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2020 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2020

作者： Hu, Rui Cai, Jiaming Zheng, Wangjie Yang, Yang Shen, Hong-Bin Shanghai Jiao Tong University Key Lab. of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Department of Computer Science and Engineering Shanghai200240 China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China Shanghai Jiao Tong University Department of Bioinformatics and Biostatistics Shanghai200240 China

ISBN: (纸本)9781728162157

Cryo-electron microscopy (cryo-EM) has become a mainstream technology for solving spatial structures of biomacromolecules, while the processing of cryo-EM images is a very challenging task. One of the great challenges is the high noise in the images. A common method is to cluster the images with close projecting angles to get mean images, which are used for 3D reconstruction. However, due to the extremely low signal-to-noise-ratio, common clustering methods often fail to obtain high-quality mean images, leading to poorly reconstructed structures. In this study, we present a new unsupervised learning framework, called NiuEM, to discriminate images captured from different angles and yield cluster-mean images. NiuEM first generates pseudo-labels and then exploits both contrastive loss and cross-entropy loss for training convolutional layers to learn feature representations. Moreover, the pseudo-labels are updated iteratively to enhance the reliability of labels. We assess the performance of NiuEM on four data sets via both visualized and quantitative experiments. Especially, two kinds of metrics are adopted to measure the performance, regarding the clustering quality and the resolution of reconstructed 3D models, respectively. The experimental results show that NiuEM achieves very competitive clustering accuracy in the comparison with the state-of-the-art image clustering methods. Moreover, the cluster mean images yielded by NiuEM lead to better initial 3D models compared with the mainstream reconstruction tools. © 2020 IEEE.

关键词： image reconstruction

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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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2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Guo, Kuo Li, Yifan Chen, Hao Shen, Hong-Bin Yang, Yang Shanghai Jiao Tong University Key Lab. of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Department of Computer Science and Engineering Shanghai200240 China Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Institute of Image Processing and Pattern Recognition Shanghai200240 China Carnegie Mellon University School of Computer Science Computational Biology Department PittsburghPA15213 United States

ISBN: (纸本)9798350337488

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. © 2023 IEEE.

关键词： alternative splicing gene ontology heterogeneous graph attention network isoform function prediction protein language model

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SliceProp: A Slice-Wise Bidirectional Propagation Model for Interactive 3D Medical image Segmentation 1

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

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1st IEEE International Conference on Medical Artificial Intelligence, MedAI 2023

作者： Xu, Xin Lu, Wenjing Lei, Jiahao Qiu, Peng Shen, Hong-Bin Yang, Yang Shanghai Jiao Tong University Key Lab. of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Department of Computer Science and Engineering Shanghai200240 China Shanghai Ninth People's Hospital Shanghai Jiao Tong University School of Medicine Department of Vascular Surgery China Shanghai Jiao Tong University Institute of Image Processing and Pattern Recognition Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China

ISBN: (纸本)9798350358780

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. © 2023 IEEE.

关键词： Medical imaging

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pNovo+: De Novo Peptide Sequencing and Assembly Using Complementary HCD and ETD Tandem Mass Spectra

pNovo+: De Novo Peptide Sequencing and Assembly Using Comple...

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第八届中国蛋白质组学大会

作者： Hao Chi Haifeng Chen Kun He Long Wu Bing Yang Rui-Xiang Sun Jianyun Liu Wen-Feng Zeng Chun-Qing Song Si-Min He Meng-Qiu Dong Key Lab of Intelligent Information Processing Institute of Computing TechnologyChinese Academy of SciencesBeijing 100190China National Institute of Biological SciencesBeijingBeijing 102206China Laboratory of Intelligent Recognition and Image ProcessingBeijing Key Laboratory of Digital MediaBeihang UniversityBeijing100191China

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Benchmarking asymmetric 3D-2D face recognition systems

Benchmarking asymmetric 3D-2D face recognition systems

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International Conference on Automatic Face and Gesture recognition

作者： Xi Zhao Wuming Zhang Georgios Evangelopoulos Di Huang Shishir K. Shah Yunhong Wang Ioannis A. Kakadiaris Liming Chen Computational Biomedicine Lab Department of Computer Science University of Houston Houston TX USA LIRIS Lab Ecole Centrale de Lyon France Laboratory of Intelligent Recognition and Image Processing School of Computer Science and Engineering Beihang University Beijing China

ISBN: (纸本)9781467355452

Asymmetric 3D-2D face recognition (FR) aims to recognize individuals from 2D face images using textured 3D face models in the gallery (or vice versa). This new FR scenario has the potential to be readily deployable in field applications while still keeping the advantages of 3D FR solutions of being more robust to pose and lighting variations. In this paper, we propose a new experimental protocol based on the UHDB11 dataset for benchmarking 3D-2D FR algorithms. This new experimental protocol allows for the study of the performance of a 3D-2D FR solution under pose and/or lighting variations. Furthermore, we also benchmarked two state of the art 3D2D FR algorithms. One is based on the Annotated Deformable Model (using manually labeled landmarks in this paper) using manually labeled landmarks whereas the other makes use of Oriented Gradient Maps along with an automatic pose estimation through random forest.

关键词： Face Lighting Probes Pipelines Solid modeling Estimation Face recognition

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Remote sensing image compression for deep space based on region of interest

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Journal of Harbin Institute of Technology(New Series) 2003年第3期10卷 300-303页

作者：王振华吴伟仁田玉龙田金文柳健 Institute for Pattern Recognition and Artificial Intelligence State Key Lab for Image Processing and Intelligent ControlHuazhong University of Science and Technology Wuhan 430074 China Institute for Pattern Recognition and Artificial Intelligence State Key Lab for Image Processing and Intelligent ControlHuazhong University of Science and Technology Wuhan 430074 China major limitation for deep space communication is the limited bandwidths available. The downlink rate using X-band with an L2 halo orbit is estimated to be of only 5.35 GB/d. However the Next Generation Space Telescope (NGST) will produce about 600 GB/d. Clearly the volume of data to downlink must be reduced by at least a factor of 100. One of the resolutions is to encode the data using very low bit rate image compression techniques. An very low bit rate image compression method based on region of interest(ROI) has been proposed for deep space image. The conventional image compression algorithms which encode the original data without any data analysis can maintain very good details and haven't high compression rate while the modern image compressions with semantic organization can have high compression rate even to be hundred and can't maintain too much details. The algorithms based on region of interest inheriting from the two previews algorithms have good semantic features and high fidelity and is therefore suitable for applications at a low bit rate. The proposed method extracts the region of interest by texture analysis after wavelet transform and gains optimal local quality with bit rate control. The Result shows that our method can maintain more details in ROI than general image compression algorithm(SPIHT) under the condition of sacrificing the quality of other uninterested areas

A major limitation for deep space communication is the limited bandwidths available. The downlinkrate using X-band with an L2 halo orbit is estimated to be of only 5.35 GB/d. However, the Next GenerationSpace Telescope (NGST) will produce about 600 GB/d. Clearly the volume of data to downlink must be re-duced by at least a factor of 100. One of the resolutions is to encode the data using very low bit rate image com-pression techniques. An very low bit rate image compression method based on region of interest(ROI) has beenproposed for deep space image. The conventional image compression algorithms which encode the original datawithout any data analysis can maintain very good details and haven' t high compression rate while the modernimage compressions with semantic organization can have high compression rate even to be hundred and can' tmaintain too much details. The algorithms based on region of interest inheriting from the two previews algorithmshave good semantic features and high fidelity, and is therefore suitable for applications at a low bit rate. Theproposed method extracts the region of interest by texture analysis after wavelet transform and gains optimal localquality with bit rate control. The Result shows that our method can maintain more details in ROI than generalimage compression algorithm(SPIHT) under the condition of sacrificing the quality of other uninterested areas.

关键词： wavelet compression ROI deep space

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An Active Landing Recovery Method for Quadrotor UAV: Localization, Tracking and Buffering Landing

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IFAC-PapersOnLine 2023年第2期56卷 3366-3372页

作者： Yongkang Xu Zhihua Chen Shoukun Wang Junzheng Wang National Key Lab of Autonomous Intelligent Unmanned Systems Beijing Institute of Technology Beijing CO 100081 P.R.China Key Laboratory of Jiangxi Province for Image Processing and Pattern Recognition and MOE Key Lab of Nondestructive Testing Technology School of Information Engineering Nanchang Hangkong University Nanchang CO 330063 P.R. China

This paper proposes a principle of fully autonomous ground mobile landing recovery of Unmanned Aerial Vehicles (UAV) for the problems of relatively fixed landing point, passive recovery, poor flexibility, and environmental adaptability, which mainly includes localization, landing point tracking, and buffering landing for quadrotor UAV. Firstly, aiming at the problem that it is difficult to accurately obtain the position of a UAV in dynamic mobile landing recovery, a target location method based on Asynchronous Multisensor Information Fusion(AMIF) and servo turntable focus tracking is proposed. Secondly, to achieve fast and high-precision tracking of UAVs, a tracking control strategy of an independently driven landing recovery system and a Stewart six-degree of freedom platform is proposed. Then, to solve the problems of large impact force and center of gravity instability in the landing process of UAV, a stationarity control algorithm based on model prediction and a compliance control algorithm based on adaptive variable impedance are designed to achieve active compliance control while adjusting the position and attitude of the receiving surface in real-time. Finally, a quadrotor unmanned landing and recovery experimental platform is built to verify the feasibility of the ground mobile landing and recovery strategy proposed in this paper and the effectiveness of the control algorithm.

关键词： Quadrotor UAV Mobile Autonomous recovery Target localization Falling point tracking Buffering landing

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A Combining Method for Tumors Detection from Near-infrared Breast Imaging

A Combining Method for Tumors Detection from Near-infrared B...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Zhicheng Wang Jian Liu Jinwen Tian Zeping Xie State Education Commission Key Laboratory for Image Processing and Intelligent Control Institute for Pattern Recognition and Artificial Intelligence Huazhong Univ. of Sci. & Tech. Wuhan 430074 China Key Lab. for Image Process. & Intelligent Control State Educ. Comm. School of Life Science & Technology Huazhong University of Science and Technology Wuhan China

This paper introduces the new qualitative and quantitative methods, which can diagnose breast tumors. Qualitative methods include blood vessel display inside and outside of pathological changes part of breast, display of equivalent pixel curves at the part of pathological changes and display of breast tumor image edge. Accordingly, three feature extraction operators are proposed, i.e. the combination operators of anisotropic gradient and smoothing operator, an improved Sobel operator and an edge sharpening operator. Furthermore, quantitative diagnostic approaches are discussed based on blood and oxygen contents according to abundant clinical data and pathological mechanism of breast tumors. The results of clinic show that the methods of combining qualitative and quantitative diagnose are effective for breast tumor images, especially for early and potential breast cancer

关键词： Breast tumors Displays Pathology Blood vessels Biomedical imaging Pixel Feature extraction Anisotropic magnetoresistance Smoothing methods Breast cancer

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Binary pattern flavored feature extractors for Facial Expression recognition: An overview

Binary pattern flavored feature extractors for Facial Expres...

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Proceedings of the International Convention MIPRO

作者： Rasmus Lyngby Kristensen Zheng-Hua Tan Zhanyu Ma Jun Guo Section of Image Analysis and Computer Graphics Technical University of Denmark Kgs. Lyngby Denmark Signal and Information Processing section (SIP) Aalborg University Aalborg Denmark Pattern Recognition and Intelligent System Lab. Beijing University of Posts and Telecommunications Beijing China

ISBN: (纸本)9781479981748

This paper conducts a survey of modern binary pattern flavored feature extractors applied to the Facial Expression recognition (FER) problem. In total, 26 different feature extractors are included, of which six are selected for in depth description. In addition, the paper unifies important FER terminology, describes open challenges, and provides recommendations to scientific evaluation of FER systems. Lastly, it studies the facial expression recognition accuracy and blur invariance of the Local Frequency Descriptor. The paper seeks to bring together disjointed studies, and the main contribution is to provide a solid overview for future research.

关键词： Feature extraction Face Face recognition Databases Three-dimensional displays Accuracy Gold

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Gait Planning and Motion Control Based on Vrep Simulation for Quadruped Robot

Gait Planning and Motion Control Based on Vrep Simulation fo...

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WRC Symposium on Advanced Robotics and Automation (WRC SARA)

作者： Linqi Zhou Zhihua Chen Jun Liu Zhi Liu Yumeng Chen Liting Zhang key Laboratory of Jiangxi Province for Image Processing and Pattern Recognition and MOE Key Lab of Nondestructive Testing Technology Nanchang Hangkong University Nanchang China State Key Laboratory of Intelligent Control and Decision of Complex Systems School of Automation Beijing Institute of Technology Beijing China

Gait planning of quadruped robots plays an important role in achieving less walking, including dynamic and static gait. In this article, a static and dynamic gait control method based on center of gravity stability margin is proposed. Firstly, the robot model and kinematics modeling are introduced. Secondly, the robot’s foot static and dynamic gait were planned and the foot trajectory was designed. Finally, two types of gait of the robot were simulated using Vrep simulation software, and the differences in stability and speed between the coordinated gait with speed and stability in the static and dynamic gait of a 12 degree of freedom robot were analyzed, verifying the effectiveness of the gait control method proposed in this paper.

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