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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Jing Gao Fa Zhang Kai Hu Xuefeng Cui Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education Xiangtan University Xiangtan China Institute of Computing Technology Chinese Academy of Sciences Beijing China Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province Xiangnan University Chenzhou China School of Medical Technology Beijing Institute of Technology Beijing China School of Computer Science and Technology Shandong University Qingdao China

ISBN: (数字)9781665468190

ISBN: (纸本)9781665468206

Recent advances in spatial transcriptomics have enabled the comprehensive measurement of transcriptional profiles while retaining the spatial contextual information. Identifying spatial domains is a critical step in the analysis of spatially resolved transcriptomics. Existing unsupervised methods perform poorly on this task owing to the large amount of noise and dropout events in the transcriptomic profiles. To address this problem, we first extend an unsupervised algorithm to a supervised learning method that can identify useful features and reduce noise hindrance. Second, inspired by the classical convolution in convolutional neural networks (CNNs), we designed a regular hexagonal convolution to compensate for the missing gene expression patterns from adjacent nodes. Compared with the graph convolution in graph neural networks (GNNs), our hexagonal convolution can preserve the relative spatial location information of different nodes in graph-structured data. Third, based on the hexagonal convolution, a novel hexagonal Convolutional Neural Network (hexCNN) is proposed for spatial transcriptomics classification. Finally, we compared the proposed hexCNN with existing methods on the DLPFC dataset. The results show that hexCNN achieves a classification accuracy of 87.2% and an average Rand index (ARI) of 78.2% (1.9% and 3.3% higher than those of GNNs).

关键词： Visualization Convolution Supervised learning Interference Spatial databases Graph neural networks Convolutional neural networks

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Timing-Driven High-Level Synthesis for Continuous-Flow Microfluidic Biochips

Timing-Driven High-Level Synthesis for Continuous-Flow Micro...

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IEEE International Symposium on Quality Electronic Design

作者： Zhengyang Ye Zhisheng Chen Youlin Pan Genggeng Liu Wenzhong Guo Tsung-Yi Ho Xing Huang College of Computer and Data Science Fuzhou University Fuzhou China Engineering Research Center of Big Data Intelligence Ministry of Education Fuzhou China Fujian Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou University Fuzhou China School of Informatics Xiamen University Xiamen China Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong China School of Computer Science Northwestern Polytechnical University Xi’an China

ISBN: (数字)9798350309270

ISBN: (纸本)9798350309287

As continuous-flow microfluidic biochips technology rapidly advances, its automated synthesis methods require adapting to increasingly complex and stringent biochemical applications. In particular, with the introduction of time-sensitive bioassays, in this work, we present a timing-driven high-level synthesis method to optimize the resource efficiency of bioassays considering the time constraints. Specifically, we investigate the existing forms of time constraints and propose a corresponding flexible modeling approach based on reaction-control which can achieve downward compatibility for physical design. Additionally, we also analyze the impact of storage and wash on time constraints. The experimental results show that our method achieves efficient execution and low devices cost while satisfying time constraints.

关键词： Costs Biochips Time factors Microfluidics Physical design

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Co-training based prediction of multi-label protein–protein interactions

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Computers in Biology and Medicine 2024年 177卷 108623-108623页

作者： Tang, Tao Zhang, Xiaocai Li, Weizhuo Wang, Qing Liu, Yuansheng Cao, Xiaofeng School of Modern Posts Nanjing University of Posts and Telecommunications 9 Wenyuan Rd Jiangsu Nanjing210023 China 1 Fusionopolis Way Singapore138632 Singapore School of Management Nanjing University of Posts and Telecommunications 9 Wenyuan Rd Jiangsu Nanjing210023 China College of Computer Science and Electronic Engineering Hunan University 2 Lushan Rd Hunan Changsha410086 China Key Laboratory of Intelligent Computing & Signal Processing of Ministry of Education Anhui University 111 Jiulong Road Anhui Hefei230601 China School of Artificial Intelligence Jilin University 2699 Qianjin St Changchun Jilin130012 China

Prediction of protein–protein interaction (PPI) types enhances the comprehension of the underlying structural characteristics and functions of proteins, which gives rise to a multi-label classification problem. The nominal features describe the physicochemical characteristics of proteins directly, establishing a more robust correlation with the interaction types between proteins than ordered features. Motivated by this, we propose a multi-label PPI prediction model referred to as CoMPPI (Co-training based Multi-Label prediction of Protein–Protein Interaction). This approach aims to maximize the utility of both ordered and nominal features extracted from protein sequences. Specifically, CoMPPI incorporates graph convolutional network (GCN) and 1D convolution operation to process the complementary subsets of features individually, leveraging both local and contextualized information in a more efficient way. In addition, two multi-type PPI datasets were constructed to eliminate the duplication in previous datasets. We compare the performance of CoMPPI with three state-of-the-art methods on three datasets partitioned using distinct schemes (Breadth-first search, Depth-first search, and Random), CoMPPI consistently outperforms the other methods across all cases, demonstrating improvements ranging from 3.81% to 32.40% in Micro-F1. The subsequent ablation experiment confirms the efficacy of employing the co-training framework for multi-label PPI prediction, indicating promising avenues for future advancements in this domain. © 2024 Elsevier Ltd

关键词： Proteins

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A Multi-scale Generalized Shrinkage Threshold Network for Image Blind Deblurring in Remote Sensing

arXiv

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arXiv 2023年

作者： Feng, Yujie Yang, Yin Fan, Xiaohong Zhang, Zhengpeng Zhang, Jianping School of Mathematics and Computational Science Xiangtan University Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory for Intelligent Computing and Information Processing The Ministry of Education Xiangtan411105 China School of Mathematics and Computational Science Xiangtan University National Center for Applied Mathematics in Hunan Hunan International Scientific and Technological Innovation Cooperation Base of Computational Science Xiangtan411105 China School of Automation and Electronic Information Xiangtan University Xiangtan411105 China

MSC Codes 54H30, 68U10, 94A08Remote sensing images are essential for many applications of the earth’s sciences, but their quality can usually be degraded due to limitations in sensor technology and complex imaging environments. To address this, various remote sensing image deblurring methods have been developed to restore sharp and high-quality images from degraded observational data. However, most traditional model-based deblurring methods usually require predefined hand-crafted prior assumptions, which are difficult to handle in complex applications. On the other hand, deep learning-based deblurring methods are often considered as black boxes, lacking transparency and interpretability. In this work, we propose a new blind deblurring learning framework that utilizes alternating iterations of shrinkage thresholds. This framework involves updating blurring kernels and images, with a theoretical foundation in network design. Additionally, we propose a learnable blur kernel proximal mapping module to improve the accuracy of the blur kernel reconstruction. Furthermore, we propose a deep proximal mapping module in the image domain, which combines a generalized shrinkage threshold with a multi-scale prior feature extraction block. This module also incorporates an attention mechanism to learn adaptively the importance of prior information, improving the flexibility and robustness of prior terms, and avoiding limitations similar to hand-crafted image prior terms. Consequently, we design a novel multi-scale generalized shrinkage threshold network (MGSTNet) that focuses specifically on learning deep geometric prior features to enhance image restoration. Experimental results on real and synthetic remote sensing image datasets demonstrate the superiority of our MGSTNet framework compared to existing deblurring methods. Copyright © 2023, The Authors. All rights reserved.

关键词： Shrinkage

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Theory of polygonal phases self-assembled from T-shaped liquid crystalline molecules

arXiv

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arXiv 2023年

作者： He, Zhijuan Wang, Xin Zhang, Pingwen Shi, An-Chang Jiang, Kai Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan411105 China School of Mathematics and Statistics Wuhan University Wuhan430072 China School of Mathematical Sciences Peking University Beijing100871 China Department of Physics and Astronomy McMaster University HamiltonONL8S 4M1 Canada

Extensive experimental studies have shown that numerous ordered phases can be formed via the self-assembly of T-shaped liquid crystalline molecules (TLCMs) composed of a rigid backbone, two flexible end chains and a flexible side chain. However, a comprehensive understanding of the stability and formation mechanisms of these intricately nanostructured phases remains incomplete. Here we fill this gap by carrying out a theoretical study of the phase behaviour of TLCMs. Specifically, we construct phase diagrams of TLCMs by computing the free energy of different ordered phases of the system. Our results reveal that the number of polygonal edges increases as the length of side chain or interaction strength increases, consistent with experimental observations. The theoretical study not only reproduces the experimentally observed phases and phase transition sequences, but also systematically analyzes the stability mechanism of the polygonal phases. Copyright © 2023, The Authors. All rights reserved.

关键词： Free energy

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Steady-state Analysis of Bipolar Transistor

Steady-state Analysis of Bipolar Transistor

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Progress in Electromagnetic Research Symposium (PIERS)

作者： Yeqiang Yan Xingang Ren Shuping He Xiaotao Huang Zhixiang Huang Anhui Province Key Laboratory of Target Recognition and Feature Extraction Luan China Information Materials and Intelligent Sensing Laboratory of Anhui Province Institute of Physical Science and Information Technology Anhui University Hefei China Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education Anhui University Hefei China Lingnan Normal University Zhanjiang China

ISBN: (纸本)9781665409889

Numerical simulation of semiconductor devices enable the quick obtain of the device physical characteristics. However, the trial productions of the semiconductor devices have the disadvantages of long cycle and high cost. Therefore, it is necessary to carry out numerical simulation investigating semiconductor devices. We propose the coupling approach and the decoupling-Gummel method to solve the semiconductor equations. The results of the two methods are compared with the commercial software. Numerical experiment indicates that the results obtained by our method are accurate. When the transistor is at a low voltage bias, the decoupling method converges faster than the coupling method. In the case of high voltage bias, the decoupling method has a slower convergence speed than the coupling method, even difficult to converge for higher voltage bias. However, the coupling method has higher memory requirements than the Gummel method. Therefore, we need to balance the advantages of the coupling method and the Gummel method when conduct the numerical simulation.

关键词： Couplings Bipolar transistors Voltage Production Numerical simulation Mathematical models Software

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RECOVERY TYPE A POSTERIORI ERROR ESTIMATION OF AN ADAPTIVE FINITE ELEMENT METHOD FOR CAHN-HILLIARD EQUATION

arXiv

引用

arXiv 2023年

作者： Chen, Yaoyao Huang, Yunqing Yi, Nianyu Yin, Peimeng School of Mathematics and Statistics Anhui Normal University Wuhu241000 China Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan411105 China Hunan Key Laboratory for Computation and Simulation in Science and Engineering School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan411105 China Multiscale Methods and Dynamics Group Computer Science and Mathematics Division Oak Ridge National Laboratory Oak RidgeTN37831 United States

In this paper, we derive a novel recovery type a posteriori error estimation of the Crank-Nicolson finite element method for the Cahn-Hilliard equation. To achieve this, we employ both the elliptic reconstruction technique and a time reconstruction technique based on three time-level approximations, resulting in an optimal a posteriori error estimator. We propose a time-space adaptive algorithm that utilizes the derived a posteriori error estimator as error indicators. Numerical experiments are presented to validate the theoretical findings, including comparing with an adaptive finite element method based on a residual type a posteriori error estimator. © 2023, CC BY-NC-ND.

关键词： Recovery

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DHMM-Based Asynchronous Finite-Time Sliding Mode Control for Markovian Jumping Lur’e Systems

Research Square

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Research Square 2021年

作者： Nie, Rong Du, Wenli Li, Zhongmei Zhou, Zhao He, Shuping Key Laboratory of Smart Manufacturing in Energy Chemical Process East China University of Science and Technology Ministry of Education Shanghai200237 China Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education School of Electrical Engineering and Automation Anhui University Hefei230601 China School of Electronic Information and Electrical Engineering Chengdu University Chengdu610106 China

This paper is concerned with the asynchronous problem for a class of Markovian jumping Lur’s system (MJLSs) via sliding mode control (SMC) in continuous-time domain. Specifically, the discrete hidden Markovian model (DHMM) is employed to describe the nonsynchronization between the controller modes and the MJLSs modes. In particular, considering the nonlinearity of MJLSs, a novel Lur’e-integral-type sliding surface is constructed. In order to ensure the finite-time stability of sliding mode dynamics and the accessibility of the specified sliding surface, the asynchronous Lur’e-type SMC law of the detector mode is presented. Finally, an example of DC motor is provided to demonstrate the effectiveness of the proposed technique. © 2021, CC BY.

关键词： Sliding mode control

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An Interpretable MRI Reconstruction Network with Two-grid-cycle Correction and Geometric Prior Distillation

arXiv

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arXiv 2022年

作者： Fan, Xiaohong Yang, Yin Chen, Ke Zhang, Jianping Dong, Ke The School of Mathematics and Computational Science Xiangtan University Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education Xiangtan411105 China The School of Mathematics and Computational Science Xiangtan University Hunan National Applied Mathematics Center Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan411105 China Centre for Mathematical Imaging Techniques Department of Mathematical Sciences The University of Liverpool Merseyside LiverpoolL6972L United Kingdom The School of Mathematics and Computational Science Xiangtan University Hunan National Applied Mathematics Center Key Laboratory of Intelligent Computing & Information Processing of Ministry of Education Xiangtan411105 China Department of Radiation Oncology Xiangtan Central Hospital Xiangtan411101 China

Although existing deep learning compressed-sensing-based Magnetic Resonance Imaging (CS-MRI) methods have achieved considerably impressive performance, explainability and generalizability continue to be challenging for such methods since the transition from mathematical analysis to network design not always natural enough, often most of them are not flexible enough to handle multi-sampling-ratio reconstruction assignments. In this work, to tackle explainability and generalizability, we propose a unifying deep unfolding multi-sampling-ratio interpretable CS-MRI framework. The combined approach offers more generalizability than previous works whereas deep learning gains explainability through a geometric prior module. Inspired by the multigrid algorithm, we first embed the CSMRI-based optimization algorithm into correction-distillation scheme that consists of three ingredients: pre-relaxation module, correction module and geometric prior distillation module. Furthermore, we employ a condition module to learn adaptively step-length and noise level, which enables the proposed framework to jointly train multi-ratio tasks through a single model. The proposed model not only compensates for the lost contextual information of reconstructed image which is refined from low frequency error in geometric characteristic k-space, but also integrates the theoretical guarantee of model-based methods and the superior reconstruction performances of deep learning-based methods. Therefore, it can give us a novel perspective to design biomedical imaging networks. Numerical experiments show that our framework outperforms state-of-the-art methods in terms of qualitative and quantitative evaluations. Our method achieves 3.18 dB improvement at low CS ratio 10% and average 1.42 dB improvement over other comparison methods on brain dataset using Cartesian sampling mask. Copyright © 2022, The Authors. All rights reserved.

关键词： Distillation

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Using Deep Active Learning to Save Sensing Cost When Estimating Overall Air Quality 15th

Using Deep Active Learning to Save Sensing Cost When Estimat...

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15th International Conference on Green, Pervasive, and Cloud computing, GPC 2020

作者： Lei, Dehao Yu, Zhiyong Li, Peiguan Han, Lei Huang, Fangwan College of Mathematics and Computer Science Fuzhou University Fuzhou China Fujian Provincial Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou University Fuzhou China Key Laboratory of Spatial Data Mining and Information Sharing Ministry of Education Fuzhou China

ISBN: (纸本)9783030642426

Air quality is widely concerned by the governments and people. To save cost, air quality monitoring stations are deployed at only a few locations, and the stations are actuated at partial time. Therefore, it is necessary to study how to actively collect a subset of air quality data to maximize the estimation accuracy of air quality at other locations and time. In order to solve this challenge, we propose the active variational adversarial model (AVAM) that selects the most valuable unlabeled samples through two iterative phases of active learning. In the first phase of our model, a candidate set with unlabeled samples is selected through traditional active learning. In the second phase, variational auto-encoder (VAE) is used to obtain the compressed representation of the candidate set and the training set with labeled samples, then a discriminator based on three-layer neural network is trained from the compressed representation. Finally the discriminator can output the most valuable unlabeled samples from the candidate set. The experimental results show that the AVAM proposed in this paper is superior to active learning models with the first or second phase only. © 2020, Springer Nature Switzerland AG.

关键词： Air quality

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