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Vision Transformers for Computational Histopathology 用于计算组织病理学的视觉转换器
IF 17.6 1区 工程技术 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2023-07-21 DOI: 10.1109/RBME.2023.3297604
Hongming Xu;Qi Xu;Fengyu Cong;Jeonghyun Kang;Chu Han;Zaiyi Liu;Anant Madabhushi;Cheng Lu
Computational histopathology is focused on the automatic analysis of rich phenotypic information contained in gigabyte whole slide images, aiming at providing cancer patients with more accurate diagnosis, prognosis, and treatment recommendations. Nowadays deep learning is the mainstream methodological choice in computational histopathology. Transformer, as the latest technological advance in deep learning, learns feature representations and global dependencies based on self-attention mechanisms, which is increasingly gaining prevalence in this field. This article presents a comprehensive review of state-of-the-art vision transformers that have been explored in histopathological image analysis for classification, segmentation, and survival risk regression applications. We first overview preliminary concepts and components built into vision transformers. Various recent applications including whole slide image classification, histological tissue component segmentation, and survival outcome prediction with tailored transformer architectures are then discussed. We finally discuss key challenges revolving around the use of vision transformers and envisioned future perspectives. We hope that this review could provide an elaborate guideline for readers to explore vision transformers in computational histopathology, such that more advanced techniques assisting in the precise diagnosis and treatment of cancer patients could be developed.
计算组织病理学侧重于自动分析千兆字节整张切片图像中包含的丰富表型信息,旨在为癌症患者提供更准确的诊断、预后和治疗建议。目前,深度学习是计算组织病理学的主流方法选择。Transformer作为深度学习的最新技术进展,基于自我注意机制学习特征表征和全局依赖关系,在该领域日益盛行。本文全面回顾了在组织病理学图像分析中用于分类、分割和生存风险回归应用的最先进的视觉变换器。我们首先概述了视觉转换器的初步概念和组件。然后讨论了近期的各种应用,包括整张切片图像分类、组织学组织成分分割,以及采用定制变换器架构的生存结果预测。最后,我们讨论了围绕视觉转换器的使用所面临的主要挑战以及对未来前景的展望。我们希望这篇综述能为读者探索视觉转换器在计算组织病理学中的应用提供详尽的指导,从而开发出更先进的技术来协助癌症患者的精确诊断和治疗。
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引用次数: 0
Beyond Supervised Learning for Pervasive Healthcare 超越监督学习,实现无处不在的医疗保健。
IF 17.6 1区 工程技术 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2023-07-20 DOI: 10.1109/RBME.2023.3296938
Xiao Gu;Fani Deligianni;Jinpei Han;Xiangyu Liu;Wei Chen;Guang-Zhong Yang;Benny Lo
The integration of machine/deep learning and sensing technologies is transforming healthcare and medical practice. However, inherent limitations in healthcare data, namely scarcity, quality, and heterogeneity, hinder the effectiveness of supervised learning techniques which are mainly based on pure statistical fitting between data and labels. In this article, we first identify the challenges present in machine learning for pervasive healthcare and we then review the current trends beyond fully supervised learning that are developed to address these three issues. Rooted in the inherent drawbacks of empirical risk minimization that underpins pure fully supervised learning, this survey summarizes seven key lines of learning strategies, to promote the generalization performance for real-world deployment. In addition, we point out several directions that are emerging and promising in this area, to develop data-efficient, scalable, and trustworthy computational models, and to leverage multi-modality and multi-source sensing informatics, for pervasive healthcare.
机器/深度学习与传感技术的融合正在改变医疗保健和医疗实践。然而,医疗保健数据固有的局限性,即稀缺性、质量和异质性,阻碍了主要基于数据和标签之间纯统计拟合的监督学习技术的有效性。在本文中,我们首先明确了机器学习在无处不在的医疗保健领域所面临的挑战,然后回顾了为解决这三个问题而开发的完全监督学习以外的当前趋势。基于纯粹的完全监督学习所固有的经验风险最小化缺点,本调查总结了七种关键的学习策略,以提高实际部署的泛化性能。此外,我们还指出了这一领域新兴且前景广阔的几个方向,以开发数据效率高、可扩展且值得信赖的计算模型,并利用多模态和多源传感信息学来实现普适性医疗保健。
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引用次数: 0
A Review of Image-Based Food Recognition and Volume Estimation Artificial Intelligence Systems 基于图像的食物识别和体积估算人工智能系统综述。
IF 17.6 1区 工程技术 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2023-06-05 DOI: 10.1109/RBME.2023.3283149
Fotios S. Konstantakopoulos;Eleni I. Georga;Dimitrios I. Fotiadis
The daily healthy diet and balanced intake of essential nutrients play an important role in modern lifestyle. The estimation of a meal's nutrient content is an integral component of significant diseases, such as diabetes, obesity and cardiovascular disease. Lately, there has been an increasing interest towards the development and utilization of smartphone applications with the aim of promoting healthy behaviours. The semi – automatic or automatic, precise and in real-time estimation of the nutrients of daily consumed meals is approached in relevant literature as a computer vision problem using food images which are taken via a user's smartphone. Herein, we present the state-of-the-art on automatic food recognition and food volume estimation methods starting from their basis, i.e., the food image databases. First, by methodically organizing the extracted information from the reviewed studies, this review study enables the comprehensive fair assessment of the methods and techniques applied for segmenting food images, classifying their food content and computing the food volume, associating their results with the characteristics of the used datasets. Second, by unbiasedly reporting the strengths and limitations of these methods and proposing pragmatic solutions to the latter, this review can inspire future directions in the field of dietary assessment systems.
日常健康饮食和必需营养素的均衡摄入在现代生活方式中发挥着重要作用。对膳食营养成分的估计是糖尿病、肥胖症和心血管疾病等重大疾病不可或缺的组成部分。最近,人们对开发和使用智能手机应用程序以促进健康行为越来越感兴趣。在相关文献中,半自动或自动、精确和实时地估算每日膳食的营养成分是一个计算机视觉问题,使用的是通过用户智能手机拍摄的食物图像。在此,我们将从食物图像数据库这一基础出发,介绍自动食物识别和食物体积估算方法的最新进展。首先,本综述研究有条不紊地整理了从综述研究中提取的信息,对用于分割食物图像、分类食物内容和计算食物体积的方法和技术进行了全面公正的评估,并将其结果与所用数据集的特点联系起来。其次,通过公正地报告这些方法的优势和局限性,并针对后者提出实用的解决方案,本综述可为膳食评估系统领域的未来发展指明方向。
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引用次数: 1
Radiomics and Deep Learning in Nasopharyngeal Carcinoma: A Review 鼻咽癌放射组学与深度学习:综述
IF 17.6 1区 工程技术 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2023-04-25 DOI: 10.1109/RBME.2023.3269776
Zipei Wang;Mengjie Fang;Jie Zhang;Linquan Tang;Lianzhen Zhong;Hailin Li;Runnan Cao;Xun Zhao;Shengyuan Liu;Ruofan Zhang;Xuebin Xie;Haiqiang Mai;Sufang Qiu;Jie Tian;Di Dong
Nasopharyngeal carcinoma is a common head and neck malignancy with distinct clinical management compared to other types of cancer. Precision risk stratification and tailored therapeutic interventions are crucial to improving the survival outcomes. Artificial intelligence, including radiomics and deep learning, has exhibited considerable efficacy in various clinical tasks for nasopharyngeal carcinoma. These techniques leverage medical images and other clinical data to optimize clinical workflow and ultimately benefit patients. In this review, we provide an overview of the technical aspects and basic workflow of radiomics and deep learning in medical image analysis. We then conduct a detailed review of their applications to seven typical tasks in the clinical diagnosis and treatment of nasopharyngeal carcinoma, covering various aspects of image synthesis, lesion segmentation, diagnosis, and prognosis. The innovation and application effects of cutting-edge research are summarized. Recognizing the heterogeneity of the research field and the existing gap between research and clinical translation, potential avenues for improvement are discussed. We propose that these issues can be gradually addressed by establishing standardized large datasets, exploring the biological characteristics of features, and technological upgrades.
鼻咽癌是一种常见的头颈部恶性肿瘤,与其他类型的癌症相比,其临床治疗方法截然不同。精准的风险分层和量身定制的治疗干预对改善生存结果至关重要。人工智能,包括放射组学和深度学习,在鼻咽癌的各种临床任务中表现出了相当大的功效。这些技术利用医学影像和其他临床数据来优化临床工作流程,最终使患者受益。在本综述中,我们将概述放射组学和深度学习在医学图像分析中的技术方面和基本工作流程。然后,我们详细回顾了它们在鼻咽癌临床诊断和治疗的七项典型任务中的应用,涵盖了图像合成、病灶分割、诊断和预后等各个方面。总结了前沿研究的创新和应用效果。认识到研究领域的异质性以及研究与临床转化之间存在的差距,讨论了潜在的改进途径。我们提出,可以通过建立标准化的大型数据集、探索特征的生物学特性以及技术升级来逐步解决这些问题。
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引用次数: 0
Systematic Development of a Simple Human Gait Index 系统开发简单人体步态指数
IF 17.6 1区 工程技术 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2023-03-24 DOI: 10.1109/RBME.2023.3279655
Abu Ilius Faisal;Tapas Mondal;M. Jamal Deen
Human gait analysis aims to assess gait mechanics and to identify the deviations from “normal” gait patterns by using meaningful parameters extracted from gait data. As each parameter indicates different gait characteristics, a proper combination of key parameters is required to perform an overall gait assessment. Therefore, in this study, we introduced a simple gait index derived from the most important gait parameters (walking speed, maximum knee flexion angle, stride length, and stance-swing phase ratio) to quantify overall gait quality. We performed a systematic review to select the parameters and analyzed a gait dataset (120 healthy subjects) to develop the index and to determine the healthy range (0.50 – 0.67). To validate the parameter selection and to justify the defined index range, we applied a support vector machine algorithm to classify the dataset based on the selected parameters and achieved a high classification accuracy (∼95%). Also, we explored other published datasets that are in good agreement with the proposed index prediction, reinforcing the reliability and effectiveness of the developed gait index. The gait index can be used as a reference for preliminary assessment of human gait conditions and to quickly identify abnormal gait patterns and possible relation to health issues.
人体步态分析旨在评估步态力学,并通过使用从步态数据中提取的有意义参数来识别偏离 "正常 "步态模式的情况。由于每个参数都表示不同的步态特征,因此需要适当组合关键参数才能进行整体步态评估。因此,在本研究中,我们从最重要的步态参数(行走速度、膝关节最大屈曲角度、步长和步幅-摆动相位比)中提取了一个简单的步态指数,用于量化整体步态质量。我们对参数的选择进行了系统回顾,并对步态数据集(120 名健康受试者)进行了分析,以制定该指数并确定健康范围(0.50 - 0.67)。为了验证参数的选择并证明所定义的指数范围,我们根据所选参数应用支持向量机算法对数据集进行了分类,并取得了较高的分类准确率(∼95%)。此外,我们还探索了其他已发表的数据集,这些数据集与所提出的指数预测结果非常吻合,从而加强了所开发步态指数的可靠性和有效性。步态指数可作为初步评估人体步态状况的参考,并能快速识别异常步态模式及可能与健康问题的关系。
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引用次数: 0
Uncertainties in the Analysis of Heart Rate Variability: A Systematic Review 心率变异性分析中的不确定性:系统回顾
IF 17.6 1区 工程技术 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2023-03-15 DOI: 10.1109/RBME.2023.3271595
Lei Lu;Tingting Zhu;Davide Morelli;Andrew Creagh;Zhangdaihong Liu;Jenny Yang;Fenglin Liu;Yuan-Ting Zhang;David A. Clifton
Heart rate variability (HRV) is an important metric with a variety of applications in clinical situations such as cardiovascular diseases, diabetes mellitus, and mental health. HRV data can be potentially obtained from electrocardiography and photoplethysmography signals, then computational techniques such as signal filtering and data segmentation are used to process the sampled data for calculating HRV measures. However, uncertainties arising from data acquisition, computational models, and physiological factors can lead to degraded signal quality and affect HRV analysis. Therefore, it is crucial to address these uncertainties and develop advanced models for HRV analysis. Although several reviews of HRV analysis exist, they primarily focus on clinical applications, trends in HRV methods, or specific aspects of uncertainties such as measurement noise. This paper provides a comprehensive review of uncertainties in HRV analysis, quantifies their impacts, and outlines potential solutions. To the best of our knowledge, this is the first study that presents a holistic review of uncertainties in HRV methods and quantifies their impacts on HRV measures from an engineer's perspective. This review is essential for developing robust and reliable models, and could serve as a valuable future reference in the field, particularly for dealing with uncertainties in HRV analysis.
心率变异性(HRV)是一项重要指标,在心血管疾病、糖尿病和心理健康等临床领域有多种应用。心率变异数据可从心电图和照相血压计信号中获取,然后利用信号过滤和数据分割等计算技术处理采样数据,计算心率变异指标。然而,数据采集、计算模型和生理因素带来的不确定性会导致信号质量下降,影响心率变异分析。因此,解决这些不确定性并开发先进的心率变异分析模型至关重要。虽然目前已有一些关于心率变异分析的综述,但它们主要集中在临床应用、心率变异方法的发展趋势或不确定性的特定方面,如测量噪声。本文全面回顾了心率变异分析中的不确定性,量化了其影响,并概述了潜在的解决方案。据我们所知,这是首次从工程师的角度对心率变异方法中的不确定性进行全面评述,并量化其对心率变异测量的影响。该综述对开发稳健可靠的模型至关重要,可作为该领域未来的重要参考资料,尤其是在处理心率变异分析中的不确定性时。
{"title":"Uncertainties in the Analysis of Heart Rate Variability: A Systematic Review","authors":"Lei Lu;Tingting Zhu;Davide Morelli;Andrew Creagh;Zhangdaihong Liu;Jenny Yang;Fenglin Liu;Yuan-Ting Zhang;David A. Clifton","doi":"10.1109/RBME.2023.3271595","DOIUrl":"10.1109/RBME.2023.3271595","url":null,"abstract":"Heart rate variability (HRV) is an important metric with a variety of applications in clinical situations such as cardiovascular diseases, diabetes mellitus, and mental health. HRV data can be potentially obtained from electrocardiography and photoplethysmography signals, then computational techniques such as signal filtering and data segmentation are used to process the sampled data for calculating HRV measures. However, uncertainties arising from data acquisition, computational models, and physiological factors can lead to degraded signal quality and affect HRV analysis. Therefore, it is crucial to address these uncertainties and develop advanced models for HRV analysis. Although several reviews of HRV analysis exist, they primarily focus on clinical applications, trends in HRV methods, or specific aspects of uncertainties such as measurement noise. This paper provides a comprehensive review of uncertainties in HRV analysis, quantifies their impacts, and outlines potential solutions. To the best of our knowledge, this is the first study that presents a holistic review of uncertainties in HRV methods and quantifies their impacts on HRV measures from an engineer's perspective. This review is essential for developing robust and reliable models, and could serve as a valuable future reference in the field, particularly for dealing with uncertainties in HRV analysis.","PeriodicalId":39235,"journal":{"name":"IEEE Reviews in Biomedical Engineering","volume":"17 ","pages":"180-196"},"PeriodicalIF":17.6,"publicationDate":"2023-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10124275","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9471426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Review of Parallel Transmit Arrays for Ultra-High Field MR Imaging 超高场磁共振成像并行传输阵列回顾。
IF 17.6 1区 工程技术 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2023-02-10 DOI: 10.1109/RBME.2023.3244132
Chang-Hoon Choi;Andrew Webb;Stephan Orzada;Mikheil Kelenjeridze;N. Jon Shah;Jörg Felder
Parallel transmission (pTX) techniques are required to tackle a number of challenges, e.g., the inhomogeneous distribution of the transmit field and elevated specific absorption rate (SAR), in ultra-high field (UHF) MR imaging. Additionally, they offer multiple degrees of freedom to create temporally- and spatially-tailored transverse magnetization. Given the increasing availability of MRI systems at 7 T and above, it is anticipated that interest in pTX applications will grow accordingly. One of the key components in MR systems capable of pTX is the design of the transmit array, as this has a major impact on performance in terms of power requirements, SAR and RF pulse design. While several reviews on pTX pulse design and the clinical applicability of UHF exist, there is currently no systematic review of pTX transmit/transceiver coils and their associated performance. In this article, we analyze transmit array concepts to determine the strengths and weaknesses of different types of design. We systematically review the different types of individual antennas employed for UHF, their combination into pTX arrays, and methods to decouple the individual elements. We also reiterate figures-of-merit (FoMs) frequently employed to describe the performance of pTX arrays and summarize published array designs in terms of these FoMs.
在超高频(UHF)磁共振成像中,需要采用并行传输(pTX)技术来应对一系列挑战,例如传输场的不均匀分布和较高的比吸收率(SAR)。此外,它们还提供了多个自由度,以创建时间和空间定制的横向磁化。鉴于 7 T 及以上的核磁共振成像系统越来越多,预计人们对 pTX 应用的兴趣也会相应增加。具有 pTX 功能的磁共振系统的关键部件之一是发射阵列的设计,因为这对功率要求、SAR 和射频脉冲设计方面的性能有重大影响。虽然已有一些关于 pTX 脉冲设计和超高频临床适用性的综述,但目前还没有关于 pTX 发射/收发线圈及其相关性能的系统综述。在本文中,我们分析了发射阵列概念,以确定不同类型设计的优缺点。我们系统地回顾了用于 UHF 的不同类型的单个天线、它们在 pTX 阵列中的组合以及解耦单个元件的方法。我们还重申了在描述 pTX 阵列性能时经常使用的优点系数 (FoM),并根据这些优点系数总结了已发布的阵列设计。
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引用次数: 0
Digital Health and Machine Learning Technologies for Blood Glucose Monitoring and Management of Gestational Diabetes 用于血糖监测和妊娠糖尿病管理的数字健康和机器学习技术。
IF 17.6 1区 工程技术 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2023-02-07 DOI: 10.1109/RBME.2023.3242261
Huiqi Y. Lu;Xiaorong Ding;Jane E. Hirst;Yang Yang;Jenny Yang;Lucy Mackillop;David A. Clifton
Innovations in digital health and machine learning are changing the path of clinical health and care. People from different geographical locations and cultural backgrounds can benefit from the mobility of wearable devices and smartphones to monitor their health ubiquitously. This paper focuses on reviewing the digital health and machine learning technologies used in gestational diabetes – a subtype of diabetes that occurs during pregnancy. This paper reviews sensor technologies used in blood glucose monitoring devices, digital health innovations and machine learning models for gestational diabetes monitoring and management, in clinical and commercial settings, and discusses future directions. Despite one in six mothers having gestational diabetes, digital health applications were underdeveloped, especially the techniques that can be deployed in clinical practice. There is an urgent need to (1) develop clinically interpretable machine learning methods for patients with gestational diabetes, assisting health professionals with treatment, monitoring, and risk stratification before, during and after their pregnancies; (2) adapt and develop clinically-proven devices for patient self-management of health and well-being at home settings (“virtual ward” and virtual consultation), thereby improving clinical outcomes by facilitating timely intervention; and (3) ensure innovations are affordable and sustainable for all women with different socioeconomic backgrounds and clinical resources.
数字健康和机器学习领域的创新正在改变临床健康和护理的路径。来自不同地理位置和文化背景的人们可以从可穿戴设备和智能手机的移动性中受益,随时随地监测自己的健康状况。本文重点回顾了用于妊娠糖尿病(一种发生在孕期的糖尿病亚型)的数字健康和机器学习技术。本文回顾了临床和商业环境中用于血糖监测设备的传感器技术、数字健康创新技术以及用于妊娠糖尿病监测和管理的机器学习模型,并讨论了未来的发展方向。尽管每六位母亲中就有一位患有妊娠糖尿病,但数字健康应用,尤其是可在临床实践中应用的技术,却发展不足。目前迫切需要:(1)为妊娠糖尿病患者开发临床可解释的机器学习方法,协助医护人员在妊娠前、妊娠中和妊娠后进行治疗、监测和风险分层;(2)改造和开发经临床验证的设备,用于患者在家庭环境中自我管理健康和福祉("虚拟病房 "和虚拟咨询),从而通过促进及时干预改善临床结果;以及(3)确保创新对不同社会经济背景和临床资源的所有妇女来说都是可负担和可持续的。
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引用次数: 2
IEEE Engineering in Medicine and Biology Society Information IEEE医学与生物工程学会信息
IF 17.6 1区 工程技术 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2023-01-05 DOI: 10.1109/RBME.2022.3228083
Presents a listing of the editorial board, board of governors, current staff, committee members, and/or society editors for this issue of the publication.
列出本期出版物的编辑委员会、董事会、现任工作人员、委员会成员和/或协会编辑。
{"title":"IEEE Engineering in Medicine and Biology Society Information","authors":"","doi":"10.1109/RBME.2022.3228083","DOIUrl":"https://doi.org/10.1109/RBME.2022.3228083","url":null,"abstract":"Presents a listing of the editorial board, board of governors, current staff, committee members, and/or society editors for this issue of the publication.","PeriodicalId":39235,"journal":{"name":"IEEE Reviews in Biomedical Engineering","volume":"16 ","pages":"C2-C2"},"PeriodicalIF":17.6,"publicationDate":"2023-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/iel7/4664312/10007429/10007531.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67744159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
IEEE Reviews in Biomedical Engineering (R-BME) Information IEEE生物医学工程(R-BME)信息综述
IF 17.6 1区 工程技术 Q1 ENGINEERING, BIOMEDICAL Pub Date : 2023-01-05 DOI: 10.1109/RBME.2022.3228079
These instructions give guidelines for preparing papers for this publication. Presents information for authors publishing in this journal.
这些说明为编写本出版物的论文提供了指导。为在本期刊上发表文章的作者提供信息。
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引用次数: 0
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