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Efficient labelling for efficient deep learning: the benefit of a multiple-image-ranking method to generate high volume training data applied to ventricular slice level classification in cardiac MRI. 高效深度学习的高效标记:将多图像排序法应用于心脏磁共振成像的心室切片水平分类,生成大量训练数据的好处。
Pub Date : 2023-04-01 DOI: 10.21037/jmai-22-55
Sameer Zaman, Kavitha Vimalesvaran, James P Howard, Digby Chappell, Marta Varela, Nicholas S Peters, Darrel P Francis, Anil A Bharath, Nick W F Linton, Graham D Cole

Background: Getting the most value from expert clinicians' limited labelling time is a major challenge for artificial intelligence (AI) development in clinical imaging. We present a novel method for ground-truth labelling of cardiac magnetic resonance imaging (CMR) image data by leveraging multiple clinician experts ranking multiple images on a single ordinal axis, rather than manual labelling of one image at a time. We apply this strategy to train a deep learning (DL) model to classify the anatomical position of CMR images. This allows the automated removal of slices that do not contain the left ventricular (LV) myocardium.

Methods: Anonymised LV short-axis slices from 300 random scans (3,552 individual images) were extracted. Each image's anatomical position relative to the LV was labelled using two different strategies performed for 5 hours each: (I) 'one-image-at-a-time': each image labelled according to its position: 'too basal', 'LV', or 'too apical' individually by one of three experts; and (II) 'multiple-image-ranking': three independent experts ordered slices according to their relative position from 'most-basal' to 'most apical' in batches of eight until each image had been viewed at least 3 times. Two convolutional neural networks were trained for a three-way classification task (each model using data from one labelling strategy). The models' performance was evaluated by accuracy, F1-score, and area under the receiver operating characteristics curve (ROC AUC).

Results: After excluding images with artefact, 3,323 images were labelled by both strategies. The model trained using labels from the 'multiple-image-ranking strategy' performed better than the model using the 'one-image-at-a-time' labelling strategy (accuracy 86% vs. 72%, P=0.02; F1-score 0.86 vs. 0.75; ROC AUC 0.95 vs. 0.86). For expert clinicians performing this task manually the intra-observer variability was low (Cohen's κ=0.90), but the inter-observer variability was higher (Cohen's κ=0.77).

Conclusions: We present proof of concept that, given the same clinician labelling effort, comparing multiple images side-by-side using a 'multiple-image-ranking' strategy achieves ground truth labels for DL more accurately than by classifying images individually. We demonstrate a potential clinical application: the automatic removal of unrequired CMR images. This leads to increased efficiency by focussing human and machine attention on images which are needed to answer clinical questions.

背景:如何从临床专家有限的标注时间中获取最大价值,是临床成像领域人工智能(AI)发展面临的一大挑战。我们提出了一种对心脏磁共振成像(CMR)图像数据进行地面实况标注的新方法,即利用多名临床专家在单个序轴上对多幅图像进行排序,而不是每次对一幅图像进行人工标注。我们采用这种策略训练深度学习(DL)模型,对 CMR 图像的解剖位置进行分类。这样就能自动去除不包含左心室(LV)心肌的切片:方法:从 300 张随机扫描图像(3,552 张独立图像)中提取匿名左心室短轴切片。每张图像相对于左心室的解剖位置采用两种不同的策略进行标注,每种策略持续5小时:(I) "一次标注一张图像":三位专家中的一位根据每张图像的位置分别标注 "太基底"、"左心室 "或 "太心尖";(II) "多张图像排序":三位独立专家根据切片的相对位置从 "最基底 "到 "最心尖 "进行排序,每8张切片为一批,直到每张图像被查看至少3次。对两个卷积神经网络进行了三向分类任务训练(每个模型使用一种标记策略的数据)。通过准确率、F1-分数和接收者操作特征曲线下面积(ROC AUC)对模型的性能进行评估:结果:在排除了有伪影的图像后,有 3323 张图像被两种策略标记。使用 "多张图像排序策略 "标签训练的模型比使用 "一次一张图像 "标签策略训练的模型表现更好(准确率为 86% 对 72%,P=0.02;F1 分数为 0.86 对 0.75;ROC AUC 为 0.95 对 0.86)。对于手动执行这项任务的临床专家而言,观察者内部的变异性较低(Cohen's κ=0.90),但观察者之间的变异性较高(Cohen's κ=0.77):我们提出的概念证明,在临床医生进行相同标记的情况下,使用 "多张图像排序 "策略并排比较多张图像,比单独对图像进行分类更能准确地获得 DL 的基本真实标签。我们展示了一种潜在的临床应用:自动移除不需要的 CMR 图像。这可以将人和机器的注意力集中在回答临床问题所需的图像上,从而提高效率。
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引用次数: 0
Defining functional requirements for a patient-centric computerized glaucoma treatment and care ecosystem 定义以患者为中心的计算机化青光眼治疗和护理生态系统的功能要求
Pub Date : 2023-02-01 DOI: 10.21037/jmai-22-33
N. Goldmann, S. Skalicky, R. Weinreb, R. P. Paletta Guedes, C. Baudouin, Xiulan Zhang, Aukje van Gestel, E. Blumenthal, P. Kaufman, R. Rothman, Ana Maria Vasquez, P. Harasymowycz, D. Welsbie, I. Goldberg
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引用次数: 0
Enabling scalable clinical interpretation of machine learning (ML)-based phenotypes using real world data 使用真实世界数据实现基于机器学习(ML)表型的可扩展临床解释
Pub Date : 2023-02-01 DOI: 10.21037/jmai-22-42
O. Parsons, N. Barlow, J. Baxter, K. Paraschin, Andrea Derix, Peter Hein, R. Dürichen
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引用次数: 0
Artificial intelligence in screening for obstructive sleep apnoea syndrome (OSAS): a narrative review 人工智能在阻塞性睡眠呼吸暂停综合征(OSAS)筛查中的应用综述
Pub Date : 2023-02-01 DOI: 10.21037/jmai-22-79
Bei Pei, Ming Xia, Hong Jiang
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引用次数: 0
Using a self-attention architecture to automate valence categorization of French teenagers' free descriptions of their family relationships. A proof of concept. 利用自关注架构对法国青少年家庭关系的自由描述进行自动效价分类。概念验证。
Pub Date : 2023-01-18 DOI: 10.1101/2023.01.16.23284557
M. Sedki, N. Vidal, P. Roux, C. Barry, M. Speranza, B. Falissard, E. Brunet-Gouet
This paper proposes a proof of concept of using natural language processing techniques to categorize valence of family relationships described in free texts written by french teenagers. The proposed study traces the evolution of techniques for word embedding. After decomposing the different texts in our possession into short texts composed of sentences and manual labeling, we tested different word embedding scenarios to train a multi-label classification model where a text can take several labels: labels describing the family link between the teenager and the person mentioned in the text and labels describing the teenager's relationship with them positive/negative/neutral valence). The natural baseline for word vector representation of our texts is to build a TF-IDF and train classical classifiers (Elasticnet logistic regression, gradient boosting, random forest, support vector classifier) after selecting a model by cross validation in each class of machine learning models. We then studied the strengths of word-vectors embeddings by an advanced language representation technique via the CamemBERT transformer model, and, again, used them with classical classifiers to compare their respective performances. The last scenario consisted in augmenting the CamemBERT with output dense layers (perceptron) representing a classifier adapted to the multi-label classification and fine-tuning the CamemBERT original layers. The optimal fine-tuning depth that achieves a bias-variance trade-off was obtained by a cross-validation procedure. The results of the comparison of the three scenarios on a test dataset show a clear improvement of the classification performances of the scenario with fine-tuning beyond the baseline and of a simple vectorization using CamemBERT without fine-tuning. Despite the moderate size of the dataset and the input texts, fine-tuning to an optimal depth remains the best solution to build a classifier.
本文提出了利用自然语言处理技术对法国青少年自由文本中描述的家庭关系的效价进行分类的概念证明。这项拟议的研究追溯了单词嵌入技术的发展。在将我们所拥有的不同文本分解成由句子和人工标注组成的短文本后,我们测试了不同的单词嵌入场景来训练一个多标签分类模型,其中文本可以采用几个标签:描述青少年和文本中提到的人之间的家庭联系的标签,以及描述青少年与他们的关系的标签(正/负/中性价)。我们文本的词向量表示的自然基线是在每类机器学习模型中通过交叉验证选择模型后,建立TF-IDF并训练经典分类器(Elasticnet逻辑回归、梯度增强、随机森林、支持向量分类器)。然后,我们通过CamemBERT转换器模型,通过先进的语言表示技术研究了词向量嵌入的强度,并再次将它们与经典分类器一起使用,以比较它们各自的性能。最后一种场景是用表示适用于多标签分类的分类器的输出密集层(感知器)来增强CamemBERT,并微调CamemBERT原始层。通过交叉验证程序获得了实现偏差-方差权衡的最佳微调深度。在测试数据集上对三种场景的比较结果表明,在基线之外进行微调后,场景的分类性能明显提高,并且在没有微调的情况下使用CamemBERT进行简单的矢量化。尽管数据集和输入文本的大小适中,但微调到最佳深度仍然是构建分类器的最佳解决方案。
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引用次数: 0
Implementing artificial intelligence in clinical practice: a mixed-method study of barriers and facilitators 在临床实践中实施人工智能:障碍和促进因素的混合方法研究
Pub Date : 2022-12-01 DOI: 10.21037/jmai-22-71
B. Schouten, M. Schinkel, A. W. Boerman, Petra van Pijkeren, Maureen Thodé, M. V. van Beneden, R. N. Nannan Panday, R. de Jonge, W. Wiersinga, P. Nanayakkara
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引用次数: 2
Deep learning applications in coronary anatomy imaging: a systematic review and meta-analysis. 深度学习在冠状动脉解剖成像中的应用:系统综述与荟萃分析。
Pub Date : 2022-12-01 DOI: 10.21037/jmai-22-36
Ebraham Alskaf, Utkarsh Dutta, Cian M Scannell, Amedeo Chiribiri

Background: The application of deep learning on medical imaging is growing in prevalence in the recent literature. One of the most studied areas is coronary artery disease (CAD). Imaging of coronary artery anatomy is fundamental, which has led to a high number of publications describing a variety of techniques. The aim of this systematic review is to review the evidence behind the accuracy of deep learning applications in coronary anatomy imaging.

Methods: The search for the relevant studies, which applied deep learning on coronary anatomy imaging, was performed in a systematic approach on MEDLINE and EMBASE databases, followed by reviewing of abstracts and full texts. The data from the final studies was retrieved using data extraction forms. A meta-analysis was performed on a subgroup of studies, which looked at fractional flow reserve (FFR) prediction. Heterogeneity was tested using tau2, I2 and Q tests. Finally, a risk of bias was performed using Quality Assessment of Diagnostic Accuracy Studies (QUADAS) approach.

Results: A total of 81 studies met the inclusion criteria. The most common imaging modality was coronary computed tomography angiography (CCTA) (58%) and the most common deep learning method was convolutional neural network (CNN) (52%). The majority of studies demonstrated good performance metrics. The most common outputs were focused on coronary artery segmentation, clinical outcome prediction, coronary calcium quantification and FFR prediction, and most studies reported area under the curve (AUC) of ≥80%. The pooled diagnostic odds ratio (DOR) derived from 8 studies looking at FFR prediction using CCTA was 12.5 using the Mantel-Haenszel (MH) method. There was no significant heterogeneity amongst studies according to Q test (P=0.2496).

Conclusions: Deep learning has been used in many applications on coronary anatomy imaging, most of which are yet to be externally validated and prepared for clinical use. The performance of deep learning, especially CNN models, proved to be powerful and some applications have already translated into medical practice, such as computed tomography (CT)-FFR. These applications have the potential to translate technology into better care of CAD patients.

背景:在最近的文献中,深度学习在医学成像中的应用越来越普遍。研究最多的领域之一是冠状动脉疾病(CAD)。冠状动脉解剖成像是基础,这导致了大量描述各种技术的出版物。本系统综述旨在回顾深度学习应用于冠状动脉解剖成像的准确性背后的证据:方法:在 MEDLINE 和 EMBASE 数据库中以系统方法搜索冠状动脉解剖成像中应用深度学习的相关研究,然后审阅摘要和全文。使用数据提取表对最终研究的数据进行了检索。对研究的一个分组进行了荟萃分析,该分组研究了分数血流储备(FFR)预测。使用 tau2、I2 和 Q 检验对异质性进行了检验。最后,使用诊断准确性研究质量评估(QUADAS)方法进行了偏倚风险分析:共有 81 项研究符合纳入标准。最常见的成像模式是冠状动脉计算机断层扫描血管造影术(CCTA)(58%),最常见的深度学习方法是卷积神经网络(CNN)(52%)。大多数研究显示了良好的性能指标。最常见的输出结果集中在冠状动脉分割、临床结果预测、冠状动脉钙化定量和 FFR 预测上,大多数研究报告的曲线下面积(AUC)≥80%。使用曼特尔-海恩泽尔(MH)法,从 8 项使用 CCTA 预测 FFR 的研究中得出的诊断几率比(DOR)为 12.5。根据Q检验(P=0.2496),各研究之间不存在明显的异质性:深度学习已被用于冠状动脉解剖成像的许多应用中,但其中大多数尚未经过外部验证并准备用于临床。深度学习的性能,尤其是 CNN 模型,被证明是强大的,一些应用已经转化为医疗实践,如计算机断层扫描(CT)-FFR。这些应用有可能将技术转化为对 CAD 患者的更好护理。
{"title":"Deep learning applications in coronary anatomy imaging: a systematic review and meta-analysis.","authors":"Ebraham Alskaf, Utkarsh Dutta, Cian M Scannell, Amedeo Chiribiri","doi":"10.21037/jmai-22-36","DOIUrl":"10.21037/jmai-22-36","url":null,"abstract":"<p><strong>Background: </strong>The application of deep learning on medical imaging is growing in prevalence in the recent literature. One of the most studied areas is coronary artery disease (CAD). Imaging of coronary artery anatomy is fundamental, which has led to a high number of publications describing a variety of techniques. The aim of this systematic review is to review the evidence behind the accuracy of deep learning applications in coronary anatomy imaging.</p><p><strong>Methods: </strong>The search for the relevant studies, which applied deep learning on coronary anatomy imaging, was performed in a systematic approach on MEDLINE and EMBASE databases, followed by reviewing of abstracts and full texts. The data from the final studies was retrieved using data extraction forms. A meta-analysis was performed on a subgroup of studies, which looked at fractional flow reserve (FFR) prediction. Heterogeneity was tested using tau<sup>2</sup>, I<sup>2</sup> and Q tests. Finally, a risk of bias was performed using Quality Assessment of Diagnostic Accuracy Studies (QUADAS) approach.</p><p><strong>Results: </strong>A total of 81 studies met the inclusion criteria. The most common imaging modality was coronary computed tomography angiography (CCTA) (58%) and the most common deep learning method was convolutional neural network (CNN) (52%). The majority of studies demonstrated good performance metrics. The most common outputs were focused on coronary artery segmentation, clinical outcome prediction, coronary calcium quantification and FFR prediction, and most studies reported area under the curve (AUC) of ≥80%. The pooled diagnostic odds ratio (DOR) derived from 8 studies looking at FFR prediction using CCTA was 12.5 using the Mantel-Haenszel (MH) method. There was no significant heterogeneity amongst studies according to Q test (P=0.2496).</p><p><strong>Conclusions: </strong>Deep learning has been used in many applications on coronary anatomy imaging, most of which are yet to be externally validated and prepared for clinical use. The performance of deep learning, especially CNN models, proved to be powerful and some applications have already translated into medical practice, such as computed tomography (CT)-FFR. These applications have the potential to translate technology into better care of CAD patients.</p>","PeriodicalId":73815,"journal":{"name":"Journal of medical artificial intelligence","volume":"5 ","pages":"11"},"PeriodicalIF":0.0,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b7/84/EMS163415.PMC7614252.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10826937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sleep’s depth detection using electroencephalogram signal processing and neural network classification 基于脑电图信号处理和神经网络分类的睡眠深度检测
Pub Date : 2022-09-01 DOI: 10.21037/jmai-22-32
M. Touil, L. Bahatti, A. El Magri
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引用次数: 2
Accuracy of predicting IgHV mutation status in chronic lymphocytic leukemia using RNA expression profiling and machine learning RNA表达谱和机器学习预测慢性淋巴细胞白血病IgHV突变状态的准确性
Pub Date : 2022-01-01 DOI: 10.21037/jmai-22-28
A. Charifa, Hong Zhang, A. Pecora, A. Ip, I. De Dios, Wanlong Ma, L. Leslie, T. Feldman, A. Goy, M. Albitar
{"title":"Accuracy of predicting IgHV mutation status in chronic lymphocytic leukemia using RNA expression profiling and machine learning","authors":"A. Charifa, Hong Zhang, A. Pecora, A. Ip, I. De Dios, Wanlong Ma, L. Leslie, T. Feldman, A. Goy, M. Albitar","doi":"10.21037/jmai-22-28","DOIUrl":"https://doi.org/10.21037/jmai-22-28","url":null,"abstract":"","PeriodicalId":73815,"journal":{"name":"Journal of medical artificial intelligence","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47427615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
A narrative review on radiotherapy practice in the era of artificial intelligence: how relevant is the medical physicist? 人工智能时代放疗实践的叙述性回顾:医学物理学家的相关性如何?
Pub Date : 2022-01-01 DOI: 10.21037/jmai-22-27
Eric Naab Manson, A. N. Mumuni, E. Fiagbedzi, I. Shirazu, H. Sulemana
Background and Objective: Artificial intelligence (AI) uses computers and machines to simulate how the human mind makes decisions and solves problems. In radiotherapy practice, AI technologies continue to be promising in image registration, synthetic computed tomography (CT), image segmentation, motion management, treatment planning, and delivery procedures, patient follow-up and quality assurance (QA). This, therefore, provides a new window of opportunity to improve upon the accuracy and output times of the manual implementation of these procedures. The goal of this review was to explore how machine learning AI technologies in radiotherapy could affect the clinical practice of medical physicists. Methods: A narrative literature review was conducted from PubMed, Science Direct and Scopus using the search terms: in the English language within 6 months. Key Content and Findings: The roles of AI and the clinical medical physicist are complementary in radiotherapy practice. Both the medical physicists and AI technology are highly needed to support the full implementation and optimization of radiotherapy procedures. Conclusions: To achieve successful implementation of AI in radiotherapy and optimize radiotherapy procedures, clinical medical physicist should receive some compulsory training in AI technologies during their education and training. They should ultimately be involved in the incorporation of machine learning technologies in radiotherapy equipment. patient-specific dosimetric of patient treatment Dosimetric measurements in phantoms one of following detectors: portal imaging The third type of looks for delivery errors in log files generated during during delivery time-series linear quality
背景与目的:人工智能(AI)使用计算机和机器来模拟人类的思维如何做出决策和解决问题。在放疗实践中,人工智能技术在图像配准、合成计算机断层扫描(CT)、图像分割、运动管理、治疗计划和交付程序、患者随访和质量保证(QA)方面继续有前景。因此,这为提高手工执行这些程序的准确性和输出时间提供了新的机会。这篇综述的目的是探讨放射治疗中的机器学习人工智能技术如何影响医学物理学家的临床实践。方法:使用检索词:在PubMed、Science Direct和Scopus中检索6个月内的英文文献。关键内容和发现:人工智能和临床医学物理学家在放射治疗实践中的作用是互补的。需要医学物理学家和人工智能技术来支持放射治疗程序的全面实施和优化。结论:为实现人工智能在放疗中的成功应用,优化放疗程序,临床医学物理学家在教育和培训过程中应接受一定的人工智能技术强制性培训。他们最终应该参与将机器学习技术整合到放射治疗设备中。病人治疗的病人特异性剂量测量幻影中的剂量测量下列探测器之一:传送门成像第三种是在传送时间序列线性质量期间生成的日志文件中查找传送错误
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引用次数: 1
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Journal of medical artificial intelligence
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