ppxscal/embedding_network huggingface dataset:
A note on the false discovery rate and inconsistent comparisons between experiments
Authors: Roger Higdon, Gerald van Belle, Eugene Kolker
Venue: Bioinformatics (2008)

Motivation: The false discovery rate (FDR) has been widely adopted to address the multiple comparisons issue in high-throughput experiments such as microarray gene-expression studies. However, while the FDR is quite useful as an approach to limit false discoveries within a single experiment, like other multiple comparison corrections it may be an inappropriate way to compare results across experiments. This article uses several examples based on gene-expression data to demonstrate the potential misinterpretations that can arise from using FDR to compare across experiments. Researchers should be aware of these pitfalls and wary of using FDR to compare experimental results. FDR should be augmented with other measures such as p-values and expression ratios. It is worth including standard error and variance information for meta-analyses and, if possible, the raw data for re-analyses. This is especially important for high-throughput studies because data are often re-used for different objectives, including comparing common elements across many experiments. No single error rate or data summary may be appropriate for all of the different objectives. Contact: Eugene.Kolker@seattlechildrens.org
Computing three-dimensional two-phase flows with a mass-conserving level set method
Authors: S. P. van der Pijl, A. Segal, C. Vuik, P. Wesseling
Venue: Computing and Visualization in Science (2008)

A method is described to compute three- dimensional two-phase flow, allowing large density ratios and coalescence and break-up of bubbles. The level set method is used to describe interfaces, and the volume-of-fluid method is used to ensure mass conservation. Efficiency in computing the interface dynamics is achieved by using a functional relation between the level set and volume-of-fluid functions. Difficulties and remedies in re-initialization of the level set function and inaccurate compution of surface tension are discussed. Test cases for validation are described, and demanding two-bubble computations to show the generality and the versatility of the method are presented.
Service-oriented approach to collaborative visualization
Authors: H. Wang, K. W. Brodlie, J. W. Handley, J. D. Wood
Venue: Concurrency and Computation: Practice Experience (2008)

This paper presents a new service-oriented approach to the design and implementation of visualization systems in a Grid computing environment. The approach evolves the traditional dataflow visualization system, based on processes communicating via shared memory or sockets, into an environment in which visualization Web services can be linked in a pipeline using the subscription and notification services available in Globus Toolkit 4. A specific aim of our design is to support collaborative visualization, allowing a geographically distributed research team to work collaboratively on visual analysis of data. A key feature of the system is the use of a formal description of the visualization pipeline, using the skML language first developed in the gViz e-Science project. This description is shared by all collaborators in a session. In co-operation with the e-Viz project, we generate user interfaces for the visualization services automatically from the skML description. The new system is called notification-service-based collaborative visualization. A simple prototype has been built and is used to illustrate the concepts. Copyright &copy; 2008 John Wiley & Sons, Ltd.
Bayesian modeling of continuously marked spatial point patterns
Authors: Matthew A. Bognar
Venue: Computational Statistics (2008)

Many analyses of continuously marked spatial point patterns assume that the density of points, with differing marks, is identical. However, as noted in the seminal paper of Goulard et al. (Scand J Stat 23:365---379, 1996), such an assumption is not realistic in many situations. For example, a stand of forest may have many more small trees than large, hence the model should allow for a higher density of points with small marks. In addition, as suggested by Ogata and Tanemura (Biometrics 41:421---433, 1985), the interaction between points should be a function of their mark, allowing, for example, the range of interaction for large trees to exceed that of smaller trees. The aforementioned articles use frequentist inferential techniques, but interval estimation presents difficulties due to the extremely complex distributional properties of the estimates; it might be possible, however, to use parametric bootstrap methodology for such inferences (Baddeley et al. in J Roy Stat Soc Ser B 67:617---666, 2005). We suggest the use of Bayesian inferential techniques. Although a Bayesian approach requires a complex, computational implementation of (reversible jump) Markov Chain Monte Carlo methodology, it enables a wide variety of inferences (including interval estimation). We demonstrate our approach by analyzing the well known Norway spruce dataset.
A More Robust Method for Multi-modality Medical Image Registration
Authors: Wang Kai, Tang Jing-tian, Xiao Jia-ying, Tang Yan, Xiao-kai Zhang
Venue: Proceedings of the 2008 International Conference on BioMedical Engineering and Informatics - Volume 01 (2008)

Radiological images are increasingly being used inhealthcare and medical research. There is, consequently, widespread interest in accurately relating information in the different images for diagnosis, treatment and basic science. The objective of registration process is to obtain a spatial transformation of a floating image to a reference image by which a similarity measure is optimized between the two images. In order to speed up the registration process and avoid local minimum, pre-alignment and Regional Mutual Information has been introduced before. Various strategies of optimization have been tested. And we select bilinear interpolation for all the tests so that the results can be well compared. Experimental results involving clinical images of CT, MR and PET in the brain or chest are presented for rigid registration. Registration with PAX provides well initial transform parameters for the optimizer. And take precision and time into account, Powell optimization is more excellent than others for registration based on RMI.
Schur positivity of skew Schur function differences and applications to ribbons and Schubert classes
Authors: Ronald C. King, Trevor A. Welsh, Stephanie J. Willigenburg
Venue: Journal of Algebraic Combinatorics: An International Journal (2008)

Some new relations on skew Schur function differences are established both combinatorially using Schützenberger's jeu de taquin, and algebraically using Jacobi-Trudi determinants. These relations lead to the conclusion that certain differences of skew Schur functions are Schur positive. Applying these results to a basis of symmetric functions involving ribbon Schur functions confirms the validity of a Schur positivity conjecture due to McNamara. A further application reveals that certain differences of products of Schubert classes are Schubert positive.
Average degree and contractibility
Authors: Matthias Kriesell
Venue: Journal of Graph Theory (2006)

It is proved that for every number k there exists a number f(k) such that every finite k-connected graph of average degree exceeding f(k) contains an edge whose contraction yields again a k-connected graph. For the proof, tree orders on certain sets of smallest separating sets of the graph in question are constructed. This leads to new canonical tree decompositions as well. &copy; 2005 Wiley Periodicals, Inc. J Graph Theory
Error estimates of proper orthogonal decomposition eigenvectors and Galerkin projection for a general dynamical system arising in fluid models
Authors: Pedro Gal&#x00e1;n del Sastre, Rodolfo Bermejo
Venue: Numerische Mathematik (2008)

We study estimates for proper orthogonal decomposition eigenvectors and eigenvalues as well as error estimates between the exact solution of a 2D Navier&#x2013;Stokes model and the numerical approach when the proper orthogonal decomposition method is considered. These estimates are also extended when bifurcation diagram are calculated using the so called p-POD or SPOD methods with a new cut-off criterion to minimize noisy modes produced by the p-POD method.
Coronavirus phylogeny based on Base-Base Correlation
Authors: Zhi-Hua Liu, Xiao Sun
Venue: International Journal of Bioinformatics Research and Applications (2008)

With more and more complete genome sequences having been released, phylogenetic analysis is entering a new era that of phylogenomics. In this paper, a novel phylogenomic method, named as Base-Base Correlation (BBC), has been proposed to infer phylogenetic relationships from complete genomes, with particular emphasis on coronavirus phylogeny. Following the high-profile publicity of SARS outbreaks, a renewed interest in coronavirus has been promoted and two novel human coronaviruses (NL63 and HKU1) have been identified. Coronavirus phylogenomics based on BBC is well consistent with that of previous studies. BBC, to study genome information structure based on information theory, provides a novel alignment-free phylogenomic methodology in postgenome informatics.
Design and Implementation of a Simulation Framework for the ARM Embedded System
Authors: Han Wan, Xiaopeng Gao, Libo Deng, Ting Yu
Venue: Proceedings of the Tenth International Conference on Computer Modeling and Simulation (2008)

This paper proposes a basic ARM full system simulation framework, a novel approach to understanding the behavior of modern embedded systems. Our simulation framework implements the kernel architecture of the ARM ISA, on which one can run and debug system or user-level programs. It has flexible software architecture, and good encapsulation of the communication between virtual peripherals and host peripherals. On the other hand, we implement a remote debugging system based on our simulation kernel, which extends remote serial protocol (RSP) of GDB and using Eclipse as the front-UI to build a platform-independent system. Since the simulation kernel has the full control of the target programs, the debugging system provides a flexible mechanism to collect the simulation information. These allowed people use or extend it to build a new ARM development environment, in order to study the embedded systems or help investigating the embedded operating system and low-level software.
Development and application of a diaphragm micro-pump with piezoelectric device
Authors: H. K. Ma, B. R. Hou, H. Y. Wu, C. Y. Lin, J. J. Gao, M. C. Kou
Venue: Microsystem Technologies (2008)

In this study, a new type of thin, compact, and light weighed diaphragm micro-pump has been successfully developed to actuate liquid by the vibration of a diaphragm. The micro-diaphragm pump with two valves is fabricated in an aluminum case by using highly accurate CNC machine, and the cross-section dimension is 28&#x00a0;mm&#x00a0;&#x00d7;&#x00a0;5&#x00a0;mm. Both valves and diaphragm are manufactured from PDMS. The amplitude of vibration by a piezoelectric device produces an oscillating flow and alters the chamber volume by the curvature change of a diaphragm. Several experimental set-ups for performance tests in a single micro-diaphragm pump, isothermal flow open system, and a closed liquid cooling system are designed and implemented. The performance of a one-side actuating micro-diaphragm pump is affected by the design of check valves, diaphragm, piezoelectric device, chamber volume, input voltage and frequency. The measured maximum flow rate of present design is 72&#x00a0;ml/min at zero total pump head in the range of operation frequency 70&#x2013;180&#x00a0;Hz.
Answering aggregate queries in data exchange
Authors: Foto Afrati, Phokion G. Kolaitis
Venue: Proceedings of the twenty-seventh ACM SIGMOD-SIGACT-SIGART symposium on Principles of database systems (2008)

Data exchange, also known as data translation, has been extensively investigated in recent years. One main direction of research has focused on the semantics and the complexity of answering first-order queries in the context of data exchange between relational schemas. In this paper, we initiate a systematic investigation of the semantics and the complexity of aggregate queries in data exchange, and make a number of conceptual and technical contributions. Data exchange is a context in which incomplete information arises, hence one has to cope with a set of possible worlds, instead of a single database. Three different sets of possible worlds have been explored in the study of the certain answers of first-order queries in data exchange: the set of possible worlds of all solutions, the set of possible worlds of all universal solutions, and a set of possible worlds derived from the CWA-solutions. We examine each of these sets and point out that none of them is suitable for aggregation in data exchange, as each gives rise to rather trivial semantics. Our analysis also reveals that, to have meaningful semantics for aggregation in data exchange, a strict closed world assumption has to be adopted in selecting the set of possible worlds. For this, we introduce and study the set of the endomorphic images of the canonical universal solution as a set of possible worlds for aggregation in data exchange. Our main technical result is that for schema mappings specified by source-to-target tgds, there are polynomial-time algorithms for computing the range semantics of every scalar aggregation query, where the range semantics of an aggregate query is the greatest lower bound and the least upper bound of the values that the query takes over the set of possible worlds. Among these algorithms, the more sophisticated one is the algorithm for the average operator, which makes use of concepts originally introduced in the study of the core of the universal solutions in data exchange. We also show that if, instead of range semantics, we consider possible answer semantics, then it is an NP-complete problem to tell if a number is a possible answer of a given scalar aggregation query with the average operator.
On the Automated Creation of Understandable Positive Security Models for Web Applications
Authors: Christian Bockermann, Ingo Mierswa, Katharina Morik
Venue: Proceedings of the 2008 Sixth Annual IEEE International Conference on Pervasive Computing and Communications (2008)

Web applications pose new security-related challengessince attacks on web applications strongly differ from thoseon client-server applications. Traditional network-basedﬁrewall systems offer no protection against this kind of at-tacks since they occur on the application-level. The cur-rent solution is the manual deﬁnition of large sets of ﬁlter-ing rules which should prevent malicious attempts from be-ing successful. We propose a new framework which shouldavoid this tedious work. The basic idea is the deﬁnition of adescription language for positive security models taking theparticularities of web applications into account. We thenpresent adaptive techniques which employ this descriptionlanguage in order to describe the valid communication toa given web application. The simplicity of the descriptionlanguage allows the easy identiﬁcation of unintentionallyincorporated vulnerabilities. Experiments for several real-world web applications demonstrate the usefulness of theproposed approach.
Compensated analog link for high power test
Authors: Jose Velazquez, Julio Montero, Raul Garduño, Trinidad Aguilar
Venue: Proceedings of the 2nd WSEAS International Conference on Circuits, Systems, Signal and Telecommunications (2008)

This paper introduces an analog fiber optic communication system for transporting signals in a high power Laboratory. Basically, the process involves converting the test signals in the range of KV and KA in to signals ranging from 200 mV to 200 V, after this these signals are modulated and finally they are transmitted by a fiber optic transceiver from the testing zone to an analog receiver located at a control room. However, several potential error sources should be minimized, among them there is dc shifting and gain variation due to temperature influence along the testing zone. Electronics and software techniques are used to reduce errors in conditioning and transmission of signals. Performances of the fiber optic transceiver were tested in bandwidth, temperature, linearity and signal to noise ratio responses; the result of using diferent compensation techniques showed remarkable improvements to performance of this fiber optic transceiver. The transmission media is optical fiber to ensure signal integrity, avoiding distortion due to EMI caused by the large currents and voltages during tests.
Public key superstructure "it's PKI Jim, but not as we know it!"
Authors: Stephen Wilson
Venue: Proceedings of the 7th symposium on Identity and trust on the Internet (2008)

While PKI has had its difficulties (like most new technologies) the unique value of public key authentication in paperless transactions is now widely acknowledged. The na&iuml;ve early vision of a single all-purpose identity system has given way to a more sophisticated landscape of multiple PKIs, used not for managing identity per se, but rather more subtle memberships, credentials and so on. It is well known that PKI's successes have mostly been in closed schemes. Until now, this fact was often regarded as a compromise; many held out hope that a bigger general purpose PKI would still eventuate. But I argue that the dominance of closed PKI over open is better understood as reflecting the reality of identity plurality, which independently is becoming the norm through the Laws of Identity and related frameworks. This paper introduces the term "Public Key Superstructure" to describe a new way to knit together existing mature PKI components to improve the utility and practicality of digital certificates. The "superstructure" draws on useful precedents in the security printing industry for manufacturing specialized security goods without complicated or un-natural liabilities, and inter-national accreditation arrangements for achieving cross-border recognition of certificates. The model rests on a crucial re-imagining of certificates as standing for relationships rather than identities. This elegant re-interpretation of otherwise standard elements could truly be a paradigm shift for PKI, for it grounds certificates in familiar, even mundane management processes. It will bring profound yet easily realized benefits for liability, cost, interoperability, scalability, accreditation, and governance.
Towards usage-based impact metrics: first results from the mesur project.
Authors: Johan Bollen, Herbert Van de Sompel, Marko A. Rodriguez
Venue: Proceedings of the 8th ACM/IEEE-CS joint conference on Digital libraries (2008)

Scholarly usage data holds the potential to be used as a tool to study the dynamics of scholarship in real time, and to form the basis for the definition of novel metrics of scholarly impact. However, the formal groundwork to reliably and validly exploit usage data is lacking, and the exact nature, meaning and applicability of usage-based metrics is poorly understood. The MESUR project funded by the Andrew W. Mellon Foundation constitutes a systematic effort to define, validate and cross-validate a range of usage-based metrics of scholarly impact. MESUR has collected nearly 1 billion usage events as well as all associated bibliographic and citation data from significant publishers, aggregators and institutional consortia to construct a large-scale usage data reference set. This paper describes some major challenges related to aggregating and processing usage data, and discusses preliminary results obtained from analyzing the MESUR reference data set. The results confirm the intrinsic value of scholarly usage data, and support the feasibility of reliable and valid usage-based metrics of scholarly impact.
Overview of the INEX 2007 Book Search track: BookSearch '07
Authors: Gabriella Kazai, Antoine Doucet
Venue: ACM SIGIR Forum (2008)

This paper provides an overview of the newly launched Book Search Track at INEX 2007 (BookSearch '07), its participants, tasks, book corpus, test topics and relevance assessments, as well as some results.
Dynamically stable optical solitons
Authors: Anjan Biswas
Venue: Proceedings of the 5th WSEAS International Conference on Applied Mathematics (2004)

The existence of a dynamically stable solition in optical fibers is established by virtue of the multiple scale perturbation technique applied in a new way to the perturbed Nonlinear Schrödinger's equation. We show that, by introducing a proper definition of the phase of the solition, one can obtain the corrections to the pulse where the standard soltion perturbation approach fails.
Constructing a system for measuring brain wave
Authors: Hsieh-Hua Yang, Jui-Chen Yu, Hung-Jen Yang, Hsiao-Chih Lin
Venue: Proceedings of the 5th WSEAS International Conference on Circuits, Systems, Electronics, Control & Signal Processing (2006)

In medical treatment, electro-encephalogram (EEG) is used to diagnose the pathological change of human body and reveal the state of mind. The brain wave machines used in medical treatment belong to the system of multi channels and they are too expansive to obtain. The purpose of the thesis is to design a set of analytical system with eight channels for the general physiological examining. The main structure of the system is based on LabVIEW operation, including pre-amplifier, systematic examining procedure of brain wave. The measurement data was recorded by data acquisition card. It recorded the instantaneous frequency and amplitude for analyzing mainly. The later section of the article focused on the usability of the self-developed brain wave machine. We achieved the testing affairs by measuring the electro-encephalogram of 14 normal persons.
Configuration-aware regression testing: an empirical study of sampling and prioritization
Authors: Xiao Qu, Myra B. Cohen, Gregg Rothermel
Venue: Proceedings of the 2008 international symposium on Software testing and analysis (2008)

Configurable software lets users customize applications in many ways, and is becoming increasingly prevalent. Researchers have created techniques for testing configurable software, but to date, only a little research has addressed the problems of regression testing configurable systems as they evolve. Whereas problems such as selective retesting and test prioritization at the test case level have been extensively researched, these problems have rarely been considered at the configuration level. In this paper we address the problem of providing configuration-aware regression testing for evolving software systems. We use combinatorial interaction testing techniques to model and generate configuration samples for use in regression testing. We conduct an empirical study on a non-trivial evolving software system to measure the impact of configurations on testing effectiveness, and to compare the effectiveness of different configuration prioritization techniques on early fault detection during regression testing. Our results show that configurations can have a large impact on fault detection and that prioritization of configurations can be effective.
On the probability distribution of data at points in real complete intersection varieties
Authors: Cruz E. Borges, Luis M. Pardo
Venue: Journal of Complexity (2008)

We show several estimates on the probability distribution of some data at points in real complete intersection varieties: norms of real affine solutions, condition number of real solution of real systems of multi-variate polynomial equations and convergence radius of Newton's operator for under-determined system of multi-variate polynomial equations.