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Performing DNA Strand Displacement with DNA Polymerase 14th

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Performing DNA Strand Displacement with DNA Polymerase

14th International Conference on Bio-inspired Computing: Theories and Applications, BIC-TA 2019

作者： Wang, Zhiyu Hu, Yingxin Chen, Zhekun Liao, Sulin Huang, Yabing Key Laboratory of Image Information Processing and Intelligent Control of Education Ministry of China School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan730074 China School of Computer Science and Technology Huazhong University of Science and Technology Wuhan730074 China Department of Pathology Renmin Hospital of Wuhan University Wuhan430060 China

ISBN: (纸本)9789811534140

Significant improvements to the dynamic DNA nano science have emerged in recent years, primarily due to the elaborate design of toehold-mediated DNA strand displacement (TMSD). However, it remains an ongoing challenge to design huge-scaled TMSD based sophisticated dynamic DNA structures without base-pair mismatching or unwanted secondary structures, because the sequence design complexity of TMSD will dramatically increase as the scale increases. Here we report a new polymerase triggered strand displacement (PTSD) mechanism to realize DNA strand displacement with the potential of constructing complicated dynamic DNA nanostructures. By employing proper polymerase with strand displacement activity, the target strand in a duplex will be displaced and freed during the polymerization. In this manner, DNA strand displacement takes place without considering the design complexity of branch migration domain. The mechanism was successfully applied in constructing one-layer and two-layer circuits in which the parameters involved were explored, suggesting that PTSD is feasible and able to be harnessed to construct cascading DNA circuits with high complexity. © 2020, Springer Nature Singapore Pte Ltd.

关键词： DNA

Temperature measurement based on electron spin resonance of magnetic nanoparticles

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arXiv 2021年

作者： Wang, Shuai Zhong, Jing Liu, Wenzhong School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China Belt and Road Joint Laboratory on Measurement and Control Technology Huazhong University of Science and Technology Wuhan430074 China Key Laboratory of Image Processing and Intelligent Control Huazhong University of Science and Technology Ministry of Education Wuhan430074 China School of Instrumentation and Optoelectronic Engineering Beihang University Beijing100191 China

Magnetic nanoparticles (MNPs) have excellent magnetic-temperature characteristic. However, current temperature measurement based on MNPs is interfered by concentration. Utilizing the electron spin resonance (ESR), we propose a highly sensitive temperature measurement method without concentration coupling. The anisotropic field is affected by temperature, thus affecting the g-value. The influence of the MNP concentration, size, and the data analysis method on temperature estimation are studied. The optimal temperature sensitivity is achieved with 15-nm MNPs while Gaussian smoothing method allows an optimal accuracy at Fe concentration of 5 mg/ml with a standard deviation of 0.07 K. Copyright © 2021, The Authors. All rights reserved.

关键词： Magnetic moments

A protocol for structured illumination microscopy with minimal reconstruction artifacts

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Biophysics Reports 2019年第2期5卷 80-90页

作者： Junchao Fan Xiaoshuai Huang Liuju Li Shan Tan Liangyi Chen Key Laboratory of Image Processing and Intelligent Control of Ministry of Education of China School of Automation Huazhong University of Science and Technology State Key Laboratory of Membrane Biology Beijing Key Laboratory of Cardiometabolic Molecular MedicineInstitute of Molecular Medicine Peking University

The imaging rate of structured illumination microscopy(SIM) reached 188 Hz recently. As the exposure time decreases, the camera detects fewer virtual photons, while the noise level remains the same. As a result, the signal-to-noise ratio(SNR) decreases sharply. Furthermore, the SNR decreases further because of photobleaching and phototoxicity. This decreased quality of SIM raw data may lead to surprising artifacts with various causes, which may confuse a new user of SIM microscopy. We summarize three significant possible sources of severe artifacts in reconstructed super-resolution(SR)images. Ultrafast motion of a biological sample or an uneven illumination pattern is the most difficult to be identified. The estimated parameter could also be incorrect, leading to artifact of regular ***, reconstruction with the Wiener method generates stochastic artifacts due to the amplification of noise during the deconvolution process. To deal with these problems, we have established a protocol to reconstruct ultrafast SIM raw data obtained in low SNR conditions. First, we checked the quality of the raw data with the image J plugin SIMcheck before reconstruction. Then, a modified parameter estimation method was used to improve the precision of the parameters. Finally, an iterative algorithm was used for SIM reconstruction under low signal-to-noise ratio conditions. This procedure effectively suppressed the artifacts in the super-resolution images reconstructed from raw data of low signal-to-noise ratio.

关键词： Ultrafast SIM Low signal-to-noise ratio Reconstruction

Tigc-Net: Transformer-Improved Graph Convolution Network for Spatio-Temporal Prediction

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SSRN

SSRN 2022年

作者： Chen, Kai Yang, Chunfeng Zhou, Zhengyuan Liu, Yao Ji, Tianjiao Sun, Weiya Chen, Yang School of Cyber Science and Engineering Southeast University Nanjing210096 China Key Laboratory of Computer Network and Information Integration Southeast University Ministry of Education Nanjing210096 China The College of Software Engineering Southeast University Nanjing210096 China Laboratory of Image Science and Technology The School of Computer Science and Engineering Southeast University Nanjing210096 China Jiangsu Key Laboratory of Molecular and Functional Imaging Department of Radiology Zhongda Hospital Southeast University Nanjing210009 China Jiangsu Provincial Joint International Research Laboratory of Medical Information Processing School of Computer Science and Engineering Southeast University Nanjing210096 China NHC Key Laboratory of Medical Virology and Viral Diseases National Institute for Viral Disease Control and Prevention Chinese Center for Disease Control and Prevention Beijing China Beijing Institute of Tracking and Communication Technology Beijing100094 China

Modeling spatio-temporal sequences is an important topic yet challenging for existing neural networks. Most of the current spatio-temporal sequence prediction methods usually capture features separately in temporal and spatial dimensions or employ multiple mutually independent local spatio-temporal graphs to represent a spatio-temporal sequence. The first kind of method mentioned above is difficult to mine the complex spatio-temporal correlations, while the other is limited for the accuracy of long-term predictions. To handle these issues, this paper proposes a Transformer-Improved Graph Convolution Network for spatio-temporal prediction. Specifically, the temporal location encoding method is exploited to derive the spatio-temporal characteristics of the sequence utilizing a spatio-temporal feature fusion network. In addition, a spatio-temporal attention network is developed to enhance the spatio-temporal correlation of the sequence, and the dynamic spatial features of sequence are further extracted through the adaptive graph convolution network. A private dataset and a public dataset are employed to demonstrate the performance of the proposed TIGC-Net. The qualitative and quantitative results show that the proposed TIGC-Net can extract dynamic spatiotemporal properties more effectively, enhance the spatio-temporal correlation of sequences and improve the prediction accuracy compared with four stateof-the-art. © 2022, The Authors. All rights reserved.

关键词： Convolution

Adaptive Fuzzy Tracking control with Global Prescribed-Time Prescribed Performance for Uncertain Strict-Feedback Nonlinear Systems

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arXiv 2022年

作者： Mao, Bing Wu, Xiaoqun Liu, Hui Xu, Yuhua Lü, Jinhu The School of Mathematics and Statistics Wuhan University Hubei430072 China Hubei Key Laboratory of Computational Science Wuhan University Hubei430072 China Research Center of Complex Network Wuhan University Hubei430072 China The School of Automation Huazhong University of Science and Technology Hubei430074 China The Key Laboratory of Image Processing and Intelligent Control of Education Ministry of China Hubei430074 China The School of Statistics and Data Science Nanjing Audit University Jiangsu211815 China The School of Automation Science and Electrical Engineering Beihang University Beijing100191 China

Adaptive fuzzy control strategies are established to achieve global prescribed performance with prescribed-time convergence for strict-feedback systems with mismatched uncertainties and unknown nonlinearities. Firstly, to quantify the transient and steady performance constraints of the tracking error, a class of prescribed-time prescribed performance functions are designed, and a novel error transformation function is introduced to remove the initial value constraints and solve the singularity problem in existing works. Secondly, based on dynamic surface control methods, controllers with or without approximating structures are established to guarantee that the tracking error achieves prescribed transient performance and converges into a prescribed bounded set within prescribed time. In particular, the settling time and initial value of the prescribed performance function are completely independent of initial conditions of the tracking error and system parameters, which improves existing results. Moreover, with a novel Lyapunov-like energy function, not only the differential explosion problem frequently occurring in backstepping techniques is solved, but the drawback of the semi-global boundedness of tracking error induced by dynamic surface control can be overcome. The validity and effectiveness of the main results are verified by numerical simulations on practical examples. Copyright © 2022, The Authors. All rights reserved.

关键词： Fuzzy control

Exploiting learnable joint groups for hand pose estimation

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arXiv 2020年

作者： Li, Moran Gao, Yuan Sang, Nong Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China Tencent AI Lab United States

In this paper, we propose to estimate 3D hand pose by recovering the 3D coordinates of joints in a group-wise manner, where less-related joints are automatically categorized into different groups and exhibit different features. This is different from the previous methods where all the joints are considered holistically and share the same feature. The benefits of our method are illustrated by the principle of multi-task learning (MTL), i.e., by separating less-related joints into different groups (as different tasks), our method learns different features for each of them, therefore efficiently avoids the negative transfer (among less related tasks/groups of joints). The key of our method is a novel binary selector that automatically selects related joints into the same group. We implement such a selector with binary values stochastically sampled from a Concrete distribution, which is constructed using Gumbel softmax on trainable parameters. This enables us to preserve the differentiable property of the whole network. We further exploit features from those less-related groups by carrying out an additional feature fusing scheme among them, to learn more discriminative features. This is realized by implementing multiple 1x1 convolutions on the concatenated features, where each joint group contains a unique 1x1 convolution for feature fusion. The detailed ablation analysis and the extensive experiments on several benchmark datasets demonstrate the promising performance of the proposed method over the state-of-the-art (SOTA) methods. Besides, our method achieves top-1 among all the methods that do not exploit the dense 3D shape labels on the most recently released FreiHAND competition at the submission date. The source code and models are available at https://***/moranli-aca/LearnableGroups-Hand. Copyright © 2020, The Authors. All rights reserved.

关键词： Convolution

FCM-RDpA: TSK fuzzy regression model construction using fuzzy C-means clustering, regularization, droprule, and powerball adabelief

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arXiv 2020年

作者： Shi, Zhenhua Wu, Dongrui Guo, Chenfeng Zhao, Changming Cui, Yuqi Wang, Fei-Yue Ministry of Education Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China State Key Laboratory for Management and Control of Complex Systems Institute of Automation Chinese Academy of Sciences Beijing China

To effectively optimize Takagi-Sugeno-Kang (TSK) fuzzy systems for regression problems, a mini-batch gradient descent with regularization, DropRule, and AdaBound (MBGD-RDA) algorithm was recently proposed. This paper further proposes FCM-RDpA, which improves MBGD-RDA by replacing the grid partition approach in rule initialization by fuzzy c-means clustering, and AdaBound by Powerball AdaBelief, which integrates recently proposed Powerball gradient and AdaBelief to further expedite and stabilize parameter optimization. Extensive experiments on 22 regression datasets with various sizes and dimensionalities validated the superiority of FCM-RDpA over MBGD-RDA, especially when the feature dimensionality is higher. We also propose an additional approach, FCM-RDpAx, that further improves FCM-RDpA by using augmented features in both the antecedents and consequents of the rules. Copyright © 2020, The Authors. All rights reserved.

关键词： Gradient methods

Path Planning Algorithm for Unmanned Surface Vessel Based on Multiobjective Reinforcement Learning

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Computational intelligence and neuroscience 2023年第1期2023卷 2146314页

作者： Caipei Yang Yingqi Zhao Xuan Cai Wei Wei Xingxing Feng Kaibo Zhou MOE Key Laboratory of Image Information Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan 430074 China. Wuhan Second Ship Design and Research Institute Wuhan 430205 China.

It is challenging to perform path planning tasks in complex marine environments as the unmanned surface vessel approaches the goal while avoiding obstacles. However, the conflict between the two subtarget tasks of obstacle avoidance and goal approaching makes the path planning difficult. Thus, a path planning method for unmanned surface vessel based on multiobjective reinforcement learning is proposed under the complex environment with high randomness and multiple dynamic obstacles. Firstly, the path planning scene is set as the main scene, and the two subtarget scenes including obstacle avoidance and goal approaching are divided from it. The action selection strategy in each subtarget scene is trained through the double deep -network with prioritized experience replay. A multiobjective reinforcement learning framework based on ensemble learning is further designed for policy integration in the main scene. Finally, by selecting the strategy from subtarget scenes in the designed framework, an optimized action selection strategy is trained and used for the action decision of the agent in the main scene. Compared with traditional value-based reinforcement learning methods, the proposed method achieves a 93% success rate in path planning in simulation scenes. Furthermore, the average length of the paths planned by the proposed method is 3.28% and 1.97% shorter than that of PER-DDQN and dueling DQN, respectively.

关键词：

Research on Public Opinion Guidance Strategy based on Interaction Constraints

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Research on Public Opinion Guidance Strategy based on Intera...

IEEE Information Technology and Mechatronics Engineering Conference (ITOEC)

作者： Yuanyuan Xu Zhan Wu Xi Chen School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China Image Processing and Intelligent Control Key Laboratory of the Education Ministry of China Wuhan China

ISBN: (数字)9781728143231

ISBN: (纸本)9781728143248

The dissemination of public opinion has a considerable impact on people's social lives, and the question of how both the government and the media can correctly guide public opinion and restore social stability is an issue that requires urgent attention. Combining the characteristics of public opinion dissemination in the network society leads to individual interaction. Considering the interaction between individual views and network topology, this paper combines the collaborative network model with the distance-constrained Hegselmann-Krause (HK) model to propose a consensus-guided strategy based on interaction constraints. It does this by changing the network topology and limiting the scope of individual interactions, thereby affecting the spread of public opinion. Based on the small-world network, the collaborative network model introduces the two parameters of Connection edge probability p and broken edge probability q, while also proposing a collaborative network model for Connection edge's breaking of the network based on the difference of individual opinion values. This paper designs simulation experiments by changing p, q, and the interaction distance, while also analyzing the results of public opinion's evolution from the perspectives of timeliness and the diversity of viewpoints. The experimental results show that when individuals are restricted from interacting with the surrounding environment and the scope of interaction between individuals is restricted, this will slow down the evolution of public opinion and increase the number of opinion clusters. By contrast, when it is encouraged, the interaction between individuals and the surrounding environment will make the entire system communicate more effectively within a short period of time, promoting the evolutionary benefits of public opinion considerably, shortening the convergence time of public opinion evolution to reach a steady state, and reducing the number of opinion clusters. The strategy is consist

关键词： Network topology Collaborative work Social network services Economics Government Bridges Media