ppxscal/embedding_network huggingface dataset:
Study of the Mini-protein Conformational Entropies at Different Temperature
Authors: Gui-zhong Liu, Xiang-hua Dou, Ji-hua Wang
Venue: Proceedings of the 2009 International Conference on Computational Intelligence and Natural Computing - Volume 01 (2009)

Based on MD simulations, we calculated the conformational entropies of a designed 10-residue peptide, or the mini-protein Chignolin’s eight residues (2-9) at four different temperature. Our results show that five conformational entropies of Chignolin’s eight residues have different jump. At 260K, the conformational entropy of Gly(7) generates three orders jump, which are being founded and that of Thr(8) generates one order jump; at 300K, the conformational entropies of Asp(3), Pro(4), and Thr(8) generates two orders jump; at 400K, the conformational entropies of Asp(3), Pro(4), Thr(6) and Thr(8) generates one order jump. The curves of conformational entropies are coincident with RMSD, however the convergence of the conformational entropies by comparing the former with the latter and this shows conformational entropies can illustrate the changes of conformations very well. The main factors influence on the residue conformational entropies are also discussed in this paper.
Using bilingual knowledge and ensemble techniques for unsupervised Chinese sentiment analysis
Authors: Xiaojun Wan
Venue: Proceedings of the Conference on Empirical Methods in Natural Language Processing (2008)

It is a challenging task to identify sentiment polarity of Chinese reviews because the resources for Chinese sentiment analysis are limited. Instead of leveraging only monolingual Chinese knowledge, this study proposes a novel approach to leverage reliable English resources to improve Chinese sentiment analysis. Rather than simply projecting English resources onto Chinese resources, our approach first translates Chinese reviews into English reviews by machine translation services, and then identifies the sentiment polarity of English reviews by directly leveraging English resources. Furthermore, our approach performs sentiment analysis for both Chinese reviews and English reviews, and then uses ensemble methods to combine the individual analysis results. Experimental results on a dataset of 886 Chinese product reviews demonstrate the effectiveness of the proposed approach. The individual analysis of the translated English reviews outperforms the individual analysis of the original Chinese reviews, and the combination of the individual analysis results further improves the performance.
A New Construction of Boolean Functions with Maximum Algebraic Immunity
Authors: Deshuai Dong, Shaojing Fu, Longjiang Qu, Chao Li
Venue: Proceedings of the 12th International Conference on Information Security (2009)

Because of the algebraic attacks, a high algebraic immunity is now an important criteria for Boolean functions used in stream ciphers. In this paper, we study the construction of Boolean functions with maximum algebraic immunity. We first present a new method to construct Boolean functions, in any number of variables, with maximum algebraic immunity(AI), and we also improve our algorithm to construct balanced functions with optimum algebraic immunity for any even number of variables. Furthermore, the enumeration and algebraic degree of the constructed Boolean functions are investigated.
Thematic Maps Service for GIS Based Urban Pipe Network Visualization System
Authors: Liutong Xu, Xiaoting Fu, Hao Lin, Yupeng Xiao, Juan Yang
Venue: Proceedings of the 2009 International Forum on Information Technology and Applications - Volume 01 (2009)

Urban pipe network pipelines are criss-crossing and have 3D (three-dimension) distribution. Plenty of attribute information and spatial data are involved. In order to display it in a more intuitive way, UPNVS (urban pipe network visualization system) is designed. The Thematic Maps service is a part of it. In this paper, we propose the Thematic Maps service, upload and edit data service, information attention service and 3D viewing service. While 3D display service concentrates on displaying simple map and unique value map. It implements the transit from 2D thematic maps to 3D and reflects the different property values of pipelines with different colors. This application enhances Thematic Maps service lively and visibility. Finally, we plug it to our UPNVS which can show the patterns and trends easily and provide the information for decision-making. At the same time, the results can also be applied to other visualization system and 3D thematic maps.
Gesture-Based Sharing of Documents in Face-to-Face Meetings
Authors: Alexander Loob, Christian Rathke
Venue: Proceedings of the 13th International Conference on Human-Computer Interaction. Part IV: Interacting in Various Application Domains (2009)

Many of the Electronic Meeting Systems on the market today only support sharing of electronic documents via email or a common user space. This kind of sharing enforces short work interruption and requires substantial mental effort than necessary. This contribution describes the development of a simple EMS, its shortcomings and the further development to a gesture-based EMS for sharing documents in face-to-face meetings. The system implements the concept of a "throwing" gesture for transferring documents to one or more participants. This gesture is explained and evaluated in further detail.
Computing word-pair antonymy
Authors: Saif Mohammad, Bonnie Dorr, Graeme Hirst
Venue: Proceedings of the Conference on Empirical Methods in Natural Language Processing (2008)

Knowing the degree of antonymy between words has widespread applications in natural language processing. Manually-created lexicons have limited coverage and do not include most semantically contrasting word pairs. We present a new automatic and empirical measure of antonymy that combines corpus statistics with the structure of a published thesaurus. The approach is evaluated on a set of closest-opposite questions, obtaining a precision of over 80%. Along the way, we discuss what humans consider antonymous and how antonymy manifests itself in utterances.
A fast Petrov-Galerkin method for solving the generalized airfoil equation
Authors: Haotao Cai
Venue: Journal of Complexity (2009)

In this paper we develop a fast Petrov-Galerkin method for solving the generalized airfoil equation using the Chebyshev polynomials. The conventional method for solving this equation leads to a linear system with a dense coefficient matrix. When the order of the linear system is large, the computational complexity for solving the corresponding linear system is huge. For this we propose the matrix truncation strategy, which compresses the dense coefficient matrix into a sparse matrix. We prove that the truncated method preserves the optimal order of the approximate solution for the conventional method. Moreover, we solve the truncated equation using the multilevel augmentation method. The computational complexity for solving this truncated linear system is estimated to be linear up to a logarithmic factor.
Privacy and perfect voyeurism
Authors: Tony Doyle
Venue: Ethics and Information Technology (2009)

I argue that there is nothing wrong with perfect voyeurism, covert watching or listening that is neither discovered nor publicized. After a brief discussion of privacy I present attempts from Stanley Benn, Daniel Nathan, and James Moor to show that the act is wrong. I argue that these authors fail to make their case. However, I maintain that, if detected or publicized, voyeurism can do grave harm and to that extent should be severely punished. I conclude with some thoughts on the stubborn intuition that perfect voyeurism is wrong despite the absence of harm.
Reusable Model-Based Testing
Authors: Erika Mir Olimpiew, Hassan Gomaa
Venue: Proceedings of the 11th International Conference on Software Reuse: Formal Foundations of Reuse and Domain Engineering (2009)

A reusable model-based testing method for software product lines (SPL) is used to create test specifications from use case and feature models, which can then be configured to test individual applications that are members of the SPL. This paper describes a feature-oriented model-based testing method for SPLs that can be used to reduce the number of reusable test specifications created to cover all use case scenarios, all features, and selected feature combinations of a SPL. These test specifications can be automatically selected and configured during feature-based test derivation to test a given application derived from the SPL. This paper also addresses what application configurations to test and how to configure test specifications for these applications. This model-based testing method was applied and evaluated on two SPL case studies.
A comparison of novel and state-of-the-art polynomial Bayesian network learning algorithms
Authors: Laura E. Brown, Ioannis Tsamardinos, Constantin F. Aliferis
Venue: Proceedings of the 20th national conference on Artificial intelligence - Volume 2 (2005)

Learning the most probable a posteriori Bayesian network from data has been shown to be an NP-Hard problem and typical state-of-the-art algorithms are exponential in the worst case. However, an important open problem in the field is to identify the least restrictive set of assumptions and corresponding algorithms under which learning the optimal network becomes polynomial. In this paper, we present a technique for learning the skeleton of a Bayesian network, called Polynomial Max-Min Skeleton (PMMS), and compare It with Three Phase Dependency Analysis, another state-of-the-art polynomial algorithm. This analysis considers both the theoretical and empirical differences between the two algorithms, and demonstrates PMMS's advantages in both respects. When extended with a greedy hill-climbing Bayesian-scoring search to orient the edges, the novel algorithm proved more time efficient, scalable, and accurate in quality of reconstruction than most state-of-the-art Bayesian network learning algorithms. The results show promise of the existence of polynomial algorithms that are provably correct under minimal distributional assumptions.
On-the-Fly Integration and Ad Hoc Querying of Life Sciences Databases Using LifeDB
Authors: Anupam Bhattacharjee, Aminul Islam, Mohammad Shafkat Amin, Shahriyar Hossain, Shazzad Hosain, Hasan Jamil, Leonard Lipovich
Venue: Proceedings of the 20th International Conference on Database and Expert Systems Applications (2009)

Data intensive applications in Life Sciences extensively use the hidden web as a platform for information sharing. Access to these heterogeneous hidden web resources is limited through the use of predefined web forms and interactive interfaces that users navigate manually, and assume responsibility for reconciling schema heterogeneity, extracting information and piping, transforming formats and so on in order to implement desired query sequences or scientific work flows. In this paper, we present a new data management system, called LifeDB, in which we offer support for currency without view materialization, and autonomous reconciliation of schema heterogeneity in one single platform through a declarative query language called BioFlow. In our approach, schema heterogeneity is resolved at run time by treating the hidden web resources as a virtual warehouses, and by supporting a set of primitives for data integration on-the-fly, extracting information and piping to other resources, and manipulating data in a way similar to traditional database systems to respond to application demands.
Evaluation of a Voice-Based Internet Browser with Untrained and Trained Users
Authors: Klaus-Peter Engelbrecht, Craig Wootton, Ina Wechsung, Sebastian Möller
Venue: Proceedings of the 5th International Conference on Universal Access in Human-Computer Interaction. Part III: Applications and Services (2009)

In our paper, we present evaluation results for VoiceBrowse, an interactive system allowing users to access content and services from the Internet via voice control. We compare two user groups, inexperienced and experienced computer users, regarding their performance and judgment of two versions of the system differing in the dialog initiative. Furthermore we investigate the usability of the systems after long-term usage (simulated by fifteen minutes practise). We find that even inexperienced computer users know from the beginning how to speak to the system, which contrasts assumptions in the related literature. Inexperienced uses perform as good as experienced users with both systems before and after the training. We also compare judgments of the systems before and after the training.
On Finding Small 2-Generating Sets
Authors: Isabelle Fagnot, Guillaume Fertin, Stéphane Vialette
Venue: Proceedings of the 15th Annual International Conference on Computing and Combinatorics (2009)

Given a set of positive integers S, we consider the problem of finding a minimum cardinality set of positive integers X (called a minimum 2-generating set of S) s.t. every element of S is an element of X or is the sum of two (non-necessarily distinct) elements of X. We give elementary properties of 2-generating sets and prove that finding a minimum cardinality 2-generating set is hard to approximate within ratio 1 + ¿ for any ¿> 0. We then prove our main result, which consists in a representation lemma for minimum cardinality 2-generating sets.
Danger Forecast of Tunnel in Excavation
Authors: Ling-qiang Yang, Jing Ma
Venue: Proceedings of the 2009 International Conference on Measuring Technology and Mechatronics Automation - Volume 03 (2009)

Based on the basic law of tunnel rock deformation and distant affection law of tunnel excavation, the method to judge tunnel rock stability according to the state of tunnel rock deformation velocity was put forward. If the deformation velocity changers less and less with the time, the deformation develop to stability. If the deformation velocity does not changer with the time, the tunnel rock locates on critical state or rheology state. If the deformation velocity equals to zero, the rock is stability. If the deformation velocity changers larger and larger with the time, the deformation state was sort into norm state and abnormal state. The abnormal state is very danger. Forecast must be put out in advance. H-K rheology modulus was used to simulate tunnel rock. The element finite method was used to simulate the processor of excavating the tunnel. A case study was show the method is right. The stability state and reinforced time was ascertained.
Design and Implementation of Distribution Network SCADA System Based on J2EE Framework
Authors: Zhao Qiang, Chen Danyan
Venue: Proceedings of the 2009 International Forum on Information Technology and Applications - Volume 01 (2009)

In this paper, the problems exposed by the third generation of SCADA (Supervisory Control And Data Acquisition) based on the C/S(Client/Server) mode are analyzed. Then, a new distribution network SCADA based on the four-tier architecture of J2EE platform is built. Because of poor information sharing and interoperability of CORBA (Common Object Request Broker Architecture) as the integration bus among application systems of power enterprises, the seamless integration between SCADA heterogeneous data platform which is based on standard IEC (International Electrical Commission) 61970, and other systems is achieved by means of Web services, and such integration is standard and open. The combination of EJB (Enterprise JavaBean) and Hibernate to implement the business logic and make data be persistent separately also makes the SCADA much more scalable and flexible. Because of its flexibility and extensibility, this new SCADA has great benefit to the automation course of electric power systems.
Clustering Based Automatic Refactorings Identification
Authors: Istvan Gergely Czibula, Gabriela Czibula
Venue: Proceedings of the 2008 10th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (2008)

The aim of this paper is to approach the problemof improving the design of an object oriented software system, by identifying the appropriate refactorings. It is well known that improving the quality of software systems design is an important issue during the evolution of object oriented software systems. This improvement can be achieved by refactoring the software system in order to improve its internal structure, but without altering the external behavior of the code. In this paper we introduce a hierarchical divisive clustering algorithm for automatic identification of refactorings that improve the internalstructure of a software system. We evaluate our approach using JHotDraw case study and a real software system, emphasizing its advantages in comparison with existing similar approaches.
A Novel Particle Swarm Optimization Method Using Clonal Selection Algorithm
Authors: Lu Hong
Venue: Proceedings of the 2009 International Conference on Measuring Technology and Mechatronics Automation - Volume 02 (2009)

Particle Swarm Optimization, a nature-inspired evolutionary algorithm, has been successful in solving a wide range of real-value optimization problems. However, little attempts have been made to extend it to discrete problems. In this paper, a new particle swarm optimization method based on the clonal selection algorithm is proposed to avoid premature convergence and guarantee the diversity of the population. The experimental results show that the new algorithm not only has great advantage of convergence property over clonal selection algorithm and PSO, but also can avoid the premature convergence problem effectively.
Numerical Modeling of the Environment Impact of Landfill Leachate Leakage on Groundwater Quality-A Field Application
Authors: Shao-gang Dong, Zhong-hua Tang, Bai-wei Liu, O. D. Orodu
Venue: Proceedings of the 2009 International Conference on Environmental Science and Information Application Technology - Volume 01 (2009)

There are more than 372 big uncontrolled landfill areas in China. Waste disposal facilities are mainly responsible for the gradual quality degradation of groundwater. This paper reports an integrated study undertaken to develop an environmental assessment of the uncontrolled sanitary landfill area of the city of Jiaxing, Zhejiang, China. The USGS modular 3D finite difference groundwater flow model (Mod- flow) and Modular 3D Finite Difference Mass Transport Model (MT3D) software were used to simulate groundwater flow and contaminant transport modeling. The results indicated that landfill leachate leakage has significant effect on groundwater quality.
Automating Termination Proofs for CHR
Authors: Paolo Pilozzi, Danny Schreye
Venue: Proceedings of the 25th International Conference on Logic Programming (2009)

We propose a constraint-based approach towards automated termination analysis of Constraint Handling Rules (CHR). Similar to such approaches for Logic Programming (LP), we define a symbolic level mapping on atoms of the program and express termination conditions using these. Then, we search for an assignment to the symbolic coefficients, validating the termination conditions. However, different from the approaches developed for LP, termination of CHR programs is concerned with multi-headed rules, while the existing constraint-based approaches in LP are developed for definite programs. These cannot be adapted directly to a multi-headed context. In the following we discuss a constraint-based approach for CHR programs and show how such an approach can be obtained by an elegant reuse of existing techniques in LP. We evaluate the approach, using our implementation, CHRisTA.
Using domain-configurable search control for probabilistic planning
Authors: Ugur Kuter, Dana Nau
Venue: Proceedings of the 20th national conference on Artificial intelligence - Volume 3 (2005)

We describe how to improve the performance of MDP planning algorithms by modifying them to use the search-control mechanisms of planners such as TLPlan, SHOP2, and TALplanner. In our experiments, modified versions of RTDP, LRTDP, and Value Iteration were exponentially faster than the original algorithms. On the largest problems the original algorithms could solve, the modified ones were about 10,000 times faster. On another set. of problems whose state spaces were more than 14,000 times larger than the original algorithms could solve, the modified algorithms took only about 1/3 second.
Eprescribing Initiatives and Knowledge Acquisition in Ambulatory Care
Authors: Ashley J. Benedict, Jesse C. Crosson, Akshatha Pandith, Robert Hannemann, Lynn A. Nuti, Vincent G. Duffy
Venue: Proceedings of the 2nd International Conference on Digital Human Modeling: Held as Part of HCI International 2009 (2009)

Electronic prescribing [eprescribing] is where prescriptions are generated through an automated data-entry process utilizing special software and a network linked to pharmacies. National and state initiatives are intended but are not yet very effective in educating and encouraging healthcare providers to use eprescribing. This study included interviews with 102 healthcare providers from 52 locations (California, Indiana, New Hampshire, and Ohio) to determine the providers' knowledge of eprescribing initiatives as well as how they acquired knowledge about these systems. Providers in New Hampshire had the most knowledge of eprescribing systems and their state initiative. Among nonusers, only two facilities were familiar with the national initiatives. Nonusers comprised 71% of the interviews. Eprescribing information was acquired through journals, conferences, pharmacies, other providers and in some cases when receiving care as a patient.
Learning to improve both efficiency and quality of planning
Authors: Tara A. Estlin, Raymond J. Mooney
Venue: Proceedings of the Fifteenth international joint conference on Artifical intelligence - Volume 2 (1997)

Most research in learning for planning has concentrated on efficiency gains. Another important goal is improving the quality of final plans. Learning to improve plan quality has been examined by a few researchers, however, little research has been done learning to improve both efficiency and quality. This paper explores this problem by using the SCOPE learning system to acquire control knowledge that improves on both of these metrics. Since SCOPE uses a very flexible training approach, we can easily focus its learning algorithm to prefer search paths that are better for particular evaluation metrics. Experimental results show that SCOPE can significantly improve both the quality of final plans and overall planning efficiency.
Multihop/Direct Forwarding (MDF) for static wireless sensor networks
Authors: Jing Deng
Venue: ACM Transactions on Sensor Networks (TOSN) (2009)

The success of Wireless Sensor Networks (WSNs) depends largely on efficient information delivery from target areas toward data sinks. The problem of data forwarding is complicated by the severe energy constraints of sensors in WSNs. In this work, we propose and analyze a data forwarding scheme, termed Multihop/Direct Forwarding (MDF), for WSNs where sensor nodes forward data traffic toward a common data sink. In the MDF scheme, a node splits outgoing traffic into at most two branches: one is sent to a node that is h units away; the other is sent directly to the data sink. The value of h is chosen to minimize the overall energy consumption of the network. The direct transmission is employed to balance the energy consumption of nodes at different locations and to avoid the so-called hot spot problem in data forwarding. In order to calculate its traffic splitting ratio, a node only needs to know the distance toward the common data sink and that of the farthest node. Our analytical and simulation results show that the MDF scheme performs close to, in terms of energy efficiency and network lifetime, the optimum data forwarding rules, which are more complex and computation intensive.