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IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes

Journal of Genetics and Genomics 2024年第4期51卷 443-453页

作者： Shuyu Liang Sicheng Xu Shichong Zhou Cai Chang Zhiming Shao Yuanyuan Wang Sheng Chen Yunxia Huang Yi Guo Department of Electronic Engineering School of Information Science and TechnologyFudan UniversityShanghai 200433China The Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention(MICCAI)of Shanghai Shanghai 200032China Shanghai Key Laboratory of Metabolic Remodeling and Health Institute of Metabolism and Integrative BiologyFudan UniversityShanghai 200433China Department of Ultrasound Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai 200032China Department of Breast Surgery Fudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai 200032China

Investigating correlations between radiomic and genomic profiling in breast cancer(BC)molecular subtypes is crucial for understanding disease mechanisms and providing personalized *** present a well-designed radiogenomic framework image–gene–gene set(IMAGGS),which detects multi-way associations in BC subtypes by integrating radiomic and genomic *** dataset consists of 721 patients,each of whom has 12 ultrasound(US)images captured from different angles and gene mutation *** better characterize tumor traits,12 multi-angle US images are fused using two distinct ***,we analyze complex many-to-many associations between phenotypic and genotypic features using a machine learning algorithm,deviating from the prevalent one-to-one relationship pattern observed in previous *** radiomic and genomic features are screened using these *** addition,gene set enrichment analysis is performed to investigate the joint effects of gene sets and delve deeper into the biological functions of BC *** further validate the feasibility of IMAGGS in a glioblastoma multiforme dataset to demonstrate the scalability of IMAGGS across different modalities and *** together,IMAGGS provides a comprehensive characterization for diseases by associating imaging,genes,and gene sets,paving the way for biological interpretation of radiomics and development of targeted therapy.

关键词： IMAGGS Radiogenomic framework "lmage-gene-geneset"associations Molecular subtypes Breast cancer

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3D Clothed Human Reconstruction From One In-the-Wild RGB image

3D Clothed Human Reconstruction From One In-the-Wild RGB Ima...

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IEEE International Conference on image processing

作者： Liangjing Shao Benshuang Chen Xinrong Chen Academy for Engineering & Technology Fudan University Shanghai China Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention

ISBN: (数字)9798350349399

ISBN: (纸本)9798350349405

In recent years, much achievement have been made in the field of 3D clothed human reconstruction. However, most of researches performed not well for reconstruction from in-the-wild images due to the domain gap between the synthetic images of training datasets and the in-the-wild images. In this study, a modular model, including clothes encoder, body encoder and cloth generator, is proposed to perform 3D clothed human reconstruction from one single-view in-the-wild RGB image. In particular, we introduce the adaptive aggregation of convolution and multi-head attention into the cloth encoder and apply the adjustment of the segmentation at the preprocessing stage. According to experiments on MSCOCO and 3DPW datasets, the proposed method achieves state-of-the-art performance on 3D clothed human reconstruction from in-the-wild images compared with previous works.

关键词： Training Solid modeling image segmentation Adaptation models Three-dimensional displays Convolution Data preprocessing

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FAST: A Dual-tier Few-Shot Learning Paradigm for Whole Slide image Classification 38

FAST: A Dual-tier Few-Shot Learning Paradigm for Whole Slide...

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38th Conference on Neural Information processing Systems, NeurIPS 2024

作者： Fu, Kexue Luo, Xiaoyuan Qu, Linhao Wang, Shuo Xiong, Ying Maglogiannis, Ilias Gao, Longxiang Wang, Manning Qilu University of Technology Shandong Academy of Sciences Jinan China Digital Medical Research Center School of Basic Medical Sciences Fudan University China Shanghai Key Lab of Medical Image Computing and Computer Assisted Intervention China Fudan University China University of Piraeus Greece Shandong Provincial Key Laboratory of Computing Power Internet and Service Computing Shandong Fundamental Research Center for Computer Science Jinan China

The expensive fine-grained annotation and data scarcity have become the primary obstacles for the widespread adoption of deep learning-based Whole Slide images (WSI) classification algorithms in clinical practice. Unlike few-shot learning methods in natural images that can leverage the labels of each image, existing few-shot WSI classification methods only utilize a small number of fine-grained labels or weakly supervised slide labels for training in order to avoid expensive fine-grained annotation. They lack sufficient mining of available WSIs, severely limiting WSI classification performance. To address the above issues, we propose a novel and efficient dual-tier few-shot learning paradigm for WSI classification, named FAST. FAST consists of a dual-level annotation strategy and a dual-branch classification framework. Firstly, to avoid expensive fine-grained annotation, we collect a very small number of WSIs at the slide level, and annotate an extremely small number of patches. Then, to fully mining the available WSIs, we use all the patches and available patch labels to build a cache branch, which utilizes the labeled patches to learn the labels of unlabeled patches and through knowledge retrieval for patch classification. In addition to the cache branch, we also construct a prior branch that includes learnable prompt vectors, using the text encoder of visual-language models for patch classification. Finally, we integrate the results from both branches to achieve WSI classification. Extensive experiments on binary and multi-class datasets demonstrate that our proposed method significantly surpasses existing few-shot classification methods and approaches the accuracy of fully supervised methods with only 0.22% annotation costs. All codes and models will be publicly available on https://***/fukexue/FAST. © 2024 Neural information processing systems foundation. All rights reserved.

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NEAT-Net: An Unsupervised Cross-View Prior Inpainting Network for CBCT Metal Artifact Reduction 46

NEAT-Net: An Unsupervised Cross-View Prior Inpainting Networ...

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46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2024

作者： Yang, Yang Tong, Zhan Zhong, Xinyun Shi, Yijie Xi, Yan Yu, Wenxue Wu, Zhan Chen, Yang First-Imaging Tech Shanghai China Southeast University Laboratory of Image Science and Technology The School of Computer Science and Engineering Nanjing China Southeast University Jiangsu Provincial Joint International Research Laboratory of Medical Information Processing The Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications Nanjing China

ISBN: (纸本)9798350371499

Intraoperative Cone-Beam Computed Tomography (CBCT) facilitates intraoperative navigation for Minimally Invasive Spine surgery (MISS). However, high-attenuation metal implants used in MISS often cause metal artifacts in the reconstructed CBCT images. Current algorithms do not consider the cross-view information in the projection-domain for metal artifact reduction (MAR). Inaccurate projection-domain inpainting results in CBCT MAR lead to tissue blurring and secondary artifacts, significantly compromising the accuracy of CBCT-guided MISS and increasing surgical risks. To address the above challenge, in this paper, we propose a novel unsupervised cross-view prior inpainting network for CBCT Metal Artifact Reduction named NEAT-Net. Firstly, a cross-view prior multi-scale inpainting module is constructed to learn the inter-view complementary information. Secondly, a hybrid feature attention module is proposed to adaptively fuse cross-view features. In addition, an unsupervised training approach is proposed to directly learn from metal-affected data. Extensive experiments are conducted to verify the effectiveness of our algorithm on a real clinical dataset. © 2024 IEEE.

关键词： computerized tomography

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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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Continuous K-space Recovery Network with image Guidance for Fast MRI Reconstruction

arXiv

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arXiv 2024年

作者： Meng, Yucong Yang, Zhiwei Duan, Minghong Shi, Yonghong Song, Zhijian 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 Academy of Engineering and Technology Fudan University Shanghai200433 China

Magnetic resonance imaging (MRI) is a crucial tool for clinical diagnosis while facing the challenge of long scanning time. To reduce the acquisition time, fast MRI reconstruction aims to restore high-quality MRI images from the undersampled k-space. Existing methods typically train deep learning models to map the undersampled data to artifact-free MRI images. However, these studies often overlook the unique properties of k-space and directly apply general networks designed for image processing to k-space recovery, leaving the precise learning of k-space largely underexplored. In this work, we propose a continuous k-space recovery network from a new perspective of implicit neural representation with image domain guidance, which boosts the performance of MRI reconstruction. Specifically, (1) an implicit neural representation based encoder-decoder structure is customized to continuously query unsampled k-values. (2) an image guidance module is designed to mine the image-domain information from the low-quality MRI images to further guide the k-space recovery. (3) a multi-stage training strategy is proposed to recover dense k-space progressively. Extensive experiments conducted on CC359, fastMRI, IXI, and SKM-TEA datasets demonstrate the effectiveness of our method and its superiority over other competitors. Implementation code will be available in https://***/XiaoMengLiLiLi/IGKR. Copyright © 2024, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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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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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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NEAT-Net: An Unsupervised Cross-View Prior Inpainting Network for CBCT Metal Artifact Reduction

NEAT-Net: An Unsupervised Cross-View Prior Inpainting Networ...

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

作者： Yang Yang Zhan Tong Xinyun Zhong Yijie Shi Yan Xi Wenxue Yu Zhan Wu Yang Chen Laboratory of Image Science and Technology the School of Computer Science and Engineering Southeast University Nanjing China First-Imaging Tech Shanghai China Jiangsu Provincial Joint International Research Laboratory of Medical Information Processing the Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications Southeast University Nanjing China

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

关键词： Training Minimally invasive surgery Accuracy Navigation Fuses Computed tomography Metals Implants Engineering in medicine and biology image reconstruction

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Dual-Source CBCT for Larger Longitudinal Coverage: System Design and image Reconstruction

Dual-Source CBCT for Larger Longitudinal Coverage: System De...

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

作者： Xusheng Zhang Tianling Lyu Yijie Shi Xinyun Zhong Zhan Wu Yan Xi Shijie Wang Yang Chen Wentao Zhu School of Software Southeast University Nanjing China Zhejiang Lab Hangzhou China Laboratory of Image Science and Technology the School of Computer Science and Engineering Southeast University Nanjing China First-Imaging Tech. Shanghai China Jiangsu Provincial Joint International Research Laboratory of Medical Information Processing the Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications Southeast University Nanjing China

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

The application of CBCT systems in intraoperative environments has become increasingly common, but concurrent CBCT systems are unsuitable for situations that require a large longitudinal imaging FoV, such as orthopedics. To increase longitudinal coverage, we developed a dual-source CBCT (DS-CBCT) system in which two ray sources are symmetrically placed along the central plane. After further analyzing its geometric characteristics, we propose an analytical reconstruction algorithm termed DT-FDK specialized for DS-CBCT, which combines cone-beam rebinning and two rays with smaller cone angles among the four conjugate rays to further suppress cone beam artifacts. The system design and reconstruction algorithm are tested on both simulated and real-scanned data. Results show that the DS-CBCT can expand the effective imaging volume by 37.1% compared to single-source CBCT systems. The reconstructed images by DT-FDK also show improved image quality compared to traditional reconstruction algorithms.

关键词： image quality Orthopedic surgery Imaging Reconstruction algorithms Engineering in medicine and biology image reconstruction System analysis and design

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