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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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Optimizing the Size of Peritumoral Region for Assessing Non-Small Cell Lung Cancer Heterogeneity Using Radiomics 12th

Optimizing the Size of Peritumoral Region for Assessing No...

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12th International Conference on Health Information Science, HIS 2023

作者： Zhang, Xingping Zhang, Guijuan Qiu, Xingting Yin, Jiao Tan, Wenjun Yin, Xiaoxia Yang, Hong Wang, Kun Zhang, Yanchun Cyberspace Institute of Advanced Technology Guangzhou University Guangzhou510006 China School of Computer Science and Technology Zhejiang Normal University Jinhua321000 China Department of Respiratory and Critical Care First Affiliated Hospital of Gannan Medical University Ganzhou341000 China Institute for Sustainable Industries and Liveable Cities Victoria University Melbourne3011 Australia Department of New Networks Peng Cheng Laboratory Shenzhen518000 China Department of Radiology First Affiliated Hospital of Gannan Medical University Ganzhou341000 China Key Laboratory of Intelligent Computing in Medical Image Ministry of Education Northeastern University Shenyang110189 China

ISBN: (纸本)9789819971077

Objectives: Radiomics has a novel value in accurately and noninvasively characterizing non-small cell lung cancer (NSCLC), but the role of peritumoral features has not been discussed in depth. This work aims to systematically assess the additional value of peritumoral features by exploring the impact of peritumoral region size. Materials and methods: A total of 370 NSCLC patients who underwent preoperative contrast-enhanced CT scans between October 2017 and September 2021 were retrospectively analyzed. The study was carefully designed with a radiomics pipeline to predict lymphovascular invasion, pleural invasion, and T4 staging. To assess the impact of peritumoral features, tumor regions of interest (ROIs) annotated by two medical experts were automatically expanded to produce peritumoral ROIs of different regional sizes, with edge thicknesses of 1 mm, 3 mm, 5 mm, and 7 mm. In a custom pipeline, prediction models were constructed using peritumoral features with different margin thicknesses and intratumoral features of the primary tumor. Results: Radiomics features combining intratumoral and peritumoral regions were created based on the best features of each ROI. Models incorporating peritumoral features yielded varying degrees of improvement in AUCs compared to models using only intratumoral features. The choice of peritumoral size may impact the degree of improvement in radiomics analysis. Conclusions: The integration of peritumoral features has shown potential for improving the predictive value of radiomics. However, selecting an appropriate peritumoral region size is constrained by various factors such as clinical issues, imaging modalities, and ROI annotations. Therefore, future radiomics studies should consider these factors and optimize peritumoral features to cater to specific applications. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd 2023.

关键词： Tumors

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Robust Point Cloud Registration Framework Based on Deep Graph Matching(TPAMI Version)

arXiv

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arXiv 2022年

作者： Fu, Kexue Luo, Jiazheng Luo, Xiaoyuan Liu, Shaolei Zhang, Chenxi Wang, Manning The Digital Medical Research Center School of Basic Medical Science Fudan University Shanghai200032 China The Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention Shanghai200032 China

3D point cloud registration is a fundamental problem in computer vision and robotics. Recently, learning-based point cloud registration methods have made great progress. However, these methods are sensitive to outliers, which lead to more incorrect correspondences. In this paper, we propose a novel deep graph matching-based framework for point cloud registration. Specifically, we first transform point clouds into graphs and extract deep features for each point. Then, we develop a module based on deep graph matching to calculate a soft correspondence matrix. By using graph matching, not only the local geometry of each point but also its structure and topology in a larger range are considered in establishing correspondences, so that more correct correspondences are found. We train the network with a loss directly defined on the correspondences, and in the test stage the soft correspondences are transformed into hard one-to-one correspondences so that registration can be performed by a correspondence-based solver. Furthermore, we introduce a transformer-based method to generate edges for graph construction, which further improves the quality of the correspondences. Extensive experiments on object-level and scene-level benchmark datasets show that the proposed method achieves state-of-the-art performance. The code is available at: https://***/fukexue/RGM. Copyright © 2022, The Authors. All rights reserved.

关键词： Topology

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RKSeg+: make full use of Runge–Kutta methods in medical image segmentation

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Multimedia Systems 2024年第2期30卷 65-65页

作者： Zhu, Mai Fu, Chong Wang, Xingwei School of Computer Science and Engineering Northeastern University Shenyang110819 China Engineering Research Center of Security Technology of Complex Network System Ministry of Education Shenyang110819 China Key Laboratory of Intelligent Computing in Medical Image Ministry of Education Northeastern University Shenyang110819 China

The dynamical system perspective has been used to build efficient image classification networks and semantic segmentation networks. Furthermore, the Runge–Kutta (RK) methods are powerful tools for building networks from the dynamical systems perspective. Hence, the Runge–Kutta segmentation network (RKSeg) for medical image segmentation was born. Skip connections and multiple scaling are often used in common models but lack mathematical explanations. RKSeg interprets and uses skip connections based on the RK methods. Therefore, RKSeg greatly improves segmentation efficiency. However, it does not explain and use multiple scales from a dynamical system perspective but only inherits the multi-scale scheme of existing models. We compensate for this shortcoming by interpreting and using multiple scales based on the RK methods. In addition, the network structure also limits the excellent image classification networks as the backbones of RKSegs. Therefore, we modify the network structure to support more image classification networks as backbones. As a result, we propose a novel network structure RKSeg+. Our proposed RKSeg+ achieves better segmentation results with fewer parameters than RKSeg. Furthermore, RKSeg+, well configured with few parameters, outperforms state-of-the-art models on six of the ten organ datasets in the medical Segmentation Decathlon. © The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2024.

关键词： Semantic Segmentation

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Rethinking Multiple Instance Learning: Developing an Instance-Level Classifier via Weakly-Supervised Self-Training

arXiv

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arXiv 2024年

作者： Ma, Yingfan Luo, Xiaoyuan Yuan, Mingzhi Chen, Xinrong Wang, Manning The Digital Medical Research Center School of Basic Medical Science Fudan University Shanghai200032 China The Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention Shanghai200032 China

Multiple instance learning (MIL) problem is currently solved from either bag-classification or instance-classification perspective, both of which ignore important information contained in some instances and result in limited performance. For example, existing methods often face difficulty in learning hard positive instances. In this paper, we formulate MIL as a semi-supervised instance classification problem, so that all the labeled and unlabeled instances can be fully utilized to train a better classifier. The difficulty in this formulation is that all the labeled instances are negative in MIL, and traditional self-training techniques used in semi-supervised learning tend to degenerate in generating pseudo labels for the unlabeled instances in this scenario. To resolve this problem, we propose a weakly-supervised self-training method, in which we utilize the positive bag labels to construct a global constraint and a local constraint on the pseudo labels to prevent them from degenerating and force the classifier to learn hard positive instances. It is worth noting that easy positive instances are instances are far from the decision boundary in the classification process, while hard positive instances are those close to the decision boundary. Through iterative optimization, the pseudo labels can gradually approach the true labels. Extensive experiments on two MNIST synthetic datasets, five traditional MIL benchmark datasets and two histopathology whole slide image datasets show that our method achieved new SOTA performance on all of them. The code will be publicly available. Impact Statement-MIL is a primary research field within weakly supervised learning and has numerous applications, such as histopathology analysis, video anomaly detection, and drug design. However, current mainstream methods in MIL predominantly rely on bag labels to train the network, consequently overlooking the potential of instance-level supervision information. In our paper, we highlight the

关键词： Self-supervised learning

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Ddfp: Data-Dependent Frequency Prompt for Source Free Domain Adaptation of medical image Segmentation

SSRN

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SSRN 2024年

作者： Yin, Siqi Liu, Shaolei Wang, Manning Digital Medical Research Center School of Basic Medical Science Fudan University Shanghai200032 China Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention Shanghai200032 China

Domain adaptation aims to address model performance degradation problem under domain gap. In the typical setting of unsupervised domain adaptation, labeled data from source domain and unlabeled data from target domain are used to train a target model. However, access to source domain medical data can be restricted due to privacy policies, in which scenario, the research attention has shifted to source free domain adaptation (SFDA) which only requires a trained source domain model and unlabeled target domain data for adaptation. Existing SFDA methods often utilize domain-dependent image style translation and self-supervision techniques to reduce domain gap and train the target domain model. However, the quality of domain-dependent style translated images and pseudo labels still leaves room for improvement. Moreover, training the entire model during adaptation is suboptimal under limited supervision. In this paper, we propose a novel SFDA framework to overcome these limitations. Specifically, to effectively mitigate the impact of domain gap in the initial training phase, we introduce pre-adaptation to derive a pre-adapted model for target model initialization and generate quality enhanced pseudo labels without introducing additional parameters. Furthermore, we propose a data-dependent frequency prompt to better translate target domain images into a source-like style individually. Subsequently, the style-related layers fine-tuning strategy tailored for SFDA is used to train the target model using the prompted target domain images and pseudo labels. Extensive experiments on cross-modality abdominal and cardiac SFDA segmentation tasks demonstrated that our proposed method outperforms the state-of-the-art baselines. Our code is available online. © 2024, The Authors. All rights reserved.

关键词： Semantic Segmentation

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A Review of intelligent image Processing Method of Pulmonary CT images

A Review of Intelligent Image Processing Method of Pulmonary...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Wenjun Tan Pan Liu Hui Guo Jinzhu Yang Xiaoxia Yin Yanchun Zhang Key Laboratory of Intelligent Computing in Medical Image Ministry of Education Northeastern University Shenyang China Cyberspace Institute of Advanced Technology Guangzhou University Guangzhou China Centre for Applied Informatics College of Engineering and Science Victoria University Melbourne Australia

ISBN: (纸本)9781728118680

Due to the high degree of air pollution, high smoking rate and poor production protection conditions during the industrialization process, the incidence of pulmonary diseases such as pulmonary cancer and chronic obstructive pulmonary disease has been maintained at a high level in the world and has shown an increasing trend, which has become one of the diseases with the highest mortality rate. In recent years, with the rapid development of artificial intelligence technology, the intelligent assisted diagnosis and surgery technology of pulmonary CT images has made great progress, and played an important role in the early diagnosis and precise treatment of pulmonary diseases. This paper mainly discusses the development history of image-assisted diagnosis and surgery technology for pulmonary diseases, as well as the method of segmentation and evaluation of pulmonary tissue and lesion, and the clinical application of pulmonary intelligent assisted diagnosis and surgery systems.

关键词： biological tissues cancer computerised tomography image segmentation lung medical image processing surgery X-Ray Computed Tomography medical image processing Lung TISSUES (BIOLOGY) Lung Diseases image segmentation Surgery Air contamination intelligent image processing Lung Cancer Chronic Obstructive Airway Disease Mortality

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A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules

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Protein & Cell 2016年第1期7卷 46-62页

作者： Hong Shan Zihao wang Fa Zhang Yong Xiong Chang-Cheng Yin Fei Sun Department of Biophysics College of Basic Medical Sciences Peking University Health Science Center Beijing 100191China National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China Key Lab of Intelligent Information Processing and Advanced Computing Research Lab Institute of Computing TechnologyChinese Academy of Sciences Beijing 100190 China University of Chinese Academy of Sciences Beijing 100049 China Department of Molecular Biophysics and Biochemistry Yale University New Haven CT 06511 USA Center for Biological Imaging Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China

Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macro- molecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate align- ments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orien- tations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimen- sional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large （60S/50S） and the small （40S/30S） subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolutionsingle particle analysis of macromolecular complexes with dynamic conformations.

关键词： cryo-electron microscopy single particleanalysis conformational heterogeneity rigid module Iocaoptimization refinement

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POS-BERT: Point Cloud One-Stage BERT Pre-Training

arXiv

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arXiv 2022年

作者： Fu, Kexue Gao, Peng Liu, Shaolei Zhang, Renrui Qiao, Yu Wang, Manning Digital Medical Research Center School of Basic Medical Sciences Fudan University China Shanghai AI Lab China Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention China

Recently, the pre-training paradigm combining Transformer and masked language modeling has achieved tremendous success in NLP, images, and point clouds, such as BERT. However, directly extending BERT from NLP to point clouds requires training a fixed discrete Variational AutoEncoder (dVAE) before pre-training, which results in a complex two-stage method called Point-BERT. Inspired by BERT and MoCo, we propose POS-BERT, a one-stage BERT pre-training method for point clouds. Specifically, we use the mask patch modeling (MPM) task to perform point cloud pre-training, which aims to recover masked patches information under the supervision of the corresponding tokenizer output. Unlike Point-BERT, its tokenizer is extra-trained and frozen. We propose to use the dynamically updated momentum encoder as the tokenizer, which is updated and outputs the dynamic supervision signal along with the training process. Further, in order to learn high-level semantic representation, we combine contrastive learning to maximize the class token consistency between different transformation point clouds. Extensive experiments have demonstrated that POS-BERT can extract high-quality pre-training features and promote downstream tasks to improve performance. Using the pretraining model without any fine-tuning to extract features and train linear SVM on ModelNet40, POS-BERT achieves the state-of-the-art classification accuracy, which exceeds Point-BERT by 3.5%. In addition, our approach has significantly improved many downstream tasks, such as fine-tuned classification, few-shot classification, part segmentation. The code and trained-models will be available at: https://***/fukexue/POS-BERT. Copyright © 2022, The Authors. All rights reserved.

关键词： Natural language processing systems

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Robust Secure Beamforming for Multi-Receiver Multi-Eavesdropper MIMO SWIPT Systems

Robust Secure Beamforming for Multi-Receiver Multi-Eavesdrop...

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GLOBECOM 2020 - 2020 IEEE Global Communications Conference

作者： Yao Yu Shumei Liu Weina Yuan Phee Lep Yeoh Branka Vucetic Yonghui Li School of Electrical and Information Engineering University of Sydney Australia Key Laboratory of Intelligent Computing in Medical Image Ministry of Education Northeastern University Shenyang China School of Information Science and Engineering East China University of Science and Technology Shanghai China

ISBN: (数字)9781728182988

ISBN: (纸本)9781728182995

In this paper, we consider a multiuser multiple-input multiple-output (MIMO) downlink communication system with simultaneous wireless information and power transfer (SWIPT). In particular, we focus on a realistic and efficient multi-receiver multi-eavesdropper MIMO SWIPT system, in which the channel state information (CSI) of each legitimate receiver and energy receiver (i.e., potential eavesdropper) is partially known to the transmitter. Based on this, we propose a robust artificial noise (AN)-aided secure transmission scheme for the system, where the channel uncertainties are modeled by the worst-case model. In the proposed scheme, we aim to maximize the worst-case achievable secrecy rate under the transmit power constraint and the energy harvesting (EH) constraint, by jointly optimizing the transmit precoding matrix and the AN covariance matrix. We utilize the S-Procedure and Taylor series approximation to transform the non-convex problem. Then, we apply the interior point method to tackle the transformed convex problem, obtaining the approximate optimal matrices and the corresponding maximum worst-case secrecy rate. Simulation results show that our proposed scheme achieves significant performance improvements in terms of convergence and the worst-case achievable secrecy rate.

关键词： Receivers Erbium MIMO communication Transmitters Covariance matrices Optimization Wireless communication

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