Ka Yung Cheng , Markus Lange-Hegermann , Jan-Bernd Hövener , Björn Schreiweis
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To address this issue, accurate and meaningful descriptors are needed for indexing fields, enabling users to efficiently search for desired images and integrate them with international standards.</p><p>This paper aims to provide concise annotation for missing or incorrectly indexed fields, incorporating essential instance-level information such as radiology modalities (e.g., X-rays), anatomical regions (e.g., chest), and body orientations (e.g., lateral) using a Deep Learning classification model - ResNet50. To demonstrate the capabilities of our algorithm in generating annotations for indexing fields, we conducted three experiments using two open-source datasets, the ROCO dataset, and the IRMA dataset, along with a custom dataset featuring SNOMED CT labels. While the outcomes of these experiments are satisfactory (Precision of >75%) for less critical tasks and serve as a valuable testing ground for image retrieval, they also underscore the need for further exploration of potential challenges. This essay elaborates on the identified issues and presents well-founded recommendations for refining and advancing our proposed approach.</p></div>","PeriodicalId":10715,"journal":{"name":"Computational and structural biotechnology journal","volume":"24 ","pages":"Pages 434-450"},"PeriodicalIF":4.4000,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2001037024002034/pdfft?md5=bd1fa074436c095e9ca887e9e8641a81&pid=1-s2.0-S2001037024002034-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Instance-level medical image classification for text-based retrieval in a medical data integration center\",\"authors\":\"Ka Yung Cheng , Markus Lange-Hegermann , Jan-Bernd Hövener , Björn Schreiweis\",\"doi\":\"10.1016/j.csbj.2024.06.006\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>A medical data integration center integrates a large volume of medical images from clinical departments, including X-rays, CT scans, and MRI scans. Ideally, all images should be indexed appropriately with standard clinical terms. However, some images have incorrect or missing annotations, which creates challenges in searching and integrating data centrally. To address this issue, accurate and meaningful descriptors are needed for indexing fields, enabling users to efficiently search for desired images and integrate them with international standards.</p><p>This paper aims to provide concise annotation for missing or incorrectly indexed fields, incorporating essential instance-level information such as radiology modalities (e.g., X-rays), anatomical regions (e.g., chest), and body orientations (e.g., lateral) using a Deep Learning classification model - ResNet50. To demonstrate the capabilities of our algorithm in generating annotations for indexing fields, we conducted three experiments using two open-source datasets, the ROCO dataset, and the IRMA dataset, along with a custom dataset featuring SNOMED CT labels. While the outcomes of these experiments are satisfactory (Precision of >75%) for less critical tasks and serve as a valuable testing ground for image retrieval, they also underscore the need for further exploration of potential challenges. 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引用次数: 0
摘要
医疗数据整合中心整合了来自临床科室的大量医疗图像,包括 X 光、CT 扫描和核磁共振扫描。理想情况下,所有图像都应使用标准临床术语进行适当索引。然而,有些图像的注释不正确或缺失,这给集中搜索和整合数据带来了挑战。为了解决这个问题,需要为索引字段提供准确而有意义的描述符,使用户能够高效地搜索所需的图像,并按照国际标准对其进行整合。本文旨在利用深度学习分类模型--ResNet50,为缺失或错误的索引字段提供简明的注释,纳入放射学模式(如 X 光)、解剖区域(如胸部)和身体方向(如侧向)等基本的实例级信息。为了证明我们的算法在为索引字段生成注释方面的能力,我们使用两个开源数据集(ROCO 数据集和 IRMA 数据集)以及一个具有 SNOMED CT 标签的自定义数据集进行了三次实验。虽然这些实验在不太重要的任务上取得了令人满意的结果(精确度为 75%),并为图像检索提供了宝贵的试验场地,但它们也强调了进一步探索潜在挑战的必要性。本文将详细阐述已发现的问题,并为完善和推进我们提出的方法提出有理有据的建议。
Instance-level medical image classification for text-based retrieval in a medical data integration center
A medical data integration center integrates a large volume of medical images from clinical departments, including X-rays, CT scans, and MRI scans. Ideally, all images should be indexed appropriately with standard clinical terms. However, some images have incorrect or missing annotations, which creates challenges in searching and integrating data centrally. To address this issue, accurate and meaningful descriptors are needed for indexing fields, enabling users to efficiently search for desired images and integrate them with international standards.
This paper aims to provide concise annotation for missing or incorrectly indexed fields, incorporating essential instance-level information such as radiology modalities (e.g., X-rays), anatomical regions (e.g., chest), and body orientations (e.g., lateral) using a Deep Learning classification model - ResNet50. To demonstrate the capabilities of our algorithm in generating annotations for indexing fields, we conducted three experiments using two open-source datasets, the ROCO dataset, and the IRMA dataset, along with a custom dataset featuring SNOMED CT labels. While the outcomes of these experiments are satisfactory (Precision of >75%) for less critical tasks and serve as a valuable testing ground for image retrieval, they also underscore the need for further exploration of potential challenges. This essay elaborates on the identified issues and presents well-founded recommendations for refining and advancing our proposed approach.
期刊介绍:
Computational and Structural Biotechnology Journal (CSBJ) is an online gold open access journal publishing research articles and reviews after full peer review. All articles are published, without barriers to access, immediately upon acceptance. The journal places a strong emphasis on functional and mechanistic understanding of how molecular components in a biological process work together through the application of computational methods. Structural data may provide such insights, but they are not a pre-requisite for publication in the journal. Specific areas of interest include, but are not limited to:
Structure and function of proteins, nucleic acids and other macromolecules
Structure and function of multi-component complexes
Protein folding, processing and degradation
Enzymology
Computational and structural studies of plant systems
Microbial Informatics
Genomics
Proteomics
Metabolomics
Algorithms and Hypothesis in Bioinformatics
Mathematical and Theoretical Biology
Computational Chemistry and Drug Discovery
Microscopy and Molecular Imaging
Nanotechnology
Systems and Synthetic Biology