ppxscal/embedding_network huggingface dataset:
Transmembrane helix prediction in proteins using hydrophobicity properties and higher-order statistics
Authors: Ilias K. Kitsas, Leontios J. Hadjileontiadis, Stavros M. Panas
Venue: Computers in Biology and Medicine (2008)

Prediction of the transmembrane (TM) helices is important in the study of membrane proteins. A novel method to predict the location and length of both single and multiple TM helices in human proteins is presented. The proposed method is based on a combination of hydrophobicity and higher-order statistics, resulting in a TM prediction tool, namely K"4HTM. A training dataset of 117 human single TM proteins and two test-datasets containing 499 and 484 human single and multiple TM proteins, respectively, were drawn from the SWISS-PROT public database and used for the optimisation and evaluation of K"4HTM. Validation results showed that K"4HTM correctly predicts the entire topology for 99.68% and 93.08% of the sequences in the single and multiple test-datasets, respectively. These results compare favourably with existing methods, such as SPLIT4, TMHMM2, WAVETM and SOSUI, constituting an alternative approach to the TM helix prediction problem.
A Reconfigurable Charging Management Platform within the Adaptive Service Provisioning Architecture of NGN
Authors: Hao Zhu, Zhengkun Mi, Rongqun Peng
Venue: Proceedings of the Fourth International Conference on Networking and Services (2008)

Adaptive charging architecture and mechanism is a hot research arena for Next Generation Service Network (NGSN). In this paper a new reconfigurable charging management platform is proposed to support adaptive charging rule generation and modification as well as reconfiguration of charging related network elements according to the static subscription charging agreement and dynamic charging information provided during the service session. The platform is a part of the Adaptive Service Provisioning Architecture (ASPA).
Gene Expression Studies with DGL Global Optimization for the Molecular Classification of Colon Cancer
Authors: Dongguang Li
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

The study attempts to analyze multiple sets of genes simultaneously, for an overall global solution to the gene’s joint discriminative ability in assigning tumors to known classes. With the workable concepts and methodologies described here an accurate classification of the type and seriousness of cancer can be made.The colon cancer microarray data can be classified 100% correctly without previous knowledge of their classes. The classification processes are automated after the gene expression data being inputted. Instead of examining a single gene at a time, the DGL method can find the global optimum solutions and construct a multi-subsets pyramidal hierarchy class predictor containing up to 23 gene subsets based on a given microarray gene expression data collection within a period of several hours. An automatically derived class predictor makes the reliable cancer classification and accurate tumor diagnosis in clinical practice possible.
On totally multicolored stars
Authors: Juan José Montellano-Ballesteros
Venue: Journal of Graph Theory (2006)

Given an edge-coloring of a graph G, a subgraph M of G will be called totally multicolored if no two edges of M receive the same color. Let h(G, K1,q) be the minimum integer such that every edge-coloring of G using exactly h(G, K1,q) colors produces at least one totally multicolored copy of K1,q (the q-star) in G. In this article, an upper bound of h(G, K1,q) is presented, as well as some applications of this upper bound. &copy; 2005 Wiley Periodicals, Inc.
Progressing problems from requirements to specifications in problem frames
Authors: Zhi Li
Venue: Proceedings of the 3rd international workshop on Applications and advances of problem frames (2008)

One of the problems with current practice in software development is that customer requirements are often not well captured, understood and analysed, and there is no clear traceable path from customer requirements to software specifications. This often leads to a mismatch between what the customer needs and what the software developer understands the customer needs. In addition to capturing, understanding and analysing requirements, requirements engineering (RE) aims to provide methods to allow software development practitioners to derive software specifications from requirements. Although work exists towards this aim, the systematic derivation of specifications from requirements remains an open problem. This paper provides a practical technique to implement the idea of problem progression as the basis for transforming requirements into specifications. The technique allows us to progress a software problem towards identifying its solution by carefully investigating the problem context and re-expressing the requirement statement until a specification is reached.
A New Approach for Bacillus Colonies Recognition: Application of Intuitionistic Fuzzy Sets Theory
Authors: Hoda Davarzani
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

This paper proposes a new approach for medical diagnosis based on laboratory empirical data using fuzzy set theory. The presented approach is based on intuitionistic fuzzy set (IFSs) theory as a special kind of fuzzy set using two new distance measures between intuitionistic fuzzy sets as a tool in pattern recognition. We will apply them in a part of progress of medical diagnosis in order to recognize bacillus colonies and then we compare its results with similar measures in regular fuzzy. Numerical results show that the proposed measures are more applicable in medical diagnosis than the similar measures in regular fuzzy ones.
Historical Perspective on Scan Compression
Authors: Rohit Kapur, Subhasish Mitra, Thomas W. Williams
Venue: IEEE Design Test (2008)

Since gaining popularity in the late 1990s, the term "scan compression" has maintained a solid hold within the IC test lexicon. In recent years, however, this technology has taken the test industry by storm. As the cost of test increased to previously unseen heights, some companies complained that the cost to test a single transistor was nearly equal to the cost of manufacturing it. Scan compression technology, however, proved to be a powerful antidote to this problem, as it catalyzed reductions in test data volume and test application time of up to 100x. As a result, the cost of test may well be contained for many years to come. This article sketches a brief history of test technology research that has led to the stunning success of scan compression. This article is not intended to attribute inventors for innovations on a fine-grained timeline. The important concepts of technologies are presented at the high level on a coarse timeline.
Bubble rap: social-based forwarding in delay tolerant networks
Authors: Pan Hui, Jon Crowcroft, Eiko Yoneki
Venue: Proceedings of the 9th ACM international symposium on Mobile ad hoc networking and computing (2008)

In this paper we seek to improve our understanding of human mobility in terms of social structures, and to use these structures in the design of forwarding algorithms for Pocket Switched Networks (PSNs). Taking human mobility traces from the real world, we discover that human interaction is heterogeneous both in terms of hubs (popular individuals) and groups or communities. We propose a social based forwarding algorithm, BUBBLE, which is shown empirically to improve the forwarding efficiency significantly compared to oblivious forwarding schemes and to PROPHET algorithm. We also show how this algorithm can be implemented in a distributed way, which demonstrates that it is applicable in the decentralised environment of PSNs.
Decision's problem with the help of imprecise data envelopment analysis (IDEA)
Authors: D. V. Derpanis, E. Foundas
Venue: Proceedings of the 9th WSEAS International Conference on Systems (2005)

The standard data envelopment analysis (DEA) method requires that the values for all inputs and outputs be known exactly. When some inputs and outputs are unknown decision variables such as bounded data, original data, and ratio bounded data, the DEA model becomes a non-linear programming problem and is called imprecise DEA (IDEA). In this study we aim to develop further the IDEA by using a kind of punishment-penalty in the DMUs (Decision Making Units) which try on their own to weight the surges and the flows in order to elect in the major degree their efficiency. This is attempted in order to avoid the fact that the record of an efficient unit is arguable.
Automatic symbolic compositional verification by learning assumptions
Authors: Wonhong Nam, P. Madhusudan, Rajeev Alur
Venue: Formal Methods in System Design (2008)

Compositional reasoning aims to improve scalability of verification tools by reducing the original verification task into subproblems. The simplification is typically based on assume-guarantee reasoning principles, and requires user guidance to identify appropriate assumptions for components. In this paper, we propose a fully automated approach to compositional reasoning that consists of automated decomposition using a hypergraph partitioning algorithm for balanced clustering of variables, and discovering assumptions using the L * algorithm for active learning of regular languages. We present a symbolic implementation of the learning algorithm, and incorporate it in the model checker NuSmv. In some cases, our experiments demonstrate significant savings in the computational requirements of symbolic model checking.
Local: a model geared towards ubiquitous learning
Authors: Jorge Barbosa, Rodrigo Hahn, Solon Rabello, Débora Barbosa
Venue: Proceedings of the 39th SIGCSE technical symposium on Computer science education (2008)

The increasing use of mobile devices and the dissemination of wireless networks have stimulated mobile and ubiquitous computing research. In this context, education is being considered one of the main application areas. New pedagogical opportunities are created through the use of location systems to track learners, and through context awareness support. This paper proposes a model to explore these opportunities using location information and context management as learning support tools. This model, called LOCAL, was conceived for small scale learning environments, but can be applied in large-scale as well. The model was implemented and the initial results show its utility to assist the teaching and learning processes.
Re-engineering Xen internals for higher-assurance security
Authors: J. McDermott, J. Kirby, B. Montrose, T. Johnson, M. Kang
Venue: Information Security Tech. Report (2008)

The Xenon project is investigating the construction of a higher-assurance open source separation kernel based on the Xen open source hypervisor. Just as the Xen open source hypervisor was initially developed from the open source Linux operating system, by simplifying Linux and modifying its design, the Xenon separation kernel is being developed from Xen. The primary goal of the Xenon project is to investigate issues in creating an open source software product with higher security assurance than conventional open source software. The Xenon project is also focused on (1) problems relating to separation kernels that support unmodified uninterpreted commercial off the shelf (COTS) guests and (2) distinctions between these kinds of separation kernels and hypervisors. This paper explains the Xenon project's approach to re-engineering Xen's internal structure into a higher-assurance form. If conventional open source software cannot be brought into this form with moderate amounts of re-engineering then higher-assurance open source software is probably not practical. Our results indicate that moderate amounts of re-engineering will be sufficient for all but a small part of the code. The remaining code is small enough to be addressed in a reasonable time, even though more effort is required.
An ontology-based planning system for e-course generation
Authors: E. Kontopoulos, D. Vrakas, F. Kokkoras, N. Bassiliades, I. Vlahavas
Venue: Expert Systems with Applications: An International Journal (2008)

Researchers in the area of educational software have always shown great interest in the automatic synthesis of learning curricula. During the recent years, with the extensive use of metadata and the emergence of the Semantic Web, this vision is gradually turning into a reality. A number of systems for curricula synthesis have been proposed. These systems are based on strong relations defined in the metadata of learning objects, which allow them to be combined with other learning objects, in order to form a complete educational program. This article presents PASER, a system for automatically synthesizing curricula using AI Planning and Semantic Web technologies. The use of classical planning techniques allows the system to dynamically construct learning paths even from disjoint learning objects, meeting the learner's profile, preferences, needs and abilities.
Proximity-preserving labeling schemes
Authors: David Peleg
Venue: Journal of Graph Theory (2000)

This article considers informative labeling schemes for graphs. Specifically, the question introduced is whether it is possible to label the vertices of a graph with short labels in such a way that the distance between any two vertices can be inferred from inspecting their labels. A labeling scheme enjoying this property is termed a proximity-preserving labeling scheme. It is shown that, for the class of n-vertex weighted trees with M-bit edge weights, there exists such a proximity-preserving labeling scheme using O(M log n + log2n) bit labels. For the family of all n-vertex unweighted graphs, a labeling scheme is proposed that using O(log2 n &middot; &kappa; &middot; n1-&kappa;) bit labels can provide approximate estimates to the distance, which are accurate up to a factor of $\sqrt{8\kappa }.$ In particular, using O(log3n) bit labels, the scheme can provide estimates accurate up to a factor of $\sqrt{2 \log n}$. (For weighted graphs, one of the log n factors in the label size is replaced by a factor logarithmic in the network's diameter.) &copy; 2000 John Wiley & Sons, Inc. J Graph Theory 33: 167&ndash;176, 2000
Solvability of nonlocal boundary value problems for ordinary differential equation of higher order with a p-Laplacian
Authors: Huihui Pang, Weigao Ge, Min Tian
Venue: Computers Mathematics with Applications (2008)

Nonlocal boundary value problems at resonance for a higher order nonlinear differential equation with a p-Laplacian are considered in this paper. By using a new continuation theorem, some existence results are obtained for such boundary value problems. An explicit example is also given in this paper to illustrate the main results.
A Modal Logic for Pawlak's Approximation Spaces with Rough Cardinality n
Authors: Philippe Balbiani, Petar Iliev, Dimiter Vakarelov
Venue: Fundamenta Informaticae (2008)

The natural modal logic corresponding to Pawlak's approximation spaces is S5, based on the box modality [R]A (and the diamond modality )R*A=&not;[R]&not;A), where R is the corresponding indiscernibility relation of the approximation space S=(W,R). However the expressive power of S5 is too weak and, for instance, we cannot express that the space S has exactly n equivalence classes (we say that S is roughly-finite and n is the rough cardinality of S). For this reason we extend the modal logic S5 with a new box modality [S]A, where S is the complement of R i.e. the discernibility relation of W. We propose a complete axiomatization, in this new language, of the logic ROUGHn corresponding to the class of approximation spaces with rough cardinality n. We prove that the satisfiability problem for ROUGHn is NP-complete.
Direct Al-Al contact using low temperature wafer bonding for integrating MEMS and CMOS devices
Authors: H. Lin, J. T. M. Stevenson, A. M. Gundlach, C. C. Dunare, A. J. Walton
Venue: Microelectronic Engineering (2008)

This paper investigates the feasibility of direct Al-Al contact using low temperature wafer bonding process for the integration of MEMS and CMOS devices. Sufficient mechanical strength oxide-oxide bonds can be achieved using an oxygen plasma assisted low temperature wafer bonding process, with Al structures present on the bonding surface. An average contact resistance of 2.6x10^-^8@Wcm^2 was measured from single contact test structures, indicating that the establishment of direct Al-Al interconnect during the bond anneal step is possible.
Propagation of positional measurement errors to agricultural field boundaries and associated costs
Authors: S. de Bruin, G. B. M. Heuvelink, J. D. Brown
Venue: Computers and Electronics in Agriculture (2008)

It has been argued that the upcoming targeted approach to managing field operations, or precision farming, requires that field boundaries are measured with cm level accuracy, thus avoiding losses such as wasted inputs, unharvested crops and inefficient use of the land. This paper demonstrates a method for verification of such claims, based on a statistical model that accounts for temporal correlation in positional measurement errors. Our implementation employs the Data Uncertainty Engine (DUE), which is free software that aids the user in defining probability distributions for uncertain spatial objects, and draws random samples from these distributions. A case study concerning the financial consequences of uncertain geometry for a farmer who uses a digital map to optimise field operations for 15ha of a potato crop is presented. The error model was parameterised on measurement scenarios representing (1) the Dutch registry of agricultural fields; (2) differential GPS-based field checks for verification of area declarations; and (3) special purpose Real Time Kinematic (RTK)-GPS surveys. We found that a farmer who has a manually digitised map of the study area would benefit from a RTK-GPS survey in a single crop year if the survey would cost less than @? 442. An independent test case showed that the results of the error model were consistent with field data.
Service-Oriented Integration of Systems for Military Capability
Authors: Duncan Russell, Nik Looker, Lu Liu, Jie Xu
Venue: Proceedings of the 2008 11th IEEE Symposium on Object Oriented Real-Time Distributed Computing (2008)

Service oriented architecture (SOA) is becoming established in computing as a means to integrate processing and data across organisations. This paper proposes that system-level integration can benefit from service oriented architectural descriptions and loose coupling between the problem domain requirements and different system solutions. The problem domain is exemplified as military capability, from the UK Ministry of Defence (MoD), in particular, Network Enabled Capability (NEC). Representations of military capability in the problem domain can be described in terms of processes. The processes are sequences of functions that can be described as services. Then different types of system solutions can implement the described services. Firstly, the paper presents an overview of conceptual SOA and in the context of military capability compares three levels of service integration: business services, systems services and computing services. Secondly, the paper presents a framework for evaluating the performance and effectiveness of service integration to compare different solutions in delivering military capability.
Relative Power Percentage and Time-Power Percentages Map Analysis of Electrogastrogram Slow Waves
Authors: Peng Cheng, Ye Datian
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 02 (2008)

In conventional analysis of electrogastrogram (EGG), the time percentage of normal slow waves is used to assess the regularity of the slow waves. A new parameter termed relative power percentage of normal slow waves is proposed in this paper to assess the regularity of slow waves from the view of power. Furthermore, the time and relative power percentage are conjoined in the Time-Power percentage map to analysis EGG slow waves. The new method is applied in the study of acupuncture regulation gastric function, and the result shows that both duration and amplitude are regulated under and after electroacupuncture. That may give illumination to mechanism study of acupuncture.
Development of a guideline-based decision support system with explanation facilities for outpatient therapy
Authors: Rick Goud, Arie Hasman, Niels Peek
Venue: Computer Methods and Programs in Biomedicine (2008)

For effective guideline implementation it is recommended to develop and apply carefully designed implementation strategies and instruments. Computerized decision support systems (CDSSs) are such instruments as they can improve guideline adherence by providing advice at the point of care. To improve the implementation of the Dutch cardiac rehabilitation guidelines a CDSS, named CARDSS, was developed. CARDSS actively provides care professionals with patient-specific, guideline-based treatment recommendations at the onset of a patient's rehabilitation trajectory. To maximize the chances of acceptance, CARDSS also provides explanation facilities and other additional information management services, and takes the working procedures specific to multidisciplinary outpatient care into account. CARDSS is currently used in over 40 Dutch cardiac rehabilitation outpatient clinics. This paper describes the development of the CARDSS system. In particular, technical issues are discussed concerning the delivery of active decision support, and the provision of advice rationales to users while taking account of dynamic clinical contexts and changing guidelines.
A Method for Evaluating Quality of Clustering DNA Fragments Encoded in Different Nucleotide Frequencies
Authors: Chon-Kit Kenneth Chan, Arthur L. Hsu, Sen-Lin Tang, Saman K. Halgamuge
Venue: Proceedings of the 2007 Frontiers in the Convergence of Bioscience and Information Technologies (2007)

The whole-genome shotgun sequencing technique has been successfully applied to environmental genomes. However, a considerable amount of DNA sequences and small contigs remain generally unassembled after the shotgun sequencing. Binning is a step of grouping these sequences based on some biological and molecular features. The combination of oligonucleotide frequency and Self-Organising Maps (SOM) clustering algorithm shows high potential as a compositional binning tool. As the previous work did not provide methods for assessing results, we proposed a systematic quantitative method to evaluate the clustering results specifically for this type of application. We used this method to investigate the suitability of each of di, tri, tetra and pentanucleotide frequencies as training feature for this binning technique. The results show that dinucleotide frequency is unable to bin 10kb DNA sequence fragments into well-clustered species groups. Furthermore, we noticed that increasing order of oligonucleotide frequency may deteriorate the assignment of DNA sequences to classes in our test, which indicates the possible existence of optimal species-specific oligonucleotide frequency. Results suggest that using trinucleotide frequency for the combination of oligonucleotide frequency and SOM as a binning process gives sufficiently good clustering quality in this case.