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Prediction of protein folding rates from structural topology and complex network properties

IPSJ Transactions on Bioinformatics 2010年 3卷 40-53页

作者： Song, Jiangning Takemoto, Kazuhiro Shen, Hongbin Tan, Hao Gromiha, M. Michael Akutsu, Tatsuya Bioinformatics Center Institute for Chemical Research Kyoto University Japan Department of Biochemistry and Molecular Biology Monash University Australia PRESTO Japan Science and Technology Agency Japan Institute of Image Processing and Pattern Recognition Shanghai Jiaotong University China Computational Biology Research Center National Institute of Advanced Industrial Science and Technology Japan

As a fundamental biological problem, revealing the protein folding mechanism remains to be one of the most challenging problems in structural bioinformatics. Prediction of protein folding rate is an important step towards our further understanding of the protein folding mechanism and the complex sequencestructure-function relationship. In this article, we develop a novel approach to predict protein folding rates for two-state and multi-state protein folding kinetics, which combines a variety of structural topology and complex network properties that are calculated from protein three-dimensional structures. To take into account the specific correlations between network properties and protein folding rates, we define two different protein residue contact networks, based on two different scales Protein Contact Network (PCN) and Long-range Interaction Network (LIN) to characterize the corresponding network features. The leave-one-out cross-validation (LOOCV) tests indicate that this integrative strategy is more powerful in predicting the folding rates from 3D structures, with the Pearson's Correlation Coefficient (CC) of 0.88, 0.90 and 0.90 for two-state, multi-state and combined protein folding kinetics, which provides an improved performance compared with other prediction work. This study provides useful insights which shed light on the network organization of interacting residues underlying protein folding process for both two-state and multi-state folding kinetics. Moreover, our method also provides a complementary approach to the current folding rate prediction algorithms and can be used as a powerful tool for the characterization of the foldomics protein data. The implemented webserver (termed PRORATE) is freely accessible at http://***/~sjn/folding/. © 2010 Information processing Society of Japan.

关键词： Forecasting

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An Enhanced Coarse-to-Fine Framework for the Segmentation of Clinical Target Volume 23rd

An Enhanced Coarse-to-Fine Framework for the Segmentation of...

引用

Anatomical Brain Barriers to Cancer Spread: Segmentation from CT and MR images Challenge, ABCs 2020, Learn2Reg Challenge, L2R 2020 and Thyroid Nodule Segmentation and Classification in Ultrasound images Challenge, TN-SCUI 2020 held in conjunction with 23rd International Conference on Medical image Computing and computer-Assisted Intervention, MICCAI 2020

作者： Chen, Huai Qian, Dahong Liu, Weiping Li, Hui Wang, Lisheng Institute of Image Processing and Pattern Recognition Department of Automation Shanghai Jiao Tong University Shanghai200240 China School of Biomedical Engineering Shanghai Jiao Tong University Shanghai200240 China Department of Algorithm and Research Shanghai Aitrox Technology Co. Ltd. Shanghai China National Key Laboratory of Science and Technology on Nano/Micro Fabrication Key Laboratory for Thin Film and Micro Fabrication of the Ministry of Education Institute of Micro-Nano Science and Technology Shanghai Jiao Tong University Shanghai200240 China

ISBN: (纸本)9783030718268

In radiation therapy, obtaining accurate boundary of the clinical target volume (CTV) is the vital step to decrease the risk of treatment failures. However, it is a time-consuming and laborious task to obtain the delineation by hand. Therefore, an automatic algorithm is urgently needed to realize accurate segmentation. In this paper, we propose an enhanced coarse-to-fine frameworkto automatically fuse the information of CT, T1 and T2 images to get the target region. This framework includes a coarse-segmentation stage to identify the region of interest (ROI) of targets and a fine-segmentation stage to iteratively refine the segmentation. In the coarse-segmentation stage, the F-loss is proposed to keep the high recall rate of the ROI. In the fine segmentation, the ROI of target will be first cropped according to the ROI obtained by coarse-segmentation and be fed into a 3D-Unet to get the initial results. Then, the prediction and medium features will be set as additional information for the next one network to refine the results. When evaluated on the validation dataset of challenge of Anatomical Brain Barriers to Cancer Spread (ABCs), our method won the 3th place in the public leaderboard. © 2021, Springer Nature Switzerland AG.

关键词： Iterative methods

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Human-in-the-loop control system based on the biped waIking - Chair robot

Human-in-the-loop control system based on the biped waIking ...

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26th Chinese Control Conference, CCC 2007

作者： Tang, Jiaoyan Zhao, Qunfei Jie, Huang Yang, Ruqing School of Mechanical Engineering Shanghai Jiaotong University Shanghai 200240 China Institute of Image Processing and Pattern Recognition Shanghai Jiaotong University Shanghai 200240 China College of Computer Science and Engineering University of Aizu Aizu Wakamatsu 965-8580 Japan

ISBN: (纸本)7900719229

This paper presents the research on stability for biped Walking-Chair robot with huamn-in-the-loop. The inherent properties of the biped system with human-in-the-loop for navigation path design and walking gait design are analyzed. Posture stability computation method based on ZMP (Zero Moement Point) theory is discussed. Some suggestions about the future research are also presented.

关键词： Robots

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Nonconvex penalties with analytical solutions for one-bit compressive sensing

arXiv

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arXiv 2017年

作者： Huang, Xiaolin Yan, Ming Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University MOE Key Laboratory of System Control and Information Processing Shanghai200240 China Department of Computational Mathematics Science and Engineering Department of Mathematics Michigan State University East LansingMI48824 United States

One-bit measurements widely exist in the real world and can be used to recover sparse signals. This task is known as one-bit compressive sensing (1bit-CS). In this paper, we propose novel algorithms based on both convex and nonconvex sparsity-inducing penalties for robust 1bit-CS. We consider the dual problem, which has only one variable and provides a sufficient condition to verify whether a solution is globally optimal or not. For positive homogeneous penalties, a globally optimal solution can be obtained in two steps: a proximal operator and a normalization step. For other penalties, we solve the dual problem, and it needs to evaluate the proximal operators for many times. Then we provide fast algorithms for finding analytical solutions for three penalties: minimax concave penalty (MCP), 0norm, and sorted 1penalty. Specifically, our algorithm is more than 200 times faster than the existing algorithm for MCP. Its efficiency is comparable to the algorithm for the 1penalty in time, while its performance is much better than 1. Among these penalties, sorted 1is most robust to noise in different settings. Copyright © 2017, The Authors. All rights reserved.

关键词： Compressed sensing

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A novel line based connected component labeling algorithm

A novel line based connected component labeling algorithm

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International Conference on computer science and Information Technology (CSIT)

作者： Yebin Fan Shengsheng Yu Hualong Zhao Department of Computer Science Huazhong University of Science and Technology Wuhan China National Key Laboratory of Science and Technology on Multi-spectral Information Processing Technologies Institute for Pattern Recognition and Artificial Intelligence Huazhong University of Science and Technology Wuhan China

This paper presents a fast connected component labeling algorithm based on line description method and optimized tree Union-Find strategy. The algorithm transforms the pixel-connected issue, which most of proposed algorithms focus on, into line-connected issue. This algorithm is comprised of three phrases, line extraction, connected component identification and label assignment. The line description method transforms the connected pixels into line form for reducing the scan time. While the new tree Union-Find strategy diminishes the redundant root compare operations. A comparison analysis is performed with other optimized famous component labeling algorithms. Our algorithm has shown an outstanding performance with respect to the processing time, which achieves 1.1~8 times as fast as the other algorithms in various test cases.

关键词： Noise

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SRSNetwork: Siamese Reconstruction-Segmentation Networks based on Dynamic-Parameter Convolution

arXiv

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arXiv 2023年

作者： Nian, Bingkun Tang, Fenghe Ding, Jianrui Zhang, Pingping Yang, Jie Kevin Zhou, S. Liu, Wei Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University China School of Biomedical Engineering Suzhou Institute for Advanced Research University of Science and Technology of China China School of Computer Science and Technology Harbin Institute of Technology China School of artificial intelligence Dalian University of Technology China

In this paper, we present a high-performance deep neural network for weak target image segmentation, including medical image segmentation and infrared image segmentation. To this end, this work analyzes the existing dynamic convolutions and proposes dynamic parameter convolution (DPConv). Furthermore, it reevaluates the relationship between reconstruction tasks and segmentation tasks from the perspective of DPConv, leading to the proposal of a dual-network model called the Siamese Reconstruction-Segmentation Network (SRSNet). The proposed model is not only a universal network but also enhances the segmentation performance without altering its structure, leveraging the reconstruction task. Additionally, as the amount of training data for the reconstruction network increases, the performance of the segmentation network also improves synchronously. On seven datasets including five medical datasets and two infrared image datasets, our SRSNet consistently achieves the best segmentation results. The code is released at https://***/fidshu/SRSNet. Copyright © 2023, The Authors. All rights reserved.

关键词： Convolution

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Dynamic Frame Interpolation in Wavelet Domain

arXiv

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arXiv 2023年

作者： Kong, Lingtong Jiang, Boyuan Luo, Donghao Chu, Wenqing Tai, Ying Wang, Chengjie Yang, Jie The Institute of Image Processing and Pattern Recognition Department of Automation Shanghai Jiao Tong University Shanghai200240 China The Youtu Lab Tencent Shanghai200233 China The School of Intelligence Science and Technology Nanjing University Suzhou215163 China

Video frame interpolation is an important low-level vision task, which can increase frame rate for more fluent visual experience. Existing methods have achieved great success by employing advanced motion models and synthesis networks. However, the spatial redundancy when synthesizing the target frame has not been fully explored, that can result in lots of inefficient computation. On the other hand, the computation compression degree in frame interpolation is highly dependent on both texture distribution and scene motion, which demands to understand the spatial-temporal information of each input frame pair for a better compression degree selection. In this work, we propose a novel two-stage frame interpolation framework termed WaveletVFI to address above problems. It first estimates intermediate optical flow with a lightweight motion perception network, and then a wavelet synthesis network uses flow aligned context features to predict multi-scale wavelet coefficients with sparse convolution for efficient target frame reconstruction, where the sparse valid masks that control computation in each scale are determined by a crucial threshold ratio. Instead of setting a fixed value like previous methods, we find that embedding a classifier in the motion perception network to learn a dynamic threshold for each sample can achieve more computation reduction with almost no loss of accuracy. On the common high resolution and animation frame interpolation benchmarks, proposed WaveletVFI can reduce computation up to 40% while maintaining similar accuracy, making it perform more efficiently against other state-of-the-arts. Code is available at https://***/ltkong218/WaveletVFI. Copyright © 2023, The Authors. All rights reserved.

关键词： Wavelet transforms

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Impulse noise removal using linear prediction model

Impulse noise removal using linear prediction model

引用

International Conference on Telecommunications in Modern Satellite, Cable and Broadcasting Service (TELSIKS)

作者： I. Prudyus S. Voloshynovskiy Y. Rytsar T. Holotyak National University Lvivska Politechnika Lviv Ukraine Coordinated Science Laboratory College of Engineering University of Illinois Urbana IL USA Department of Image Processing and Pattern Recognition Institute of Physics and Mechanics National Academy of Sciences Lviv Ukraine

Noise removal is an important problem in many applications. In this paper a new two-step scheme of the decision-based impulse noise removal method by means of contaminated pixel detection is proposed and comparison with direct order statistic filtering is given. The proposed methods satisfy both objective and subjective image quality.

关键词： Predictive models Statistics Noise reduction Pixel Electronic mail image quality Nonlinear filters Filtering algorithms Data analysis Statistical analysis

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Learning data-adaptive nonparametric kernels

arXiv

引用

arXiv 2018年

作者： Liu, Fanghui Huang, Xiaolin Gong, Chen Yang, Jie Li, Li Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai200240 China Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information Ministry of Education School of Computer Science and Engineering Nanjing University of Science and Technology Nanjing210094 China Department of Automation Tsinghua University

Kernel methods have been extensively used in a variety of machine learning tasks such as classification, clustering, and dimensionality reduction. For complicated practical tasks, the traditional kernels, e.g., Gaussian kernel and sigmoid kernel, or their combinations are often not sufficiently flexible to fit the data. In this paper, we present a Data-Adaptive Nonparametric Kernel (DANK) learning framework in a data-driven manner. To be specific, in model formulation, we impose an adaptive matrix on the kernel/Gram matrix in an entry-wise strategy. Since we do not specify the formulation of the adaptive matrix, each entry in the adaptive matrix can be directly and flexibly learned from the data. Therefore, the solution space of the learned kernel is largely expanded, which makes our DANK model flexible to capture the data with different local statistical properties. Specifically, the proposed kernel learning framework can be seamlessly embedded to support vector machines (SVM) and support vector regression (SVR), which has the capability of enlarging the margin between classes and reducing the model generalization error. Theoretically, we demonstrate that the objective function of our DANK model embedded in SVM/SVR is gradient-Lipschitz continuous. Thereby, the training process for kernel and parameter learning in SVM/SVR can be efficiently optimized in a unified framework. Further, to address the scalability issue in nonparametric kernel learning framework, we decompose the entire optimization problem in DANK into several smaller easy-to-solve problems, so that our DANK model can be efficiently approximated by this partition. The effectiveness of this approximation is demonstrated by both empirical studies and theoretical guarantees. Experimentally, the proposed DANK model embedded in SVM/SVR achieves encouraging performance on various classification and regression benchmark datasets when compared with other representative kernel learning based algorithms. Copyrig

关键词： Matrix algebra

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Robust occupancy detection from stereo images

Robust occupancy detection from stereo images

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International Conference on Intelligent Transportation

作者： B. Alefs M. Clabian H. Bischof W. Kropatsch F. Khairallah Advanced Computer Vision GmbH-ACV Vienna Austria Advanced Computer Vision GmbH-ACV Austria Institute for Computer Graphics and Vision Graz University of Technology Graz Austria Pattern Recognition and Image Processing Group Institute of Computer Aided Automation Computer Science Department University of Technology Vienna Vienna Austria TRW Automotive GmbH Farmington Hills MI USA

Vehicle occupants that are out-of-position can be deadly injured by the deployment of the air bag in a crash situation. In recent years many different sensors and systems have been proposed to detect the type of occupant and the position of the occupant's head. This work presents a method for classification and occupant's head detection based on passive stereo vision. The proposed system uses depth surface analysis and scene statistics together with support vector machines for classification and selection of head candidates. Evaluation of the method shows 99% correct for classification and 98% correct for head detection, using large sets of image data, and image sequences recorded in a driving vehicle.

关键词： Robustness Magnetic heads Vehicle crash testing Sensor systems Stereo vision Layout Statistical analysis Support vector machines Support vector machine classification Vehicle detection

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