Analysis method and algorithm design of biological sequence problem based on generalized k-mer vector

K-mer can be used for the description of biological sequences and k-mer distribution is a tool for solving sequences analysis problems in bioinformatics.We can use k-mer vector as a representation method of the k-mer distribution of the biological sequence.Problems,such as similarity calculations or sequence assembly,can be described in the k-mer vector space.It helps us to identify new features of an old sequence-based problem in bioinformatics and develop new algorithms using the concepts and methods from linear space theory.In this study,we defined the k-mer vector space for the generalized biological sequences.The meaning of corresponding vector operations is explained in the biological context.We presented the vector/matrix form of several widely seen sequence-based problems,including read quantification,sequence assembly,and pattern detection problem.Its advantages and disadvantages are discussed.Also,we implement a tool for the sequence assembly problem based on the concepts of k-mer vector methods.It shows the practicability and convenience of this algorithm design strategy.

CONSTRUCTION METHODS AND ALGORITHM DESIGN OF WAVELET BASES

Based on the brief introduction of the principles of wavelet analysis, this paper gives a summary of several typical wavelet bases from the point of view of perfect reconstruction of signals and emphasizes that designing wavelet bases which are used to decompose the signal into a two-band form is equivalent to designing a two-band filter bank with perfect or nearly perfect property. The generating algorithm corresponding to Daubechies bases and some simulated results are also given in the paper.

Approach of generating parallel programs from parallelized algorithm design strategies

Today, parallel programming is dominated by message passing libraries, such as message passing interface （MPI）. This article intends to simplify parallel programming by generating parallel programs from parallelized algorithm design strategies. It uses skeletons to abstract parallelized algorithm design strategies, as well as parallel architectures. Starting from problem specification, an abstract parallel abstract programming language＋ （Apla＋） program is generated from parallelized algorithm design strategies and problem-specific function definitions. By combining with parallel architectures, implicity of parallelism inside the parallelized algorithm design strategies is exploited. With implementation and transformation, C＋＋ and parallel virtual machine （CPPVM） parallel program is finally generated. Parallelized branch and bound （B＆B） algorithm design strategy and paraUelized divide and conquer （D ＆ C） algorithm design strategy are studied in this article as examples. And it also illustrates the approach with a case study.

An Incremental Approach to Automatic Algorithm Design

This paper presents an incremental approach to automatic algorithm design, which can be described by algebraic specifications precisely and conveniently. The definitions of selection operator and extension operator which can bedefined by strategy relations and transformations are given in order to model theprocess of finding the solution of a problem. Also discussed is its object-orientedimplementation. The functional specification and the design specification for an algorithm are given in one framework so that the correctness of the algorithm can beeasily proved.

The Key Path of the Shape Optimization Design of Isotropic Material Pressure Vessels

An optimization design was conducted for the shape of the pressure vessel with a thin-shell shell. During this process, the optimization calculation was performed with the aid of the genetic algorithm toolbox included in Matlab. Firstly, through the parametric modeling function of APDL, models such as arc-shaped, parabolic, elliptical, and those generated by the fitting curve command were successfully constructed. Meanwhile, the relevant settings of material properties were accomplished, and the static analysis was conducted. Secondly, the optimization calculation process was initiated using the genetic algorithm toolbox in Matlab. Eventually, through analysis and judgment, the model generated by the fitting curve command was relatively superior within the category of the best shape.

Algorithms for automatic measurement of SIS-type hysteretic underdamped Josephson junction’s parameters by current-voltage characteristics

Some electrical parameters of the SIS-type hysteretic underdamped Josephson junction(JJ)can be measured by its current-voltage characteristics(IVCs).Currents and voltages at JJ are commensurate with the intrinsic noise level of measuring instruments.This leads to the need for multiple measurements with subsequent statistical processing.In this paper,the digital algorithms are proposed for the automatic measurement of the JJ parameters by IVC.These algorithms make it possible to implement multiple measurements and check these JJ parameters in an automatic mode with the required accuracy.The complete sufficient statistics are used to minimize the root-mean-square error of parameter measurement.A sequence of current pulses with slow rising and falling edges is used to drive JJ,and synchronous current and voltage readings at JJ are used to realize measurement algorithms.The algorithm performance is estimated through computer simulations.The significant advantage of the proposed algorithms is the independence from current source noise and intrinsic noise of current and voltage meters,as well as the simple implementation in automatic digital measuring systems.The proposed algorithms can be used to control JJ parameters during mass production of superconducting integrated circuits,which will improve the production efficiency and product quality.

Real-time Design Constraints in Implementing Active Vibration Control Algorithms

Although computer architectures incorporate fast processing hardware resources, high performance real-time implementation of a complex control algorithm requires an efficient design and software coding of the algorithm so as to exploit special features of the hardware and avoid associated architecture shortcomings. This paper presents an investigation into the analysis and design mechanisms that will lead to reduction in the execution time in implementing real-time control algorithms. The proposed mechanisms are exemplified by means of one algorithm, which demonstrates their applicability to real-time applications. An active vibration control （AVC） algorithm for a flexible beam system simulated using the finite difference （FD） method is considered to demonstrate the effectiveness of the proposed methods. A comparative performance evaluation of the proposed design mechanisms is presented and discussed through a set of experiments.

New Optimization Method, the Algorithms of Changes, for Heat Exchanger Design

Heat exchangers are widely used in the process engineering such as the chemical industries, the petroleum industries, and the HVAC applications etc. An optimally designed heat exchanger cannot only help the optimization of the equipment size but also the reduction of the power consumption. In this paper, a new optimization approach called algorithms of changes (AOC) is proposed for design and optimization of the shell-tube heat exchanger. This new optimization technique is developed based on the concept of the book of changes (I Ching) which is one of the oldest Chinese classic texts. In AOC, the hexagram operations in I Ching are generalized to binary string case and an iterative process, which imitates the I Ching inference, is defined. Before applying the AOC to the heat exchanger design problem, the new optimization method is examined by the benchmark optimization problems such as the global optimization test functions and the travelling salesman problem (TSP). Based on the TSP results, the AOC is shown to be superior to the genetic algorithms (GA). The AOC is then used in the optimal design of heat exchanger. The shell inside diameter, tube outside diameter, and baffles spacing are treated as the design (or optimized) variables. The cost of the heat exchanger is arranged as the objective function. For the heat exchanger design problem, the results show that the AOC is comparable to the GA method. Both methods can find the optimal solution in a short period of time.

Genetic Algorithms for the Optimal Design of Electromagnetic Micro-Motors

The genetic algorithm (GA) to the design of electromagnetic micro motor to optimize parameter design. Besides the different oversize from macro motor, the novel structure of micro motor which the rotor is set between the two stators make its design different, too. There are constraint satisfaction problems CSP) in the design. It is shown that the use GA offers a high rate of global convergence and the ability to get the optimal design of electromagnetic micro motors.

Satellite Constellation Design with Adaptively Continuous Ant System Algorithm

The ant system algorithm （ASA） has proved to be a novel meta-heuristic algorithm to solve many multivariable problems. In this paper, the earth coverage of satellite constellation is analyzed and a n ＋ 1^ -fold coverage rate is put forward to evaluate the coverage performance of a satellite constellation. An optimization model of constellation parameters is established on the basis of the coverage performance. As a newly developed method, ASA can be applied to optimize the constellation parameters. In order to improve the ASA, a rule for adaptive number of ants is proposed, by which the search range is obviously enlarged and the convergence speed increased. Simulation results have shown that the ASA is more quick and efficient than other methodV211.71s.

Selection diagram of design algorithms for neutron-focusing supermirrors

The neutron supermirror is an important neutron optical device that can significantly improve the efficiency of neutron transport in neutron guides and has been widely used in research neutron sources.Three types of algorithms,including approximately ten algorithms,have been developed for designing high-efficiency supermirror structures.In addition to its applications in neutron guides,in recent years,the use of neutron supermirrors in neutronfocusing mirrors has been proposed to advance the development of neutron scattering and neutron imaging instruments,especially those at compact neutron sources.In this new application scenario,the performance of supermirrors strongly affects the instrument performance;therefore,a careful evaluation of the design algorithms is needed.In this study,we examine two issues:the effect of nonuniform film thickness distribution on a curved substrate and the effect of the specific neutron intensity distribution on the performance of neutron supermirrors designed using existing algorithms.The effect of film thickness nonuniformity is found to be relatively insignificant,whereas the effect of the neutron intensity distribution over Q(where Q is the magnitude of the scattering vector of incident neutrons)is considerable.Selection diagrams that show the best design algorithm under different conditions are obtained from these results.When the intensity distribution is not considered,empirical algorithms can obtain the highest average reflectivity,whereas discrete algorithms perform best when the intensity distribution is taken into account.The reasons for the differences in performance between algorithms are also discussed.These findings provide a reference for selecting design algorithms for supermirrors for use in neutron optical devices with unique geometries and can be very helpful for improving the performance of focusing supermirror-based instruments.

Immune Genetic Algorithm for Optimal Design

A computing model employing the immune and genetic algorithm (IGA) for the optimization of part design is presented. This model operates on a population of points in search space simultaneously, not on just one point. It uses the objective function itself, not derivative or any other additional information and guarantees the fast convergence toward the global optimum. This method avoids some weak points in genetic algorithm, such as inefficient to some local searching problems and its convergence is too early. Based on this model, an optimal design support system (IGBODS) is developed.IGBODS has been used in practice and the result shows that this model has great advantage than traditional one and promises good application in optimal design.

An Adaptive Differential Evolution Algorithm to Solve Constrained Optimization Problems in Engineering Design

Differential evolution (DE) algorithm has been shown to be a simple and efficient evolutionary algorithm for global optimization over continuous spaces, and has been widely used in both benchmark test functions and real-world applications. This paper introduces a novel mutation operator, without using the scaling factor F, a conventional control parameter, and this mutation can generate multiple trial vectors by incorporating different weighted values at each generation, which can make the best of the selected multiple parents to improve the probability of generating a better offspring. In addition, in order to enhance the capacity of adaptation, a new and adaptive control parameter, i.e. the crossover rate CR, is presented and when one variable is beyond its boundary, a repair rule is also applied in this paper. The proposed algorithm ADE is validated on several constrained engineering design optimization problems reported in the specialized literature. Compared with respect to algorithms representative of the state-of-the-art in the area, the experimental results show that ADE can obtain good solutions on a test set of constrained optimization problems in engineering design.

Genetic Algorithm for Injection Mould Design and Moulding

Obtaining the optimal values of the parameters for th e design of a required mould and the operation of the moulding process are diffi cult, this is due to the complexity of product geometry and the variation of pla stic material properties. The typical parameters for the mould design and mouldi ng process are melt flow length, injection pressure, holding pressure, back pres sure, injection speed, melt temperature, mould temperature, clamping force, inje ction time, holding time and cooling time. This paper discusses the difficulties of using the current computer aided optimization methods to acquire the values of the parameters. A method that is based on the concept of genetic algorithm is proposed to overcome the difficulties. The proposed method describes in details on how to attain the optimal values of the parameters form a given product geom etry.

A Generic Design Model for Evolutionary Algorithms

A generic design model for evolutionary algorithms is proposed in this paper. The model, which was described by UML in details, focuses on the key concepts and mechanisms in evolutionary algorithms. The model not only achieves separation of concerns and encapsulation of implementations by classification and abstraction of those concepts, it also has a flexible architecture due to the application of design patterns. As a result, the model is reusable, extendible, easy to understand, easy to use, and easy to test. A large number of experiments applying the model to solve many different problems adequately illustrate the generality and effec-tivity of the model.

Optimal Design of Materials for DJMP Based on Genetic Algorithm

The genetic algorithm was used in optimal design of deep jet method pile.The cost of deep jet method pile in one unit area of foundation was taken as the objective function.All the restrains were listed following the corresponding specification.Suggestions were proposed and the modified.The real-coded Genetic Algorithm was given to deal with the problems of excessive computational cost and premature convergence.Software system of optimal design of deep jet method pile was developed.

Design of Process Centrifugal Compressor： an Adapted Algorithm

Considering the essential and influential role of centrifugal compressors in a wide range of industries makes most of engineers research and study on design and optimization of centrifugal compressors. Centrifugal compressors are the key to part ofoil, gas and petrochemical industries as well as gas pipeline transports. Since complete 3D design of the compressor consumes a considerable amount of time, most of active companies in the field, are profoundly interested in obtaining a design outline before taking any further steps in designing the entire machine. In this paper, a numerical algorithm, named ACDA （adapted compressor design algorithm） for fast and accurate preliminary design of centrifugal compressor is presented. The design procedure is obtained under real gas behavior, using an appropriate equation of state. Starting from impeller inlet, the procedure is continued on by resulting in numerical calculation for other sections including impeller exit, volute and exit diffuser. Clearly, in any step suitable correction factors are employed in order to conclude in precise numerical results. Finally, the achieved design result is compared with available reference data.

Series-parallel Hybrid Vehicle Control Strategy Design and Optimization Using Real-valued Genetic Algorithm

Despite the series-parallel hybrid electric vehicle inherits the performance advantages from both series and parallel hybrid electric vehicle, few researches about the series-parallel hybrid electric vehicle have been revealed because of its complex co nstruction and control strategy. In this paper, a series-parallel hybrid electric bus as well as its control strategy is revealed, and a control parameter optimization approach using the real-valued genetic algorithm is proposed. The optimization objective is to minimize the fuel consumption while sustain the battery state of charge, a tangent penalty function of state of charge（SOC） is embodied in the objective function to recast this multi-objective nonlinear optimization problem as a single linear optimization problem. For this strategy, the vehicle operating mode is switched based on the vehicle speed, and an ＂optimal line＂ typed strategy is designed for the parallel control. The optimization parameters include the speed threshold for mode switching, the highest state of charge allowed, the lowest state of charge allowed and the scale factor of the engine optimal torque to the engine maximum torque at a rotational speed. They are optimized through numerical experiments based on real-value genes, arithmetic crossover and mutation operators. The hybrid bus has been evaluated at the Chinese Transit Bus City Driving Cycle via road test, in which a control area network-based monitor system was used to trace the driving schedule. The test result shows that this approach is feasible for the control parameter optimization. This approach can be applied to not only the novel construction presented in this paper, but also other types of hybrid electric vehicles.

“私教”还是“枪手”:基于大模型的计算机实践教学探索

以大模型为代表的新一代人工智能技术正深刻影响传统教学模式。在计算机实践教学过程中,如果大模型被合理应用,它可以充当学生的“私教”,辅助学生的个性化学习;否则大模型可能沦为学生完成作业的“枪手”,削弱学生的独立思考及实践能力。该文首先论述了计算机实践教学的层次,并分析了大模型对各个层次实践教学的正面和负面影响。然后,以“算法设计与分析”课程为案例,设计了面向算法设计实践的大模型应用模式,包括过程报告、逆向思考和集中考核等主要形式,初步应用结果表明,84.8%的学生在课程中使用大模型,其中51%的学生认可大模型的帮助作用,大模型应用显著提高了课程实践作业的完成度。

Satellite constellation design with genetic algorithms based on system performance

Satellite constellation design for space optical systems is essentially a multiple-objective optimization problem. In this work, to tackle this challenge, we first categorize the performance metrics of the space optical system by taking into account the system tasks（i.e., target detection and tracking）. We then propose a new non-dominated sorting genetic algorithm（NSGA） to maximize the system surveillance performance. Pareto optimal sets are employed to deal with the conflicts due to the presence of multiple cost functions. Simulation results verify the validity and the improved performance of the proposed technique over benchmark methods.