ppxscal/embedding_network huggingface dataset:
Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions
Authors: David W. Ritchie, Dima Kozakov, Sandor Vajda
Venue: Bioinformatics (2008)

Motivation: Predicting how proteins interact at the molecular level is a computationally intensive task. Many protein docking algorithms begin by using fast Fourier transform (FFT) correlation techniques to find putative rigid body docking orientations. Most such approaches use 3D Cartesian grids and are therefore limited to computing three dimensional (3D) translational correlations. However, translational FFTs can speed up the calculation in only three of the six rigid body degrees of freedom, and they cannot easily incorporate prior knowledge about a complex to focus and hence further accelerate the calculation. Furthemore, several groups have developed multi-term interaction potentials and others use multi-copy approaches to simulate protein flexibility, which both add to the computational cost of FFT-based docking algorithms. Hence there is a need to develop more powerful and more versatile FFT docking techniques. Results: This article presents a closed-form 6D spherical polar Fourier correlation expression from which arbitrary multi-dimensional multi-property multi-resolution FFT correlations may be generated. The approach is demonstrated by calculating 1D, 3D and 5D rotational correlations of 3D shape and electrostatic expansions up to polynomial order L=30 on a 2 GB personal computer. As expected, 3D correlations are found to be considerably faster than 1D correlations but, surprisingly, 5D correlations are often slower than 3D correlations. Nonetheless, we show that 5D correlations will be advantageous when calculating multi-term knowledge-based interaction potentials. When docking the 84 complexes of the Protein Docking Benchmark, blind 3D shape plus electrostatic correlations take around 30 minutes on a contemporary personal computer and find acceptable solutions within the top 20 in 16 cases. Applying a simple angular constraint to focus the calculation around the receptor binding site produces acceptable solutions within the top 20 in 28 cases. Further constraining the search to the ligand binding site gives up to 48 solutions within the top 20, with calculation times of just a few minutes per complex. Hence the approach described provides a practical and fast tool for rigid body protein-protein docking, especially when prior knowledge about one or both binding sites is available. Availability: http://www.csd.abdn.ac.uk/hex/ Contact: d.w.ritchie@abdn.ac.uk
I-MINDS: A Multiagent System for Intelligent Computer- Supported Collaborative Learning and Classroom Management
Authors: Leen-Kiat Soh, Nobel Khandaker, Hong Jiang
Venue: International Journal of Artificial Intelligence in Education (2008)

I-MINDS provides a computer-supported collaborative learning (CSCL) infrastructure and environment for learners in synchronous learning and classroom management applications for instructors, for large classroom or distance education situations. For supporting the instructor, I-MINDS includes a teacher agent. The teacher agent allows the instructor to interact with students, manage Q&A; sessions, administer quizzes, post evaluations, form groups and monitor individual and group performances. For computer-supported collaborative learning, I-MINDS, which stands for Intelligent Multiagent Infrastructure for Distributed Systems in Education, provides a student agent for each student. Each student agent monitors and models its user and carries out group formation with other student agents behind-the-scene. I-MINDS provides standard online collaborative features such as chat rooms and whiteboards and implements a structured cooperative learning mechanism called Jigsaw. The system also incorporates multiagent coalition formation algorithms for forming peer groups. I-MINDS also provides a group agent for each peer group that monitors and evaluates its assigned peer group. I-MINDS has been deployed and evaluated in an introductory computer science course (CS1). Results show that intelligent tools such as I-MINDS can be used in a real-time environment to support student cooperative learning activities, and also as a testbed to collect instructional or pedagogical data for better understanding of student collaborative learning. This paper describes the I-MINDS framework, implementation, deployment, and test results comprehensively.
Computer Jobs with the Growing Information Technology Professional Services Sector [2007] Companies-Contacts-Links - IT Services Firms - Midwest States
Authors: Info Tech Employment
Venue:  (2007)

The solid and growing information technology professional services sector continues to increase headcount. Discover computer jobs in this robust sector of the industry with Computer Jobs with the Growing Information Technology Professional Services Sector [2007]: Career Guide - Companies-Contacts-Links -8 Regional Editions. So that jobseekers can find employers close to home, there are eight editions available , which cover eight US regions: New England States, Mid-Atlantic States, Potomac Region, Southern States, Midwest States, Western States, West Coast States, and Northwestern States. In the "Companies-Contacts-Links" section, technology jobseekers gain access to current URLs and recruiter/personnel e-mail addresses of IT service providers in their region. These providers have active government and corporate contracts to supply information technology services and staff. In the "Articles" section, 21 Advisory and Analytical articles discuss leading IT jobs, skill sets, positioning tools, job classifications and pay scales. Analytical Articles: C++ Computer . Java and JavaScript . Visual Basic . Sun Solaris, Unix, Linux, Network Tech Jobs . Oracle, SQL, FoxPro, Sybase, Database Management . Software Programmer; Software Engineer . Network Programmer, Network Systems . Telecommunications . Web Developer . IT Procurement, IT Training, Project Management . IT Security . Computer Graphics, Computer Animation. Advisory Articles: Careers in IT . Hiring Options: IT Outsourcers, IT Service Providers, In-House IT Staff. Telecommuting IT Careers, Entry-Level Tech Jobs . Resumes . Skills Employers Require of IT Professionals; Training Opportunities, Building a Successful Computer Career. These editions give sure-fire direction to good employment in all 50 U.S. States.
Synchronization of neural networks based on parameter identification and via output or state coupling
Authors: Xuyang Lou, Baotong Cui
Venue: Journal of Computational and Applied Mathematics (2008)

For neural networks with all the parameters unknown, we focus on the global robust synchronization between two coupled neural networks with time-varying delay that are linearly and unidirectionally coupled. First, we use Lyapunov functionals to establish general theoretical conditions for designing the coupling matrix. Neither symmetry nor negative (positive) definiteness of the coupling matrix are required; under less restrictive conditions, the two coupled chaotic neural networks can achieve global robust synchronization regardless of their initial states. Second, by employing the invariance principle of functional differential equations, a simple, analytical, and rigorous adaptive feedback scheme is proposed for the robust synchronization of almost all kinds of coupled neural networks with time-varying delay based on the parameter identification of uncertain delayed neural networks. Finally, numerical simulations validate the effectiveness and feasibility of the proposed technique.
Satellite-based assessment of the impact of sea-surface winds on regional atmospheric circulations over the Korean Peninsula
Authors: S. -H. Lee, D. -H. Kim, H. -W. Lee
Venue: International Journal of Remote Sensing (2008)

In order to clarify the impact of sea-wind satellite-data assimilation under fair and calm weather conditions over the Korean Peninsula, several numerical experiments were carried out. The numerical model used in this study was the Fifth Mesoscale Model (MM5), verified by many previous studies; satellite data of sea winds were gathered by the QuikSCAT sensor launched on ADEOS II. During the daytime, the change in mesoscale circulations according to the assimilation of sea-wind data increased in the coastal area and decreased deep inland. Although variations in mesoscale circulations due to satellite-based sea-wind data assimilation occurred near the coastal area, the mixing height far inland over the Korean Peninsula often changed according to the intensity of inflow from the surrounding seas and that of the topographic effect. In this study, a lower mixing height inland was generated by a numerical simulation using QuikSCAT sea-wind data assimilation. The lower mixing height was caused by strong westerly and weak easterly winds from the Yellow Sea and the East Sea, respectively. The validation of the sea-wind influence was verified quantitatively by RMSD and IOA analyses. The accuracy of weather forecasting increased at the East Sea and Korea Strait and decreased at the Yellow Sea. These different accuracy levels were caused by the inhomogeneity of sea-wind data quality. The maintenance of the uniform quality of satellite-based data on sea wind is an important factor in the reasonable forecasting of mesoscale circulations.
Comparison of algorithms for pre-processing of SELDI-TOF mass spectrometry data
Authors: Alejandro Cruz-Marcelo, Rudy Guerra, Marina Vannucci, Yiting Li, Ching C. Lau, Tsz-Kwong Man
Venue: Bioinformatics (2008)

Motivation: Surface-enhanced laser desorption and ionization (SELDI) time of flight (TOF) is a mass spectrometry technology. The key features in a mass spectrum are its peaks. In order to locate the peaks and quantify their intensities, several pre-processing steps are required. Though different approaches to perform pre-processing have been proposed, there is no systematic study that compares their performance. Results: In this article, we present the results of a systematic comparison of various popular packages for pre-processing of SELDI-TOF data. We evaluate their performance in terms of two of their primary functions: peak detection and peak quantification. Regarding peak quantification, the performance of the algorithms is measured in terms of reproducibility. For peak detection, the comparison is based on sensitivity and false discovery rate. Our results show that for spectra generated with low laser intensity, the software developed by Ciphergen Biosystems (ProteinChip© Software 3.1 with the additional tool Biomarker Wizard) produces relatively good results for both peak quantification and detection. On the other hand, for the data produced with either medium or high laser intensity, none of the methods show uniformly better performances under both criteria. Our analysis suggests that an advantageous combination is the use of the packages MassSpecWavelet and PROcess, the former for peak detection and the latter for peak quantification. Contact:rguerra@rice.edu; marina@rice.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Estimating stem volume by tree crown area and tree shadow area extracted from pan-sharpened Quickbird imagery in open Crimean juniper forests
Authors: I. Ozdemir
Venue: International Journal of Remote Sensing (2008)

Although open forests represent approximately 30% of the world's forest resources, there is a clear lack of reliable inventory data to allow sustainable management of this valuable resource from semi-arid areas. This paper demonstrates that the low ground cover of open forest offers a unique opportunity for deriving single tree attributes from high-resolution satellite imagery, allowing reliable biomass estimation. More particularly, this study investigates the relationship between field-measured stem volume and tree attributes, including tree crown area and tree shadow area, measured from pan-sharpened Quickbird imagery with a 0.61 m resolution in a sparse Crimean juniper (Juniperus excelsa M.Bieb.) forest in south-western Turkey. First tree shadows and crowns were identified and delineated as individual polygons. Both visual delineation and computer-aided automatic classification methods were tested. After delineation, stem volume as a function of these image-measured attributes was modelled using linear regression. The statistical analyses indicated that stem volume was correlated with both shadow area and crown area. The best model for stem volume using shadow area resulted in an adjusted R 2 = 0.67, with a root mean square error (RMSE) of 12.5%. The model for stem volume using crown area resulted in an adjusted R 2 = 0.51, with a RMSE of 15.2%. The results showed that pan-sharpened Quickbird imagery is suitable for estimating stem volume and may be useful in reducing the time required for obtaining inventory data in open Crimean juniper forests and other similar open forests.
Similarity solutions to the power-law generalized Newtonian fluid
Authors: Wenjie Gao, Junyu Wang
Venue: Journal of Computational and Applied Mathematics (2008)

The authors of this paper study a second-order nonlinear parabolic equation with a background describing the motion of the power-law generalized Newtonian fluid. The existence of similarity solutions is obtained and the asymptotic behavior of the solution is studied.
3-Valued abstraction: More precision at less cost
Authors: Sharon Shoham, Orna Grumberg
Venue: Information and Computation (2008)

This paper investigates both the precision and the model checking efficiency of abstract models designed to preserve branching time logics w.r.t. a 3-valued semantics. Current abstract models use ordinary transitions to over approximate the concrete transitions, while they use hyper transitions to under approximate the concrete transitions. In this work, we refer to precision measured w.r.t. the choice of abstract states, independently of the formalism used to describe abstract models. We show that current abstract models do not allow maximal precision. We suggest a new class of models and a construction of an abstract model which is most precise w.r.t. any choice of abstract states. As before, the construction of such models might involve an exponential blowup, which is inherent by the use of hyper transitions. We therefore suggest an efficient algorithm in which the abstract model is constructed during model checking, by need. Our algorithm achieves maximal precision w.r.t. the given property while remaining quadratic in the number of abstract states. To complete the picture, we incorporate it into an abstraction-refinement framework.
Conditioning probabilistic databases
Authors: Christoph Koch, Dan Olteanu
Venue: Proceedings of the VLDB Endowment (2008)

Past research on probabilistic databases has studied the problem of answering queries on a static database. Application scenarios of probabilistic databases however often involve the conditioning of a database using additional information in the form of new evidence. The conditioning problem is thus to transform a probabilistic database of priors into a posterior probabilistic database which is materialized for subsequent query processing or further refinement. It turns out that the conditioning problem is closely related to the problem of computing exact tuple confidence values. It is known that exact confidence computation is an NP-hard problem. This has led researchers to consider approximation techniques for confidence computation. However, neither conditioning nor exact confidence computation can be solved using such techniques. In this paper we present efficient techniques for both problems. We study several problem decomposition methods and heuristics that are based on the most successful search techniques from constraint satisfaction, such as the Davis-Putnam algorithm. We complement this with a thorough experimental evaluation of the algorithms proposed. Our experiments show that our exact algorithms scale well to realistic database sizes and can in some scenarios compete with the most efficient previous approximation algorithms.
Failure of electronic devices due to condensation
Authors: C. Schimpf, K. Feldmann, C. Matzner, A. Steinke
Venue: Microsystem Technologies (2008)

The increasing usage of electronic devices and the progressive trend of miniaturisation in automotive applications require different installation locations. According to varying locations, different climate conditions will occur. In this article, the influence of condensation on the reliability of electronic devices is examined. For the detection of failures or the loss of functionality it is essential to determine the occurrence of condensation. A new microsensor based on the CCC-principle (condensate controlled capacitance) allows the measurement of the condensed water mass directly. Depending on the gaps of special designed stray field capacity in combination with a water drop sensitive detection system, a change of the capacity with increasing water mass is shown. It is necessary to analyse failure mechanisms like corrosion induced leakage currents and electrochemical migration. For the research of these failure mechanisms special test patterns were designed and assembled. These samples were exposed to a certain climate profile, which produces a reproducible and defined amount of condensation, this can occur in certain locations in automotives. On the bases of these test patterns, which consist of both combs with different spaces and chip capacities with variable sizes, diverse influences were examined. Beside field strength also the surface metallisation and the cleanliness of the samples were investigated and quantified.
Fuzzy logic supported sketch based image information enhancement
Authors: A. R. Varkonyi-Koczy
Venue: International Journal of Advanced Intelligence Paradigms (2008)

Recently, the importance of information enhancement methods in digital image processing has increased significantly. Typical examples are searching for similar objects/images in large databases and understanding the objects in images. The main points of these tasks are to extract the most characteristic features of the objects in the images and/or to separate the 'significant' and 'unimportant' parts of these features. This paper describes a new edge processing method which is able to extract the 'primary', i.e. those edges which can advantageously be used in sketch based image retrieval algorithms.
Erlang for Concurrent Programming
Authors: Jim Larson
Venue: Queue (2008)

What role can programming languages play in dealing with concurrency? One answer can be found in Erlang, a language designed for concurrency from the ground up. One of Erlang's key features is its small, yet powerful set of concurrency primitives that help developers reason about the behaviour of concurrent programs. But is it scalable? And how well does it perform? In this article, Jim Larson from Google introduces Erlang and shows how it can be used to implement concurrent programs correctly and quickly.
Key-dependent message security under active attacks - BRSIM/UC-soundness of Dolev-Yao-style encryption with key cycles
Authors: Michael Backes, Birgit Pfitzmann, Andre Scedrov
Venue: Journal of Computer Security (2008)

Key-dependent message (KDM) security was introduced by Black, Rogaway and Shrimpton to address the case where key cycles occur among encryptions, e.g., a key is encrypted with itself. It was mainly motivated by key cycles in Dolev-Yao models, i.e., symbolic abstractions of cryptography by term algebras, and a corresponding computational soundness result was later shown by Ad&atilde;o et al. However, both the KDM definition and this soundness result do not allow the general active attacks typical for Dolev-Yao models or for security protocols in general. We extend these definitions to obtain a soundness result under active attacks. We first present a definition AKDM (adaptive KDM) as a KDM equivalent of authenticated symmetric encryption, i.e., it provides chosen-ciphertext security and integrity of ciphertexts for key cycles. However, this is not yet sufficient for the desired computational soundness result and thus we define DKDM (dynamic KDM) that additionally allows limited dynamic revelation of keys. We show that DKDM is sufficient for computational soundness, even in the strong sense of blackbox reactive simulatability (BRSIM)/UC and in cases with joint terms with other operators. We also build on current KDM-secure schemes to construct schemes secure under the new definitions. Moreover, we prove implications or construct separating examples, respectively, for new definitions and existing ones for symmetric encryption.
Ranking Web Pages from User Perspectives of Social Bookmarking Sites
Authors: Chia-Hao Lo, Wen-Chih Peng, Meng-Fen Chiang
Venue: Proceedings of the 2008 IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology - Volume 01 (2008)

Recently, the growth of social bookmark sites (e.g.,\\del.icio.us) brings a new way to organize and share web pages. Specially, the social bookmarking sites contain many bookmarks of users, and users, who bookmark web pages, would frequently browse these pages in the future. Therefore, we argue that social bookmarking sites provide the readers' perspective and are able to take the perspective into consideration in ranking web pages. In this paper, we propose two ranking algorithms, ExpertVoteRank and RecommendationPageRank, to reveal the diverse information of web pages in the social bookmarking sites. The concept of both algorithms are based on the views of readers: ExpertVoteRank takes advantage of experts of readers, while RecommendationPageRank applies recommendations from crowds to web pages. Note that we collected about 90 millions data. Experiments show that both algorithms have effectiveness to rank web pages according to the viewpoint of users.
Genetic approach for dynamic OVSF code allocation in 3G wireless networks
Authors: Mustafa Karakoc, Adnan Kavak
Venue: Applied Soft Computing (2009)

Orthogonal variable spreading factor (OVSF) codes provide variable data rate transmissions for different bandwidth requirements in 3G WCDMA networks. In order to effectively utilize limited OVSF resources, many works in the literature have focused on dynamic code assignment (DCA) schemes. This paper investigates genetic algorithm (GA) based approach for dynamic OVSF code assignment in WCDMA networks. Different from existing conventional code assignment (CCA) and dynamic code assignment schemes, population is adaptively constructed according to existing traffic density in the OVSF code-tree. In order to improve the ability of the GA, we employ so-called ''dominance & diploidy'' structure to adapt to changing traffic conditions. Performances of these two methods are evaluated in terms of blocking probability and spectral efficiency, and also compared with CCA and DCA. The simulation results show that the GA, especially with diploid structure, provides reduced code blocking probability and improved spectral efficiency in the system when compared to the CCA and DCA schemes. In addition to these, different GA operators are also tested under varying traffic loads to increase the overall system performance.