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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

作者： Ji, Haoping Wang, Yanfeng Sun, Junwei Henan Key Lab of Information-Based Electrical Appliances Zhengzhou University of Light Industry Zhenzhou450002 China School of Electrical and Information Engineering Zhengzhou University of Light Industry Zhenzhou450002 China

ISBN: (纸本)9789811912559

As a typical dna nanotechnology, dna strand displacement reaction has attracted many scholars to investigate. In this paper, a four-variable chaotic system is proposed by multiplication, degradation, and adjustment dna strand displacement modules, and the dynamic behaviors of designed chaotic system are analysed by the software of Matlab and Visual DSD. the simulation results show that our strand displacement chaotic system can realize the production of chaotic signals. Our work uses biological reactions to achieve the construction of chaotic systems, which can provide a reference for the future researches of chaotic system. © 2022, Springer Nature Singapore Pte Ltd.

关键词： Chaotic systems

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

16th International Conference on Bio-Inspired Computing: The...

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

ISBN: (纸本)9789811912528

the proceedings contain 67 papers. the special focus in this conference is on Bio-Inspired computing: theories and Applications. the topics include: Firefly Algorithm with Opposition-Based Learning;a Multi-direction Prediction Multi-objective Hybrid Chemical Reaction Optimization Algorithm for Dynamic Multi-objective Optimization;optimal Overbooking Appointment Scheduling in Hospitals Using Evolutionary Markov Decision Process;an Improved Bare-Bones Multi-objective Artificial Bee Colony Algorithm;surrogate-Assisted Artificial Bee Colony Algorithm;a Hybrid Multi-objective Coevolutionary Approach for the Multi-user Agile Earth Observation Satellite Scheduling Problem;a Node Influence Based Memetic Algorithm for Community Detection in Complex Networks;water Wave Optimization with Distributed-Learning Refraction;a Differential Evolution Algorithm for Multi-objective Mixed-Variable Optimization Problems;Implementation and Application of NSGA-III Improved Algorithm in Multi-objective Environment;solving Satellite Range Scheduling Problem with Learning-Based Artificial Bee Colony Algorithm;Synchronization of Chaos with a Single Driving Variable Feedback Control Based on dna Strand Displacement;an Optimization Method of Course Scheduling Problem Based on Improved Genetic Algorithm;A Multi-UUV Formation Control and Reorganization Method Based on Path Tracking Controller and Improved Ant Colony Algorithm;an Effective Data Balancing Strategy Based on Swarm Intelligence Algorithm for Malicious Code Detection and Classification;an Optimization Task Scheduling Model for Multi-robot Systems in Intelligent Warehouses;feature Selection Method Based on Ant Colony Optimization Algorithm and Improved Neighborhood Discernibility Matrix;a Cuckoo Quantum Evolutionary Algorithm for the Graph Coloring Problem;attribute Selection Method Based on Artificial Bee Colony Algorithm and Neighborhood Discrimination Matrix Optimization;black Widow Spider Algorithm Based on Differential Evolution and

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

16th International Conference on Bio-Inspired Computing: The...

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16th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2021

ISBN: (纸本)9789811912559

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A privacy-preserving image retrieval scheme based secure kNN, dna coding and deep hashing

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MULTIMEDIA TOOLS AND APPLICATIONS 2021年第15期80卷 22733-22755页

作者： Cheng, Shu-Li Wang, Lie-Jun Huang, Gao Du, An-Yu Xinjiang Univ Coll Informat Sci & Engn Urumqi 830046 Peoples R China Tsinghua Univ Dept Automat Beijing 100084 Peoples R China

In recent years, information leakage incidents occur frequently. Ciphertext domain search has become a hot spot in multimedia technology and software engineering. therefore, how to mine valuable information safely and effectively is very important. In this paper, we present the CBIR solution and complete the relevant software development. the proposed method not only outsources CBIR services but also avoids privacy leaks. Our main contributions are reflected in two aspects: improving search efficiency and protecting user privacy. For one thing, we propose a novel privacy protection algorithm to encrypt images. For the other thing, we propose an integrated deep hash algorithm to extract the high-level features of images. In the index encryption process, we use secure kNN to encrypt the index. through experimental analysis and argumentation, the proposed privacy protection algorithm has a lower correlation coefficient and a better information entropy. It is secure enough and can resist common types of attacks encountered during data transmission. the proposed secure image retrieval algorithm is tested on two datasets. Compared with the same type of algorithm, the proposed algorithm has better retrieval performance. In short, the privacy reservation scheme guarantees the security and effectiveness of the system.

关键词： Multimedia Privacy protection Deep hash Cloud computing Image encryption Secure kNN

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16th international conference on Parallel computing Technologies, PaCT 2021

16th International Conference on Parallel Computing Technolo...

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16th international conference on Parallel computing Technologies, PaCT 2021

ISBN: (纸本)9783030863586

the proceedings contain 36 papers. the special focus in this conference is on Parallel computing Technologies. the topics include: High-Efficiency Specialized Support for Dense Linear Algebra Arithmetic in LuNA System;efficient Cluster Parallelization Technology for Aerothermodynamics Problems;computational Aspects of Solving Grid Equations in Heterogeneous computing Systems;optimized Hybrid Execution of Dense Matrix-Matrix Multiplication on Clusters of Heterogeneous Multicore and Many-Core Platforms;Parallelization of Robust Multigrid Technique Using OpenMP Technology;Network Reliability Calculation with Use of GPUs;implicit Data Layout Optimization for Portable Parallel programming in C++;On Defragmentation Algorithms for GPU-Native Octree-Based AMR Grids;zipped Data Structure for Adaptive Mesh Refinement;A New Model-Based Approach to Performance Comparison of MPI Collective Algorithms;automatic Parallel Tiled Code Generation Based on Dependence Approximation;Scalability Issues in FFT Computation;High Performance Implementation of Boris Particle Pusher on DPC++. A First Look at oneAPI;Evaluating the Performance of Kunpeng 920 Processors on Modern HPC Applications;optimization of Resources Allocation in High Performance Distributed computing with Utilization Uncertainty;influence of Execution Time Forecast Accuracy on the Efficiency of Scheduling Jobs in a Distributed Network of Supercomputers;Performance Estimation of a BOINC-Based Desktop Grid for Large-Scale molecular Docking;consensus-Free Ledgers When Operations of Distinct Processes are Commutative;design and Implementation of Highly Scalable Quantifiable Data Structures;optimal Concurrency for List-Based Sets;Deterministic OpenMP and the LBP Parallelizing Manycore Processor;mobile Agents Operating on a Grid: Some Non-conventional Issues in Parallel computing;parallel Computations in Integrated Environment of Engineering Modeling and Global Optimization.

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A Novel Autonomous molecular Mechanism Based on Spatially Localized dna Computation 15th

A Novel Autonomous Molecular Mechanism Based on Spatially Lo...

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15th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2020

作者： Wang, Yue Qian, Mengyao Hu, Wenxiao Wang, Luhui Dong, Yafei School of Computer Science Shaanxi Normal University Xi’an Shaanxi710119 China College of Life Science Shaanxi Normal University Xi’an Shaanxi710119 China

ISBN: (纸本)9789811613531

Contemporary dna synthesis technology matures, and the development provides intriguing possibilities for dynamic manipulation of dna self-assembly, which plays a pivotal role in the behavior of designing versatile nanodevices and generating controllable networks. Similarly, in synthetic molecular circuits, the spatially localized architecture furnishes a different strategy, allowing for immobilized dna molecules in close vicinity to each other. Herein, the formal modeling language was utilized to mark the address with a specific sequence of location tags, thus a set of routes were precisely arranged at the nanoscale. Beyond building a collection of separate modules, computer simulations were used to explore further complex assemblies of the building blocks. By orchestrating a series of dna strand displacement operations locally, autonomous movement and addressing operations were realized, completing the group transport and partition storage of dissimilar molecules. the nanodevice gives the dna molecule its mechanical properties and follows an embedded "molecular program". the simulation results of the Visual DSD tool provided qualitative and quantitative proof for the operation of the system. © 2021, Springer Nature Singapore Pte Ltd.

关键词： dna

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computing with chemical reaction networks: a tutorial

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NATURAL computing 2019年第1期18卷 119-137页

作者： Brijder, Robert Hasselt Univ Diepenbeek Belgium

Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we discuss a method to implement arbitrary (abstract) CRNs in a test tube using dna. Finally, we discuss relationships between CRNs and other models of computation.

关键词： Chemical reaction networks dna strand displacement Population protocols Petri nets

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Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual international Biocuration conference in Padua, Italy

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DATABASE-thE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2024年第2024期2024卷 baae073页

作者： Martinez, Karina Agirre, Jon Akune, Yukie Aoki-Kinoshita, Kiyoko F. Arighi, Cecilia Axelsen, Kristian B. Bolton, Evan Bordeleau, Emily Edwards, Nathan J. Fadda, Elisa Feizi, Ten Hayes, Catherine Ives, Callum M. Joshi, Hiren J. Krishna Prasad, Khakurel Kossida, Sofia Lisacek, Frederique Liu, Yan Luetteke, thomas Ma, Junfeng Malik, Adnan Martin, Maria Mehta, Akul Y. Neelamegham, Sriram Panneerselvam, Kalpana Ranzinger, Rene Ricard-Blum, Sylvie Sanou, Gaoussou Shanker, Vijay thomas, Paul D. Tiemeyer, Michael Urban, James Vita, Randi Vora, Jeet Yamamoto, Yasunori Mazumder, Raja George Washington Univ Sch Med & Hlth Sci Dept Biochem & Mol Med Ross HallRoom 540 2300 1 St NW Washington DC 20037 USA Univ York Dept Chem York Struct Biol Lab Wentworth Way York YO10 5DD England Imperial Coll London Glycosci Lab Hammersmith CampusDu Cane Rd London W12 0NN England Soka Univ Glycan & Life Syst Integrat Ctr GaLSIC 1-236 Tangi Machi Hachioji Tokyo 1928577 Japan Univ Delaware Dept Comp & Informat Sci 18 Amstel Ave Newark DE 19716 USA Swiss Inst Bioinformat SIB Swiss Prot Grp CMU1 Rue Michel Servet CH-1211 Geneva 4 Switzerland NIH Natl Ctr Biotechnol Informat Natl Lib Med 8600 Rockville Pike Bethesda MD 20894 USA Univ British Columbia Michael Smith Labs 2185 East Mall Vancouver BC V6T 1Z4 Canada Georgetown Univ Dept Biochem & Mol & Cellular Biol 2115 Wisconsin Ave NW Washington DC 20007 USA Maynooth Univ Dept Chem Kilcock Rd Maynooth W23 AH3Y Co Kildare Ireland Maynooth Univ Hamilton Inst Kilcock Rd Maynooth W23 AH3Y Co Kildare Ireland Swiss Inst Bioinformat SIB Proteome Informat Grp Route Drize 7 CH-1227 Geneva Switzerland Univ Copenhagen Fac Hlth Sci Copenhagen Ctr Glyc Dept Cellular & Mol Med Blegdamsvej 3 DK-2200 Copenhagen Denmark Extreme Light Infrastructure ERIC ELI Beamlines Facil Za Radn 835 Dolni Brezany 25241 Czech Republic Univ Montpellier UM Inst Human Genet IGH Natl Ctr Sci Res CNRS IMGT Int ImMunoGeneT Informat Syst 141 Rue Cardonille F-34090 Montpellier France Justus Liebig Univ Giessen Inst Vet Physiol & Biochem Frankfurter Str 100 D-35392 Giessen Germany Georgetown Univ Med Ctr Lombardi Comprehens Canc Ctr Dept Oncol 3900 Reservior Rd NW Washington DC 20007 USA European Bioinformat Inst EMBL EBI European Mol Biol Lab Wellcome Genome Campus Cambridge CB10 1SD England Harvard Med Sch Beth Israel Deaconess Med Ctr Natl Ctr Funct Glyc Dept Surg 330 Brookline Ave Boston MA 02215 USA Univ Buffalo State Univ New York Dept Chem & Biol Engn 906 Furnas Hall Buffalo NY 14260 USA Univ Buffalo State

Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information focus primarily on the macromolecules within the central dogma of molecular biology (dna, RNA, proteins). To gain a better understanding of organisms, there is a need to capture the functional impact of glycans and glycosylation on biological processes. A workshop titled "Functional impact of glycans and their curation" was held in conjunction with the 16th Annual international Biocuration conference to discuss ongoing worldwide activities related to glycan function curation. this workshop brought together subject matter experts, tool developers, and biocurators from over 20 projects and bioinformatics resources. Participants discussed four key topics for each of their resources: (i) how they curate glycan function-related data from publications and other sources, (ii) what type of data they would like to acquire, (iii) what data they currently have, and (iv) what standards they use. their answers contributed input that provided a comprehensive overview of state-of-the-art glycan function curation and annotations. this report summarizes the outcome of discussions, including potential solutions and areas where curators, data wranglers, and text mining experts can collaborate to address current gaps in glycan and glycosylation annotations, leveraging each other's work to improve their respective resources and encourage impactful data sharing among *** URL: https://***/Glycan_Function_Workshop_2023

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Verification in staged tile self-assembly

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NATURAL computing 2019年第1期18卷 107-117页

作者： Schweller, Robert Winslow, Andrew Wylie, Tim Univ Texas Rio Grande Valley Dept Comp Sci Edinburg TX 78539 USA

We prove the unique assembly and unique shape verification problems, benchmark measures of self-assembly model power, are coNP(NP)-hard and contained in PSPACE (and in II2sP for staged systems with s stages). En route... 详细信息

关键词： dna computing Biocomputing 2HAM Hierarchical

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A Block-Based Systolic Array on an HBM2 FPGA for dna Sequence Alignment 16th

A Block-Based Systolic Array on an HBM2 FPGA for DNA Sequenc...

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16th international Symposium on Applied Reconfigurable computing

作者： Ben Abdelhamid, Riadh Yamaguchi, Yoshiki Univ Tsukuba Grad Sch Syst & Informat Engn 1-1-1 Ten Ou Dai Tsukuba Ibaraki 3058573 Japan Univ Tsukuba Fac Engn Informat & Syst 1-1-1 Ten Ou Dai Tsukuba Ibaraki 3058573 Japan

ISBN: (纸本)9783030445331;9783030445348

Revealing the optimal local similarity between a pair of genomic sequences is one of the most fundamental issues in bioinformatics. the Smith-Waterman algorithm is a method that was developed for that specific purpose. With the continuous advances in the computer field, this method becomes widely used to an extent where it expanded its reach to cover a broad range of applications, even in areas such as network packet inspections and pattern matching. this algorithm is based on Dynamic programming and is guaranteed to find the optimal local sequence alignment between two base pairs. the computational complexity is O(mn), where m and n are defined as the number of the elements of a query and a database sequence, respectively. Researchers have investigated several manners to accelerate the calculation using CPU, GPU, Cell B.E., and FPGA. Most of them have proposed a data-reuse approach because the Smith-Waterman algorithm has rather high "bytes per operation";in other words, the Smith-Waterman algorithm requires large memory bandwidth. In this paper, we try to minimize the impact of the memory bandwidth bottleneck through the implementation of a block-based systolic array approach that maximizes the usage of memory banks in HBM2 (High Bandwidth Memory). the proposed approach demonstrates a higher performance in terms of GCUPS (Giga Cell Update Per Second) compared to one of the best cases reported in previous works, and also achieves a significant improvement in power efficiency. For example, our implementation could reach 429.39 GCUPS while achieving a power efficiency of 7.68 GCUPS/W. With a different configuration, it could reach 316.73 GCUPS while hitting a peak power efficiency of 8.86 GCUPS/W.

关键词： dna sequence alignment Smith-Waterman algorithm Systolic array HBM2 High Level Synthesis Reconfigurable High Performance computing

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