ppxscal/embedding_network huggingface dataset:
A geometric framework for robust nearest neighbor analysis of protein structure and function
Authors: Jack S. Snoeyink
Venue:  (2006)

A protein is a long chain of amino acids, also called residues. In solution the protein chain folds into a compact three-dimensional shape that determines the protein's function. Nearest-neighbor analysis of protein structures, represented as one point per residue, identifies pairs, triples and quadruples of residues that interact or pack together. Such analysis has been used to score protein packing and interactions; to detect repeating elements of protein structure; to compare two protein structures; and to find packing patterns in families of proteins that are related to their function. However, point coordinates of protein structures are determined experimentally and are thus imprecise. I explore whether nearest-neighbor analysis done on precise points still applies for imprecise points. My dissertation introduces two new geometric techniques for robust neighbor analysis, almost-Delaunay simplices and Delaunay probability, that capture imprecision in the input points, and demonstrates several applications in the analysis of protein structure. The almost-Delaunay simplices quantify possible changes in the nearest neighbors, given the maximum motion allowed for any point. For 3D points, they define new sets of neighboring pairs, triples and quadruples that may arise, called the almost-Delaunay edges, triangles and tetrahedra. The Delaunay probability estimates the probability that a set of points really are nearest neighbors, given the expected amplitude of random motion for all points. These techniques establish a framework in which existing applications of nearest-neighbor analysis can often be adapted to make them more robust for imprecise points, and entirely new applications can be designed that were not possible previously. Using the almost-Delaunay tetrahedra, I observe that the nearest neighbors in a protein structure are more stable than in other protein-like structures, such as artificially folded decoys and structures predicted from protein sequences. I adapt a statistical score for protein packing to use my geometric framework, and show that the score is robust when used to distinguish well-packed proteins from decoys, and that the framework may make it more robust when analyzing the packing at each residue. I identify packing signatures for repeating elements of protein structure, particularly for alpha-helices, and detect these elements with high accuracy. Finally, I use changes in the neighboring residues between two or more snapshots of a protein undergoing motion to identify flexible residues. Using the almost-Delaunay edges, I derive a sparse and robust graph representation of protein structure to support mining frequent substructures from protein families. From these I identify fingerprints, specific substructures that characterize protein families, and use them to infer the function of protein structures with unknown function.
A Reflective Database-Oriented Framework for Autonomic Managers
Authors: Wendy Powley, Pat Martin
Venue: Proceedings of the International Conference on Autonomic and Autonomous Systems (2006)

The trend towards autonomic systems emphasizes the need for implementation frameworks for autonomic features. In this paper we describe a general framework for the development of autonomic managers, that is, components that can manage their own behaviour. Our approach uses concepts and tools from relational database management systems as well as reflective programming techniques to implement the components of the autonomic manager.
Data Acquisition in Sensor Networks with Large Memories
Authors: D. Zeinalipour-Yazti, Neema,  V. Kalogeraki, D. Gunopulos, W. Najjar
Venue: Proceedings of the 21st International Conference on Data Engineering Workshops (2005)

Sensor Networks will soon become ubiquitous, making them essential tools for monitoring the activity and evolution of our surrounding environment. However such environments are expected to generate vast amounts of temporal data that needs to be processed in a power-effective manner. To this date sensor nodes feature small amounts of memory which mostly limits their capabilities to queries that only refer to the current point in time. In this paper we initiate a study on the deployment of large memories at sensor nodes. Such an approach gives birth to an array of new temporal and top-k queries which have been extensively studied by the database community. Our discussion is in the context of the RISE (RIverside SEnsor) hardware platform, in which sensor nodes feature external flash card memories that provides them several Megabytes of storage.
Modeling an emergency operations center with agents
Authors: Margaret L. Loper, Bart Presnell
Venue: Proceedings of the 37th conference on Winter simulation (2005)

The Georgia Emergency Management Agency (GEMA) operates the State Operations Center, which is the centralized hub for all communications regarding state operations, with respect to emergency response. The Center provides three primary functions: Request for Information, Request for Assistance, and Media Relations. The Center has responsibility for the entire process of servicing an emergency, from instigation to communication to execution to ending service for the emergency. To accomplish this, the Center is set up like a production facility, which follows a well-defined process articulated in a plan. In this project, we worked with GEMA to develop a simulation of the Center. The simulation, called GEMASim, models the information flow among people working within the Center, as well as the flow of information coming into and leaving the Center. Data is presented on the initial experiments with GEMASim using two different scenarios.
Dynamically reducing pressure on the physical register file through simple register sharing
Authors: L. Tran, N. Nelson, Fung Ngai, S. Dropsho, M. Huang
Venue: Proceedings of the 2004 IEEE International Symposium on Performance Analysis of Systems and Software (2004)

Using register renaming and physical registers, modern microprocessors eliminate false data dependences from reuse of the instruction set defined registers (logical registers). High performance processors that have longer pipelines and a greater capacity to exploit instruction-level parallelism have more instructions in-flight and require more physical registers. Simultaneous multithreading architectures further exacerbate this register pressure. This paper evaluates two register sharing techniques for reducing register usage. The first technique dynamically combines physical registers having the same value the second technique combines the demand of several instructions updating the same logical register and share physical register storage among them. While similar techniques have been proposed previously, an important contribution of this paper is to exploit only special cases that provide most of the benefits of more general solutions but at a very low hardware complexity. Despite the simplicity, our design reduces the required number of physical registers by more than 10% on some applications, and provides almost half of the total benefits of an aggressive (complex) scheme. More importantly, we show the simpler design to reduce register pressure has significant performance effects in a simultaneous multithreaded (SMT) architecture where register availability can be a bottleneck. Our results show an average of 25.6% performance improvement for an SMT architecture with 160 registers or, equivalently, similar performance as an SMT with 200 registers (25% more) but no register sharing.
Resolution analysis in signal recovery
Authors: S. Dharanipragada, K. S. Arun
Venue: Proceedings of the Acoustics, Speech, and Signal Processing, 1995. on International Conference - Volume 02 (1995)

Resolution analysis for the problem of signal recovery from finitely many linear samples is the subject of the paper. The classical Rayleigh limit serves only as a lower bound on resolution since it does not assume any recovery strategy and is based only on observed data. The authors show that details finer than the Rayleigh limit can be recovered by simple linear processing that incorporates prior information. They first define a measure of resolution based on allowable levels of error that is more appropriate for current signal recovery strategies than the Rayleigh definition. In the practical situation in which only finitely many noisy observations are available, one must restrict the class of signals in order to make the resolution measure meaningful. They consider the set of bandlimited and essentially time-limited signals since it describes most signals encountered in practice. For this set they show how to precompute resolution limits from knowledge of measurement functionals, signal-to-noise ratio, passband, energy concentration regions, energy concentration factor, and a prescribed level of error tolerance. In the process they also derive an algorithm for high resolution signal recovery. They illustrate the results with an example.
Learning to rank networked entities
Authors: Alekh Agarwal, Soumen Chakrabarti, Sunny Aggarwal
Venue: Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining (2006)

Several algorithms have been proposed to learn to rank entities modeled as feature vectors, based on relevance feedback. However, these algorithms do not model network connections or relations between entities. Meanwhile, Pagerank and variants find the stationary distribution of a reasonable but arbitrary Markov walk over a network, but do not learn from relevance feedback. We present a framework for ranking networked entities based on Markov walks with parameterized conductance values associated with the network edges. We propose two flavors of conductance learning problems in our framework. In the first setting, relevance feedback comparing node-pairs hints that the user has one or more hidden preferred communities with large edge conductance, and the algorithm must discover these communities. We present a constrained maximum entropy network flow formulation whose dual can be solved efficiently using a cutting-plane approach and a quasi-Newton optimizer. In the second setting, edges have types, and relevance feedback hints that each edge type has a potentially different conductance, but this is fixed across the whole network. Our algorithm learns the conductances using an approximate Newton method.
The Design of Internet Collaborative Learning System Structure with the Integration of 3D Virtual Instruments
Authors: Fu-Chien Kao, Tien-Hsin Feng, Chia-Liang Kuo
Venue: Proceedings of the Fourth IEEE International Workshop on Technology for Education in Developing Countries (2006)

The collaborative learning approach has in the past decades gained significant recognition. It is a group instruction design, which combines education theory and social psychology. Most web-based collaborative learning systems today provide a network environment that is conducive to the students' online study of theory-based curriculums in a collaborative learning format. Few however explore how a network based collaborative environment involving the practical operation of instrumentation can be established. To transplant the six characteristics of traditional collaborative learning (including characteristics such as heterogeneous grouping, positive interdependence, positive face-to-face interaction, individual learning performance assessments, social skills and the group process) into the network collaborative learning environment, this paper proposes the design of a network collaborative learning system with remotely operated 3D virtual instruments. To express the six characteristics through network collaborative learning, this research uses Access Grid tools and Remote Control Parameter Delivering Technology to design the structure of the system, and integrate traditional elements to create a web-based collaborative learning environment based around documentation, video conferences or 3D virtual sets. The proposed system functions contain (1) face-to-face voice communications (2) real-time text chat (3) electronic whiteboard instruction (4) SCORM learning content sharing (5) VOD video-conferencing instruction (6) recording of the group learning process (7) individual learning performance assessment. This means that the proposed system structure and functionalities are a true translation of traditional collaborative characteristics into an Internet-based collaborative learning environment.
Curve Shape Modification and Similarity Evaluation
Authors: Tetsuzo Kuragano, Akira Yamaguchi
Venue: Proceedings of the International Conference on Computational Inteligence for Modelling Control and Automation and International Conference on Intelligent Agents Web Technologies and International Commerce (2006)

In Computer Aided Aesthetic Design, designers evaluate the quality of a designed curve by looking at its curvature or radius of curvature plots. If the quality of a designed curve does not meet a designer's demand, they usually modify the control points of the curve interactively. But the definition of the quality of a designed curve is ambiguous and no official standards are given. Therefore, in this paper, a criterion of a fair curve is established. A five degree B-spline curve and curvature are expressed. Feature of curvature distribution and radius of curvature distribution are discussed. The radius of curvature specification to modify the shape of a B-spline curve is described. To modify the shape of the B-spline curve, the least-squares method is introduced to minimize the difference between the B-spline curve radius of curvature and the specified radius of curvature. Correlation matching for similarity evaluation is described. The discrete values of radius of curvature are considered as the components of a multi dimensional vector for the curve. Similarity between two curves is calculated by normalizing the dot product of the vectors. Curve shape similarity evaluation is tried by giving examples. Examples show the numerical similarity evaluation matches our visual recognition of curve shape similarity. Assuming a curve with constant variation of radius of curvature distribution is fair, the similarity of the designed curve to a fair curve is evaluated.
Graph-based Approach to Context-adaptable PNS and its Application Scenarios
Authors: Masayuki Kawabata, Ryo Nishide, Mayumi Ueda, Shinichi Ueshima
Venue: Proceedings of the 21st International Conference on Data Engineering Workshops (2005)

Recently, the remarkable advance on mobile terminal technologies has enabled us to develop full-scaled navigation systems for pedestrians. In most systems developed so far, researches have been focused on visualization effect on maps to users to guide pedestrians to their destination smoothly. The authors present a context-adaptable pedestrian navigation system, which provides users with the preferable route, considering the conditions of each area and the objectives of users. A graph-based approach is employed utilizing metadata to represent logical space built over the real space, and a scoring scheme is provided by partitioning target region to its edges, which enables to expand target region. The usability of this system in many environments is examined by numerical simulations. The authors also discuss the possibilities of the system in practical settings in an open area, temporarily built-up sites.
Arabic word recognition by classifiers and context
Authors: Nadir Farah, Labiba Souici, Mokhtar Sellami
Venue: Journal of Computer Science and Technology (2005)

Given the number and variety of methods used for handwriting recognition, it has been shown that there is no single method that can be called the "best". In recent years, the combination of different classifiers and the use of contextual information .have become major areas of interest in improving recognition results. This paper addresses a case study on the combination of multiple classifiers and the integration of syntactic level information for the recognition of handwritten Arabic literal amounts. To the best of our knowledge, this is the first time either of these methods has been applied to Arabic word recognition. Using three individual classifiers with high level global features, we performed word recognition experiments. A parallel combination method was tested for all possible configuration cases of the three chosen classifiers. A syntactic analyzer makes a final decision on the candidate words generated by the best configuration scheme. The effectiveness of contextual knowledge integration in our application is confirmed by the obtained results.
Long-wavelength lasers based on metamorphic quantum dots
Authors: A. E. Zhukov, A. R. Kovsh, V. M. Ustinov, N. N. Ledentsov, Zh. I. Alferov
Venue: Microelectronic Engineering (2005)

We study a novel approach to extend a spectral range of GaAs-based structures up to 1.6@mm. The dependence of quantum dot (QD) light emission on the bandgap of surrounding matrix is employed by forming a QD array inside a metamorphic InGaAs epilayer. Specific growth regimes and the design of the metamorphic transient layers can provide a mirror-like morphology in combination with the effective dislocation trapping. It is shown that the wavelength of the QD emission can be controllably tuned in the 1.4-1.6@mm range by varying the composition of the metamorphic InGaAs matrix. Details of formation, fabrication and characterization of metamorphic-based diode lasers are presented. We demonstrate a lasing wavelength as long as 1488-1515nm in the 20-80^oC temperature interval. The minimum threshold current density of that is 700A/cm^2 at room temperature. The external differential efficiency and the maximum pulsed power exceed 50% and 7W, respectively. Issues of the metamorphic-based long-wavelength surface-emitting laser are also addressed.
Low-power software configurable modulator for wireless communications
Authors: Jenshan Lin
Venue:  (2006)

We examined a software configurable modulator with the potential to generate different modulation schemes. The modulator uses a "digital" approach unlike the "mixing" or "multiplying" approach used by conventional analog modulators. The digital approach uses the phasor combining technique to generate the modulated signal constellation. The phasor combing method is essentially to weigh and sum up two phasors, or two LO signals with different phases (e.g., in quadrature) to generate a desired phasor that represents the modulated signal on the constellation. We designed and tested 2 test modulator circuits realizing an MSK-like modulation scheme based on the design approach: one with a fixed data pattern and the other for arbitrary data patterns. Experimental results showed that, compared to a conventional modulator with similar functions, the proposed modulator has the advantages of low power consumption (&sim;3.6 mW excluding output buffers), high data rate (up to &sim;100 Mbps), broad operating frequency range (up to &sim;3 GHz), and less circuit complexity in terms of necessary accompanying circuit components for function and performance purposes. We also present the design and experimental results of a direct conversion transmitter that uses the modulator. The transmitter consists of a voltage controlled oscillator (VCO), the modulator circuit for arbitrary bit patterns, and a power amplifier (PA). The power consumption of the whole transmitter is &sim;129 mW, and the output power level is &sim;3 dBm. The transmitter can be used for a ZigBee-ready personal area network, or other similar wireless networks. It has the advantages of higher data rate and lower error vector magnitude (EVM) than the normal specifications for such networks. We also designed and built a board-level modulator a core modulator chip with the same architecture as the integrated modulator circuit. Control signals and bias currents can be applied off-chip by on-board circuit components. The board was tested for offset quadrature phase shift keying (OQPSK) modulation, and the minimum shift keying (MSK) function can be developed by properly designed on-board circuitry. The phasor combining approach can potentially allow a modulator to generate different modulation schemes such as QPSK, MSK, and even quadrature amplitude modulation (QAM). These modulation schemes are widely used in today's wireless communications. Therefore, the proposed modulator may be well suited for a software defined radio.
How can agent know the global information without close coordination?
Authors: Satoshi Kurihara, Shinya Sato, Kensuke Fukuda, Toshiharu Sugawara
Venue: Proceedings of the fifth international joint conference on Autonomous agents and multiagent systems (2006)

In the multi-agent systems, even if each agent behaves selfish or cooperative, its behavior influences the other agents' behaviors and their behaviors influence its behavior cyclically. Thereore a certain information about the relative position of each agent among all the agents may be able to be extracted only from its behavior. If this information can be extracted, each agent has the possibility to improve its efficiency only by seeing its own behavior without knowing about the information of the other agents. In this paper, we verified this hypothesis by using the competitive multi-agent simulation environment named Minority Game, and confirmed that each agent's performance gain was actually possible. This analytical technique may be especially useful for massively multi-agent systems.
Industrial Semantics and Magic
Authors: Charles Petrie, Christoph Bussler
Venue: IEEE Internet Computing (2006)

It's time for academic research in semantics to be industrially relevant. Yes, industry generally adapts slowly to new ideas, but the problem is compounded by academics' confusion about the issues they're solving - and those that industry would like solved.
Modelling WS-RF based Enterprise Applications
Authors: A. Akram, J Kewley, R. Allan
Venue: Proceedings of the 10th IEEE on International Enterprise Distributed Object Computing Conference Workshops (2006)

The Web Service Resource Framework (WS-RF) specifications originated from the Grid paradigm which has no widespread programming methodology and lacks established design models. The flexibility and richness of WS-RF specifications are ideal for the complex, unpredictable and inter-dependent components in an Enterprise Application. This paper presents a Model-Driven approach for WS-RF to meet the requirements of Enterprise Applications (EAs) spread across multiple domains and institutes. This Model-Driven approach addresses cross-platform interoperability, quality of service, design reuse, systematic development and compliance to user requirements at the design level.
Personal space in virtual reality
Authors: Laurie M. Wilcox, Robert S. Allison, Samuel Elfassy, Cynthia Grelik
Venue: ACM Transactions on Applied Perception (TAP) (2006)

Improving the sense of &ldquo;presence&rdquo; is a common goal of three-dimensional (3D) display technology for film, television, and virtual reality. However, there are instances in which 3D presentations may elicit unanticipated negative responses. For example, it is well established that violations of interpersonal space cause discomfort in real-world situations. Here we ask if people respond similarly when viewing life-sized stereoscopic images. Observers rated their level of comfort in response to animate and inanimate objects in live and virtual (stereoscopic projection) viewing conditions. Electrodermal activity was also recorded to monitor their physiological response to these stimuli. Observers exhibited significant negative reactions to violations of interpersonal space in stereoscopic 3D displays, which were equivalent to those experienced in the natural environment. These data have important implications for the creation of 3D media and the use of virtual reality systems.