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SS-Pro:a simplified siamese contrastive learning approach for protein surface representation

Frontiers of computer Science 2024年第5期18卷 243-245页

作者： Ao SHEN Mingzhi YUAN Yingfan MA Manning WANG Digital Medical Research Center School of Basic Medical ScienceFudan UniversityShanghai 200032China Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention Shanghai 200032China

Protein surface serves as an important representation of protein structure,revealing how protein interacts with other biomolecules to perform its *** forms the basis for pharmaceutical and fundamental biological research[1].Datadriven deep learning methods in protein surface representation face challenges of label scarcity,since labeled data are typically obtained through wet lab experiments.

关键词： revealing representation simplified

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Typicality-and instance-dependent label noise-combating:a novel framework for simulating and combating real-world noisy labels for endoscopic polyp classification

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Visual computing for Industry,Biomedicine,and Art 2024年第1期7卷 300-315页

作者： Yun Gao Junhu Fu Yuanyuan Wang Yi Guo School of Information Science and Technology Fudan UniversityShanghai 200433China Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai Shanghai 200433China

Learning with noisy labels aims to train neural networks with noisy *** models handle instance-inde-pendent label noise(IIN)well;however,they fall short with real-world *** medical image classification,atypical samples frequently receive incorrect labels,rendering instance-dependent label noise(IDN)an accurate representa-tion of real-world ***,the current IDN approaches fail to consider the typicality of samples,which hampers their ability to address real-world label noise *** alleviate the issues,we introduce typicality-and instance-dependent label noise(TIDN)to simulate real-world noise and establish a TIDN-combating framework to combat label ***,we use the sample’s distance to decision boundaries in the feature space to repre-sent *** TIDN is then generated according to *** establish a TIDN-attention module to combat label noise and learn the transition matrix from latent ground truth to the observed noisy labels.A recursive algorithm that enables the network to make correct predictions with corrections from the learned transition matrix is *** experiments demonstrate that the TIDN simulates real-world noise more closely than the existing IIN and ***,the TIDN-combating framework demonstrates superior classification performance when training with simulated TIDN and actual real-world noise.

关键词： Noisy label Instance-dependent label noise Noisy label simulation Real-world label noise Polyp classification

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Weakly Semi-supervised Whole Slide image Classification by Two-level Cross Consistency Supervision

arXiv

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arXiv 2025年

作者： Qu, Linhao Li, Shiman Luo, Xiaoyuan Liu, Shaolei Guo, Qinhao Wang, Manning Song, Zhijian Digital Medical Research Center School of Basic Medical Science Fudan University Shanghai China Shanghai Key Lab of Medical Image Computing and Computer Assisted Intervention Shanghai China Department of Gynecologic Oncology Shanghai Cancer Center Fudan University Shanghai China Department of Oncology Shanghai Medical College Fudan University Shanghai China

computer-aided Whole Slide image (WSI) classification has the potential to enhance the accuracy and efficiency of clinical pathological diagnosis. It is commonly formulated as a Multiple Instance Learning (MIL) problem, where each WSI is treated as a bag and the small patches extracted from the WSI are considered instances within that bag. However, obtaining labels for a large number of bags is a costly and time-consuming process, particularly when utilizing existing WSIs for new classification tasks. This limitation renders most existing WSI classification methods ineffective. To address this issue, we propose a novel WSI classification problem setting, more aligned with clinical practice, termed Weakly Semi-supervised Whole slide image Classification (WSWC). In WSWC, a small number of bags are labeled, while a significant number of bags remain unlabeled. The MIL nature of the WSWC problem, coupled with the absence of patch labels, distinguishes it from typical semi-supervised image classification problems, making existing algorithms for natural images unsuitable for directly solving the WSWC problem. In this paper, we present a concise and efficient framework, named CroCo, to tackle the WSWC problem through two-level Cross Consistency supervision. CroCo comprises two heterogeneous classifier branches capable of performing both instance classification and bag classification. The fundamental idea is to establish cross-consistency supervision at both the bag-level and instance-level between the two branches during training. Extensive experiments conducted on four datasets demonstrate that CroCo achieves superior bag classification and instance classification performance compared to other comparative methods when limited WSIs with bag labels are available. To the best of our knowledge, this paper presents for the first time the WSWC problem and gives a successful resolution. Copyright © 2025, The Authors. All rights reserved.

关键词： Semi-supervised learning

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Research of an electromagnetic tracking method based on two electrically-controlled magnetic sources

Research of an electromagnetic tracking method based on two ...

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IEEE Advanced Information Technology, Electronic and Automation Control Conference, IAEAC 2015

作者： Sha, Min Wang, Yifeng Ding, Ning Fang, Zuxiang Wu, Xiaomei Department of Electronic Engineering Fudan University Shanghai China Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention Shanghai China

ISBN: (纸本)9781479919796

This paper presents an electromagnetic tracking method based on two electrically-controlled magnetic sources. Each source consists of three mutual orthogonal coils. The method can skillfully determine the rotation angles of the maximum magnetic flux density vector (MMFD V) generated by a magnetic source according to the Biot-Savart Law. Then the position of the sensor can be calculated with a noniterative geometrical algorithm in real time. Simulation results demonstrate a good performance of this method. © 2015 IEEE.

关键词： Finite element method

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The virtual endoscope of neurosurgery used for transnasal approach

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9th International Symposium on Linear Drives for Industry Applications, LDIA 2013

作者： Mo, Jun Cong Yao, De Min Digital Medical Research Center of Shanghai Medical College Fudan University Shanghai 200032 China Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention Shanghai 200032 China

ISBN: (纸本)9783037858639

This paper presents and implements an automatic roaming and fast virtual endoscopic neurosurgery system for transsexual approach, which can be compatible with the fiber-optic endoscopic transnasal approach in the skull base surgery, and accurately locate the position and their mutual relations among the lesions, tumors and surrounding vital anatomical structures. The system uses a multithreaded RayCasting volume-rendering algorithm based on the graphics processor (GPU). It reconstructs the nasal three-dimensional structure in the skull base surgery, and optimizes the centerline extraction that can be carried out automatically. In real-time display, it improves the translucent rendering optical model, taking into account lighting model important parameter-the image gradient translucent degree of non-linear effects, and can fully display the skull surface and internal implied the interface and internal details. © (2013) Trans Tech Publications, Switzerland.

关键词： Neurosurgery

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An Ultrasonic Backscatter Instrument for Cancellous Bone Evaluation in Neonates

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Engineering 2015年第3期1卷 336-343页

作者： Chengcheng Liu Rong Zhang Ying Li Feng Xu Dean Ta Weiqi Wang Department of Electronic Engineering Fudan University Department of Neonatology Children’s Hospital of Fudan University Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention (MICCAI) of Shanghai

Ultrasonic backscatter technique has shown promise as a noninvasive cancellous bone assessment tool. A novel ultrasonic backscatter bone diagnostic （UBBD） instrument and an in vivo application for neonatal bone evaluation are introduced in this study. The UBBD provides several advantages, including noninvasiveness, non- ionizing radiation, portability, and simplicity. In this study, the backscatter signal could be measured within 5 s using the UBBD. Ultrasonic backscatter measurements were performed on 467 neonates （268 males and 199 females） at the left calcaneus. The backscatter signal was measured at a central frequency of 3.5 MHz. The delay （-/-1） and duration （7-2） of the backscatter signal of interest （SOl） were varied, and the apparent integrated backscatter （AIB）, frequency slope of apparent backscatter （FSAB）, zero frequency intercept of apparent backscatter （FIAB）, and spectral centroid shift （SCS） were calculated. The results showed that the SOl selection had a direct influence on cancellous bone evaluation. The AIB and FIAB were positively correlated with the gestational age （｜R｜ up to 0.45, P 〈 0.001） when -/-1 was short （〈 8 μS）, while negative correlations （｜R｜ up to 0.56, P 〈 0.001） were commonly observed for T1 〉 10 IJS. Moderate positive correlations （IRI up to 0.45, P 〈 0.001） were observed for FSAB and SCS with gestational age when 71 was long （〉 10 μs）. The 7-2 mainly introduced fluctuations in the observed correlation coefficients. The moderate correlations observed with UBBD demonstrate the feasibility of using the backscatter signal to evaluate neonatal bone status. This study also proposes an explicit standard for in vivo SOl selection and neonatal cancellous bone assessment.

关键词： ultrasonic backscatter cancellous bone evaluation signal of interest (SOI) backscatter instrument neonatal bone status

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Interoperative fundus image and report sharing in compliance with integrating the healthcare enterprise conformance and web access to digital imaging and communication in medicine persistent object protocol

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International Journal of Ophthalmology(English edition) 2013年第6期6卷 879-883页

作者： Hui-Qun Wu Zheng-Min Lv Xing-Yun Geng Kui Jiang Le-Min Tang Guo-Min Zhou Jian-Cheng Dong Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention(MICCAI) of Shanghai Department of Medical Informatics Medical School of Nantong University Department of Medical Image Engineering Medical School of Nantong University Department of Anatomy Histology and EmbryologySchool of Basic Medical Sciences

AIM:To address issues in interoperability between different fundus image systems,we proposed a web eyepicture archiving and communication system(PACS)framework in conformance with digital imaging and communication in medicine(DICOM)and health level 7(HL7)protocol to realize fundus images and reports sharing and communication through ***:Firstly,a telemedicine-based eye care work flow was established based on integrating the healthcare enterprise(IHE)Eye Care technical ***,a browser/server architecture eye-PACS system was established in conformance with the web access to DICOM persistent object(WADO)protocol,which contains three ***:In any client system installed with web browser,clinicians could log in the eye-PACS to observe fundus images and *** internet mail extensions(MIME)type of a structured report is saved as pdf/html with reference link to relevant fundus image using the WADO syntax could provide enough information for *** functions provided by open-source Oviyam could be used to query,zoom,move,measure,view OICOM fundus ***:Such web eye-PACS in compliance to WADO protocol could be used to store and communicate fundus images and reports,therefore is of great significance for teleophthalmology.

关键词： picture archiving and communication system teleophthalmology integrating the healthcare enterprise web access to DICOM persistent object

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Dual Attention Poser: Dual Path Body Tracking Based on Attention

Dual Attention Poser: Dual Path Body Tracking Based on Atten...

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2023 IEEE/CVF Conference on computer Vision and Pattern Recognition Workshops, CVPRW 2023

作者： Di, Xinhan Dai, Xiaokun Zhang, Xinkang Chen, Xinrong Fudan Universiry Academy for Engineering&Technology China Deepearthgo Fudan University Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention China

ISBN: (纸本)9798350302493

Currently, mixed reality head-mounted displays tracking the full body of users is an important human-computer interaction mode through the pose of the head and the hands. Unfortunately, users' virtual representation and experience is limited due to high reconstruction error when simple transformer network architecture is applied. In this paper, we present a novel model, named Dual Attention Poser, which can learn the whole body reconstruction at a high accuracy. The proposed model consists of three key modules. Among them, dual-path attention encoder is designed to extract feature of the sparse signals. Cross attention mixer module enable the fusion of representation in the double path. Attention-gated-mlp decoder is applied to decode the hidden feature from the sparse input through attention gate. Test results on the AMASS dataset show that Dual Attention Poser can reduce the error by up to 18.2% in comparison with the state-of-the-art results. © 2023 IEEE.

关键词： Network architecture

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STCA-Net: Multi-channel ECG Space-Time-Channel Attention Model for Noninvasive Prediction of Catheter Ablation in Atrial Fibrillation 3

STCA-Net: Multi-channel ECG Space-Time-Channel Attention Mod...

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3rd International Conference on Pattern Recognition and Machine Learning, PRML 2022

作者： Zhong, Gaoyan Liu, Sen Wang, Yueyi Yang, Cuiwei Fudan University Center for Biomedical Engineering Shanghai China The Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai Shanghai China

ISBN: (数字)9781665499507

ISBN: (纸本)9781665499507

Atrial Fibrillation (AF) remains a high recurrence rate after Catheter Ablation (CA). It is of certain clinical significance to predict the recurrence of AF before CA using preoperative electrocardiogram (ECG) signals. The Body Surface Potential Mapping Signals (BSPMs) can be processed into Three-dimensional (3D) video frame signals using isopotential map. By applying space, time and channel attention to emphasize meaningful features, we proposed the space-time-channel attention module (STCA-Net) for large-scale supervised learning. Compare with C3D-Net, the experiment of 14 patients collected in the clinic shows that C3D-Net with space-time-channel attention (STCA) can achieve better performance, and can achieve 0.858 accuracy for the experiment of identifying patients' recurrence. The experimental results show that STCA-Net contributes to a good prediction of CA in AF. © 2022 IEEE.

关键词： Electrocardiograms

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Surface-based automatic coarse registration of head scans

Surface-based automatic coarse registration of head scans

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作者： Li, Fang Song, Zhijian Digital Medical Research Center Fudan University Shanghai200032 China Key Laboratory of Medical Imaging Computing Computer Assisted Intervention of Shanghai Shanghai200032 China

Surface registration is widely used in image-guided neurosurgery to achieve spatial registration between the patient space and the image space. Coarse registration, followed by fine registration, is an important premise to ensure the robustness and efficiency of surface registration. In this paper, a coarse registration algorithm based on the principal axes is proposed to achieve this goal. The extraction of the principal axes relies on the approximated surface with an adaptive Gaussian kernel, the width of which is consistent with neighborhood relation so that it is applicable for various scanning data. Determining the corresponding centers of translation is another problem for aligning different scanning data, which is solved through heuristics. Six pairs of points on two surfaces with the farthest projections on the principal axes were regarded as the candidates of translation centers, and then through tentative alignments of local regions around them, a pair of candidates with the minimum registration error was selected as the optimal translation centers. Automatic registration of two scans of a head phantom is presented in this paper. Experimental results confirmed the robustness of the algorithm and its feasibility in clinical applications. © 2014 - IOS Press and the authors.

关键词： Neurosurgery

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