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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Jiang, Hanjing Wang, Meineng Zhang, Luping Huang, Yu-An Li, Yangyuan Huang, Yabing Huazhong University of Science and Technology Key Laboratory of Image Information Processing and Intelligent Control Education Ministry of China Institute of Artificial Intelligence School of Artificial Intelligence and Automation Hubei Wuhan430074 China China University of Mining and Technology School of Computer Science and Technology Xuzhou221116 China Yichun University School of Mathematics and Computer Science Yichun336000 China East China University of Technology School of Information Engineering Nanchang330013 China Northwestern Polytechnical University School of Computer Science Xi'an710129 China Renmin Hospital Wuhan University Department of Pathology Wuhan430060 China

ISBN: (纸本)9798350386226

The advent of single-cell RNA sequencing (scRNA-seq) has facilitated the acquisition of high-resolution data regarding cell heterogeneity across various tissues. A fundamental and critical step in the analysis of scRNA-seq data is cell type identification. An appropriate graph construction strategy can reflect the topological structure between cells and allows for detailed exploration of the relationships between cells and genes. Given the sparsity of scRNA-seq data and the pronounced noise generated by shallow sequencing, choosing an appropriate graph construction strategy has become a significant challenge. In this paper, we propose a single-cell clustering method, named Sc-PNNMF, based on structural perturbation of nonnegative matrix factorization. Sc-PNNMF employs a structural perturbation algorithm to optimize the gene expression matrix. The optimized matrix guides the matrix factorization process, effectively overcoming the impact of data sparsity and significant noise in gene expression data on the graph construction strategy. We compared the clustering abilities of Sc-PNNMF with five other methods on ten real datasets. © 2024 IEEE.

关键词： Non-negative matrix factorization

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Fuzzy control for Uncertain Vehicle Active Suspension Systems via Dynamic Sliding-Mode Approach

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IEEE Transactions on Systems, Man, and Cybernetics: Systems 2017年第1期47卷 24-32页

作者： Wen, Shiping Chen, Michael Z. Q. Zeng, Zhigang Yu, Xinghuo Huang, Tingwen School of Automation Huazhong University of Science and Technology Wuhan430074 China Key Laboratory of Image Processing and Intelligent Control of Education Ministry of China Wuhan430074 China Department of Mechanical Engineering University of Hong Kong Hong Kong Hong Kong Platform Technologies Research Institute RMIT University MelbourneVIC3001 Australia Texas A and M University at Qatar Doha23874 Qatar

This paper investigates the fuzzy control issue for uncertain active suspension systems via dynamic sliding-mode method. The Takagi-Sugeno fuzzy approach is adopted on the background of the varying masses to describe the prescribed nonlinear system in order to achieve the design targets via the method of sector nonlinearity. This paper employs the dynamic sliding-mode scheme to control nonlinear active suspension systems. In the proposed sliding-mode control scheme, the sliding surface function is formed linearly with the system states and control inputs. Then, a fuzzy dynamic term is utilized to construct the sliding-mode feedback controller. In existing results, the sliding mode is achieved and maintained with no consideration of the system perturbations. Thus, sufficient conditions are proposed to make the sliding surface reachable with the existence of the system perturbations to make the augmented system stable. Finally, simulation results are presented to verify the effectiveness of the proposed schemes. © 2013 IEEE.

关键词： Robust control

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Towards an inclusive computational model of visual cortex

Towards an inclusive computational model of visual cortex

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IEEE Symposium on Bioinformatics and Bioengineering (BIBE)

作者： M. Gheiratmand H. Soltanian-Zadeh H. Khaloozadeh Electrical Engineering Department K.N. Toosi University of Technology Tehran Iran Radiology Department Henry Ford Health System Image Analysis and Communications Laboratory Detroit MI USA School of Cognitive Sciences Institute for Studies Theoretical Physics and Mathematics (IPM) Tehran Iran Control and Intelligent Processing Center of Excellence Electrical and Computer Engineering Department University of Tehran Tehran Iran

Understanding the primatespsila visual system has been one of the challenging problems of different groups of scientists for years. Though many studies, from physiology and neuroscience to computer vision, are done on different aspects of visual processing in the cortex, a comprehensive computational model of visual cortex is still missing. We have implemented a computational model of object recognition in ventral visual pathway in our previous work. This hierarchical model covers visual areas V1/V2, V4/PIT, and AIT sending inputs to the Prefrontal Cortex (PFC) for categorization. To extend our model, in this work, we have added a simple model of motion detection in neurons of areas V1 and MT of the dorsal stream to our previous model. This has enabled the model to perform another principal function of the visual cortex, i.e., motion perception.

关键词： Brain modeling Computational modeling Neurons Biological system modeling Object recognition Motion analysis Solid modeling Visual system Computer vision Motion detection

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Underwater image enhancement via histogram similarity-oriented color compensation complemented by multiple attribute adjustment

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intelligent Marine Technology and Systems 2023年第1期1卷 1-15页

作者： Wang, Hao Frery, Alejandro C. Li, Mingjie Ren, Peng College of Control Science and Engineering China University of Petroleum (East China) Qingdao China College of Mathematics and Statistics Victoria University of Wellington Wellington New Zealand Key Laboratory of Intelligent Perception and Image Understanding of the Ministry of Education Xidian University Xi’an China South China Sea Institute of Planning and Environmental Research State Oceanic Administration Guangzhou China College of Oceanography and Space Informatics China University of Petroleum (East China) Qingdao China

Underwater images are often influenced by color casts, low contrast, and blurred details. We observe that images taken in natural settings typically have similar histograms across color channels, while underwater images do not. To improve the natural appearance of an underwater image, it is critical to improve the histogram similarity across its color channels. To address this problem, we develop a histogram similarity-oriented color compensation method that corrects color casts by improving the histogram similarity across color channels in the underwater image. In addition, we apply the multiple attribute adjustment method, including max-min intensity stretching, luminance map-guided weighting, and high-frequency edge mask fusion, to enhance contrast, saturation, and sharpness, effectively addressing problems of low contrast and blurred details and eventually enhancing the overall appearance of underwater images. Particularly, the method proposed in this work is not based on deep learning, but it effectively enhances a single underwater image. Comprehensive empirical assessments demonstrated that this method exceeds state-of-the-art underwater image enhancement techniques. To facilitate public assessment, we made our reproducible code available at https://***/wanghaoupc/UIE_HS2CM2A.

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Isoform Function Prediction Based on Heterogeneous Graph Attention Networks

Isoform Function Prediction Based on Heterogeneous Graph Att...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Kuo Guo Yifan Li Hao Chen Hong-Bin Shen Yang Yang Department of Computer Science and Engineering Shanghai Jiao Tong University and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China Computational Biology Department School of Computer Science Carnegie Mellon University Pittsburgh PA USA

Isoforms refer to different mRNA molecules transcribed from the same gene, which can be translated into proteins with varying structures and functions. Predicting the functions of isoforms is an essential topic in bioinformatics as it can provide valuable insights into the intricate mechanisms of gene regulation and biological processes. Conventionally, gene function labels are standardized in Gene Ontology (GO) terms. However, traditional methods for predicting isoform function are largely limited by the absence of isoform-specific labels, sparse annotations, and the vast number of GO terms. To address these issues, we propose HANIso, a deep learning-based method for isoform function prediction. HANIso leverages a pretrained protein language model to extract features from protein sequences. It also integrates heterogeneous information, such as isoform sequence features, GO annotations, and isoform interaction data, using a Heterogeneous Graph Attention Network (HAN). This allows the model to learn the importance of different sources of information and their semantic relationships through the attention mechanism. Our method can predict function labels at both the gene level and isoform level. We conduct experiments on two species datasets, and the results demonstrate that our method outperforms existing methods on both AUROC and AUPRC. HANIso has the potential to overcome the limitations of traditional methods and provide a more accurate and comprehensive understanding of isoform function.

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Utility-Oriented Underwater image Quality Assessment Based on Transfer Learning

arXiv

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arXiv 2022年

作者： Chen, Weiling Lin, Rongfu Liao, Honggang Zhao, Tiesong Gu, Ke Le Callet, Patrick Fujian Key Lab for Intelligent Processing and Wireless Transmission of Media Information Fuzhou University Fuzhou350108 China Peng Cheng Laboratory Shenzhen518000 China The Faculty of Information Technology Beijing University of Technology Engineering Research Center of Intelligent Perception and Autonomous Control Ministry of Education Beijing Key Laboratory of Computational Intelligence and Intelligent System Beijing Artificial Intelligence Institute Beijing100124 China Équipe Image Perception et Interaction Laboratoire des Sciences du Numérique de Nantes Université de Nantes France

The widespread image applications have greatly promoted the vision-based tasks, in which the image Quality Assessment (IQA) technique has become an increasingly significant issue. For user enjoyment in multimedia systems, the IQA exploits image fidelity and aesthetics to characterize user experience;while for other tasks such as popular object recognition, there exists a low correlation between utilities and perceptions. In such cases, the fidelity-based and aesthetics-based IQA methods cannot be directly applied. To address this issue, this paper proposes a utility-oriented IQA in object recognition. In particular, we initialize our research in the scenario of underwater fish detection, which is a critical task that has not yet been perfectly addressed. Based on this task, we build an Underwater image Utility Database (UIUD) and a learning-based Underwater image Utility Measure (UIUM). Inspired by the top-down design of fidelity-based IQA, we exploit the deep models of object recognition and transfer their features to our UIUM. Experiments validate that the proposed transfer-learning-based UIUM achieves promising performance in the recognition task. We envision our research provides insights to bridge the researches of IQA and computer vision. Copyright © 2022, The Authors. All rights reserved.

关键词： Multimedia systems

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BoostTree and BoostForest for Ensemble Learning

arXiv

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arXiv 2020年

作者： Zhao, Changming Wu, Dongrui Huang, Jian Yuan, Ye Zhang, Hai-Tao Peng, Ruimin Shi, Zhenhua Key Laboratory of the Ministry of Education for Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China Shenzhen Huazhong University of Science and Technology Research Institute Shenzhen China The Autonomous Intelligence Unmanned Systems Engineering Research Center of Ministry of Education of China The State Key Lab of Digital Manufacturing Equipment and Technology Wuhan China

Bootstrap aggregating (Bagging) and boosting are two popular ensemble learning approaches, which combine multiple base learners to generate a composite model for more accurate and more reliable performance. They have been widely used in biology, engineering, healthcare, etc. This paper proposes BoostForest, which is an ensemble learning approach using BoostTree as base learners and can be used for both classification and regression. BoostTree constructs a tree model by gradient boosting. It increases the randomness (diversity) by drawing the cut-points randomly at node splitting. BoostForest further increases the randomness by bootstrapping the training data in constructing different BoostTrees. BoostForest generally outperformed four classical ensemble learning approaches (Random Forest, Extra-Trees, XGBoost and LightGBM) on 35 classification and regression datasets. Remarkably, BoostForest tunes its parameters by simply sampling them randomly from a parameter pool, which can be easily specified, and its ensemble learning framework can also be used to combine many other base learners. Copyright © 2020, The Authors. All rights reserved.

关键词： Classification (of information)

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SliceProp: A Slice-Wise Bidirectional Propagation Model for Interactive 3D Medical image Segmentation

SliceProp: A Slice-Wise Bidirectional Propagation Model for ...

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Medical Artificial Intelligence (MedAI), IEEE International Conference on

作者： Xin Xu Wenjing Lu Jiahao Lei Peng Qiu Hong-Bin Shen Yang Yang Department of Computer Science and Engineering Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai Jiao Tong University Shanghai China Department of Vascular Surgery Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai Jiao Tong University Shanghai China

Interactive medical image segmentation methods have become increasingly popular in recent years. These methods combine manual labeling and automatic segmentation, reducing the workload of annotation while maintaining high accuracy. However, most current interactive segmentation frameworks are limited to 2D image data, and are not suitable for 3D image data due to the large size and high complexity of 3D data, as well as the challenges posed by information asymmetry and sparse annotation. In this paper, we propose SliceProp, an interactive segmentation framework that implements slice-wise Label Bidirectional Propagation (LBP) for 3D medical image segmentation. SliceProp extends the interactive 2D image segmentation algorithm to 3D image segmentation, and can handle 3D data with large size and high complexity. Moreover, equipped with a Backtracking Feedback Check (BFC) module, SliceProp effectively addresses the issues of information asymmetry and spatial sparse annotation in 3D medical image segmentation. Additionally, we adopt an uncertainty-based criterion to pri-oritize the slices to be refined interactively, which enhances the efficiency of the interaction process by enabling the model to focus on the regions with the most unreliable predictions. SliceProp is evaluated on two datasets and achieves promising results compared to state-of-the-art methods.

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T-TIME: Test-Time Information Maximization Ensemble for Plug-and-Play BCIs

arXiv

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arXiv 2024年

作者： Li, Siyang Wang, Ziwei Luo, Hanbin Ding, Lieyun Wu, Dongrui Ministry of Education Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China Shenzhen Huazhong University of Science and Technology Research Institute Shenzhen China Henan Key Laboratory of Brain Science and Brain Computer Interface Technology School of Electrical and Information Engineering Zhengzhou University China School of Civil and Hydraulic Engineering Huazhong University of Science and Technology Wuhan430074 China

Objective: An electroencephalogram (EEG)-based brain-computer interface (BCI) enables direct communication between the human brain and a computer. Due to individual differences and non-stationarity of EEG signals, such BCIs usually require a subject-specific calibration session before each use, which is time-consuming and user-unfriendly. Transfer learning (TL) has been proposed to shorten or eliminate this calibration, but existing TL approaches mainly consider offline settings, where all unlabeled EEG trials from the new user are available. Methods: This paper proposes Test-Time Information Maximization Ensemble (T-TIME) to accommodate the most challenging online TL scenario, where unlabeled EEG data from the new user arrive in a stream, and immediate classification is performed. T-TIME initializes multiple classifiers from the aligned source data. When an unlabeled test EEG trial arrives, T-TIME first predicts its labels using ensemble learning, and then updates each classifier by conditional entropy minimization and adaptive marginal distribution regularization. Our code is publicized. Results: Extensive experiments on three public motor imagery based BCI datasets demonstrated that T-TIME outperformed about 20 classical and state-of-the-art TL approaches. Significance: To our knowledge, this is the first work on test time adaptation for calibration-free EEG-based BCIs, making plug-and-play BCIs possible. © 2024, CC BY.

关键词： Calibration

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Boosting discriminative model for moving cast shadow detection

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Jisuanji Xuebao/Chinese Journal of Computers 2007年第8期30卷 1295-1301页

作者： Zha, Yu-Fei Chu, Ying Wang, Xun Ma, Shi-Ping Bi, Du-Yan Signal and Information Processing Laboratory Engineering College Air Force Engineering University Xi'an 710038 China Key Laboratory for Image Processing and Intelligent Control Institute of Pattern Recognition and Artificial Intelligence Huazhong Univ. of Sci. and Technol. Wuhan 430074 China

Moving cast shadow causes serious problem while segmenting and extracting foreground from image sequences, due to the misclassification of moving shadow as foreground. This paper proposes a Boosting discriminative model to eliminate cast shadow on Discriminative Random Fields (DRFs). The method combines different features for Boosting to discriminate cast shadow from moving objects, then temporal and spatial coherence of shadow and foreground are incorporated on Discriminative Random Fields and the problem can be solved by graph cut. Firstly, moving objects are obtained by background subtraction;secondly, shadow candidates can be derived through pre-processing moving objects, in terms of the shadow physical property;thirdly, color information and texture information is derived by comparing shadow and foreground points in current image with corresponding points in background image, which are selected as features for Boosting;finally, temporal and spatial coherence of shadow and foreground is employed on Discriminative Random Fields and discriminate shadow and foreground by graph cut accurately.

关键词： image processing

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