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IEEE International Conference on Systems Biology

作者： Mingjun Wang Hong-Bin Shen Tatsuya Akutsu Jiangning Song State Engineering Laboratory for Industrial Enzymes Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences (CAS) Tianjin China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai China Bioinformatics Center Institute for Chemical Research Kyoto University Uji Kyoto Japan Department of Biochemistry and Molecular Biology Faculty of Medicine Monash University Melbourne VIC Australia

Single amino acid polymorphisms (SAPs) are the most abundant form of known genetic variations associated with human diseases. It is of great interest to study the sequence-structure-function relationship underlying SAPs. In this work, we collected the human variant data from three databases and divided them into three categories, i.e. cancer somatic mutations (CSM), Mendelian disease-related variant (SVD) and neutral polymorphisms (SVP). We built support vector machine (SVM) classifiers to predict these three classes of SAPs, using the optimal features selected by a random forest algorithm. Consequently, 280 sequence-derived and structural features were initially extracted from the curated datasets from which 18 optimal candidate features were further selected by random forest. Furthermore, we performed a stepwise feature selection to select characteristic sequence and structural features that are important for predicting each SAPs class. As a result, our predictors achieved a prediction accuracy (ACC) of 84.97, 96.93, 86.98 and 88.24%, for the three classes, CSM, SVD and SVP, respectively. Performance comparison with other previously developed tools such as SIFT, SNAP and Polyphen2 indicates that our method provides a favorable performance with higher Sensitivity scores and Matthew's correlation coefficients (MCC). These results indicate that the prediction performance of SAPs classifiers can be effectively improved by feature selection. Moreover, division of SAPs into three respective categories and construction of accurate SVM-based classifiers for each class provides a practically useful way for investigating the difference between Mendelian disease-related variants and cancer somatic mutations.

关键词： Support vector machines Accuracy Proteins Feature extraction Humans Amino acids Databases

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Learning data-adaptive non-parametric kernels

The Journal of Machine Learning Research

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The Journal of Machine Learning Research 2020年第1期21卷 8590-8628页

作者： Fanghui Liu Xiaolin Huang Chen Gong Jie Yang Li Li Department of Electrical Engineering ESAT-STADIUS KU Leuven Belgium Institute of Image Processing and Pattern Recognition Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China PCA Lab Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information of Ministry of Education School of Computer Science and Engineering Nanjing University of Science and Technology China and Department of Computing Hong Kong Polytechnic University Hong Kong SAR China Department of Automation BNRist Tsinghua University China

In this paper, we propose a data-adaptive non-parametric kernel learning framework in margin based kernel methods. In model formulation, given an initial kernel matrix, a data-adaptive matrix with two constraints is imposed in an entry-wise scheme. Learning this data-adaptive matrix in a formulation-free strategy enlarges the margin between classes and thus improves the model flexibility. The introduced two constraints are imposed either exactly (on small data sets) or approximately (on large data sets) in our model, which provides a controllable trade-off between model flexibility and complexity with theoretical demonstration. In algorithm optimization, the objective function of our learning framework is proven to be gradient-Lipschitz continuous. Thereby, kernel and classifier/regressor learning can be efficiently optimized in a unified framework via Nesterov's acceleration. For the scalability issue, we study a decomposition-based approach to our model in the large sample case. The effectiveness of this approximation is illustrated by both empirical studies and theoretical guarantees. Experimental results on various classification and regression benchmark data sets demonstrate that our non-parametric kernel learning framework achieves good performance when compared with other representative kernel learning based algorithms.

关键词： support vector machines non-parametric kernel learning gradient-Lipschitz continuous

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3D RoI-aware U-net for accurate and efficient colorectal tumor segmentation

arXiv

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arXiv 2018年

作者： Huang, Yi-Jie Dou, Qi Wang, Zi-Xian Liu, Li-Zhi Jin, Ying Li, Chao-Feng Wang, Lisheng Chen, Hao Xu, Rui-Hua Institute of Image Processing and Pattern Recognition Department of Automation Shanghai Jiao Tong University China Imsight Medical Technology Co. Ltd. China Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong Sun Yat-sen University Cancer Center State Key Laboratory of Oncology in South China Collaborative Innovation Center for Cancer Medicine Guangzhou China

Segmentation of colorectal cancerous regions from 3D Magnetic Resonance (MR) images is a crucial procedure for radiotherapy which conventionally requires accurate delineation of tumour boundaries at an expense of labor, time and reproducibility. While deep learning based methods serve good baselines in 3D image segmentation tasks, small applicable patch size limits effective receptive field and degrades segmentation performance. In addition, Regions of interest (RoIs) localization from large whole volume 3D images serves as a preceding operation that brings about multiple benefits in terms of speed, target completeness, reduction of false positives. Distinct from sliding window or non-joint localization-segmentation based models, we propose a novel multitask framework referred to as 3D RoI-aware U-Net (3D RU-Net), for RoI localization and in-region segmentation where the two tasks share one backbone encoder network. With the region proposals from the encoder, we crop multi-level RoI in-region features from the encoder to form a GPU memory-efficient decoder for detail-preserving segmentation and therefore enlarged applicable volume size and effective receptive field. To effectively train the model, we designed a Dice formulated loss function for the global-to-local multi-task learning procedure. Based on the efficiency gains demonstrated by the proposed method, we went on to ensemble models with different receptive fields to achieve even higher performance costing minor extra computational expensiveness. Extensive experiments were subsequently conducted on 64 cancerous cases with a four-fold cross-validation, and the results showed significant superiority in terms of accuracy and efficiency over conventional state-of-the art frameworks. In conclusion, the proposed method has a huge potential for extension to other 3D object segmentation tasks from medical images due to its inherent generalizability. The code for the proposed method is publicly available. Copyright ©

关键词： Signal encoding

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Vehicle Routing Problem with Time Windows using Hybrid Metaheuristic Dragonfly Algorithm and Variable Neighborhood Search: Work on Progress

Vehicle Routing Problem with Time Windows using Hybrid Metah...

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International Conference on Electrical Engineering, Computer Science and Informatics (EECSI)

作者： Yunita Yunita Deris Stiawan Dian Palupi Rini Doctoral Student at Faculty of Computer Science Sriwijaya University Intelligent System Research Group Faculty of Computer Science Sriwijaya University Palembang South Sumatera Communication Network and Information Security Research Group Faculty of Computer Science Sriwijaya University Palembang South Sumatera Image Processing dan Pattern Recognition Laboratory Group Faculty of Computer Science Sriwijaya University Palembang South Sumatera

ISBN: (数字)9798350355314

ISBN: (纸本)9798350355321

One of the problems with Smart Transportation is the problem of cost and travel time. This problem is known as the Variable Routing Problem (VRP). In some real cases, in addition to considering route selection, there are limitations on the capacity and time period for the vehicle to serve each customer known as Time Windows, so VRP has developed into Variable Routing Problem with Time Windows (VRPTW). One way to solve VRPTW is to use metaheuristic methods. However, the metaheuristic method has a weakness, which are it can get stuck in local optimums and fail to find better global solutions. To overcome this, a combination with other methods or known as hybrid is needed. The formulation of this research problem is how to develop a Smart transportation model using a metaheuristic hybrid algorithm. The purpose of this study is to develop a Smart transportation model using a metaheuristic hybrid algorithm. The method used is to combine two metaheuristic algorithms, which are the Dragonfly Algorithm (DA) and the Variable Neighborhood Search (VNS). The result of this research is a new algorithm model which is a hybrid between DA and VNS. Through a combination of global exploration using DA and local exploitation using VNS, this algorithm is expected to be able to find a better solution and faster convergence in solving VRPTW problems

关键词： Electrical engineering Computer science Costs Metaheuristics Vehicle routing Routing Search problems Smart transportation Informatics Convergence

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MARL-based calibration for cameras with large FOV

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Optica Acta: International Journal of Optics 2024年第1-3期71卷

作者： Xinyu Yang Fuhan Chen Jingwen Jiang Hui Xie Qiaofeng Ou Key Laboratory of Jiangxi Province for Image Processing and Pattern Recognition School of Information Engineering Nanchang Hangkong University Nanchang People’s Republic of China

Achieving high-precision measurements in a large field of view (FOV) is a challenging task. The accuracy of vision measurements is determined by the quality of camera calibration, which is influenced by the pose of the target. To obtain suitable target pose, a target pose optimization method based on multi-agent reinforcement learning (MARL) is proposed. Firstly, the target pose optimization problem is modelled as a Markov decision process (MDP). Secondly, a multi-agent proximal policy optimization (MAPPO) algorithm for target pose optimization is designed by parameter sharing mechanism. Finally, optimization algorithm is adopted to camera calibration process. The calibration experiment was carried out under the large FOV of 4600 mm × 2300 mm. The results show that the back-projection error was 0.198 mm, the relative error of the diagonal length of target (505.847 mm) was 0.789 mm, and the success rate of large FOV camera calibration was 98.5%.

关键词： Camera calibration large FOV target pose optimization MARL MDP MAPPO

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Constructing multi-modality and multi-classifier radiomics predictive models through reliable classifier fusion

arXiv

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arXiv 2017年

作者： Zhou, Zhiguo Zhou, Zhi-Jie Hao, Hongxia Li, Shulong Chen, Xi Zhang, You Folkert, Michael Wang, Jing Department of Radiation Oncology UT Southwestern Medical Center DallasTX United States High-Tech Institute of Xi'an Xi'an China Department of Information and Control Engineering Xi'an University of Technology Xi'an China School of Computer Science and Technology Key Laboratory of Intelligent Perception and Image Understanding of Ministry of Education Xidian University Xi'an China School of Biomedical Engineering Southern Medical Unversity Guangzhou China Institute of Image Processing and Pattern Recognition Xi'an Jiaotong Unversity Xi'an China

Radiomics aims to extract and analyze large numbers of quantitative features from medical images and is highly promising in staging, diagnosing, and predicting outcomes of cancer treatments. Nevertheless, several challenges need to be addressed to construct an optimal radiomics predictive model. First, the predictive performance of the model may be reduced when features extracted from an individual imaging modality (e.g. PET, CT, MRI) are blindly combined into a single predictive model. Second, because many different types of classifiers are available to construct a predictive model, selecting an "optimal" classifier for a particular application is still challenging. In this work, we developed multi-modality and multi-classifier radiomics predictive models that address the aforementioned issues in currently available models. Specifically, a new reliable classifier fusion strategy was proposed to optimally combine output from different modalities and classifiers. In this strategy, modality-specific classifiers were first trained, and an analytic evidential reasoning (ER) rule was developed to fuse the output score from each modality to construct an optimal predictive model. One public datasets and two clinical case studies were performed to validate model performance. The experimental results indicated that the proposed ER rule based radiomics models outperformed the traditional models that rely on a single classifier or simply use combined features from different modalities. Copyright © 2017, The Authors. All rights reserved.

关键词： Diagnosis

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Unsupervised Learning of Depth and Pose Based on Monocular Camera and Inertial Measurement Unit (IMU)

Unsupervised Learning of Depth and Pose Based on Monocular C...

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IEEE International Conference on Robotics and Automation (ICRA)

作者： Yanbo Wang Hanwen Yang Jianwei Cai Guangming Wang Jingchuan Wang Yi Huang University of Michigan-Shanghai Jiao Tong University Joint Institute Shanghai Jiao Tong University Shanghai China School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai China Department of Automation Shanghai Jiao Tong University Shanghai China Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai Weitong Vision Technology Co. Ltd.

The main content of the research in this paper is the estimation of depth and pose based on monocular vision and Inertial Measurement Unit (IMU). The usual depth estimation network and pose estimation network require depth ground truth or pose ground truth as a supervised signal for training, while the depth ground truth and pose ground truth are hard to obtain, and monocular vision based depth estimation cannot predict absolute depth. In this paper, with the help of IMU, which is inexpensive and widely used, we can obtain angular velocity and acceleration information. Two new supervision signals are proposed and the calculation expressions are given. Among them, the model trained with acceleration constraint shows a good ability to estimate the absolute depth during the test. It can be considered that the model can estimate the absolute depth. We also derive the method of estimating the scale factor during the test from the acceleration constraint, and also achieve good results as the acceleration constraint does. In addition, this paper also studies the method of using IMU information as pose network input and as selecting conditions. Moreover, it analyzes and discusses the experimental results. At the same time, we also evaluate the effect of the pose estimation of the relevant models. This article starts by reviewing the achievements and deficiencies of the work in this field, combines the use of IMU, puts forward three new methods such as a new loss function, and conducts a test analysis and discussion of relevant indicators on the KITTI data set.

关键词：

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Abnormal resting-state EEG power and impaired inhibition control in young smokers

引用

Neuroscience Letters 2021年第0期761卷 136120-136120页

作者： Dong, Fang Li, Xiaojian Zhang, Yunmiao Jia, Shaodi Zhang, Shidi Xue, Ting Ren, Yan Lv, Xiaoqi Yuan, Kai Yu, Dahua Inner Mongolia Key Laboratory of Pattern Recognition and Intelligent Image Processing School of Information Engineering Inner Mongolia University of Science and Technology Baotou 014010 Inner Mongolia China College of Information Engineering Inner Mongolia University of Technology Hohhot 010051 Inner Mongolia China School of Life Science and Technology Xidian University Xi'an 710071 Shaanxi China

Exposure to nicotine during adolescence may cause neurophysiological changes and increase the risks of developing nicotine dependence;it can even lead to lifelong smoking. The intake of nicotine may also lead to abnormal patterns of oscillatory brain activity and inhibition control deficits. However, little is known about the specific relationship between oscillatory brain activity during the resting state and inhibition control capacity in young smokers. In the present study, we acquired resting-state electroencephalography (EEG) data from thirty-four young smokers and 39 age-matched non-smoking controls. Inhibition control performance was measured by a Go/NoGo task. Compared with non-smoking controls, we detected reduced low-frequency delta band activity in the frontal, central and posterior cortices of young smokers. Furthermore, young smokers committed more errors in response to infrequent NoGo trials. Notably, we demonstrated that delta absolute power in the frontal region was negatively correlated with NoGo errors and that alpha power in the central region was positively correlated with NoGo errors in non-smoking controls but not in young smokers. These findings may suggest that these inhibitory control processes were associated with alterations in oscillatory brain activity during the resting state. Our findings suggest that alterations of power spectra in delta bands may act as a useful biomarker of inhibitory control performance and provide a scientific basis for the diagnosis and treatment of nicotine addiction in adolescents. © 2021 Elsevier B.V.

关键词： Brain oscillations Electroencephalography (EEG) Inhibition control Resting state Young smokers

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CNN-based invertible wavelet scattering for the investigation of diffusion properties of the in vivo human heart in diffusion tensor imaging

arXiv

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arXiv 2019年

作者： Deng, Zeyu Wang, Lihui Kuai, Zixiang Chen, Qijian Cheng, Xinyu Yang, Feng Yang, Jie Zhu, Yuemin Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province College of Computer Science and Technology Guizhou University Guiyang550025 China Imaging Center Harbin Medical University Cancer Hospital Harbin150081 China School of Computer and Information Technology Beijing Jiaotong University Beijing100044 China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai200240 China University Lyon INSA Lyon CNRS Inserm IRP Metislab CREATIS UMR5220 U1206 LyonF-69621 France

In vivo diffusion tensor imaging (DTI) is a promising technique to investigate noninvasively the fiber structures of the in vivo human heart. However, signal loss due to motions remains a persistent problem in in vivo cardiac DTI. We propose a novel motion-compensation method for investigating in vivo myocardium structures in DTI with free-breathing acquisitions. The method is based on an invertible Wavelet Scattering achieved by means of Convolutional Neural Network (WSCNN). It consists of first extracting translation-invariant wavelet scattering features from DW images acquired at different trigger delays and then mapping the fused scattering features into motion-compensated spatial DW images by performing an inverse wavelet scattering transform achieved using CNN. The results on both simulated and acquired in vivo cardiac DW images showed that the proposed WSCNN method effectively compensates for motion-induced signal loss and produces in vivo cardiac DW images with better quality and more coherent fiber structures with respect to existing methods, which makes it an interesting method for measuring correctly the diffusion properties of the in vivo human heart in DTI under free breathing. Copyright © 2019, The Authors. All rights reserved.

关键词： Diffusion tensor imaging

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Relationship between pulmonary nodule malignancy and surrounding pleurae, airways and vessels: a quantitative study using the public LIDC-IDRI dataset

arXiv

引用

arXiv 2021年

作者： Qin, Yulei Gu, Yun Zhang, Hanxiao Yang, Jie Wang, Lihui Wang, Zhexin Yao, Feng Zhu, Yue-Min Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Shanghai200240 China Institute of Medical Robotics Shanghai Jiao Tong University Shanghai200240 China CREATIS INSA Lyon CNRS UMR 5220 INSERM U1206 Université de Lyon Villeurbanne69621 France Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province School of Computer Science and Technology Guizhou University Guiyang550025 China Department of Thoracic Surgery Shanghai Chest Hospital Shanghai Jiao Tong University Shanghai200025 China

Objectives: To investigate whether the pleurae, airways and vessels surrounding a nodule on non-contrast computed tomography (CT) can discriminate benign and malignant pulmonary nodules. Materials and Methods: The LIDC-IDRI dataset, one of the largest publicly available CT database, was exploited for study. A total of 1556 nodules from 694 patients were involved in statistical analysis, where nodules with average scorings 3 were respectively denoted as benign and malignant. Besides, 339 nodules from 113 patients with diagnosis ground-truth were independently evaluated. Computer algorithms were developed to segment pulmonary structures and quantify the distances to pleural surface, airways and vessels, as well as the counting number and normalized volume of airways and vessels near a nodule. Odds ratio (OR) and Chi-square (χ2) testing were performed to assess the correlation between features of surrounding structures and nodule malignancy. A non-parametric receiver operating characteristic (ROC) analysis was conducted in logistic regression to evaluate discrimination ability of each structure. Results: For the benign and malignant groups, the average distances from nodules to pleural surface, airways and vessels are respectively (6.56, 5.19), (37.08, 26.43) and (1.42, 1.07) mm. The correlation between nodules and the counting number of airways and vessels that contact or project towards nodules are respectively (OR=22.96, χ2=105.04) and (OR=7.06, χ2=290.11). The correlation between nodules and the volume of airways and vessels are (OR=9.19, χ2=159.02) and (OR=2.29, χ2=55.89). The areas-under-curves (AUCs) for pleurae, airways and vessels are respectively 0.5202, 0.6943 and 0.6529. Conclusion: Our results show that malignant nodules are often surrounded by more pulmonary structures compared with benign ones, suggesting that features of these structures could be viewed as lung cancer biomarkers. © 2021, CC BY.

关键词： Computerized tomography

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