also proposes speeding up the computation of PFM and BSFT parameters by considering the top few Gaussians only. Results show that PFM performs slightly better than FM and that the fast approach can reduce computation time substantially. Among the approaches investigated, the fast BSFT (fBSFT) strikes a good balance between computational complexity and error rates, and FW and STG are the best in terms of error rates but with higher computational complexity. It was also found that fusion of the scores derived from systems using fBSFT and STG can reduce the error rate further. This study advocates that fBSFT, FW, and STG have the highest potential for robust speaker verification over telephone networks because they achieve good performance without any a priori knowledge of the communication channel.
Node Connectivity in Vehicular Ad Hoc Networks with Structured Mobility
Authors: Ivan W. H. Ho, Kin K. Leung, John W. Polak, Rahul Mangharam
Venue: Proceedings of the 32nd IEEE Conference on Local Computer Networks (2007)

Vehicular Ad hoc NETworks (VANETs) is a subclass of Mobile Ad hoc NETworks (MANETs). However, automotive ad hoc networks will behave in fundamentally different ways than the predominated models in MANET research. Driver behaviour, mobility constraints and high speeds create unique characteristics in the network. All of these constraints have implications on the VANET architecture at the physical, link, network, and application layers. To facilitate the cross-layer designs for VANETs, understanding of the relationship between mobility and network connectivity is of paramount importance. In this paper, we focus on studying transport systems with structured mobility (e.g., bus systems), which have unique characteristics on the road such as fixed routes that have never been explored in previous work. The main contributions of this paper are three-fold: 1) we provide an analytical framework including the design requirements of the mobility model for realistic vehicular network studies, and metrics for evaluating node connectivity in vehicular networks; 2) we demonstrate, through simulation, the impacts of marco- and micro-mobility models, and various transport elements on network connectivity; and 3) we show that multi-hop paths perform dramatically poorer than single-hop links in vehicular networks. Specifically, twohop and three-hop (communication) paths can only respectively achieve less than 27% and 13% of the average duration of single-hop links. Such kind of knowledge of the performance of multi-hop transmission will be significant for the studies of routing algorithm and other networking functions in vehicular networks.
Similarity Measurement of Web Sessions by Sequence Alignment
Authors: Chaofeng Li, Yansheng Lu
Venue: Proceedings of the 2007 IFIP International Conference on Network and Parallel Computing Workshops (2007)

The task of clustering web sessions is to group web sessions based on similarity and consists of maximizing the intra-group similarity while minimizing the inter-group similarity. The first and foremost question needed to be considered in clustering web sessions is how to measure the similarity between web sessions. However, there are many shortcomings in traditional measurements. This paper analyses the shortcomings of traditional methods and introduces a new method to measure similarities between web pages, which considers not only the URL but also the viewing time of the visited web page. Then we propose a new method to measure the similarity of web sessions using sequence alignment and the similarity of web page access. Finally, we conclude this paper and propose the future research directions.
A Comparison of Measures of Control Flow Complexity
Authors: A. L. Baker
Venue: IEEE Transactions on Software Engineering (1980)

In attempting to describe the quality of computer software, one of the more frequently mentioned measurable attributes is complexity of the flow of control. During the past several years, there have been many attempts to quantify this aspect of computer programs, approaching the problem from such diverse points of view as graph theory and software science. Most notable measures in these areas are McCabe's cyclomatic complexity and Halstead's software effort. More recently, Woodward et al. proposed a complexity measure based on the number of crossings, or "knots," of arcs in a linearization of the flowgraph.
Fourier Spectrum-Based Signature Test: A Genetic CAD Toolbox for Reliable RF Testing Using Low-Performance Test Resources
Authors: G. Srinivasan, A. Chatterjee
Venue: Proceedings of the 16th Asian Test Symposium (2007)

At the present time, coordinated EDA tools for RF/mixed-signal pin test do not exist. In this paper, a CAD tool for efficient production testing of highperformance RF systems using low-cost baseband ATE is presented. The CAD tool consists of a custom developed genetic ATPG for spectral (Fourier spectrum) signature-based alternate (to full specification-based tests) test of RF systems and involves co-simulation of scalable behavioral-level models of the RF System-Under-Test, baseband ATE test instrumentation, loadboard resources, and DfT resources for fast test vector optimization/generation. The CAD tool also enables the evaluation of various low-cost ATE architectures on the impact of the generated tests to provide a cost-effective solution.
A Faster FPT Algorithm for the Maximum Agreement Forest Problem
Authors: Michael Hallett, Catherine Mccartin
Venue: Theory of Computing Systems (2007)

Given two unrooted, binary trees, T1 and T2, leaf labelled bijectively by a set of species L, the Maximum Agreement Forest (MAF) problem asks to find a minimum cardinality collection F = {t1, ..., tk} of phylogenetic trees where each element of F is a subtree of both T1 and T2, the elements of F are pairwise disjoint, and the leaf labels for the elements of F partition the leaf label set L. We give an efficient fixed-parameter tractable (FPT) algorithm for the MAF problem, significantly improving on an FPT algorithm given in [2]. Whereas the algorithm from [2] has a running time of O(k3k) + p(|L|), our algorithm runs in time O(4k · k5) + p(|L|), where k bounds the size of the agreement forest and p(·) is a low order polynomial.
The "art" of programming gossip-based systems
Authors: Patrick Eugster, Pascal Felber, Fabrice Le Fessant
Venue: ACM SIGOPS Operating Systems Review (2007)

How does one best go about building actual gossip-based protocols? Trying to answer this question has brought us to address two preliminary questions, namely (1) what the intrinsics of such systems or protocols are, and (2) what kind of applications would in the end be built on top of such protocols. We address the first question by arguing that gossip-based protocols are all built following one and the same pattern, and describing three building blocks which we claim are used to support this recurrent pattern---most notably a source of randomness. We validate these claims by devising simplified versions of well-known protocols, in a layered fashion, on top of a conceptual interface describing these basic services. The second question is addressed by arguing that gossip-based protocols exhibit some probabilistic or imperfect flavor (e.g., probabilistic or partial completion), and by proposing to take such probabilistic behavior into account when devising interfaces for applications building on top of gossip-based protocols. We argue for inherent support for these probabilities in the programming model.
A Computer Adventure Game Applied in E-Learning
Authors: Pei-Chi Ho, Chun-Hsiung Huang, Szu-Ming Chung
Venue: Proceedings of the The 2007 International Conference on Intelligent Pervasive Computing (2007)

Based on the constructivism and situated learning theory, knowledge should not be isolated from its own cultural context. A computer game can use various designs to construct a complex plot and a logical story line. Through exploring, objects collecting, thinking, problem solving, a learner's motivation can be stimulated and reinforced in the course of game playing, which is the major application of instructional design in E-learning. This study intends to discuss and apply the teaching theory in a Computer Adventure Game (AVG) by using Flash, which resulted as an AVG called Ataiyal Legend. Keywords: Computer adventure game, Flash game, E-learning, Ataiyal Tribal Culture
An Accurate Jitter Estimation Technique for Efficient High Speed I/O Testing
Authors: Dongwoo Hong, Kwang-Ting (Tim) Cheng
Venue: Proceedings of the 16th Asian Test Symposium (2007)

This paper describes a technique for estimating total jitter that, along with a loopback-based margining test, can be applied to test high speed serial interfaces. We first present the limitations of the existing estimation method, which is based on the dual-Dirac model. The accuracy of the existing method is extremely sensitive to the choice of the fitting region and the ratio of deterministic jitter to random jitter. Then, we propose a high-order polynomial fitting technique and demonstrate its value for a more efficient and accurate total jitter estimation at a very low Bit-Error-Rate level. The estimation accuracy is also analyzed with respect to different numbers of measurement points for fitting. This analysis shows that only a very small number (i.e., 4) of measurement points is needed for achieving accurate estimation.
Efficient Automata-Based Assertion-Checker Synthesis of SEREs for Hardware Emulation
Authors: Marc Boule, Zeljko Zilic
Venue: Proceedings of the 2007 Asia and South Pacific Design Automation Conference (2007)

In this paper, we present a method for generating checker circuits from sequential-extended regular expressions (SEREs). Such sequences form the core of increasingly-used Assertion-Based Verification (ABV) languages. A checker generator capable of transforming assertions into efficient circuits allows the adoption of ABV in hardware emulation. Towards that goal, we introduce the algorithms for sequence fusion and length matching intersection, two SERE operators that are not typically used over regular expressions. We also develop an algorithm for generating failure detection automata, a concept critical to extending regular expressions for ABV, as well as present our efficient symbol encoding. Experiments with complex sequences show that our tool outperforms the best known checker generator.
Replacing Lost or Stolen E-Passports
Authors: Jianming Yong, Elisa Bertino
Venue: Computer (2007)

The launch of e-passports raises concerns about how travellers can replace them if they're lost or stolen.
On adopting Content-Based Routing in service-oriented architectures
Authors: Gianpaolo Cugola, Elisabetta Di Nitto
Venue: Information and Software Technology (2008)

Two requirements of SOAs are the need for a global discovery agency, which assists requesters in finding their required services, and the need for new interaction paradigms, which overcome the limitations of the usual request/reply style. Content-Based Routing (CBR) holds the promise of addressing both these aspects with a single technology and a single routing infrastructure. To provide arguments for our hypothesis, we review the on going efforts for service retrieval and asynchronous communication in SOAs, identify their limitations and the advantages, and discuss how incorporating CBR into SOAs allows to solve most limitations, but also poses some interesting challenges.
Optimization of pattern matching algorithm for memory based architecture
Authors: Cheng-Hung Lin, Yu-Tang Tai, Shih-Chieh Chang
Venue: Proceedings of the 3rd ACM/IEEE Symposium on Architecture for networking and communications systems (2007)

Due to the advantages of easy re-configurability and scalability, the memory-based string matching architecture is widely adopted by network intrusion detection systems (NIDS). In order to accommodate the increasing number of attack patterns and meet the throughput requirement of networks, a successful NIDS system must have a memory-efficient pattern-matching algorithm and hardware design. In this paper, we propose a memory-efficient pattern-matching algorithm which can significantly reduce the memory requirement. For total Snort string patterns, the new algorithm achieves 29% of memory reduction compared with the traditional Aho-Corasick algorithm [5]. Moreover, since our approach is orthogonal to other memory reduction approaches, we can obtain substantial gain even after applying the existing state-of-the-art algorithms. For example, after applying the bit-split algorithm [9], we can still gain an additional 22% of memory reduction.
A Segmentation Method Based on Gray-Scale Morphological Filter and Watershed Algorithm for Touching Objects Image
Authors: Ning Lu, Xizheng Ke
Venue: Proceedings of the Fourth International Conference on Fuzzy Systems and Knowledge Discovery - Volume 03 (2007)

In the process of intellectualized visional testing prod- ucts, valid image information is often collected to analysis for objective parameters such as quantity, size, and shape and so on. Because there is phenomenon of touch, the ob- jects needs to be segmented accurately. A watershed seg- mentation algorithm based on distance image using gray- scale morphological pretreating is presented in this essay. First, distance transform is applied to the binary image. And then opening operations of gray-scale morphology are applied to remove small light details in distance image be- fore applying watershed algorithm. Thus oversegmentation was controlled and touching objects were segmented pre- cisely. The result of the experiments shows that touching objects can be segmented with the accuracy near 100% with this method, that the shape of the object is not to be changed, which can meet the demand of analysis of object characteristics in intellectualized visional testing process, and that it has a practical value.
Preface
Authors: Tse-Yun Feng
Venue: IEEE Transactions on Computers (1984)

The year 1984 marks the 100th anniversary of The Institute of Electrical and Electronics Engineers. This Specification Issue of the IEEE TRANSACTIONS ON COMPUTERS is devoted to the Institute's landmark Centennial event. The ACM Portal is published by the Association for Computing Machinery. Copyright © 2010 ACM, Inc. Terms of Usage Privacy Policy Code of Ethics Contact Us Useful downloads: Adobe Acrobat QuickTime Windows Media Player Real Player