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Discrimination between leucine-rich glioma-inactivated 1 antibody encephalitis and gamma-aminobutyric acid B receptor antibody encephalitis based on ResNet18. 基于ResNet18的富亮氨酸胶质瘤失活1抗体脑炎与γ -氨基丁酸B受体抗体脑炎的鉴别
4区 计算机科学 Q1 Arts and Humanities Pub Date : 2023-08-18 DOI: 10.1186/s42492-023-00144-5
Jian Pan, Ruijuan Lv, Qun Wang, Xiaobin Zhao, Jiangang Liu, Lin Ai

This study aims to discriminate between leucine-rich glioma-inactivated 1 (LGI1) antibody encephalitis and gamma-aminobutyric acid B (GABAB) receptor antibody encephalitis using a convolutional neural network (CNN) model. A total of 81 patients were recruited for this study. ResNet18, VGG16, and ResNet50 were trained and tested separately using 3828 positron emission tomography image slices that contained the medial temporal lobe (MTL) or basal ganglia (BG). Leave-one-out cross-validation at the patient level was used to evaluate the CNN models. The receiver operating characteristic (ROC) curve and the area under the ROC curve (AUC) were generated to evaluate the CNN models. Based on the prediction results at slice level, a decision strategy was employed to evaluate the CNN models' performance at patient level. The ResNet18 model achieved the best performance at the slice (AUC = 0.86, accuracy = 80.28%) and patient levels (AUC = 0.98, accuracy = 96.30%). Specifically, at the slice level, 73.28% (1445/1972) of image slices with GABAB receptor antibody encephalitis and 87.72% (1628/1856) of image slices with LGI1 antibody encephalitis were accurately detected. At the patient level, 94.12% (16/17) of patients with GABAB receptor antibody encephalitis and 96.88% (62/64) of patients with LGI1 antibody encephalitis were accurately detected. Heatmaps of the image slices extracted using gradient-weighted class activation mapping indicated that the model focused on the MTL and BG for classification. In general, the ResNet18 model is a potential approach for discriminating between LGI1 and GABAB receptor antibody encephalitis. Metabolism in the MTL and BG is important for discriminating between these two encephalitis subtypes.

本研究旨在利用卷积神经网络(CNN)模型区分富含亮氨酸的胶质瘤失活1 (LGI1)抗体脑炎和γ -氨基丁酸B (GABAB)受体抗体脑炎。这项研究共招募了81名患者。分别使用含有内侧颞叶(MTL)或基底神经节(BG)的3828张正电子发射断层扫描图像切片对ResNet18、VGG16和ResNet50进行训练和测试。在患者水平上使用留一交叉验证来评估CNN模型。生成接收者工作特征(ROC)曲线和ROC曲线下面积(AUC)来评价CNN模型。基于切片水平的预测结果,采用决策策略评估CNN模型在患者水平的性能。ResNet18模型在切片(AUC = 0.86,准确率= 80.28%)和患者水平(AUC = 0.98,准确率= 96.30%)上表现最佳。其中,在切片水平上,73.28%(1445/1972)的GABAB受体抗体脑炎图像切片和87.72%(1628/1856)的LGI1抗体脑炎图像切片被准确检测出来。在患者水平上,GABAB受体抗体脑炎患者的准确率为94.12% (16/17),LGI1抗体脑炎患者的准确率为96.88%(62/64)。使用梯度加权类激活映射提取的图像切片热图表明,该模型将重点放在MTL和BG上进行分类。总的来说,ResNet18模型是区分LGI1和GABAB受体抗体脑炎的潜在方法。MTL和BG的代谢是区分这两种脑炎亚型的重要指标。
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引用次数: 0
Hyperparameter optimization for cardiovascular disease data-driven prognostic system. 心血管疾病数据驱动预后系统的超参数优化。
4区 计算机科学 Q1 Arts and Humanities Pub Date : 2023-08-01 DOI: 10.1186/s42492-023-00143-6
Jayson Saputra, Cindy Lawrencya, Jecky Mitra Saini, Suharjito Suharjito

Prediction and diagnosis of cardiovascular diseases (CVDs) based, among other things, on medical examinations and patient symptoms are the biggest challenges in medicine. About 17.9 million people die from CVDs annually, accounting for 31% of all deaths worldwide. With a timely prognosis and thorough consideration of the patient's medical history and lifestyle, it is possible to predict CVDs and take preventive measures to eliminate or control this life-threatening disease. In this study, we used various patient datasets from a major hospital in the United States as prognostic factors for CVD. The data was obtained by monitoring a total of 918 patients whose criteria for adults were 28-77 years old. In this study, we present a data mining modeling approach to analyze the performance, classification accuracy and number of clusters on Cardiovascular Disease Prognostic datasets in unsupervised machine learning (ML) using the Orange data mining software. Various techniques are then used to classify the model parameters, such as k-nearest neighbors, support vector machine, random forest, artificial neural network (ANN), naïve bayes, logistic regression, stochastic gradient descent (SGD), and AdaBoost. To determine the number of clusters, various unsupervised ML clustering methods were used, such as k-means, hierarchical, and density-based spatial clustering of applications with noise clustering. The results showed that the best model performance analysis and classification accuracy were SGD and ANN, both of which had a high score of 0.900 on Cardiovascular Disease Prognostic datasets. Based on the results of most clustering methods, such as k-means and hierarchical clustering, Cardiovascular Disease Prognostic datasets can be divided into two clusters. The prognostic accuracy of CVD depends on the accuracy of the proposed model in determining the diagnostic model. The more accurate the model, the better it can predict which patients are at risk for CVD.

除其他外,基于医学检查和患者症状的心血管疾病预测和诊断是医学上最大的挑战。每年约有1790万人死于心血管疾病,占全世界死亡总数的31%。及时的预后和充分考虑患者的病史和生活方式,可以预测心血管疾病并采取预防措施来消除或控制这种危及生命的疾病。在这项研究中,我们使用了来自美国一家主要医院的各种患者数据集作为CVD的预后因素。数据是通过监测918例患者获得的,这些患者的成人标准为28-77岁。在这项研究中,我们提出了一种数据挖掘建模方法,使用Orange数据挖掘软件来分析无监督机器学习(ML)中心血管疾病预后数据集的性能、分类精度和聚类数量。然后使用各种技术对模型参数进行分类,例如k近邻、支持向量机、随机森林、人工神经网络(ANN)、naïve贝叶斯、逻辑回归、随机梯度下降(SGD)和AdaBoost。为了确定聚类的数量,我们使用了各种无监督的ML聚类方法,如k-means、分层聚类和基于密度的空间聚类。结果表明,模型性能分析和分类精度最好的是SGD和ANN,两者在Cardiovascular Disease Prognostic数据集上的得分均为0.900。基于大多数聚类方法的结果,如k-means和分层聚类,心血管疾病预后数据集可以分为两个聚类。CVD的预后准确性取决于所提出的模型在确定诊断模型时的准确性。模型越准确,就越能更好地预测哪些患者有患心血管疾病的风险。
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引用次数: 0
Survey of methods and principles in three-dimensional reconstruction from two-dimensional medical images. 二维医学图像三维重建的方法和原理综述。
4区 计算机科学 Q1 Arts and Humanities Pub Date : 2023-07-27 DOI: 10.1186/s42492-023-00142-7
Mriganka Sarmah, Arambam Neelima, Heisnam Rohen Singh

Three-dimensional (3D) reconstruction of human organs has gained attention in recent years due to advances in the Internet and graphics processing units. In the coming years, most patient care will shift toward this new paradigm. However, development of fast and accurate 3D models from medical images or a set of medical scans remains a daunting task due to the number of pre-processing steps involved, most of which are dependent on human expertise. In this review, a survey of pre-processing steps was conducted, and reconstruction techniques for several organs in medical diagnosis were studied. Various methods and principles related to 3D reconstruction were highlighted. The usefulness of 3D reconstruction of organs in medical diagnosis was also highlighted.

近年来,由于互联网和图形处理单元的进步,人体器官的三维重建受到了人们的关注。在未来几年,大多数患者护理将转向这种新模式。然而,由于涉及大量的预处理步骤,从医学图像或一组医学扫描中开发快速准确的3D模型仍然是一项艰巨的任务,其中大部分依赖于人类的专业知识。本文综述了医学诊断中几种器官的预处理步骤,并对其重建技术进行了研究。重点介绍了三维重建的各种方法和原理。还强调了器官三维重建在医学诊断中的有用性。
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引用次数: 0
Vision transformer architecture and applications in digital health: a tutorial and survey. 数字健康领域的视觉转换器架构与应用:教程与调查。
4区 计算机科学 Q1 Arts and Humanities Pub Date : 2023-07-10 DOI: 10.1186/s42492-023-00140-9
Khalid Al-Hammuri, Fayez Gebali, Awos Kanan, Ilamparithi Thirumarai Chelvan

The vision transformer (ViT) is a state-of-the-art architecture for image recognition tasks that plays an important role in digital health applications. Medical images account for 90% of the data in digital medicine applications. This article discusses the core foundations of the ViT architecture and its digital health applications. These applications include image segmentation, classification, detection, prediction, reconstruction, synthesis, and telehealth such as report generation and security. This article also presents a roadmap for implementing the ViT in digital health systems and discusses its limitations and challenges.

视觉转换器(ViT)是一种用于图像识别任务的先进架构,在数字医疗应用中发挥着重要作用。医疗图像占数字医疗应用数据的 90%。本文将讨论 ViT 架构的核心基础及其数字医疗应用。这些应用包括图像分割、分类、检测、预测、重建、合成以及远程医疗(如报告生成和安全)。本文还介绍了在数字医疗系统中实施 ViT 的路线图,并讨论了其局限性和挑战。
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引用次数: 0
DB-DCAFN: dual-branch deformable cross-attention fusion network for bacterial segmentation. DB-DCAFN:用于细菌分割的双分支可变形交叉注意融合网络。
4区 计算机科学 Q1 Arts and Humanities Pub Date : 2023-07-04 DOI: 10.1186/s42492-023-00141-8
Jingkun Wang, Xinyu Ma, Long Cao, Yilin Leng, Zeyi Li, Zihan Cheng, Yuzhu Cao, Xiaoping Huang, Jian Zheng

Sputum smear tests are critical for the diagnosis of respiratory diseases. Automatic segmentation of bacteria from sputum smear images is important for improving diagnostic efficiency. However, this remains a challenging task owing to the high interclass similarity among different categories of bacteria and the low contrast of the bacterial edges. To explore more levels of global pattern features to promote the distinguishing ability of bacterial categories and maintain sufficient local fine-grained features to ensure accurate localization of ambiguous bacteria simultaneously, we propose a novel dual-branch deformable cross-attention fusion network (DB-DCAFN) for accurate bacterial segmentation. Specifically, we first designed a dual-branch encoder consisting of multiple convolution and transformer blocks in parallel to simultaneously extract multilevel local and global features. We then designed a sparse and deformable cross-attention module to capture the semantic dependencies between local and global features, which can bridge the semantic gap and fuse features effectively. Furthermore, we designed a feature assignment fusion module to enhance meaningful features using an adaptive feature weighting strategy to obtain more accurate segmentation. We conducted extensive experiments to evaluate the effectiveness of DB-DCAFN on a clinical dataset comprising three bacterial categories: Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. The experimental results demonstrate that the proposed DB-DCAFN outperforms other state-of-the-art methods and is effective at segmenting bacteria from sputum smear images.

痰涂片检查对呼吸道疾病的诊断至关重要。痰涂片图像中细菌的自动分割对提高诊断效率具有重要意义。然而,由于不同类别细菌之间的高类间相似性和细菌边缘的低对比度,这仍然是一项具有挑战性的任务。为了探索更多层次的全局模式特征以提高细菌类别的区分能力,同时保持足够的局部细粒度特征以确保模糊细菌的准确定位,我们提出了一种新的双分支可变形交叉注意融合网络(DB-DCAFN)用于准确的细菌分割。具体而言,我们首先设计了一个由多个卷积和变压器块并行组成的双支路编码器,以同时提取多级局部和全局特征。然后,我们设计了一个稀疏的、可变形的交叉注意模块来捕获局部和全局特征之间的语义依赖关系,从而有效地弥合语义鸿沟,融合特征。此外,我们设计了一个特征分配融合模块,使用自适应特征加权策略增强有意义的特征,以获得更准确的分割。我们进行了广泛的实验来评估DB-DCAFN在包括三种细菌类别的临床数据集上的有效性:鲍曼不动杆菌、肺炎克雷伯菌和铜绿假单胞菌。实验结果表明,所提出的DB-DCAFN优于其他最先进的方法,可以有效地从痰涂片图像中分割细菌。
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引用次数: 0
Editorial: advances in deep learning techniques for biomedical imaging. 社论:生物医学成像中深度学习技术的进展。
4区 计算机科学 Q1 Arts and Humanities Pub Date : 2023-06-21 DOI: 10.1186/s42492-023-00139-2
Chuang Niu, Ge Wang
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引用次数: 0
Beyond the horizon: immersive developments for animal ecology research. 超越地平线:动物生态学研究的沉浸式发展。
4区 计算机科学 Q1 Arts and Humanities Pub Date : 2023-06-20 DOI: 10.1186/s42492-023-00138-3
Ying Zhang, Karsten Klein, Falk Schreiber, Kamran Safi

More diverse data on animal ecology are now available. This "data deluge" presents challenges for both biologists and computer scientists; however, it also creates opportunities to improve analysis and answer more holistic research questions. We aim to increase awareness of the current opportunity for interdisciplinary research between animal ecology researchers and computer scientists. Immersive analytics (IA) is an emerging research field in which investigations are performed into how immersive technologies, such as large display walls and virtual reality and augmented reality devices, can be used to improve data analysis, outcomes, and communication. These investigations have the potential to reduce the analysis effort and widen the range of questions that can be addressed. We propose that biologists and computer scientists combine their efforts to lay the foundation for IA in animal ecology research. We discuss the potential and the challenges and outline a path toward a structured approach. We imagine that a joint effort would combine the strengths and expertise of both communities, leading to a well-defined research agenda and design space, practical guidelines, robust and reusable software frameworks, reduced analysis effort, and better comparability of results.

现在有了更多关于动物生态学的数据。这种“数据洪流”给生物学家和计算机科学家都带来了挑战;然而,它也为改进分析和回答更全面的研究问题创造了机会。我们的目标是提高人们对动物生态学研究人员和计算机科学家之间跨学科研究的当前机会的认识。沉浸式分析(IA)是一个新兴的研究领域,研究如何使用沉浸式技术,如大型显示墙、虚拟现实和增强现实设备,来改善数据分析、结果和沟通。这些调查有可能减少分析工作,并扩大可以解决的问题范围。我们建议生物学家和计算机科学家共同努力,为动物生态学研究中的人工智能奠定基础。我们讨论了潜力和挑战,并概述了通往结构化方法的路径。我们设想,联合的努力将结合两个社区的优势和专业知识,导致定义良好的研究议程和设计空间、实用指南、健壮和可重用的软件框架、减少分析工作,以及更好的结果可比性。
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引用次数: 0
Systematic review of digital twin technology and applications. 数字孪生技术及其应用系统综述。
4区 计算机科学 Q1 Arts and Humanities Pub Date : 2023-05-30 DOI: 10.1186/s42492-023-00137-4
Jun-Feng Yao, Yong Yang, Xue-Cheng Wang, Xiao-Peng Zhang

As one of the most important applications of digitalization, intelligence, and service, the digital twin (DT) breaks through the constraints of time, space, cost, and security on physical entities, expands and optimizes the relevant functions of physical entities, and enhances their application value. This phenomenon has been widely studied in academia and industry. In this study, the concept and definition of DT, as utilized by scholars and researchers in various fields of industry, are summarized. The internal association between DT and related technologies is explained. The four stages of DT development history are identified. The fundamentals of the technology, evaluation indexes, and model frameworks are reviewed. Subsequently, a conceptual ternary model of DT based on time, space, and logic is proposed. The technology and application status of typical DT systems are described. Finally, the current technical challenges of DT technology are analyzed, and directions for future development are discussed.

数字孪生(digital twin, DT)作为数字化、智能化、服务化的重要应用之一,突破了物理实体在时间、空间、成本、安全等方面的限制,扩展和优化了物理实体的相关功能,提升了物理实体的应用价值。这一现象在学术界和工业界得到了广泛的研究。在本研究中,对各行业学者和研究人员所使用的数据挖掘概念和定义进行了总结。解释了DT与相关技术之间的内在联系。确定了DT发展历史的四个阶段。综述了该技术的基本原理、评价指标和模型框架。随后,提出了基于时间、空间和逻辑的DT概念三元模型。介绍了典型DT系统的技术及应用现状。最后,分析了当前DT技术面临的技术挑战,并对未来的发展方向进行了讨论。
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引用次数: 4
Translating radiology reports into plain language using ChatGPT and GPT-4 with prompt learning: results, limitations, and potential. 使用 ChatGPT 和 GPT-4 将放射学报告翻译成通俗易懂的语言,并进行及时学习:结果、局限性和潜力。
4区 计算机科学 Q1 Arts and Humanities Pub Date : 2023-05-18 DOI: 10.1186/s42492-023-00136-5
Qing Lyu, Josh Tan, Michael E Zapadka, Janardhana Ponnatapura, Chuang Niu, Kyle J Myers, Ge Wang, Christopher T Whitlow

The large language model called ChatGPT has drawn extensively attention because of its human-like expression and reasoning abilities. In this study, we investigate the feasibility of using ChatGPT in experiments on translating radiology reports into plain language for patients and healthcare providers so that they are educated for improved healthcare. Radiology reports from 62 low-dose chest computed tomography lung cancer screening scans and 76 brain magnetic resonance imaging metastases screening scans were collected in the first half of February for this study. According to the evaluation by radiologists, ChatGPT can successfully translate radiology reports into plain language with an average score of 4.27 in the five-point system with 0.08 places of information missing and 0.07 places of misinformation. In terms of the suggestions provided by ChatGPT, they are generally relevant such as keeping following-up with doctors and closely monitoring any symptoms, and for about 37% of 138 cases in total ChatGPT offers specific suggestions based on findings in the report. ChatGPT also presents some randomness in its responses with occasionally over-simplified or neglected information, which can be mitigated using a more detailed prompt. Furthermore, ChatGPT results are compared with a newly released large model GPT-4, showing that GPT-4 can significantly improve the quality of translated reports. Our results show that it is feasible to utilize large language models in clinical education, and further efforts are needed to address limitations and maximize their potential.

名为 ChatGPT 的大型语言模型因其类似人类的表达和推理能力而受到广泛关注。在本研究中,我们研究了使用 ChatGPT 将放射学报告翻译成通俗易懂的语言供患者和医疗服务提供者使用的可行性,从而使他们受到教育,改善医疗服务。本研究收集了二月上半月 62 份低剂量胸部计算机断层扫描肺癌筛查扫描和 76 份脑磁共振成像转移筛查扫描的放射报告。根据放射科医生的评估,ChatGPT 可以成功地将放射科报告翻译成通俗易懂的语言,在五分制中平均得分 4.27 分,信息缺失 0.08 处,信息错误 0.07 处。就 ChatGPT 提供的建议而言,这些建议普遍具有相关性,如继续随访医生和密切监测任何症状,在总共 138 个病例中,ChatGPT 根据报告中的发现提供了约 37% 的具体建议。ChatGPT 的回复也有一定的随机性,偶尔会出现过于简化或忽略信息的情况,这可以通过更详细的提示来缓解。此外,我们还将 ChatGPT 的结果与新发布的大型模型 GPT-4 进行了比较,结果表明 GPT-4 可以显著提高翻译报告的质量。我们的研究结果表明,在临床教育中使用大型语言模型是可行的,但还需要进一步努力解决其局限性并最大限度地发挥其潜力。
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引用次数: 0
EM-Gaze: eye context correlation and metric learning for gaze estimation. EM-Gaze:用于凝视估计的眼球上下文相关性和度量学习。
4区 计算机科学 Q1 Arts and Humanities Pub Date : 2023-05-05 DOI: 10.1186/s42492-023-00135-6
Jinchao Zhou, Guoan Li, Feng Shi, Xiaoyan Guo, Pengfei Wan, Miao Wang

In recent years, deep learning techniques have been used to estimate gaze-a significant task in computer vision and human-computer interaction. Previous studies have made significant achievements in predicting 2D or 3D gazes from monocular face images. This study presents a deep neural network for 2D gaze estimation on mobile devices. It achieves state-of-the-art 2D gaze point regression error, while significantly improving gaze classification error on quadrant divisions of the display. To this end, an efficient attention-based module that correlates and fuses the left and right eye contextual features is first proposed to improve gaze point regression performance. Subsequently, through a unified perspective for gaze estimation, metric learning for gaze classification on quadrant divisions is incorporated as additional supervision. Consequently, both gaze point regression and quadrant classification performances are improved. The experiments demonstrate that the proposed method outperforms existing gaze-estimation methods on the GazeCapture and MPIIFaceGaze datasets.

近年来,深度学习技术已被用于估计凝视--这是计算机视觉和人机交互中的一项重要任务。以往的研究在从单目人脸图像预测 2D 或 3D 注视方面取得了重大成就。本研究提出了一种用于移动设备 2D 注视估计的深度神经网络。它实现了最先进的二维注视点回归误差,同时显著改善了显示屏象限划分上的注视分类误差。为此,我们首先提出了一种基于注意力的高效模块,它能关联并融合左右眼的上下文特征,从而提高注视点回归性能。随后,通过统一的注视估计视角,将用于象限划分的注视分类的度量学习作为附加监督纳入其中。因此,注视点回归和象限分类的性能都得到了提高。实验证明,在 GazeCapture 和 MPIIFaceGaze 数据集上,所提出的方法优于现有的注视估计方法。
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引用次数: 0
期刊
Visual Computing for Industry, Biomedicine, and Art
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