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IEEE Symposium Series on Computational Intelligence (SSCI)

作者： Tianye Shu Yang Nan Ke Shang Hisao Ishibuchi Department of Computer Science and Engineering Guangdong Provincial Key Laboratory of Brain-inspired Intelligent Computation Southern University of Science and Technology Shenzhen China

In evolutionary multi-objective optimization (EMO), one important issue is to efficiently remove dominated solutions from a large number of solutions examined by an EMO algorithm. An efficient approach to remove dominated solutions from a large solution set is to partition it into small subsets. Dominated solutions are removed from each subset independently. This partition method is fast but cannot guarantee to remove all dominated solutions. To further remove remaining dominated solutions, a simple idea is to iteratively perform this approach. In this paper, we first examine three partition methods (random, objective value-based and cosine similarity-based methods) and their iterative versions through computational experiments on artificial test problems (DTLZ and WFG) and real-world problems. Our results show that the choice of an appropriate partition method is problem dependent. This observation motivates us to use a hybrid approach where different partition methods are used in an iterative manner. The results show that all dominated solutions are removed by the hybrid approach in most cases. Then, we examine the effects of the following factors on the computation time and the removal performance: the number of objectives, the shape of the Pareto front, and the number of subsets in each partition method.

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Controllability analysis of transcriptional regulatory networks for Saccharomyces cerevisiae 44

Controllability analysis of transcriptional regulatory netwo...

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44th Annual Conference of the IEEE Industrial Electronics Society, IECON 2018

作者： Liu, Suling Wang, Pei Xu, Qiong Chen, Aimin Lü, Jinhu School of Mathematics and Statistics Henan University Kaifeng China School of Mathematics and Statistics Institute of Applied Mathematics Laboratory of Data Analysis Technology Henan University Kaifeng China School of Mathematics and Statistics Institute of Applied Mathematics Henan University Kaifeng China School of Automation Science and Electrical Engineering State Key Laboratory of Software Development Environment Beijing Advanced Innovation Center for Big Data Brain Machine Intelligence Beihang University Beijing China

ISBN: (纸本)9781509066841

Structural controllability of complex networks has been a research focus in recent years. However, few works considered the structural controllability of biological networks, especially for dynamic biological networks. In this paper, structural controllability of one static and five dynamic transcriptional regulatory networks (TRNs) for Saccharomyces cerevisiae (S. cerevisiae) have been investigated. The five dynamic networks included two endogenous and three exogenous ones. We clarified the controllability properties of these networks, as well as explored the differences among different types of networks. Our results revealed that the structural properties of different types of networks are significantly different. We found that the TRNs are rather difficult to be fully controlled. However, the dynamic TRNs were relatively easier to be controlled than the static one, and one needs relatively more external inputs to control the exogenous TRNs than the endogenous ones. Based on the structural controllability analysis of subnetworks with the same sizes, as well as randomly perturbed networks by preserving degree distributions, we further illustrated that the structural controllability of the six networks may be mainly dominated by their degree distributions. Our investigations clarify the control properties of TRNs in S. cerevisiae, it provides some insights on real-world control of biological networks. © 2018 IEEE.

关键词： Complex networks

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DeepNFT: Towards Precise Neurofibrillary Tangle Detection via Improving Multi-scale Feature Fusion and Adversary

DeepNFT: Towards Precise Neurofibrillary Tangle Detection vi...

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2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

作者： Jiang, Yankai Zhang, Lei Li, Yiming He, Xiangyang Huang, Hanxiao Zhu, Keqing Tao, Yubo Lin, Hai State Key Laboratory of CADCG College of Computer Science and Technology Zhejiang University Hangzhou China Zhejiang University School of Medicine China Brain Bank and Department of Neurology in Second Affiliated Hospital Key Laboratory of Medical Neurobiology of Zhejiang Province Department of Neurobiology Hangzhou China Department of Pathology Zhejiang University School of Medicine Hangzhou China

ISBN: (纸本)9781665401265

Detecting neurofibrillary tangles is an important procedure in the assessment of the intensity and distribution pattern of hippocampal tau pathology, which are the principal clinical phenotypes associated with Alzheimer's disease. Existing deep learning based detectors still face a critical obstacle: the difficulty in detecting extremely small objects in high resolution images. In this paper, we propose a deep learning framework, named DeepNFT, which combines the multilevel feature aggregation pyramid network (MFAPN) and the adversarial feature generation module (AFGM) to acquire precise detection results with significantly reduced false positives. To prove its universality and robustness, DeepNFT has been validated on two datasets. Experiments show the significant performance gain of our proposed approach over state-of-the-art detectors. Ablation study shows our network components improve the performance of various backbones and detectors. © 2021 IEEE.

关键词： Generative adversarial networks

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Noninvasive Tracking of Every Individual in Unmarked Mouse Groups Using Multi-Camera Fusion and Deep Learning

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Neuroscience Bulletin 2023年第6期39卷 893-910页

作者： Feng Su Yangzhen Wang Mengping Wei Chong Wang Shaoli Wang Lei Yang Jianmin Li Peijiang Yuan Dong-Gen Luo Chen Zhang Department of Neurobiology School of Basic Medical SciencesBeijing Key Laboratory of Neural Regeneration and RepairCapital Medical UniversityBeijing100069China Chinese Institute for Brain Research Beijing102206China State Key Laboratory of Translational Medicine and Innovative Drug Development Nanjing210000China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China School of Life Sciences Tsinghua UniversityBeijing100084China School of Biological Science and Medical Engineering Beihang UniversityBeijing100191China The Key Laboratory of Developmental Genes and Human Disease Institute of Life SciencesSoutheast UniversityNanjing210096JiangsuChina Institute for Artificial Intelligence the State Key Laboratory of Intelligence Technology and SystemsBeijing National Research Center for Information Science and TechnologyDepartment of Computer Science and TechnologyTsinghua UniversityBeijing100084China School of Mechanical Engineering and Automation Beihang UniversityBeijing100191China

Accurate and efficient methods for identifying and tracking each animal in a group are needed to study complex behaviors and social *** tracking methods(e.g.,marking each animal with dye or surgically implanting microchips)can be invasive and may have an impact on the social behavior being *** overcome these shortcomings,video-based methods for tracking unmarked animals,such as fruit flies and zebrafish,have been ***,tracking individual mice in a group remains a challenging problem because of their flexible body and complicated interaction *** this study,we report the development of a multi-object tracker for mice that uses the Faster region-based convolutional neural network(R-CNN)deep learning algorithm with geometric transformations in combination with multi-camera/multi-image fusion *** system successfully tracked every individual in groups of unmarked mice and was applied to investigate chasing *** proposed system constitutes a step forward in the noninvasive tracking of individual mice engaged in social behavior.

关键词： Noninvasive tracking Deep learning Multi-camera Mouse group Social interaction

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Evolutionary multi-objective optimization algorithm framework with three solution sets

arXiv

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arXiv 2020年

作者： Ishibuchi, Hisao Pang, Lie Meng Shang, Ke Guangdong Provincial Key Laboratory of Brain-inspired Intelligent Computation Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen China

It is assumed in the evolutionary multi-objective optimization (EMO) community that a final solution is selected by a decision maker from a non-dominated solution set obtained by an EMO algorithm. The number of solutions to be presented to the decision maker can be totally different. In some cases, the decision maker may want to examine only a few representative solutions from which a final solution is selected. In other cases, a large number of non-dominated solutions may be needed to visualize the Pareto front. In this paper, we suggest the use of a general EMO framework with three solution sets to handle various situations with respect to the required number of solutions. The three solution sets are the main population of an EMO algorithm, an external archive to store promising solutions, and a final solution set which is presented to the decision maker. The final solution set is selected from the archive. Thus the population size and the archive size can be arbitrarily specified as long as the archive size is not smaller than the required number of solutions. The final population is not necessarily to be a good solution set since it is not presented to the decision maker. Through computational experiments, we show the advantages of this framework over the standard final population and final archive frameworks. We also discuss how to select a final solution set and how to explain the reason for the selection, which is the first attempt towards an explainable EMO framework. © 2020, CC BY.

关键词： Decision making

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Two-Stage Lazy Greedy Inclusion Hypervolume Subset Selection for Large-Scale Problem

Two-Stage Lazy Greedy Inclusion Hypervolume Subset Selection...

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IEEE International Conference on Systems, Man and Cybernetics

作者： Yang Nan Tianye Shu Hisao Ishibuchi Department of Computer Science and Engineering Guangdong Provincial Key Laboratory of Brain-inspired Intelligent Computation Southern University of Science and Technology Shenzhen China

Hypervolume subset selection (HSS) is a hot topic in the evolutionary multi-objective optimization (EMO) community since hypervolume is the most widely-used performance indicator. In the literature, most HSS algorithms were designed for small-scale HSS (e.g., environmental selection: select $N$ solutions from $2N$ solutions where $N$ is the population size). Few researchers focus on large-scale HSS as a post-processing procedure in an unbounded external archive framework (i.e., subset selection from all examined solutions). In this paper, we propose a two-stage lazy greedy inclusion HSS (TGI-HSS) algorithm for large-scale HSS. In the first stage of TGI- HSS, a small solution set is selected from a large-scale candidate set using an efficient subset selection method (which is not based on exact hypervolume calculation). In the second stage, the final subset is selected from the small solution set using an existing efficient HSS algorithm. Experimental results show that the computational time can be significantly reduced by the proposed algorithm in comparison with other state-of-the-art HSS algorithms at the cost of only a small deterioration of the selected subset quality.

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How to Find a Large Solution Set to Cover the Entire Pareto Front in Evolutionary Multi-Objective Optimization

How to Find a Large Solution Set to Cover the Entire Pareto ...

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IEEE International Conference on Systems, Man and Cybernetics

作者： Lie Meng Pang Yang Nan Hisao Ishibuchi Department of Computer Science and Engineering Guangdong Provincial Key Laboratory of Brain-inspired Intelligent Computation Southern University of Science and Technology Shenzhen China

Recently, it has been pointed out in many studies that the performance of evolutionary multi-objective optimization (EMO) algorithms can be improved by selecting solutions from all examined solutions stored in an unbounded external archive. This is because in general the final population is not the best subset of the examined solutions. To obtain a good final solution set in such a solution selection framework, subset selection from a large candidate set (i.e., all examined solutions) has been studied. However, since good subsets cannot be obtained from poor candidate sets, a more important issue is how to find a good candidate set, which is the focus of this paper. In this paper, we first visually demonstrate that the entire Pareto front is not covered by the examined solutions through computational experiments using MOEA/D, NSGA-III and SMS-EMOA on DTLZ test problems. That is, the examined solution set stored in the unbounded archive has some large holes (i.e., some uncovered area of the Pareto front). Next, to evaluate the quality of the examined solution set (i.e., to measure the size of the largest hole), we propose the use of a variant of the inverted generational distance (IGD) indicator. Then, we propose a simple modification of EMO algorithms to improve the quality of the examined solution set. Finally, we demonstrate the effectiveness of the proposed modification through computational experiments.

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Algorithm configurations of MOEA/D with an unbounded external archive

arXiv

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arXiv 2020年

作者： Pang, Lie Meng Ishibuchi, Hisao Shang, Ke Guangdong Provincial Key Laboratory of Brain-inspired Intelligent Computation Department of Computer Science and Engineering Southern University of Science and Technology Shenzhen China

In the evolutionary multi-objective optimization (EMO) community, it is usually assumed that the final population is presented to the decision maker as the result of the execution of an EMO algorithm. Recently, an unbounded external archive was used to evaluate the performance of EMO algorithms in some studies where a pre-specified number of solutions are selected from all the examined non-dominated solutions. In this framework, which is referred to as the solution selection framework, the final population does not have to be a good solution set. Thus, the solution selection framework offers higher flexibility to the design of EMO algorithms than the final population framework. In this paper, we examine the design of MOEA/D under these two frameworks. First, we show that the performance of MOEA/D is improved by linearly changing the reference point specification during its execution through computational experiments with various combinations of initial and final specifications. Robust and high performance of the solution selection framework is observed. Then, we examine the use of a genetic algorithm-based offline hyper-heuristic method to find the best configuration of MOEA/D in each framework. Finally, we further discuss solution selection after the execution of an EMO algorithm in the solution selection framework. Copyright © 2020, The Authors. All rights reserved.

关键词： Heuristic methods

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Effects of Initialization Methods on the Performance of Surrogate-Based Multiobjective Evolutionary Algorithms

Effects of Initialization Methods on the Performance of Surr...

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IEEE Symposium Series on Computational Intelligence (SSCI)

作者： Jinyuan Zhang Hisao Ishibuchi Linjun He Yang Nan Department of Computer Science and Engineering Guangdong Provincial Key Laboratory of Brain-inspired Intelligent Computation Southern University of Science and Technology Shenzhen China

Initialization plays a crucial role in surrogate-based multiobjective evolutionary algorithms (MOEAs) when tackling computationally expensive multiobjective optimization problems. During the initialization process, solutions are generated to train surrogate models. Consequently, the accuracy of these surrogate models depends on the quality of the initial solutions, which in turn directly impacts the performance of surrogate-based MOEAs. Despite the widespread use of Latin hypercube sampling as an initialization method in surrogate-based MOEAs, there is a lack of comprehensive research examining the effectiveness of different initialization methods. Additionally, the impact of the number of initial solutions on the performance of surrogate-based MOEAs remains largely unexplored. This paper aims to bridge these research gaps by comparing the usefulness of two commonly employed initialization methods (i.e., random sampling and Latin hypercube sampling) in surrogate-based MOEAs. Furthermore, it investigates how varying the number of initial solutions influences the performance of surrogate-based MOEAs.

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Ensemble R2-based Hypervolume Contribution Approximation

Ensemble R2-based Hypervolume Contribution Approximation

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IEEE Symposium Series on Computational Intelligence (SSCI)

作者： Guotong Wu Tianye Shu Yang Nan Ke Shang Hisao Ishibuchi Department of Computer Science and Engineering Guangdong Provincial Key Laboratory of Brain-inspired Intelligent Computation Southern University of Science and Technology Shenzhen China

The hypervolume-based multi-objective evolutionary algorithms (HV-MOEAs) have proven to be highly effective in solving multi-objective optimization problems. However, the computation time of the hypervolume calculation increases significantly as the number of objectives increases. To address this issue, an R2-based hypervolume contribution approximation (R2-HVC) method was proposed. Nevertheless, the original R2-HVC generates a large number of vectors and computes the HVC only once. In this study, we propose an ensemble method based on the R2-HVC method. By using a small number of vectors for repetitive computation and majority voting, the ensemble method can reduce the probability of making incorrect choices. Experimental results show that the proposed method can improve the approximation accuracy while maintaining a similar computation time to the original R2-HVC method.

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