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FAS-UNet: A Novel FAS-driven Unet to Learn Variational Image Segmentation

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arXiv 2022年

作者： Zhu, Hui Shu, Shi Zhang, Jianping The School of Mathematics and Computational Science Xiangtan University Key Laboratory of Intelligent Computing & Information Processing Ministry of Education China The School of Mathematics and Computational Science Xiangtan University Hunan Key Laboratory for Computation and Simulation in Science and Engineering Xiangtan411105 China The School of Mathematics and Computational Science Xiangtan University Hunan National Applied Mathematics Center China

Solving variational image segmentation problems with hidden physics is often expensive and requires different algorithms and manually tunes model parameter. The deep learning methods based on the U-Net structure have obtained outstanding performances in many different medical image segmentation tasks, but designing such networks requires a lot of parameters and training data, not always available for practical problems. In this paper, inspired by traditional multi-phase convexity Mumford-Shah variational model and full approximation scheme (FAS) solving the nonlinear systems, we propose a novel variational-model-informed network (denoted as FAS-Unet) that exploits the model and algorithm priors to extract the multi-scale features. The proposed model-informed network integrates image data and mathematical models, and implements them through learning a few convolution kernels. Based on the variational theory and FAS algorithm, we first design a feature extraction sub-network (FAS-Solution module) to solve the model-driven nonlinear systems, where a skip-connection is employed to fuse the multi-scale features. Secondly, we further design a convolution block to fuse the extracted features from the previous stage, resulting in the final segmentation possibility. Experimental results on three different medical image segmentation tasks show that the proposed FAS-Unet is very competitive with other state-of-the-art methods in qualitative, quantitative and model complexity evaluations. Moreover, it may also be possible to train specialized network architectures that automatically satisfy some of the mathematical and physical laws in other image problems for better accuracy, faster training and improved generalization. The code is available at https://***/zhuhui100/FASUNet. Copyright © 2022, The Authors. All rights reserved.

关键词： Image segmentation

A Novel Preference-Driven Dynamic Multi-Objective Evolutionary Algorithm for Solving Dynamic Multi-Objective Problems

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SSRN

SSRN 2023年

作者： Wang, Xueqing Zheng, Jinhua Hou, Zhanglu Liu, Yuan Zou, Juan Xia, Yizhang Yang, Shengxiang Key Laboratory of Intelligent Computing and Information Processing Ministry of Education School of Computer Science School of Cyberspace Science Xiangtan University Hunan Province Xiangtan China School of Computer Science School of Cyberspace Science of Xiangtan University Xiangtan411105 China School of Computer Science and Informatics De Montfort University LeicesterLE1 9BH United Kingdom

Most research on dynamic multi-objective optimization primarily concentrates on tracking the true Pareto optimal front (POF) and Pareto optimal set (POS) quickly and accurately when the environment undergoes changes. However, there are real-world scenarios where it is necessary to simultaneously solve changing objective functions and satisfy the preference of Decision Makers (DMs). Specifically, the DMs may be only interested in a partial region of the POF, known as the region of interest (ROI), rather than requiring the entire POF. To meet the challenge of simultaneously predicting a changing POF and/or POS and dynamic ROI, this paper proposes a new dynamic multi-objective evolutionary algorithm (DMOEAs) based on the preference. The proposed algorithm comprises three main components: an evolutionary direction adjustment strategy based on changing reference points to accommodate preference shifts, an angle-based search strategy for tracking the varying ROI, and a hybrid prediction strategy combining linear prediction models and population manifold estimation within the ROI to ensure convergence and distribution in unchanged preference scenarios. Experimental studies conducted on 16 widely used benchmark problems and empirical results demonstrate the significant advantages of the proposed algorithm over existing state-of-the-art DMOEAs. © 2023, The Authors. All rights reserved.

关键词： Evolutionary algorithms

Hexagonal Convolutional Neural Network for Spatial Transcriptomics Classification

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Hexagonal Convolutional Neural Network for Spatial Transcrip...

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

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

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

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

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

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

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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

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

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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

Steady-state Analysis of Bipolar Transistor

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Steady-state Analysis of Bipolar Transistor

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

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

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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