ppxscal/embedding_network huggingface dataset:
Bio-Workflows with BizTalk: Using a Commercial Workflow Engine for eScience
Authors: Asbjorn Rygg, Scott Mann, Paul Roe, On Wong
Venue: Proceedings of the First International Conference on e-Science and Grid Computing (2005)

Workflow is an important enabling technology for eScience. Research into workflow systems for eScience has yielded several specialized workflow engines. In this paper we investigate the nature of scientific workflow and describe how an existing business workflow engine, Microsoft's BizTalk, can be adapted to support scientific workflow, and some advantages of doing this. We demonstrate how BizTalk is able to support scientific workflow through the implementation of two real bioinformatics workflows. These workflows are enacted through a novel web based interface making them widely accessible.
Christos Faloutsos speaks out: on power laws, fractals, the future of data mining, sabbaticals, and more
Authors: Marianne Winslett
Venue: ACM SIGMOD Record (2005)

Welcome to this installment of ACM SIGMOD Record's series of interviews with distinguished members of the database community. I'm Marianne Winslett, and today I have here with me Christos Faloutsos, who is a professor of computer science at Carnegie Mellon University. Christos recieved the Presidential Young Investigator Award from the National Science Foundation in 1989. He received the 1997 VLDB Ten Year Paper Award for his paper on R+ trees, and the SIGMOD 1994 Best Paper Award for a paper on fast subsequence matching in time series databases. Christos is a member of the SIGKDD Executive Committee, and he has wide-ranging interests in data mining, database performance, and spatial and multimedia databases. His PhD is from the University of Toronto. So, Christos, welcome!
Image Indexing and Retrieval for a Vietnamese Folk Paintings Gallery
Authors: Binh Pham
Venue: Proceedings of the Digital Image Computing on Techniques and Applications (2005)

Cultural aspects such as history, tradition, beliefs and social customs are often depicted in paintings, both explicitly and implicitly. This paper discusses our experience and difficulties encountered while creating a multimedia Vietnamese Traditional Paintings Gallery for the purpose of dissemination and analysis of information regarding the cultural and artistic aspects of these painting . Issues regarding indexing and retrieval are analysed, which provide the motivations for our own approach which combines keyword and visual features-based methods with iconclass-based method used in arts and humanities. The use of XML-based language to express semantic content and Bayesian inference network to cater for vague queries are also discussed.
Pattern Recognition Method to Detect Vulnerable Spots in an RNA Sequence for Bacterial Resistance to the Antibiotic Spectinomycin
Authors: Alexander Churkin, Danny Barash
Venue: Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR'05) - Workshops - Volume 03 (2005)

This paper describes an efficient pattern recognition method for detecting vulnerable spots within an RNA sequence. Mutations in these spots may lead to a structural change that directly relates to a change in functionality. Previously, the concept was tried on RNA genetic control elements called ¿riboswitches¿ and other known RNA switches. Here, the concept is extended to assist in planning in-vivo experiments in general, using a new tool that we have developed called RNAMute. We apply the package RNAMute on an RNA transcript that was shown experimentally to inactivate spectinomycin resistance in Escherichia coli by creating a library of point mutations using PCR and screening to locate those mutations. Our prediction, conducted independently of the known experimental results, succeeds in matching the inactivating point mutations that were obtained by the selection experiment. Validation of the method with data available from laboratory experiment supports its use as a general predictive tool.
BIT: A Very Compact Scheme System for Microcontrollers
Authors: Danny Dubé, Marc Feeley
Venue: Higher-Order and Symbolic Computation (2005)

We present a compact implementation of Scheme for microcontrollers that includes a real-time garbage collector. The compiler runs on a normal workstation and produces byte-code from the source program. A smart linker links the byte-code with the runtime module. We demonstrate that with this system it is clearly possible to run realistic Scheme programs on a microcontroller with as little as 3 to 4 KB of RAM. Programs that access the whole Scheme library require only 13 KB of ROM. As a byproduct of this research, we designed a novel space-efficient real-time GC algorithm.
Mires: a publish/subscribe middleware for sensor networks
Authors: Eduardo Souto, Germano Guimar&#x00e3;es, Glauco Vasconcelos, Mardoqueu Vieira, Nelson Rosa, Carlos Ferraz, Judith Kelner
Venue: Personal and Ubiquitous Computing (2005)

A wireless sensor network (WSN) consists of a large number of small devices with computational power, wireless communication and sensing capability. These networks have been developed for a wide range of applications, such as habitat monitoring, object tracking, precision agriculture, building monitoring and military systems. Meanwhile, middleware systems have also been proposed in to facilitate both the development of these applications and provide common application services. The development of middleware for sensor networks, however, places new challenges on middleware developers due to the low availability of resources and processing capacity of the sensor nodes. In this context, this paper presents the design and implementation of a middleware for WSN named Mires. Mires incorporates characteristics of message-oriented middleware by allowing applications communicate in a publish/subscribe way. In order to illustrate the proposed middleware, we have also developed an environment-monitoring application and a data aggregation service.
Video inpainting and restoration techniques
Authors: Rong-Chi Chang, Louis H. Lin, Chia-Ton Tian, Timothy K. Shih
Venue: Proceedings of the 13th annual ACM international conference on Multimedia (2005)

Aged films may contain defects such as spikes or dirt, as well as long vertical defect lines. These defects were produced in file development or due to improper maintenance of films. We present a series of algorithms, which can detect and restore defects. In addition, the restoration technique is used with a motion tracking mechanism. Objects can be removed and holes can be inpainted. We aim to demonstrate three tools for 1) spike detection and restoration, 2) long vertical line detection and repairing, and 3) object removal and inpainting. Results of restored video clips show that our mechanisms are practical with good inpainted video quality.
Time-Parameterized Sensing Task Model for Real-Time Tracking
Authors: Min-Young Nam, Chang-Gun Lee, Kanghee Kim, Marco Caccamo
Venue: Proceedings of the 26th IEEE International Real-Time Systems Symposium (2005)

This paper proposes a novel task model whose physical and temporal parameters are specified as time-parameterized functions and their values are finally determined at the actual dispatch time. This model is clearly differentiated from the classical task model where parameters are fixed at the job release time. The new model better suits sensing tasks in tracking applications, since the sensor parameters such as field-of-view and measurement duration can be properly adjusted at the actual sensing time. The new model, however, creates the cyclic dependency between task parameters and scheduling behavior, that is, the task parameters depend on scheduling behavior and the latter in turn depends on the former. This cyclic dependency makes the schedulability check even more difficult. We handle this difficultyby iterative convergence and probabilistic schedulability envelope, which provides an efficient online schedulability check. The experimental study shows that the new model significantly improves the effective capacity of tracking systems without losing track accuracy.
A model and architecture for pseudo-random generation with applications to /dev/random
Authors: Boaz Barak, Shai Halevi
Venue: Proceedings of the 12th ACM conference on Computer and communications security (2005)

We present a formal model and a simple architecture for robust pseudorandom generation that ensures resilience in the face of an observer with partial knowledge/control of the generator's entropy source. Our model and architecture have the following properties:Resilience. The generator's output looks random to an observer with no knowledge of the internal state. This holds even if that observer has complete control over data that is used to refresh the internal state.Forward security. Past output of the generator looks random to an observer, even if the observer learns the internal state at a later time.Backward security/Break-in recovery. Future output of the generator looks random, even to an observer with knowledge of the current state, provided that the generator is refreshed with data of sufficient entropy.Architectures such as above were suggested before. This work differs from previous attempts in that we present a formal model for robust pseudo-random generation, and provide a formal proof within this model for the security of our architecture. To our knowledge, this is the first attempt at a rigorous model for this problem.Our formal modeling advocates the separation of the entropy extraction phase from the output generation phase. We argue that the former is information-theoretic in nature, and could therefore rely on combinatorial and statistical tools rather than on cryptography. On the other hand, we show that the latter can be implemented using any standard (non-robust) cryptographic PRG.We also discuss the applicability of our architecture for applications such as /dev/(u)random in Linux and pseudorandom generation on smartcards.
Spatial Error Concealment Using Directional Extrapolation
Authors: Yan Zhao, Hexin Chen, Xuefen Chi, Jesse S. Jin
Venue: Proceedings of the Digital Image Computing on Techniques and Applications (2005)

A new spatial error concealment algorithm based on directional extrapolation is presented. Practical communication channels are not error free. Data corruption or loss may be caused by network congestion, signal fade, various noise, etc. Error concealment is an important and practical scheme to solve such problems. Spatial error concealment is aimed at masking the effect of missing blocks by making use of the properties of smoothness and edge continuity in the spatial domain of an image or intra frame. This paper presents a spatial directional extrapolation algorithm that addresses concealment of missing image blocks on pixel-by-pixel basis. After determining the direction of edge which traverses the to-be-recovered pixel, the pixel is recovered by extrapolation along the corresponding direction. Experimental results demonstrate the performance improvement of the proposed method over conventional algorithms.
CanTree: A Tree Structure for Efficient Incremental Mining of Frequent Patterns
Authors: Carson Kai-Sang Leung, Quamrul I. Khan, Tariqul Hoque
Venue: Proceedings of the Fifth IEEE International Conference on Data Mining (2005)

Since its introduction, frequent-pattern mining has been the subject of numerous studies, including incremental updating. Many existing incremental mining algorithms are Apriori-based, which are not easily adoptable to FP-tree based frequent-pattern mining. In this paper, we propose a novel tree structure, called CanTree (Canonical-order Tree), that captures the content of the transaction database and orders tree nodes according to some canonical order. By exploiting its nice properties, the CanTree can be easily maintained when database transactions are inserted, deleted, and/or modified. For example, the CanTree does not require adjustment, merging, and/or splitting of tree nodes during maintenance. No rescan of the entire updated database or reconstruction of a new tree is needed for incremental updating. Experimental results show the effectiveness of our CanTree.
Bridging the Gap between Systems Design
Authors: David Garlan, William K. Reinholtz, Bradley Schmerl, Nicholas D. Sherman, Tony Tseng
Venue: Proceedings of the 29th Annual IEEE/NASA on Software Engineering Workshop (2005)

A challenging problem for software engineering practitioners is moving from high-level system architectures produced by system engineers to deployable software produced by software engineers. In this paper we describe our experience working with NASA engineers to develop an approach and toolset for automating the generation of space systems software from architectural specifications. Our experience shows that it is possible to leverage the space systems domain, formal architectural specifications, and component technology to provide retargetable code generators for this class of software.
Dynamic voltage and frequency scaling for energy-efficient system design
Authors: Massoud Pedram
Venue:  (2005)

Demand for low power consumption in battery-powered computer systems has risen sharply. This is due to the fact that extending the service lifetime of these systems by reducing their power dissipation is a key customer requirement. Dynamic voltage and frequency scaling (DVFS) techniques have proven to be a highly effective in achieving low power consumption in various computer systems. The key idea behind DVFS technique is to adaptively scale the supply voltage level of the CPU so as to provide &ldquo;just-enough&rdquo; circuit speed to process the system workload while meeting total computation time and/or throughput constraints, and thereby, reduce the energy dissipation. This thesis presents intra-process DVFS techniques targeted toward both non real-time and real-time applications running on embedded system platforms. To enhance the amount of the CPU energy saving by DVFS, a technique called &ldquo;workload decomposition&rdquo; is proposed whereby the workload of a target program is decomposed in two parts: on-chip and off-chip. The on-chip workload signifies the CPU clock cycles that are required to execute instructions inside the CPU, whereas the off-chip workload captures the number of external memory access clock cycles that are required to perform external memory transactions. When combined with a DVFS technique to minimize the energy consumption, this workload decomposition method results in higher energy savings for memory-intensive applications. Notice that on-chip and off-chip workload cause different amount of power dissipation because on-chip workload requires the CPU to be executed while off-chip workload requires a proper system component such as memory. So, if the task workload is decomposed into on-chip and off-chip component, the system energy variation according to the CPU frequency can be predicted very accurately, which enables the development of a more effective DVFS approach for the system energy reduction. The proposed techniques have been implemented on two real computing systems: (1) the XScale-based embedded system platform built at USC and (2) the PXA255-processor based BitsyX system from ADS Inc. Energy savings with the proposed DVFS policies have been obtained by performing current measurements on real hardware.
Heterogeneous Floorplanning for FPGAs
Authors: Yan Feng, Dinesh P. Mehta
Venue: Proceedings of the 19th International Conference on VLSI Design held jointly with 5th International Conference on Embedded Systems Design (2006)

The large size of modern FPGAs has caused researchers to consider deploying hierarchical techniques in their design. In this paper, we consider the floorplanning of FPGAs. We present a two-step approach for the floorplanning of modern FPGAs that we believe is cleaner and more versatile than recent floorplanners. The steps, based on resource-aware fixed outline simulated annealing and constrained floorplanning, are adapted to address the heterogeneous nature of FPGA floorplanning. Experiments demonstrate the viability of our approach.
An Exploration of Electrolessly Cu/Ni Plated Polyester Fabrics as E-Textiles
Authors: Jayoung Cho, Jihye Moon, Gilsoo Cho, Keesam Jeong
Venue: Proceedings of the Ninth IEEE International Symposium on Wearable Computers (2005)

Electrolessly Cu/Ni plated fabrics are favorable to be used as e-textiles owing to the excellent conductivity and the properties peculiar to fabrics. Nevertheless, durability is less ensured compared with Cu-based conductive lines. Therefore, we investigate the influence of abrasion and laundering on the electrical resistance of electrolessly Cu/Ni plated fabrics, and the effect of polyurethane sealing for the electrical durability.
Change Impact Analysis for Requirement Evolution using Use Case Maps
Authors: Jameleddine Hassine, Juergen Rilling, Jacqueline Hewitt
Venue: Proceedings of the Eighth International Workshop on Principles of Software Evolution (2005)

Changing customer needs and computer technology are the driving factors influencing software evolution. There is a need to assess the impact of these changes on existing software systems. Requirement specification is gaining increasingly attention as a critical phase of software systems development process. In particular for larger systems, it quickly becomes difficult to comprehend what impact a requirement change might have on the overall system or parts of the system. Thus, the development of techniques and tools to support the evolution of requirement specifications becomes an important issue. In this paper we present a novel approach to change impact analysis at the requirement level. We apply both slicing and dependency analysis at the Use Case Map specification level to identify the potential impact of requirement changes on the overall system. We illustrate our approach and its applicability with a case study conducted on a simple telephony system.
Induction of Word and Phrase Alignments for Automatic Document Summarization
Authors: Hal Daumé,  III, Daniel Marcu
Venue: Computational Linguistics (2005)

Current research in automatic single-document summarization is dominated by two effective, yet na&iuml;ve approaches: summarization by sentence extraction and headline generation via bag-of-words models. While successful in some tasks, neither of these models is able to adequately capture the large set of linguistic devices utilized by humans when they produce summaries. One possible explanation for the widespread use of these models is that good techniques have been developed to extract appropriate training data for them from existing document/abstract and document/headline corpora. We believe that future progress in automatic summarization will be driven both by the development of more sophisticated, linguistically informed models, as well as a more effective leveraging of document/abstract corpora. In order to open the doors to simultaneously achieving both of these goals, we have developed techniques for automatically producing word-to-word and phrase-to-phrase alignments between documents and their human-written abstracts. These alignments make explicit the correspondences that exist in such document/abstract pairs and create a potentially rich data source from which complex summarization algorithms may learn. This paper describes experiments we have carried out to analyze the ability of humans to perform such alignments, and based on these analyses, we describe experiments for creating them automatically. Our model for the alignment task is based on an extension of the standard hidden Markov model and learns to create alignments in a completely unsupervised fashion. We describe our model in detail and present experimental results that show that our model is able to learn to reliably identify word- and phrase-level alignments in a corpus of document, abstract pairs.
Friends Reunited? Evolutionary Robotics and Representational Explanation
Authors: Michael Wheeler
Venue: Artificial Life (2005)

Robotics as practiced within the artificial life community is no longer the bitter enemy of representational explanation in the way that it sometimes seemed to be in the heady, revolutionary days of the 1990s. This rapprochement is, however, fragile, because the field of evolutionary robotics continues to pose two important challenges to the idea that real-time intelligent action must or should be explained by appeal to inner representations. The first of these challenges, the threat from nontrivial causal spread, occurs when extra-neural factors account for the kind of adaptive richness and flexibility normally associated with representation-based control. The second, the threat from continuous reciprocal causation, occurs when the causal contributions made by the systemic components collectively responsible for behavior generation are massively context-sensitive and variable over time. I argue that while the threat from nontrivial causal spread can be resisted, the threat from continuous reciprocal causation provides a stern test for our representational intuitions.
Evaluation of Corner Detectors for Structure from Motion Problems
Authors: Tristrom Cooke, Robert Whatmough
Venue: Proceedings of the Digital Image Computing on Techniques and Applications (2005)

This paper is motivated by the problem of finding a 3D model of a building based on a video sequence from an air-borne platform. The first step in such a process is usually the detection of corners, which are then tracked throughout the image sequence. This paper describes a measure of performance of corner detectors for this type of problem, and then uses this to evaluate a suite of commonly used algorithms from the literature. Three simple new corner detectors have also been described.
Supporting Mixed Presence Groupware in Tabletop Applications
Authors: Peter Hutterer, Benjamin S. Close, Bruce H. Thomas
Venue: Proceedings of the First IEEE International Workshop on Horizontal Interactive Human-Computer Systems (2006)

In this paper we present the Transparent Input Device Layer framework to extend Java applications with support for multiple distributed input devices, a major requirement for tabletop applications. This overcomes a key restriction of current graphical environments to support only a single system cursor and one keyboard, and allows the cursor and keyboard control of applications to be performed by input devices that are connected to other hosts on the network. Applications can be developed with this framework and therefore allow operations such as simultaneous drag-and-drop by multiple users. Additionally, we have created a wrapper application to inject support for multiple input devices into legacy applications at runtime-without the need for code alteration or recompilation. We present two tabletop applications that make use of our framework: One is a graphical front-end to a military course of action scheduling application and was developed with the framework. The second application, a component based data visualisation application, employs the injection wrapper application to gain support for distributed multiple input devices at runtime.