ppxscal/embedding_network huggingface dataset:
Classifying G Protein-Coupled Receptors with Multiple Physicochemical Properties
Authors: Jingyi Yang, Jitender Deogun
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

Automated annotation of G protein-coupled receptors (GPCRs) has been an intriguing topic because of the important role of GPCRs in pharmaceutical research. The diverse nature of GPCRs results in the lack of overall sequence homolog among members, making the classification of GPCRs a challenging task. In this paper, we propose a new method to classify GPCRs based on only their primary sequences. We extract feature vectors from protein sequences based on various physicochemical properties and use the Support Vector Machine (SVM) for the classification. When features derived from multiple properties are used together, we obtain the accuracy of 97.61% on GPCR Level I subfamily classification and 99.94% on GPCR superfamily recognition in double cross-validation tests. The results compare favorably with those reported in previous publications.
Robust construction of the three-dimensional flow complex
Authors: Frederic Cazals, Aditya Parameswaran, Sylvain Pion
Venue: Proceedings of the twenty-fourth annual symposium on Computational geometry (2008)

The Delaunay triangulation and its dual the Voronoi diagram are ubiquitous geometric complexes. From a topological standpoint, the connection has recently been made between these cell complexes and the Morse theory of distance functions. In particular, in the generic setting, algorithms have been proposed to compute the flow complex--the stable and unstable manifolds associated to the critical points of the distance function to a point set. As algorithms ignoring degenerate cases and numerical issues are bound to fail on general inputs, this paper develops the first complete and robust algorithm to compute the flow complex. First, we present complete algorithms for the flow operator, unraveling a delicate interplay between the degenerate cases of Delaunay and those which are flow specific. Second, we sketch how the flow operator unifies the construction of stable and unstable manifolds. Third, we discuss numerical issues related to predicates on cascaded constructions. Finally, we report experimental results with CGAL's filtered kernel, showing that the construction of the flow complex incurs a small overhead w.r.t. the Delaunay triangulation when moderate cascading occurs. These observations provide important insights on the relevance of the flow complex for (surface) reconstruction and medial axis approximation, and should foster flow complex based algorithms. In a broader perspective and to the best of our knowledge, this paper is the first one reporting on the effective implementation of a geometric algorithm featuring cascading.
An algorithm for finding symmetric Grobner bases in infinite dimensional rings
Authors: Matthias Aschenbrenner, Christopher J. Hillar
Venue: Proceedings of the twenty-first international symposium on Symbolic and algebraic computation (2008)

A symmetric ideal I ⊂ R = K[x1,x2,...] is an ideal that is invariant under the natural action of the infinite symmetric group. We give an explicit algorithm to find Grobner bases for symmetric ideals in the infinite dimensional polynomial ring R. This allows for symbolic computation in a new class of rings. In particular, we solve the ideal membership problem for symmetric ideals of R.
Multilevel frames for sparse tensor product spaces
Authors: Helmut Harbrecht, Reinhold Schneider, Christoph Schwab
Venue: Numerische Mathematik (2008)

For Au&#x00a0;=&#x00a0;f with an elliptic differential operator $${A:\mathcal{H} \rightarrow \mathcal{H}'}$$ and stochastic data f, the m-point correlation function $${{\mathcal M}^m u}$$ of the random solution u satisfies a deterministic equation with the m-fold tensor product operator A (m) of A. Sparse tensor products of hierarchic FE-spaces in $${\mathcal{H}}$$ are known to allow for approximations to $${{\mathcal M}^m u}$$ which converge at essentially the rate as in the case m&#x00a0;=&#x00a0;1, i.e. for the deterministic problem. They can be realized by wavelet-type FE bases (von Petersdorff and Schwab in Appl Math 51(2):145&#x2013;180, 2006; Schwab and Todor in Computing 71:43&#x2013;63, 2003). If wavelet bases are not available, we show here how to achieve the fast computation of sparse approximations of $${{\mathcal M}^m u}$$ for Galerkin discretizations of A by multilevel frames such as BPX or other multilevel preconditioners of any standard FEM approximation for A. Numerical examples illustrate feasibility and scope of the method.
Spamulator: the Internet on a laptop
Authors: John Aycock, Heather Crawford, Rennie deGraaf
Venue: ACM SIGCSE Bulletin (2008)

We have developed an Internet simulator - the "Spamulator" - for a course on spam and spyware, a simulator that allows us to simulate the network services provided by a million domains. The Spamulator is lightweight in its resource usage, running on a single computer, and we currently have implementations for two different platforms. Students interact with the Spamulator using unmodified client software, like web browsers. Alternatively, students can write their own software to use the simulated Internet using any programming language, without contrived constraints or special libraries. Furthermore, the Spamulator is extensible, making it useful as a research tool. It could easily be used for assignments on networking, peer-to-peer networks, distributed systems, and its lightweight nature allows large-scale experiments to be conducted even by underequipped institutions. We discuss the motivation, design, and implementation of the Spamulator, and our experience with it in the spam and spyware class.
Seven key decision factors for selecting e-learning
Authors: John Huddlestone, Jonathon Pike
Venue: Cognition, Technology and Work (2008)

E-learning is increasingly being adopted as a routine instructional media, and has moved from a niche solution in the defence and aerospace industries, to one that is adopted across the vast majority of industries and within education worldwide. E-learning is not however suited for all types of learning outcome or for all instructional situations. In this paper we describe a new instructional media selection model which enables the assessment of suitability of e-learning to a particular learning outcome. Following a review of media selection theory, seven key decision areas were identified. These consideration areas are; Learning Task, Media Attributes, Grouping Strategy, Learning Context, Learner Characteristics, Instructional Management and Cost Effectiveness. The paper focuses on the identification of the key decision factors for selecting e-learning and the development of detailed guidance within each decision area to enable an assessment of suitability of e-learning to be made. Finally we outline the dependencies and interactions between decision areas to illustrate the compromises inherent in instructional media selection, and to produce a model of these inter-relationships.
Authentication in stealth distributed hash tables
Authors: Andrew MacQuire, Andrew Brampton, Idris A. Rai, Nicholas J. P. Race, Laurent Mathy
Venue: Journal of Systems Architecture: the EUROMICRO Journal (2008)

Most existing DHT algorithms assume that all nodes have equal capabilities. This assumption has previously been shown to be untrue in real deployments, where the heterogeneity of nodes can actually have a detrimental effect upon performance. We now acknowledge that nodes on the same overlay may also differ in terms of their trustworthiness. However, implementing and enforcing security policies in a network where all nodes are treated equally is a non-trivial task. We therefore extend our previous work on Stealth DHTs to consider the differentiation of nodes based on their trustworthiness rather than their capabilities alone.
Waveprint: Efficient wavelet-based audio fingerprinting
Authors: Shumeet Baluja, Michele Covell
Venue: Pattern Recognition (2008)

In this paper, we present Waveprint, a novel method for audio identification. Waveprint uses a combination of computer-vision techniques and large-scale data-stream processing algorithms to create compact fingerprints of audio data that can be efficiently matched. The resulting system has excellent identification capabilities for small snippets of audio that have been degraded in a variety of manners, including competing noise, poor recording quality and cell-phone playback. We explicitly measure the tradeoffs between performance, memory usage, and computation through extensive experimentation. The system is more efficient in terms of memory usage and computation, while being more accurate when compared with previous state of the art systems. The applications of Waveprint include song identification for end-consumer use, copyright protection for audio assets, copyright protection for television assets and synchronization of off-line audio sources, such as live television.
Huffman Coding with Non-sorted Frequencies
Authors: Shmuel T. Klein, Dana Shapira
Venue: Proceedings of the Data Compression Conference (2008)

A standard way of implementing Huffman's optimal code construction algorithm is by using a sorted sequence of frequencies. Several aspects of the algorithm are investigated as to the consequences of relaxing the requirement of keeping the frequencies in order. Using only partial order may speed up the code construction, which is important in some applications, at the cost of increasing the size of the encoded file. In an application to packet transmission, using partial order may even improve the compressibility.
Effecting change: coordination in large-scale software development
Authors: Andrew Begel
Venue: Proceedings of the 2008 international workshop on Cooperative and human aspects of software engineering (2008)

Large-scale software development requires coordination within and between very large engineering teams, each of which may be located in different locations and time zones. Numerous studies, and indeed, a whole conference (ICGSE), are dedicated to discovering the causes of problems with distributed development in the software industry. Microsoft has long had product teams too large to be considered co-located, even when sitting in neighboring buildings on the same campus. Recently, it has been expanding its engineering workforce into India and China, and our research is showing that Microsoft is encountering many of the coordination problems that go along with differences of location, time zone, and culture. As we go forward, our research has been changing from learning about the problem to experimenting with solutions. What are the best practices for improving coordination? Can they be applied to all software teams? How does one move past simple readings of research results towards effective intervention?
Characterize branching distance in terms of (η,α)-bisimilarity
Authors: Jinjin Zhang, Zhaohui Zhu
Venue: Information and Computation (2008)

In order to describe approximate equivalence between processes, the notion of branching distance has been introduced in the framework of quantitative transition systems. This paper introduces the notion of (@h,@a)-bisimilarity and explores the relationship between it and the branching distance.
Who Searches the Searchers? Community Privacy in the Age of Monolithic Search Engines
Authors: Jonathan A. Poritz
Venue: The Information Society (2007)

Privacy has largely been equated with every individual's right to privacy. Accordingly, current efforts to protect privacy on the Internet have sought anonymity by breaking, where possible, links with personally identifiable information (PII)-all uses of aggregated data stripped of PII are considered legitimate. This article argues that we need to use a broader concept, general or group identifying information (GII), because even aggregated data stripped of PII violate privacy at the community level. The search engine companies, or anyone else with access to their log files, can use these data to generate a moment-by-moment view of what is on the collective mind. Such a view can be used in a variety of ways, some with deep economic and even political impact. In order to frame this discussion, it is necessary to examine some of the realities of the search engine-mediated associative interface to the World Wide Web. While this interface has enormous benefits for the networked world, it also fundamentally changes a number of issues underlying various current debates about Internet governance.
Covering cliques with spanning bicliques
Authors: André Kündgen
Venue: Journal of Graph Theory (1998)

The edges of the complete graph on n vertices can be covered by &lceil;lg n&rceil; spanning complete bipartite subgraphs. However, the sum of the number of edges in these subgraphs is roughly (n2-4)lg n, while a cover consisting of n - 1 spanning stars uses only (n - 1)2 edges. We will show that the covering by spanning stars has the smallest total number of edges among all coverings of the clique by spanning complete bipartite subgraphs, except when n is 4 or 8. &copy; 1998 John Wiley & Sons, Inc. J Graph Theory 27: 223&ndash;227, 1998
CUBA: an architecture for efficient CPU/co-processor data communication
Authors: Isaac Gelado, John H. Kelm, Shane Ryoo, Steven S. Lumetta, Nacho Navarro, Wen-mei W. Hwu
Venue: Proceedings of the 22nd annual international conference on Supercomputing (2008)

Data-parallel co-processors have the potential to improve performance in highly parallel regions of code when coupled to a general-purpose CPU. However, applications often have to be modified in non-intuitive and complicated ways to mitigate the cost of data marshalling between the CPU and the co-processor. In some applications the overheads cannot be amortized and co-processors are unable to provide benefit. The additional effort and complexity of incorporating co-processors makes it difficult, if not impossible, to effectively utilize co-processors in large applications. This paper presents CUBA, an architecture model where co-processors encapsulated as function calls can efficiently access their input and output data structures through pointer parameters. The key idea is to map the data structures required by the co-processor to the co-processor local memory as opposed to the CPU's main memory. The mapping in CUBA preserves the original layout of the shared data structures hosted in the co-processor local memory. The mapping renders the data marshalling process unnecessary and reduces the need for code changes in order to use the co-processors. CUBA allows the CPU to cache hosted data structures with a selective write-through cache policy, allowing the CPU to access hosted data structures while supporting efficient communication with the co-processors. Benchmark simulation results show that a CUBA-based system can approach optimal transfer rates while requiring few changes to the code that executes on the CPU.
So how can I ask for it?
Authors: Wolfgang Neijdl
Venue: Proceedings of the 2008 international workshop on Data management in peer-to-peer systems (2008)

More and more information is available both on our personal computers and on the Web, and the current search engines do a great job to make it accessible. Exploiting information structures as well as social information can make them still better. In this talk I will present some ongoing work at L3S addressing these challenges, done in the context of three projects focusing on personal information management and search (NEPOMUK and iSearch) as well as audio-visual and social search (PHAROS). Regarding information structures, I will talk about ongoing work aiming at querying large amounts of heterogeneous structured data without requiring detailed schema knowledge to formulate appropriate queries. Regarding social information, I will discuss first experiments on music recommendation and retrieval, using tags and user profiles from Last.fm
A learning approach to semantic image analysis
Authors: G. Th. Papadopoulos, P. Panagi, S. Dasiopoulou
Venue: Proceedings of the 2nd international conference on Mobile multimedia communications (2006)

In this paper, a learning approach coupling Support Vector Machines (SVMs) and a Genetic Algorithm (GA) is presented for knowledge-assisted semantic image analysis in specific domains. Explicitly defined domain knowledge under the proposed approach includes objects of the domain of interest and their spatial relations. SVMs are employed using low-level features to extract implicit information for each object of interest via training in order to provide an initial annotation of the image regions based solely on visual features. To account for the inherent visual information ambiguity, fuzzy spatial relations along with the previously computed initial annotations are supplied to a genetic algorithm, which decides on the globally most plausible annotation. Experiments with images of the beach vacation domain demonstrate the performance of the proposed approach.
A Scrambling Method for Fingerprint Positioning Based on Temporal Diversity and Spatial Dependency
Authors: Sheng-Po Kuo, Yu-Chee Tseng
Venue: IEEE Transactions on Knowledge and Data Engineering (2008)

Signal strength fluctuation is one of the major problems in a fingerprint-based localization system. To alleviate this problem, we propose a scrambling method to exploit temporal diversity and spatial dependency of collected signal samples. We present how to apply these properties to enhance the positioning accuracy of several existing schemes. Simulation studies and experimental results show that the scrambling method can greatly improve positioning accuracy, especially when the tracked object has some degree of mobility.
Model of a Four-Position Unbalanced Hydraulic Valve
Authors: S. Mick Andic
Venue: Proceedings of the Tenth International Conference on Computer Modeling and Simulation (2008)

The present paper proposes and models a four-position unbalanced valve that was introduced by the author in 2006 [1] in a hydraulic system used to save and recover braking power. The valve modulates the oil flow from a free-wheeling mode to braking-and-storing energy, to full braking, to recovering energy and accelerating a load. The valve design achieves this by combining the operating characteristics of the sliding and the rotary operation. The key goals of the present analysis are to demonstrate that the four-position operation is attainable, and to evaluate the valve stability during the transient and the steady state modes of operation and compare it with the stability of the conventional stepped-spool valves. The normal, freewheeling position of the valve is determined by locating its spool in between the two springs of unequal stiffness, thus making it “unbalanced”. The solid model of the proposed design is presented and analysed here.
Performance comparison of scheduling algorithms in network mobility environment
Authors: Yaning Wang, Linghang Fan, Dan He, Rahim Tafazolli
Venue: Computer Communications (2008)

Network mobility (NEMO) supports a network moving as a whole, and this may cause the bandwidth on its wireless link varying with time and locations. The quick and frequent bandwidth fluctuation makes the resource reservation and admission control lack of scalability but with heavy overhead. A feasible solution for this problem is using scheduling algorithms to optimise the resource distribution based on the varying available bandwidth. In this paper, the performance comparison of several well-known priority queue (PQ) and fair queue (FQ) scheduling algorithms are given and their advantages and disadvantages in the NEMO environment are analysed. Moreover, a novel scheduling algorithm, named adaptive rotating priority queue (ARPQ), is proposed to avoid the problems of the existing algorithms. ARPQ operates with a ''priority first, fairness second'' policy and guarantees the delay bounds for the flows with higher priorities and maintain the reasonable throughput for the flows with lower priorities. The simulation results show that ARPQ outperforms all the existing scheduling algorithms in mobile networks, whose capacities are time-varying and location-dependent.
RAILWAY PASSENGER TRAFFIC VOLUME PREDICTION BASED ON NEURAL NETWORK
Authors: Wang Zhuo, Jia Li-Min, Qin Yong, Wang Yan-hui
Venue: Applied Artificial Intelligence (2007)

In order to overcome the shortcomings of the methods in railway passenger traffic volume prediction, an improved BP neural network method is adopted to predict railway passenger traffic volume. By analyzing the improved BP neural network theory, the neural network prediction model of railway passenger traffic volume is set up. The network learning and training simulation experiment is carried out on the data of railway passenger traffic volume from 1980-1998. Comparing with standard BP neural network, the improved BP neural network presents more accurate and reliable prediction results and faster learning speed. The improved BP neural network provides a new and feasible thought to predict railway passenger traffic volume, which can also be used to predict other relative problems.
An analysis of services for the mobile tourist
Authors: Esther Meng-Yoke Tan, Dion Hoe-Lian Goh, Yin-Leng Theng, Schubert Foo
Venue: Proceedings of the 4th international conference on mobile technology, applications, and systems and the 1st international symposium on Computer human interaction in mobile technology (2007)

Mobile tourism services have become an essential tool for supporting tourists around the world. Our research aims to identify desirable and undesirable features for mobile tourism services from the tourists' perspective. Focus group discussions and surveys were conducted to gather tourists' needs, exploring the problems faced. This paper presents our findings highlighting desirable design features being maps and transportation information, and unpopular features such as gaming activities. The results also reflect differences in preferences between business/leisure travelers and frequent/infrequent travelers. We believe results of our work are useful in providing design insights for mobile service providers when deciding on features to be included in tourist-friendly information-rich systems, and the types of services customized for specific tourist groups.
ASA: advanced secure architecture for preventing unauthorized access in personal computer platforms and BIOS
Authors: Lourdes López, José-F Martínez, Alfonso Muñoz, Vicente Hernández, Antonio Dasilva, Ana-B García
Venue: Proceedings of the 2007 Euro American conference on Telematics and information systems (2007)

This paper proposes an architecture for Personal Computers (PC) to avoid BIOS alteration and unauthorized access to resources. This proposal is based on results obtained from study of most popular PC platforms security mechanisms. Authentication controls which are established in PC platform in order to grant operating system booting or BIOS integrity of code mechanism incorporated to secure and avoid executing disallowed code are quite easy to break. The architecture described in the present work (Advanced Secure Architecture - ASA) increase the overall information and system security since prevents an unauthorized platform booting and it provides procedures for BIOS code authentication. On the other hand, ASA overcomes the users' authentication challenge in a corporative environment as well as it offers a very flexible way to specify the Personal Computers Corporation set that a user is allowed to access.
Generation of a top-of-canopy Digital Elevation Model (DEM) in tropical rain forest regions using radargrammetry
Authors: Y. Chen, P. Shi, l. Deng, J. Li
Venue: International Journal of Remote Sensing (2007)

A feasibility study is prepared for creating a top-of-canopy Digital Elevation Model (DEM) based on Radarsat data from the tropical rain forest regions of Malaysia. Through a case study, the accuracy of the generated DEM is verified, showing reasonable accuracy.