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5th World Robot Conference Symposium on Advanced Robotics and Automation, WRC SARA 2023

作者： Zhou, Linqi Chen, Zhihua Liu, Jun Liu, Zhi Chen, Yumeng Zhang, Liting Nanchang Hangkong University Key Laboratory of Jiangxi Province for Image Processing and Pattern Recognition Moe Key Lab of Nondestructive Testing Technology Nanchang330063 China Beijing Institute of Technology State Key Laboratory of Intelligent Control and Decision of Complex Systems School of Automation Beijing100081 China

ISBN: (纸本)9798350307320

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. © 2023 IEEE.

关键词： Robot programming

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RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs

RBP-Former: Joint Prediction of RNA-protein Binding Sites on...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Li, Yichong Liu, Xiaojian Cheng, Fan Pan, Xiaoyong Yang, Yang Shanghai Jiao Tong University Department of Computer Science and Engineering Shanghai200240 China Shanghai Jiao Tong University Institute of Image Processing and Pattern Recognition Shanghai200240 China Ministry of Education of China Key Laboratory of System Control and Information Processing Shanghai200240 China Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai200240 China

ISBN: (纸本)9798350386226

RNA-binding proteins (RBPs) are essential for gene expression, and the complex RNA-protein interaction mechanisms require analysis of global RNA information. Therefore, accurate prediction of RBP binding sites on full-length RNA transcripts is crucial for understanding these mechanisms and their roles in diseases. While machine learning methods can predict RBP binding to RNA fragments, extending this to full-length transcripts presents challenges due to sequence length and data imbalance. In this paper, we introduce RBP-Former, a binding site joint prediction model designed specifically for full-length RNA transcripts that can be used for multiple RBPs. This model processes information at both coarse and fine-grained levels to fully exploit sequence data and its interactions with multiple RBPs. We develop multi-level imbalance learning strategies, achieving favorable results on imbalanced data. Our method outperforms existing methods in predicting binding sites on full-length RNA transcripts for multiple RBPs, demonstrating its effectiveness in handling imbalanced label and sample distributions. © 2024 IEEE.

关键词： Binding sites

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Unsupervised Learning of Gaussian Mixture Model with Application to Image Segmentation

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Chinese Journal of Electronics 2023年第3期19卷 451-456页

作者： Bo Li Wenju Liu Lihua Dou School of Automation Beijing Institute of Technology Beijing China Key Laboratory of Complex System Intelligent Control and Decision Ministry of Education Beijing Institute of Technology Beijing China National Laboratory of Pattern Recognition Institute of Automation Chinese Academy of Sciences Beijing China

Density estimation via Gaussian mixture modeling has been successfully applied to image segmentation, speech processing and other fields relevant to clustering analysis and Probability density function (PDF) modeling. Finite Gaussian mixture model is usually used in practice and the selection of number of mixture components is a significant problem in its application. For example, in image segmentation, it is the donation of the number of segmentation regions. The determination of the optimal model order therefore is a problem that achieves widely attention. This paper proposes a degenerating model algorithm that could simultaneously select the optimal number of mixture components and estimate the parameters for Gaussian mixture model. Unlike traditional model order selection method, it does not need to select the optimal number of components from a set of candidate models. Based on the investigation on the property of the elliptically contoured distributions of generalized multivariate analysis, it select the correct model order in a different way that needs less operation times and less sensitive to the initial value of EM. The experimental results show the effectiveness of the algorithm.

关键词： Training Image segmentation Analytical models Parameter estimation Estimation Probability density function Speech processing

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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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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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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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RBP-Former: Joint Prediction of RNA-protein Binding Sites on Full-length RNA Transcripts for Multiple RBPs

RBP-Former: Joint Prediction of RNA-protein Binding Sites on...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Yichong Li Xiaojian Liu Fan Cheng Xiaoyong Pan Yang Yang Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai China Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai China

ISBN: (数字)9798350386226

ISBN: (纸本)9798350386233

关键词： Proteins Protein engineering Accuracy RNA Machine learning Predictive models Data models Gene expression Bioinformatics Diseases

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Local Neighbor Propagation on Graphs for Robust Feature Matching

SSRN

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SSRN 2023年

作者： Guo, Hanlin Xiao, Guobao Su, Lumei Zhou, Jiaxing Wang, Dahan Xiamen Key Laboratory of Frontier Electric Power Equipment and Intelligent Control School of Electrical Engineering and Automation Xiamen University of Technology China Fujian Key Laboratory of Sensing and Computing for Smart Cities School of Information Science and Engineering Xiamen University China College of Computer and Control Engineering Minjiang University China Fujian Key Laboratory of Pattern Recognition and Image Understanding School of Computer and Information Engineering Xiamen University of Technology China

Establishing reliable correspondences between two sets of feature points is a critical preprocessing step in many computer vision and pattern recognition tasks. In this paper, we propose a novel robust Local Neighbor Propagation on Graphs based feature matching (LNPG) method, to obtain good correspondences for feature matching. LNPG starts from a novel neighborhood graph construction strategy. The strategy leverages the spatial consistency constraint to generate a series of neighborhood sets, and employs the residual information to preserve the local neighborhood relationships of potential inliers (i.e., true matches). Subsequently, LNPG incorporates local neighbor propagation into the graph to enhance connections between data in different neighborhoods, by using the path-based similarity measurement and the adaptive graph partition. In addition, LNPG includes a novel consistency-filtering-based clustering algorithm for robust feature matching. This clustering algorithm introduces a reliable neighborhood consistency measure function and an effective cluster merging criterion for cluster detection and cluster merging during the clustering process, respectively. Overall, LNPG not only effectively distinguishes inliers from outliers, but also reliably classifies inliers into different transformation models between pairs of images. Experiments on publicly available datasets with different types of image transformations show the superiority of our LNPG in comparison with other state-of-the-art methods. © 2023, The Authors. All rights reserved.

关键词： Clustering algorithms

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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

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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

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