Identification of sequence repetitions in immunoglobulin folds

A lot of evidence suggests that many proteins with the symmetric structures have evolved by internal duplication and fusion. Meanwhile many internal sequence repeats correspond to functional and structural units. These proteins, which have internal structural symmetry, this means that their sequences should be made up of identical repeats. However, many of these repeat signals can only be seen at the structural level yet. We have developed a de novo algorithm, modified recurrence correlation analysis, to detect the symmetries in the primary sequences of immunoglobulin folds (Ig folds), which adopt highly symmetrical tertiary structures while their sequences appear nearly random. Using this method, we show that the internal repetitions of the immunoglobulin folds could be identified directly at the sequence level. These results may give us some help to study the hypotheses about the origin of Ig folds by duplication of simpler fragments and it may also give us some helps to understand the relationship between the sequences and their tertiary structures.     

Invariability,orbits and fuzzy attractors

In this paper, we present a generalization of a new systemic approach to abstract fuzzy systems. Using a fuzzy relations structure will retain the information provided by degrees of membership. In addition, to better suit the situation to be modelled, it is advisable to use T-norm or T-conorm distinct from the minimum and maximum, respectively. This gain in generality is due to the completeness of the work on a higher level of abstraction. You cannot always reproduce the results obtained previously, and also sometimes different definitions with different views are obtained. In any case this approach proves to be much more effective when modelling reality.     

Bootstrap analysis of multiple repetitions of experiments using an interval-valued multiple comparison procedure

A new bootstrap test is introduced that allows for assessing the significance of the differences between stochastic algorithms in a cross-validation with repeated folds experimental setup. Intervals are used for modeling the variability of the data that can be attributed to the repetition of learning and testing stages over the same folds in cross validation. Numerical experiments are provided that support the following three claims: (1) Bootstrap tests can be more powerful than ANOVA or Friedman test for comparing multiple classifiers. (2) In the presence of outliers, interval-valued bootstrap tests achieve a better discrimination between stochastic algorithms than nonparametric tests. (3) Choosing ANOVA, Friedman or Bootstrap can produce different conclusions in experiments involving actual data from machine learning tasks.     

On maximal repetitions of arbitrary exponent

The first two authors have shown [1,2] (Kolpakov and Kucherov, 1999, 2000) that the sum of the exponents (and thus the number) of maximal repetitions of exponent at least 2 in a word (also called runs) is linear with respect to the length of the word. The exponent 2 in the definition of a run may seem arbitrary. In this paper, we consider maximal repetitions of exponent strictly greater than 1.     

The automatic recognition of handprinted Chinese characters — A method of extracting an ordered sequence of strokes

In this paper, a method of recognizing handprinted Chinese characters by extracting and composing an ordered sequence of strokes is presented. A computer simulation for three hundred Chinese characters has been done, and the results are satisfactory.     

Periodicity in software vulnerability discovery,patching and exploitation

Periodicity in key processes related to software vulnerabilities need to be taken into account for assessing security at a given time. Here, we examine the actual multi-year field datasets for some of the most used software systems (operating systems and Web-related software) for potential annual variations in vulnerability discovery processes. We also examine weekly periodicity in the patching and exploitation of the vulnerabilities. Accurate projections of the vulnerability discovery process are required to optimally allocate the effort needed to develop patches for handling discovered vulnerabilities. A time series analysis that combines the periodic pattern and longer-term trends allows the developers to predict future needs more accurately. We analyze eighteen datasets of software systems for annual seasonality in their vulnerability discovery processes. This analysis shows that there are indeed repetitive annual patterns. Next, some of the datasets from a large number of major organizations that record the result of daily scans are examined for potential weekly periodicity and its statistical significance. The results show a 7-day periodicity in the presence of unpatched vulnerabilities, as well as in the exploitation pattern. The seasonal index approach is used to examine the statistical significance of the observed periodicity. The autocorrelation function is used to identify the exact periodicity. The results show that periodicity needs to be considered for optimal resource allocations and for evaluation of security risks.     

Periodicity, directionality, and randomness: Wold features forimage modeling and retrieval

One of the fundamental challenges in pattern recognition is choosing a set of features appropriate to a class of problems. In applications such as database retrieval, it is important that image features used in pattern comparison provide good measures of image perceptual similarities. We present an image model with a new set of features that address the challenge of perceptual similarity. The model is based on the 2D Wold decomposition of homogeneous random fields. The three resulting mutually orthogonal subfields have perceptual properties which can be described as “periodicity,” “directionality,” and “randomness,” approximating what are indicated to be the three most important dimensions of human texture perception. The method presented improves upon earlier Wold-based models in its tolerance to a variety of local inhomogeneities which arise in natural textures and its invariance under image transformation such as rotation. An image retrieval algorithm based on the new texture model is presented. Different types of image features are aggregated for similarity comparison by using a Bayesian probabilistic approach. The, effectiveness of the Wold model at retrieving perceptually similar natural textures is demonstrated in comparison to that of two other well-known pattern recognition methods. The Wold model appears to offer a perceptually more satisfying measure of pattern similarity while exceeding the performance of these other methods by traditional pattern recognition criteria. Examples of natural scene Wold texture modeling are also presented     

Design,implementation, and performance of an automatic configuration service for distributed component systems

Component technology promotes code reuse by enabling the construction of complex applications by assembling off‐the‐shelf components. However, components depend on certain characteristics of the environment in which they execute. They depend on other software components and on hardware resources. In existing component architectures, the application developer is left with the task of resolving those dependencies, i.e. making sure that each component has access to all the resources it needs and that all the required components are loaded. Nevertheless, according to encapsulation principles, developers should not be aware of the component internals. Thus, it may be difficult to find out what a component really needs. In complex systems, such as the ones found in modern distributed environments, this manual approach to dependency management can lead to disastrous results. Current systems rely heavily on manual configuration by users and system administrators. This is tolerable now, when users have to manage a few computers. But, in the near future, people will have to deal with thousands of computing devices and it will no longer be acceptable to require the user to configure each of them. This paper presents the results of our 6 year research (from 1998 to 2003) in the area of automatic configuration, describing an integrated architecture for managing dependencies in distributed component‐based systems. The architecture supports automatic configuration and dynamic resource management in distributed heterogeneous environments. We describe a concrete implementation of this architecture, present experimental results, and compare our approach to other works in the area. Copyright © 2005 John Wiley & Sons, Ltd.     

基于系统行为序列的Petri网自动建模方法

要想用Petri网对系统进行有效的模拟和分析,就必须先建立起可靠准确的Petri网模型,目前很少有文献专门研究Petri网对系统的建模问题。对此,提出了基于系统行为序列的Petri网自动建模方法。该方法将系统所有行为序列组合为正规语言表达式,对于不同的系统,给出标注函数(即变迁和系统行为的映射关系),就可以建立起系统的Petri网模型。给出了电话呼叫业务建立用户Petri网模型的一个实例。该方法形式化强、通用性好,建立的模型标准规范,并且可实现机器自动建模,在目前的系统建模研究方面取得了进展。     

Noncombinatorial detection of regular repetitions under perspective skew

We present a geometric framework for the efficient detection of regular repetitions of planar (but not necessarily coplanar) patterns. At the heart of our system, lie the fixed structures of the transformations that describe these regular configurations. The approach detects a number of symmetric configurations that have traditionally been dealt with separately, in that all configurations corresponding to planar homologies are detected. These include important cases such as periodicities, mirror symmetries, and reflections about a point. The approach can handle perspective distortions. It avoids to get trapped in combinatorics; through invariant-based hashing for pattern matching and through Hough transforms for the detection of fixed structures. Additional efficiency and robustness are obtained from the system's ability to "reason" about the consistency of multiple homologies. The performance of the system is demonstrated with several examples.     

Periodicity and arithmetic-periodicity in hexadecimal games

We investigate 1-, 2- and some k-digit (k⩾3) hexadecimal games with the help of a new arithmetic-periodicity theorem. We also note that not all hexadecimal games are periodic or arithmetic-periodic.     

Arnold变换的周期性与安全性分析

Arnold变换是通信安全中数字图像置乱技术之一。该文分析了Arnold变换的周期性,探讨了其周期性与安全性之间的关系,提出了一种有效克服其周期性的实现方法,其基本思想是将图像的所有像素分成多组,每组采用不同的参数进行置乱,实验表明用该置乱后的图像不再出现周期性现象,可有效提高Arnold变换及其推广的安全性。     

An IR and visible image sequence automatic registration method based on optical flow

IR–visible camera registration is required for multi-sensor fusion and cooperative processing. Image sequences can provide motion information, which is useful for sequence registration. The existing methods mainly focus on registration using moving objects which are observed by both cameras. However, accurate motion feature extraction for a whole moving object is difficult, because of the complex environment and different imaging mechanism of two sensors. To overcome this problem, we use motion features associated with single pixels in the two image sequences to carry out automatic registration. A normalized optical flow time sequence for each image pixel is constructed. The matching of pixels between the IR image and the visible light image is carried out using a fast similarity measurement and a three stage correspondence selection method. Finally cascaded random sample consensus is adopted to remove outlying matches, and least-square method and Levenberg–Marquardt method are used to estimate the transformation from the IR image to the visible image. The effectiveness of our method is demonstrated using several real datasets and simulated datasets.     

Periodicity in generations of automata

A class of automata which build other automata is defined. These automata are called Turing machine automata because each one contains a Turing machine which acts as its computer-brain and which completely determines what its offspring, if any, will be. We show that for the descendants of an arbitrary progenitor Turing machine automaton there are exactly three possibilities: (1) there is a sterile descendant after an arbitrary number of generations, (2) after a delay of an arbitrary number of generations, the descendants repeat in generations with an arbitrary period, or (3) the descendants are aperiodic. We also show what sort of computing ability may be realized by the descendants in each of the possibilities. Furthermore, it is determined whether there are effective procedures for distinguishing between the various possibilities, and the exact degree of unsolvability is computed for those decision problems for which there is no effective procedure. Lastly, we discuss the relevance of the results to biology and pose several questions.Department of Computer Science. The research for this paper was supported in part by Kansas General Research Grant 3683-5038.     

Periodicity of Kalman-based scheduled filters

In this paper, the sensor scheduling problem for estimation is tackled, in which a set of sensors must share a common network to communicate their measurements. It is shown that, under some mild conditions, a Kalman-based scheduled filter results in a periodic selection of the sensors. In those cases, the computational cost and energy consumption can be reduced, as the sensors can await asleep between two consecutive measurements. A suboptimal one-step ahead strategy is thoroughly studied as a possible example of observation scheme.     

TaylUR, an arbitrary-order diagonal automatic differentiation package for Fortran 95

We present TaylUR, a Fortran 95 module to automatically compute the numerical values of a complex-valued function's derivatives with respect to several variables up to an arbitrary order in each variable, but excluding mixed derivatives. Arithmetic operators and Fortran intrinsics are overloaded to act correctly on objects of a defined type taylor, which encodes a function along with its first few derivatives with respect to the user-defined independent variables. Derivatives of products and composite functions are computed using Leibniz's rule and Faà di Bruno's formula. TaylUR makes heavy use of operator overloading and other Fortran 95 features such as elemental functions.

Program summary

Program title: TaylURCatalogue identifier:ADXR_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXR_v1_0Program obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions:noneProgramming language:Fortran 95Computer:Any computer with a conforming Fortran 95 compilerOperating system:Any system with a conforming Fortran 95 compilerNo. of lines in distributed program, including test data, etc.:6286No. of bytes in distributed program, including test data, etc:14 994Distribution format:tar.gzNature of problem:Problems that require potentially high orders of derivatives with respect to some variables, such as e.g. expansions of Feynman diagrams in particle masses in perturbative Quantum Field Theory, and which cannot be treated using existing Fortran modules for automatic differentiation [C.W. Straka, ADF95: Tool for automatic differentiation of a FORTRAN code designed for large numbers of independent variables, Comput. Phys. Comm. 168 (2005) 123-139, arXiv:cs.MS/0503014; S. Stamatiadis, R. Prosmiti, S.C. Farantos, auto_deriv: Tool for automatic differentiation of a FORTRAN code, Comput. Phys. Comm. 127 (2000) 343-355].Solution method:Arithmetic operators and Fortran intrinsics are overloaded to act correctly on objects of a defined type taylor, which encodes a function along with its first few derivatives with respect to the user-defined independent variables. Derivatives of products and composite functions are computed using Leibniz's rule and Faà di Bruno's formula.Restrictions:Memory and CPU time constraints may restrict the number of variables and Taylor expansion order that can be achieved. Loss of numerical accuracy due to cancellation may become an issue at very high orders.Unusual features:No mixed higher-order derivatives are computed. The complex conjugation operation assumes all independent variables to be real.Running time:The running time of TaylUR operations depends linearly on the number of variables. Its dependence on the Taylor expansion order varies from linear (for linear operations) through quadratic (for multiplication) to exponential (for elementary function calls).     

舵机自动测试系统的设计与实现

为更灵活准确的测试舵机性能和寿命,研制了基于工控机、力矩加载器、力矩传感器、角度传感器的舵机性能和寿命自动测试系统。测试系统采用NI公司生产的便携式一体化PXI机箱和高精度多功能采集卡,在测试过程中实时监测采集舵机控制器的电压电流和舵机位置信号;采用Lab VIEW编程平台开发了相应的测试软件,设计了友好的人机交互界面,实现了舵机产品的参数测量及合格性判断。通过实验比对新旧测试系统对同一舵机产品测试数据,证明新测试系统测试精度和测试效率都更高。     

A Coarse-Grained Multicomputer algorithm for the detection of repetitions

The paper presents a Coarse-Grained Multicomputer algorithm that solves the problem of detection of repetitions. This algorithm can be implemented in the CGM model with P processors in in time and O(P) communication steps. It is the first CGM algorithm for this problem. We present also experimental results showing that the CGM algorithm is very efficient.