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MCALIGN2: Faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution

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BMC BIOINFORMATICS 2006年第1期7卷 292-292页

作者： Wang, Jun Keightley, Peter D. Johnson, Toby Univ Edinburgh Sch Biol Sci Inst Evolutionary Biol Edinburgh EH9 3JT Midlothian Scotland

Background: Non-coding DNA sequences comprise a very large proportion of the total genomic content of mammals, most other vertebrates, many invertebrates, and most plants. Unraveling the functional significance of non-coding DNA depends on how well we are able to align non-coding DNA sequences. However, the alignment of non-coding DNA sequences is more difficult than aligning protein-coding sequences. Results: Here we present an improved pair-hidden-Markov-Model (pair HMM) based method for performing global pairwise alignment of non-coding DNA sequences. The method uses an explicit model of indel length frequency distribution which can be specified, and allows any time reversible model of nucleotide substitution. The method uses a deterministic global optimiser to find the alignment with the highest posterior probability. We test MCALIGN2 in simulations, and compare it to a previous Monte Carlo based method (MCALIGN), to the pair HMM method of Knudsen and Miyamoto, and to a heuristic method (AVID) that performed very well in a previous simulation study. We show that the pair HMM methods have excellent performance for all combinations of parameter values we have considered. MCALIGN2 is up to ten times faster than MCALIGN. MCALIGN2 is more accurate in resolving indels given an accurate explicit model than heuristic methods, but is computationally slower. Conclusion: MCALIGN2 produces better quality alignments by explicitly using biological knowledge about the indel length distribution and time reversible models of nucleotide substitution. As a result, it can outperform other available sequence alignment methods for the cases we have considered to align non-coding DNA sequences.

关键词： Monte Carlo dynamic programming method General Time Reversible Model General Time Reversible Indel Event

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Energy management strategy of series-parallel hybrid transmission integrating map information and personalized driving characteristics

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ETRANSPORTATION 2024年 22卷

作者： Zhao, Junwei Xu, Xiangyang Guo, Wei Dong, Peng Yao, Kun Liu, Xuewu Beihang Univ Sch Transportat Sci & Engn Dept Automot Engn Beijing 100191 Peoples R China GAC Automot Res & Dev Ctr Guangzhou 511434 Peoples R China

The integration of multi-source intelligent and connected information during a driving trip, along with its online application to globally optimized energy management strategies, has emerged as a crucial technical approach for enhancing the energy-saving effectiveness of hybrid transmissions. However, the action mode of such information and the optimization calculation efficiency of existing dynamic programming (DP) methods limit the online application of the aforementioned strategies with global optimization capabilities. To address these problems, the present study proposes a hierarchical energy management strategy that follows the reference trajectory of the battery state of charge (SoC) and comprehensively considers the multi- source information on the driving trip. First, a global speed prediction model based on personalized driving characteristics is proposed to obtain an accurate driving cycle input for the space-domain DP method. Second, the aforementioned tasks as well as the working-mode decision of the hybrid transmission and the multi-power- source torque distribution calculation tasks are deployed in the dual-core controller. Finally, the hierarchical energy management strategy is verified via vehicle testing. Compared with the DP strategy, the proposed strategy has an energy-saving potential of 4.17% that is yet to be realized. Furthermore, compared with the charge-depleting and charge-sustaining (CD-CS) strategy, the proposed strategy reduces fuel consumption by 0.38 L per 100 km, and its energy-saving effect is significant. This study is the first to apply the DP method to the vehicle controller, thereby facilitating the online application of energy management strategies with global optimization capabilities.

关键词： Series-parallel hybrid transmission Energy management strategy dynamic programming method Online application Testing and verification

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Optimal control for uncertain stochastic dynamic systems with jump and application to an advertising model

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APPLIED MATHEMATICS AND COMPUTATION 2021年 407卷 126337-126337页

作者： Chen, Xin Zhu, Yuanguo Sheng, Linxue Nanjing Univ Sci & Technol Sch Sci Nanjing 210094 Jiangsu Peoples R China Nanjing Univ Finance & Econ Sch Appl Math Nanjing 210023 Jiangsu Peoples R China

Randomness is an objective indeterminacy, while uncertainty is a subjective indetermi-nacy. As an effective methodology, chance theory is applicable for disposing of indetermi-nacy composing of both uncertainty and randomness. Based on chance theory, the optimal control for uncertain stochastic dynamic systems described by both a stochastic differen-tial equation driven by the standard Wiener process and an uncertain differential equation driven by the Liu process and V & minus;n jumps process is considered. Then the principle of optimality is presented by drawing on the dynamic programming method. Particularly, the equation of optimality is established to solve the proposed problem. Furthermore, the opti-mal control problems with linear and quadratic objective functions are discussed by using the obtained equation. As an application, an advertising problem is analyzed, the corre-sponding optimal pricing policies and advertising strategies are provided. (c) 2021 Elsevier Inc. All rights reserved.

关键词： Optimal control Chance theory dynamic programming method Advertising model

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Enterprise Profit Maximization in the Range of Products and Production Rate Selection Problems

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IFAC Proceedings Volumes 1983年第12期16卷 487-493页

作者： J. Gutenbaum A. Jakubowski System Research Institute Polish Academy of Sciences. Newelska 6 01-477 Warsaw Poland

In conditions of monopolistic position of enterprises, they exhibit unrestrained tendency to increase the prices of their products, without taking care for full utilization of their production capacities. Such a situation may occur in the planned and as well as the free-market national economy. The decision center is able to counteract this tendency by introducing a proper system of income taxes, which results in the optimal prices providing the maximal profit. Simultaneously, due to the high level of the prime costs of small production series, there exists some threshold value in the relation between profit and production rate. If the production rate is less than this value, it is unprofitable. For reasons mentioned, the problem of enterprise profit optimization in the case of production capacities constrained, is a non-trivial mathematical programming problem. It is a mixed discrete-continuous optimization problem: the decision variables connected with selecting ranges of products are of discrete (zero-one) type: the decision variables associated with the choice of the optimal production rate are continuous. The paper presents an optimization algorithm which can be used to solve this mixed discrete-continuous decision problem. The worked out method can be also applied to other socio-economic decision problems of similar type.

关键词： Enterprise profit maximization production capacities constraints discrete-continuous decision problem optimization algorithm dynamic programming method

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Consumption-portfolio choice with subsistence consumption and risk aversion change at retirement

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JOURNAL OF INEQUALITIES AND APPLICATIONS 2018年第1期2018卷 165-165页

作者： Lee, Ho-Seok Kwangwoon Univ Dept Math Seoul South Korea

This paper considers subsistence consumption of an economic agent both before and after retirement in analyzing the optimal consumption, portfolio, and retirement problem. We allow the relative risk aversion of the economic agent to make a one-off jump at retirement. With a Cobb-Douglas utility function, we obtain explicit expressions for the optimal policies. Numerical results show that, whereas post-retirement subsistence consumption tends to delay retirement, pre-retirement subsistence consumption and the magnitude of jump in relative risk aversion may stimulate early retirement. Also, the consumption drop at retirement deepens as post-retirement subsistence consumption increases, but it weakens as pre-retirement subsistence consumption increases.

关键词： dynamic programming method Free boundary value problem Optimal stopping time Risk aversion change Subsistence consumption

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Optimal Operating Scenario for Polerood Hydropower Station to Maximize Peak Shaving and Produced Profit

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INTERNATIONAL JOURNAL OF RENEWABLE ENERGY DEVELOPMENT-IJRED 2018年第3期7卷 233-239页

作者： Feshalami, Behzad Forouzi Ferdowsi Univ Mashhad Dept Mech Engn Mashhad Khorasan Razavi Iran

This paper deals with the optimization of the daily operation of Polerood hydropower station being constructed in the north of Iran. dynamic programming method (DP) is applied as the preferred optimization tool owing to the fact that it guarantees the optimal solution and is applicable to the present problem. Produced profit and peak-shaving are the two objectives considered separately in this study. The results show that the optimal water management of the case study through charging and discharging the reservoir at the appropriate times led to 4% increase in the produced profit. In another part of this study, the optimal performance strategies regarding to the two objectives (produced profit and peak-shaving) are compared. The observed similarity between the two performance strategies implies the substantial dependence of the electricity price and the network demand level. The paper ends with the profitability study of the project and the sensitivity analysis of the results to various economic parameters.

关键词： Polerood Hydropower Station Performance Optimization dynamic programming method Profit Peak Shaving

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Back-translation for discovering distant protein homologies in the presence of frameshift mutations

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ALGORITHMS FOR MOLECULAR BIOLOGY 2010年第1期5卷 6-6页

作者： Girdea, Marta Noe, Laurent Kucherov, Gregory Univ Lille 1 CNRS Lab Informat Fondamentale Lille Lille France Ctr Rech Lille Nord Europe Inst Natl Rech Informat & Automat Lille France French Russian JV Poncelet Lab Moscow Russia

Background: Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. Results: We developed a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamic programming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. Our implementation is freely available at http://***/path/. Conclusions: Our approach allows to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.

关键词： Codon dynamic programming method Codon Substitution dynamic programming Matrix Codon Substitution Model

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An optimal consumption and investment problem with stochastic hyperbolic discounting

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ADVANCES IN DIFFERENCE EQUATIONS 2019年第1期2019卷 211-211页

作者： Shin, Yong Hyun Roh, Kum-Hwan Sookmyung Womens Univ Dept Math Seoul South Korea Sookmyung Womens Univ Res Inst Nat Sci Seoul South Korea Hannam Univ Dept Math Daejeon South Korea

In this paper, we analyze the optimal consumption and investment problem of an agent by incorporating the stochastic hyperbolic preferences with constant relative risk aversion utility. Using the dynamic programming method, we deal with the optimization problem in a continuous-time model. And we provide the closed-form solutions of the optimization problem.

关键词： Portfolio selection Stochastic hyperbolic discounting dynamic programming method

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Mission Planning for Electromagnetism Environment Monitors Satellite Based on Heuristic Tabu Search Algorithm

Mission Planning for Electromagnetism Environment Monitors S...

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第27届中国控制与决策会议

作者： Zhenhai Lin School of Automation Science and Electrical Engineering Beihang University

ISBN: (纸本)9781479970186

The electromagnetism environment monitors satellite(EEMS) is a kind of earth observing *** is an important means to gain electronic intelligence of space,and has a special effect on prompt *** problem of mission planning for EEMS is a serious problem involving a lot of complex *** on analyzing the principle of EEMS,this paper puts forward the essential hypotheses of the problem and gives a basic pretreatment method firstly,and then establishes the constraints satisfaction problem(CSP) models for the ***,a heuristic tabu search algorithm(HTS) is designed for the mission planning for *** last,the paper utilizes HTS and dynamic programming method to solve the problems with different scales *** results show that the problem of mission planning for EEMS can be solved effectively with this method.

关键词： Electromagnetism environment monitors satellite Mission planning Constraints satisfaction problem models Heuristic tabu search algorithm dynamic programming method

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APPLICATION OF FUZZY ADAPTIVE CONTROL FOR OPTIMAL LOAD DISTRIBUTION OF PLANT

APPLICATION OF FUZZY ADAPTIVE CONTROL FOR OPTIMAL LOAD DISTR...

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2012 IEEE 2nd International Conference on Cloud Computing and Intelligence Systems

作者： Xiaodan Zhang College of Electrical and Information Engineering from Beihua University

A new kind of fuzzy adaptive method is proposed to transfer the multi-objective function to single objective function under the same constraint conditions. Based on multiple dynamic programming models, an improved dynamic programming method with different step-length to the solution for an optimal distribution of generators in an electrical power plant has been developed. This method overcomes the problem that due to improper selection of searching step-length. The experimental results show that the dynamic programming method based on fuzzy adaptive theory has a good energy-saving effect and engineering application value.

关键词： Load distribution Adaptive Fuzzy multi-objective dynamic programming method

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