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International Core Journal of Engineering 2024年第3期10卷 205-212页

作者： Binghua Hu Haiyan Wang Kelin Wu Zhihui Li

By studying the characteristics of certain practical questions, this paper proposes an operating process assessing system based on the needleman-wunsch algorithm, aiming to address the general lack of universality, insufficient emphasis on assessing the operating process, and excessive subjectivity in the current practical assessing methods. This system converts operating steps into operation sequences. It utilizes the needleman-wunsch algorithm to compare the standard operation sequences with the actual operation sequence, thus assessing the operating process. The results indicate that this system applies to operation questions, meets manual scoring requirements, and can objectively reflect students' operation abilities.

关键词： Operating Process Automatic Assessing Method Sequences Alignment needleman-wunsch algorithm

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Analysis and experimental evaluation of the needleman-wunsch algorithm for trajectory comparison

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EXPERT SYSTEMS WITH APPLICATIONS 2021年 165卷 114068-114068页

作者： Cavojsky, Maros Drozda, Martin Balogh, Zoltan Slovak Univ Technol Bratislava Fac Elect Engn & Informat Technol Bratislava Slovakia Constantine Philosopher Univ Dept Informat Nitra Slovakia

We evaluate whether the needleman-wunsch algorithm is suitable for user trajectory comparison. The problem that we aim to solve is pair-wise user trajectory comparison. Similar user trajectories are then clustered with respect to their similarity, where clusters emerge in a non-supervised way. We assume that user position, provided by GPS (Global positioning system), is normally distributed around user actual position. This assumption allows us to derive a model for setting score for match, penalty for gap and penalty for mismatch, which are an input to the needleman-wunsch algorithm. Our model implies that, in scenarios where actual user position is unknown and must be thus estimated from measured positions, the needleman-wunsch algorithm may be prevented from applying mismatches. In an experimental evaluation, we apply two data sets that contain recorded user positions and we show that our approach based on the needleman wunsch algorithm is capable of correct classification of user trajectories into groups. Unlike in existing literature, we show that in GPS based user trajectory comparison, it is indeed not necessary to consider mismatches when applying the needleman-wunsch algorithms. This leads to a simplified string editing problem known as Longest Common Subsequence (LCS). We compare our approach with Edit Distance on Real sequence (EDR) in order to provide an insight into the performance of our approach. Applying the needleman-wunsch algorithm has helped to solve several problems that emerge in GPS based user trajectory comparison such as interrupted GPS service due to satellite occlusion and various signal propagation phenomena such as signal reflection, fading etc. In order to improve the efficiency of the needleman wunsch algorithm, we apply Move ability to identify when such detrimental conditions could occur. We also apply linear approximation in order to enhance user GPS trajectories with missing points, what further improves the efficiency of user traj

关键词： needleman-wunsch algorithm GPS (Global positioning system) Sequence alignment String edit distance User trajectory comparison and experimental evaluation

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Comparison of User Trajectories with the needleman-wunsch algorithm 10

Comparison of User Trajectories with the Needleman-Wunsch Al...

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10th European-Alliance-for-Innovation (EAI) International Conference on Mobile Computing, Applications, and Services (MobiCASE)

作者： Cavojsky, Maros Drozda, Martin Slovak Univ Technol Bratislava Fac Elect Engn & Informat Technol Bratislava Slovakia

ISBN: (纸本)9783030284688;9783030284671

We show that the needleman-wunsch algorithm for sequence alignment can be efficiently applied to comparing user trajectories, where user locations are provided by Global positioning system (GPS). We compare our approach based on this algorithm with other approaches such as the pairwise method and the proximity method. We describe all steps necessary to apply the needleman-wunsch algorithm when comparing user trajectories. In our experiments we use two different data sets: a data set that we collected with 455 mobile devices distributed among our students and the Geolife data set (Microsoft Research Asia). We conclude that our approach based on the needleman-wunsch algorithm performs better than other approaches, especially, in terms of true negatives, false positives and false negatives, while still offering improvement in terms of true positives.

关键词： GPS needleman-wunsch algorithm Sequence alignment User movement patterns Experimental evaluation

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Multithreaded Parallel Sequence Alignment Based on needleman-wunsch algorithm 19

Multithreaded Parallel Sequence Alignment Based on Needleman...

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19th Annual IEEE International Conference on Bioinformatics and Bioengineering (BIBE)

作者： Gancheva, Veska Georgiev, Ivaylo Tech Univ Sofia Dept Programming & Comp Technol Sofia Bulgaria Stephan Angeloff Inst Microbiol Sofia Bulgaria

ISBN: (纸本)9781728146171

Biocomputing and molecular biology are areas that change knowledge and skills for acquisition, storing, management, analysis, interpretation and dissemination of biological information. This requires the utilization of high performance computers and innovative software tools for management of the vast information, as well as deployment of innovative algorithmic techniques for analysis, interpretation and prognostication of data in order to get to insight of the design and validation of life-science experiments. Sequence alignment is an important method in DNA and protein analysis. The paper describes the computational challenges in biological sequence processing. The great challenges are to propose parallel computational models and parallel program implementations based on the algorithms for biological sequence alignment. An investigation of the efficiency of sequence alignment based on parallel multithreaded program implementation of needleman-wunsch algorithm is presented in this paper. Parallel computational model based on needleman-wunsch algorithm is designed. The proposed parallel model is verified by multithreaded parallel program implementation utilizing OpenMP. A number of experiments have been carried out for the case of various data sets and a various number of threads. Parallel performance parameters execution time and speedup are estimated experimentally. The performance estimation and scalability analyses show that the suggested model has good scalability both in respect to the workload and machine size.

关键词： bioinformatics DNA needleman-wunsch algorithm OpenMP parallel performance sequence alignment

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A teaching approach from the exhaustive search method to the needleman-wunsch algorithm

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BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION 2017年第3期45卷 194-204页

作者： Xu, Zhongneng Yang, Yayun Huang, Beibei Jinan Univ Dept Ecol Guangzhou 510632 Guangdong Peoples R China Univ Rovira & Virgili Dept Engn Quim 26 Ave Dels Paisos Catalans Tarragona 43007 Spain Univ Texas MD Anderson Canc Ctr Dept Expt Therapeut Unit 36 Houston TX 77030 USA

The needleman-wunsch algorithm has become one of the core algorithms in bioinformatics;however, this programming requires more suitable explanations for students with different major backgrounds. In supposing sample sequences and using a simple store system, the connection between the exhaustive search method and the needleman-wunsch algorithm was analyzed to more thoroughly explain this algorithm. The present study could benefit the teaching and learning of the needleman-wunsch algorithm. (c) 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):194-204, 2017.

关键词： needleman-wunsch algorithm exhaustive search sequence alignment teaching

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Tree Alignment Based on needleman-wunsch algorithm for Sensor Selection in Smart Homes

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SENSORS 2017年第8期17卷 1902-1902页

作者： Chua, Sook-Ling Foo, Lee Kien Multimedia Univ Fac Comp & Informat Persiaran Multimedia Cyberjaya 63100 Selangor Malaysia

Activity recognition in smart homes aims to infer the particular activities of the inhabitant, the aim being to monitor their activities and identify any abnormalities, especially for those living alone. In order for a smart home to support its inhabitant, the recognition system needs to learn from observations acquired through sensors. One question that often arises is which sensors are useful and how many sensors are required to accurately recognise the inhabitant's activities? Many wrapper methods have been proposed and remain one of the popular evaluators for sensor selection due to its superior accuracy performance. However, they are prohibitively slow during the evaluation process and may run into the risk of overfitting due to the extent of the search. Motivated by this characteristic, this paper attempts to reduce the cost of the evaluation process and overfitting through tree alignment. The performance of our method is evaluated on two public datasets obtained in two distinct smart home environments.

关键词： sensor selection tree alignment needleman-wunsch algorithm activity recognition smart homes

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Research on Pairwise Sequence Alignment needleman-wunsch algorithm

Research on Pairwise Sequence Alignment Needleman-Wunsch Alg...

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2017 5th International Conference on Mechatronics,Materials,Chemistry and Computer Engineering(ICMMCCE 2017)

作者： Xiantao Jiang Xueliang Fu Gaifang Dong Honghui Li College of Computer and Information Engineering Inner Mongolia Agricultural University

The pairwise sequence alignment algorithm, needleman-wunsch is one of the most basic algorithms in biological information processing. However, the needleman-wunsch algorithm based on dynamic programming gets optimal alignment results with high time complexity and space complexity,which is *** paper proposes an improved algorithm of needleman-wunsch, and demonstrates the algorithm by experiment. With the same score and accuracy, we compare and analyze the running time before and after improvement. The experimental results show that the improved algorithm can reduce the time complexity of needleman-wunsch algorithm.

关键词： Bioinformatics Pairwise sequence alignment needleman-wunsch algorithm Dynamic programming

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Sensitive inference of alignment-safe intervals from biodiverse protein sequence clusters using EMERALD

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GENOME BIOLOGY 2023年第1期24卷 1页

作者： Grigorjew, Andreas Gynter, Artur Dias, Fernando H. C. Buchfink, Benjamin Drost, Hajk-Georg Tomescu, Alexandru I. Univ Helsinki Dept Comp Sci Helsinki Finland Max Planck Inst Biol Comp Biol Grp Tubingen Germany

Sequence alignments are the foundations of life science research, but most innovation so far focuses on optimal alignments, while information derived from suboptimal solutions is ignored. We argue that one optimal alignment per pairwise sequence comparison is a reasonable approximation when dealing with very similar sequences but is insufficient when exploring the biodiversity of the protein universe at tree-of-life scale. To overcome this limitation, we introduce pairwise alignment-safety to uncover the amino acid positions robustly shared across all suboptimal solutions. We implement EMERALD, a software library for alignment-safety inference, and apply it to 400k sequences from the SwissProt database.

关键词： Sequence alignment Dynamic programming needleman-wunsch algorithm Protein folding Suboptimal alignments

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Malicious Variant Text Alignment algorithm Based on Improved Soundshape Codes 3

Malicious Variant Text Alignment Algorithm Based on Improved...

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3rd International Conference on Electronic Information Engineering and Computer Science, EIECS 2023

作者： Li, Huiying Yang, Bei Wan, Fangjie Academy of Cyberspace Security of Zhengzhou University Zhengzhou China Zhengzhou University School of Computer and Artificial Intelligence Zhengzhou China

ISBN: (纸本)9798350316674

In order to improve the extraction ability of illegal information from various platforms in the network, this paper proposes a non-equal-length malicious foreign characters alignment algorithm based on improved soundshape code combined with needleman-wunsch algorithm. The algorithm first uses the improved soundshape code to transform Chinese characters into a special coding sequence that integrates soundshape, morphological and semantic features, and then according to the principle of maximizing the sum of the similarity of characters at each position in the sequence, the needleman-wunsch sequence comparison algorithm combining the character similarity function is utilized to complete the alignment of the original text with the deformed text by correspondence and padding. Experiments were conducted on a constructed dataset containing malicious variants, and the results show that the algorithm improves the alignment effect due to reduced character padding and accurate text correspondence. © 2023 IEEE.

关键词： Chinese character similarity needleman-wunsch algorithm Soundshape Code text alignment

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Identifying Bus Lines and Outliers in Bus Routes of Rio de Janeiro 27

Identifying Bus Lines and Outliers in Bus Routes of Rio de J...

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27th International Conference on Knowledge Based and Intelligent Information and Engineering Sytems, KES 2023

作者： Cavojsky, Maros Faculty of Electrical Engineering and Information Technology Slovak University of Technology Ilkovicova 3 Bratislava84104 Slovakia

Public transportation systems play a vital role in the mobility of cities and the quality of life of their residents. With the advent of GPS technology, it is now possible to collect vast amounts of data on the movements of public buses. In this study, we investigate if it is possible to use approach based on needleman-wunsch algorithm (NWA) for identifying bus lines from logged GPS tracks of buses based on a timetable from the year 2020 in Rio de Janeiro, Brazil. Further we discuss possible drawbacks of that approach and reasons why such approach could not be efficiently used. As alternative we introduce approach that relies solely on the order of bus stops encoded in geohash codes to identify the correct bus line of track, eliminating the inaccuracies caused by location interpolation used in NWA. Our findings suggest that approach based on NWA could not be efficiently used for labeling logged GPS bus tracks by bus lines because of interpolation and global alignment. But introduced alternative approach could reliable assign to bus tracks their bus line. Such approach is also able to filter out inaccurate bus tracks and outliers. Detecting anomalies and outliers can provide valuable insights into the transportation patterns of cities, and analyzing the data from public transportation systems can inform the development of more efficient and effective transportation policies. © 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (https://***/licenses/by-nc-nd/4.0)

关键词： Bus routes Geohash GPS dataset needleman-wunsch algorithm

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