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arXiv 2025年

作者： Luo, Gongning Xu, Mingwang Chen, Hongyu Liang, Xinjie Tao, Xing Ni, Dong Jeong, Hyunsu Kim, Chulhong Stock, Raphael Baumgartner, Michael Kirchhoff, Yannick Rokuss, Maximilian Maier-Hein, Klaus Yang, Zhikai Fan, Tianyu Boutry, Nicolas Tereshchenko, Dmitry Moine, Arthur Charmetant, Maximilien Sauer, Jan Du, Hao Bai, Xiang-Hui Raikar, Vipul Pai Montoya-Del-Angel, Ricardo Martí, Robert Luna, Miguel Lee, Dongmin Qayyum, Abdul Mazher, Moona Guo, Qihui Wang, Changyan Awasthi, Navchetan Zhao, Qiaochu Wang, Wei Wang, Kuanquan Wang, Qiucheng Dong, Suyu School of Computer Science and Technology Harbin Institute of Technology Harbin150001 China Department of Mathematics Faculty of Science National University of Singapore Singapore National-Regional Key Technology Engineering Laboratory for Medical Ultrasound School of Biomedical Engineering Shenzhen University Medical School Shenzhen University Shenzhen China Laboratory Shenzhen University Shenzhen China School of Biomedical Engineering and Informatics Nanjing Medical University Nanjing China Pohang Korea Republic of Heidelberg Division of Medical Image Computing Heidelberg Germany Faculty of Mathematics and Computer Science Heidelberg University Germany Heidelberg Germany HIDSS4Health - Helmholtz Information and Data Science School for Health Karlsruhe Heidelberg Germany Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Germany Department of Biomedical Engineering and Health KTH Royal Institute of Technology Stockholm Sweden France FathomX Singapore Saw Swee Hock School of Public Health National University of Singapore Singapore Philips Research University of Girona Spain Department of Robotics and Mechatronics Engineering DGIST Korea Republic of Department of Interdisciplinary Studies of Artificial Intelligence DGIST Korea Republic of National Heart and Lung Institute Faculty of Medicine Imperial College London London United Kingdom Centre for Medical Image Computing Department of Computer Science University College London London United Kingdom Lab School of Communication and Information Engineering Shanghai University Shanghai China Faculty of Science Mathematics and Computer Science Informatics Institute University of Amsterdam Amsterdam1090 GH Netherlands Department of Biomedical Engineering and Physics Amsterdam UMC Amsterdam1081 HV Netherlands Xi’an Jiaotong-Liverpool University China Department of Ultrasound Harbin Medical University Cancer Hospital No. 150 Haping Road Nangang

Breast cancer is one of the most common causes of death among women worldwide. Early detection helps in reducing the number of deaths. Automated 3D Breast Ultrasound (ABUS) is a newer approach for breast screening, which has many advantages over handheld mammography such as safety, speed, and higher detection rate of breast cancer. Tumor detection, segmentation, and classification are key components in the analysis of medical images, especially challenging in the context of 3D ABUS due to the significant variability in tumor size and shape, unclear tumor boundaries, and a low signal-to-noise ratio. The lack of publicly accessible, well-labeled ABUS datasets further hinders the advancement of systems for breast tumor analysis. Addressing this gap, we have organized the inaugural Tumor Detection, Segmentation, and Classification Challenge on Automated 3D Breast Ultrasound 2023 (TDSC-ABUS2023). This initiative aims to spearhead research in this field and create a definitive benchmark for tasks associated with 3D ABUS image analysis. In this paper, we summarize the top-performing algorithms from the challenge and provide critical analysis for ABUS image examination. We offer the TDSC-ABUS challenge as an open-access platform at https://***/ to benchmark and inspire future developments in1algorithmic research. © 2025, CC BY.

关键词： Image segmentation

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Using Machine Learning to Develop Smart Reflex Testing Protocols

arXiv

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arXiv 2023年

作者： McDermott, Matthew Dighe, Anand Szolovits, Peter Luo, Yuan Baron, Jason MIT Computer Science and Artificial Intelligence Lab BostonMA United States Harvard Medical School Department of Biomedical Informatics United States Department of Pathology Massachusetts General Hospital BostonMA United States Harvard Medical School BostonMA United States MGB HealthCare System SomervilleMA United States Department of Preventive Medicine Northwestern University ChicagoIL United States

Objective: Reflex testing protocols allow clinical laboratories to perform second line diagnostic tests on existing specimens based on the results of initially ordered tests. Reflex testing can support optimal clinical laboratory test ordering and diagnosis. In current clinical practice, reflex testing typically relies on simple "if-then" rules;however, this limits their scope since most test ordering decisions involve more complexity than a simple rule will allow. Here, using the analyte ferritin as an example, we propose an alternative machine learning-based approach to "smart" reflex testing with a wider scope and greater impact than traditional rule-based approaches. Methods: Using patient data, we developed a machine learning model to predict whether a patient getting CBC testing will also have ferritin testing ordered, consider applications of this model to "smart" reflex testing, and evaluate the model by comparing its performance to possible rule-based approaches. Results: Our underlying machine learning models performed moderately well in predicting ferritin test ordering and demonstrated greater suitability to reflex testing than rule-based approaches. Using chart review, we demonstrate that our model may improve ferritin test ordering. Finally, as a secondary goal, we demonstrate that ferritin test results are missing not at random (MNAR), a finding with implications for unbiased imputation of missing test results. Conclusions: Machine learning may provide a foundation for new types of reflex testing with enhanced benefits for clinical diagnosis and laboratory utilization management. © 2023, CC BY.

关键词： Decision support systems

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Explainable AI for Bioinformatics: Methods, Tools, and Applications

arXiv

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arXiv 2022年

作者： Karim, Md. Rezaul Islam, Tanhim Beyan, Oya Lange, Christoph Cochez, Michael Rebholz-Schuhmann, Dietrich Decker, Stefan Department of Data Science and Artificial Intelligence Fraunhofer FIT Germany Chair of Computer Science 5 - Information Systems and Databases RWTH Aachen University Germany University of Cologne Faculty of Medicine University Hospital Cologne Institute for Biomedical Informatics Germany Department of Computer Science Vrije Univeriteit Amsterdam Netherlands Elsevier Discovery Lab Amsterdam Netherlands ZBMED - Information Center for Life Sciences Germany Faculty of Medicine University of Cologne Germany

Artificial intelligence (AI) systems utilizing deep neural networks (DNNs) and machine learning (ML) algorithms are widely used for solving important problems in bioinformatics, biomedical informatics, and precision medicine. However, complex DNNs or ML models, which are often perceived as opaque and black-box, can make it difficult to understand the reasoning behind their decisions. This lack of transparency can be a challenge for both end-users and decision-makers, as well as AI developers. Additionally, in sensitive areas like healthcare, explainability and accountability are not only desirable but also legally required for AI systems that can have a significant impact on human lives. Fairness is another growing concern, as algorithmic decisions should not show bias or discrimination towards certain groups or individuals based on sensitive attributes. Explainable artificial intelligence (XAI) aims to overcome the opaqueness of black-box models and provide transparency in how AI systems make decisions. Interpretable ML models can explain how they make predictions and the factors that influence their outcomes. However, most state-of-the-art interpretable ML methods are domain-agnostic and evolved from fields like computer vision, automated reasoning, or statistics, making direct application to bioinformatics problems challenging without customization and domain-specific adaptation. In this paper, we discuss the importance of explainability in the context of bioinformatics, provide an overview of model-specific and model-agnostic interpretable ML methods and tools, and outline their potential caveats and drawbacks. Besides, we discuss how to customize existing interpretable ML methods for bioinformatics problems. Nevertheless, we demonstrate how XAI methods can improve transparency through case studies in bioimaging, cancer genomics, and text mining (GitHub repo: https://***/rezacsedu/XAI-for-bioinformatics. Our review aims to provide valuable insights and se

关键词： Bioinformatics

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Application of Kronecker convolutions in deep learning technique for automated detection of kidney stones with coronal CT images

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Information sciences 2023年 640卷

作者： Patro, Kiran Kumar Allam, Jaya Prakash Neelapu, Bala Chakravarthy Tadeusiewicz, Ryszard Acharya, U Rajendra Hammad, Mohamed Yildirim, Ozal Plawiak, Pawel Department of Electronics and Communication Engineering Aditya Institute of Technology and Management AP Tekkali532201 India Department of Electronics and Communication Engineering National Institute of Technology Rourkela Odisha Rourkela769008 India Department of Biotechnology and Medical Engineering National Institute of Technology Rourkela Odisha Rourkela769008 India AGH University of Science and Technology Department of Biocybernetics and Biomedical Engineering Krakow Poland School of Mathematics Physics and Computing University of Southern Queensland Springfield Australia EIAS Data Science Lab College of Computer and Information Sciences Prince Sultan University Riyadh11586 Saudi Arabia Department of Information Technology Faculty of Computers and Information Menoufia University Shibin El Kom32511 Egypt Department of Software Engineering Firat University Elazig Turkey Department of Computer Science Faculty of Computer Science and Telecommunications Cracow University of Technology Warszawska 24 Krakow31-155 Poland Institute of Theoretical and Applied Informatics Polish Academy of Sciences Baltycka 5 Gliwice44-100 Poland

Kidney stone disease is a serious public health concern that is getting worse with changes in diet, obesity, medical conditions, certain supplements etc. A kidney stone also called a renal calculus, is a hard buildup of urine minerals that form in the kidneys. Computed tomography (CT) is one of the imaging models used to identify kidney stones by clinical experts. Due to the low resolution of these images, sometimes detecting kidney stones is tedious with the naked eye, which may lead to false alarms. In this work, a computer-based diagnosis system with a deep learning technique has been developed as a practical solution to aid clinicians in their diagnosis. The traditional convolutional neural network (CNN)-based deep learning technology can detect stones in the kidney. Still, it suffers from the performance and standard implementation of the convolution operations in convolution layers. A Kronecker product-based convolution technique is incorporated in the proposed deep learning architecture to reduce the redundancy in feature maps without convolution overlapping. Our proposed method helps to make the network more effective by extracting abstract and in-depth features from the input images. The publicly available GitHub kidney stone CT scans are utilized to develop the proposed architecture. Our automated model detected kidney stones with an accuracy of 98.56% utilizing CT images. Our system is more effective than the most recent and cutting-edge techniques developed for identifying kidney stones of any size, including the smallest ones. © 2023 The Author(s)

关键词： Convolution

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DUBLINE: A DEEP UNFOLDING NETWORK FOR B-LINE DETECTION IN LUNG ULTRASOUND IMAGES

arXiv

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arXiv 2023年

作者： Yang, Tianqi Anantrasirichai, Nantheera Karakuş, Oktay Allinovi, Marco Koydemir, Hatice Ceylan Achim, Alin Visual Information Lab University of Bristol Bristol United Kingdom School of Computer Science and Informatics Cardiff University Cardiff United Kingdom Nephrology Dialysis and Transplantation Careggi University Hospital Florence Italy Department of Biomedical Engineering Texas A&M University United States Center for Remote Health Technologies and Systems Texas A&M Engineering Experiment Station United States

In the context of lung ultrasound, the detection of B-lines, which are indicative of interstitial lung disease and pulmonary edema, plays a pivotal role in clinical diagnosis. Current methods still rely on visual inspection by experts. Vision-based automatic B-line detection methods have been developed, but their performance has yet to improve in terms of both accuracy and computational speed. This paper presents a novel approach to posing B-line detection as an inverse problem via deep unfolding of the Alternating Direction Method of Multipliers (ADMM). It tackles the challenges of data la-belling and model training in lung ultrasound image analysis by harnessing the capabilities of deep neural networks and model-based methods. Our objective is to substantially enhance diagnostic accuracy while ensuring efficient real-time capabilities. The results show that the proposed method runs more than 90 times faster than the traditional model-based method and achieves an F1 score that is 10.6% higher. © 2023, CC BY.

关键词： Inverse problems

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Discriminative Radial Domain Adaptation

arXiv

引用

arXiv 2023年

作者： Huang, Zenan Wen, Jun Chen, Siheng Zhu, Linchao Zheng, Nenggan The Qiushi Academy for Advanced Studies Zhejiang University Zhejiang Hangzhou310007 China The College of Computer Science and Technology Zhejiang University Zhejiang Hangzhou310007 China The Department of Biomedical Informatics Harvard Medical School BostonMA02115 United States Cooperative Medianet Innovation Center Shanghai Jiao Tong University Shanghai200240 China Shanghai AI Laboratory Shanghai200240 China College of Computer Science and Technology Zhejiang University Hangzhou China and Zhejiang Lab Zhejiang Hangzhou311121 China

Domain adaptation methods reduce domain shift typically by learning domain-invariant features. Most existing methods are built on distribution matching, e.g., adversarial domain adaptation, which tends to corrupt feature discriminability. In this paper, we propose Discriminative Radial Domain Adaptation (DRDA) which bridges source and target domains via a shared radial structure. It’s motivated by the observation that as the model is trained to be progressively discriminative, features of different categories expand outwards in different directions, forming a radial structure. We show that transferring such an inherently discriminative structure would enable to enhance feature transferability and discriminability simultaneously. Specifically, we represent each domain with a global anchor and each category a local anchor to form a radial structure and reduce domain shift via structure matching. It consists of two parts, namely isometric transformation to align the structure globally and local refinement to match each category. To enhance the discriminability of the structure, we further encourage samples to cluster close to the corresponding local anchors based on optimal-transport assignment. Extensively experimenting on multiple benchmarks, our method is shown to consistently outperforms state-of-the-art approaches on varied tasks, including the typical unsupervised domain adaptation, multi-source domain adaptation, domain-agnostic learning, and domain generalization. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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State-of-the-Art Deep Learning Methods on Electrocardiogram Data: Systematic Review

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JMIR Medical informatics 2022年第8期10卷 e38454页

作者： Petmezas, Georgios Stefanopoulos, Leandros Kilintzis, Vassilis Tzavelis, Andreas Rogers, John A. Katsaggelos, Aggelos K. Maglaveras, Nicos Lab of Computing Medical Informatics and Biomedical-Imaging Technologies The Medical School Aristotle University of Thessaloniki Thessaloniki Greece Department of Biomedical Engineering Northwestern University Evanston IL United States Department of Material Science Northwestern University Evanston IL United States Department of Electrical and Computer Engineering Northwestern University Evanston IL United States

Background: Electrocardiogram (ECG) is one of the most common noninvasive diagnostic tools that can provide useful information regarding a patient’s health status. Deep learning (DL) is an area of intense exploration that leads the way in most attempts to create powerful diagnostic models based on physiological signals. Objective: This study aimed to provide a systematic review of DL methods applied to ECG data for various clinical applications. Methods: The PubMed search engine was systematically searched by combining “deep learning” and keywords such as “ecg,” “ekg,” “electrocardiogram,” “electrocardiography,” and “electrocardiology.” Irrelevant articles were excluded from the study after screening titles and abstracts, and the remaining articles were further reviewed. The reasons for article exclusion were manuscripts written in any language other than English, absence of ECG data or DL methods involved in the study, and absence of a quantitative evaluation of the proposed approaches. Results: We identified 230 relevant articles published between January 2020 and December 2021 and grouped them into 6 distinct medical applications, namely, blood pressure estimation, cardiovascular disease diagnosis, ECG analysis, biometric recognition, sleep analysis, and other clinical analyses. We provide a complete account of the state-of-the-art DL strategies per the field of application, as well as major ECG data sources. We also present open research problems, such as the lack of attempts to address the issue of blood pressure variability in training data sets, and point out potential gaps in the design and implementation of DL models. Conclusions: We expect that this review will provide insights into state-of-the-art DL methods applied to ECG data and point to future directions for research on DL to create robust models that can assist medical experts in clinical decision-making. ©Georgios Petmezas, Leandros Stefanopoulos, Vassilis Kilintzis, Andreas Tzavelis, John A Rogers

关键词： clinical decision CNN convolutional neural networks decision support deep learning diagnostic tools ECG ECG databases electrocardiogram long short-term memory LSTM residual neural network ResNet

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Deep and handcrafted feature supported diabetic retinopathy detection: A study

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Procedia computer science 2023年 218卷 2675-2683页

作者： Seifedine Kadry Rubén González Crespo Enrique Herrera-Viedma Sujatha Krishnamoorthy Venkatesan Rajinikanth Faculty of Applied Computing and Technology Noroff University College Kristiansand 94612 Norway Computer Science Department School of Engineering and Technology Universidad Internacional de La Rioja 26006 Andalusian Spain Research Institute in Data Science and Computational Intelligence University of Granada Granada Spain Zhejiang Bioinformatics International Science and Technology Cooperation Center Wenzhou-Kean University Zhejiang Province China Wenzhou Municipal Key Lab of Applied Biomedical and Biopharmaceutical Informatics Wenzhou-Kean University Zhejiang Province China Department of Electronics and Instrumentation Engineering St. Joseph's College of Engineering OMR Chennai 600119 Tamil Nadu India

The eye is the prime sensory organ in physiology, and the abnormality in the eye severely influences the vision system. Therefore, eye irregularity is commonly assessed using imaging schemes, and Fundus Retinal Image (FRI) supported eye screening is one of the ophthalmological practices. This work proposed a Deep-Learning Procedure (DLP) to recognize Diabetic Retinopathy (DR) in FI. The proposed work presents the experimental work with different DLP methods found in the literature. This work is executed with two modes; (i) DR detection using conventional deep-features and (ii) DR discovery using deep ensemble features. To demonstrate this work, 1800 fundus images (900 regular and 900 DR class) are considered for the assessment, and the advantage of proposed plan is confirmed using various performance metrics. The experimental outcome of this study confirms that the AlexNet-based detection provides a better detection (>96%), and the deep ensemble features of AlexNet, VGG16, and ResNet18 provide a detection accuracy of >98% on the chosen FRI database.

关键词： Eye abnormality Diabetic retinopathy Fundus imaging Deep-Learning Classification

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Automatic detection of lung nodule in CT scan slices using CNN segmentation schemes: A study

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Procedia computer science 2023年 218卷 2786-2794页

作者： Seifedine Kadry Enrique Herrera-Viedma Rubén González Crespo Sujatha Krishnamoorthy Venkatesan Rajinikanth Faculty of Applied Computing and Technology Noroff University College Kristiansand 94612 Norway Research Institute in Data Science and Computational Intelligence University of Granada Granada Andalusian Spain Computer Science Department School of Engineering and Technology Universidad Internacional de La Rioja 26006 Spain Zhejiang Bioinformatics International Science and Technology Cooperation Center Wenzhou-Kean University Zhejiang Province China Wenzhou Municipal Key Lab of Applied Biomedical and Biopharmaceutical Informatics Wenzhou-Kean University Zhejiang Province China Department of Electronics and Instrumentation Engineering St. Joseph's College of Engineering OMR Chennai 600119 Tamil Nadu India

The lung is one of the prime respiratory organs in human physiology, and its abnormality will severely disrupt the respiratory system. Lung Nodule (LN) is one of the abnormalities, and early screening and treatment are necessary to reduce its harshness. The proposed work aims to implement the Convolutional-Neural-Network (CNN) segmentation methodology to extract the LN in various lung CT slices, such as axial, coronal, and sagittal planes. This work consists of the following phases; (i) Image collection and pre-processing, (ii) Ground-truth generation, (iii) CNN-supported segmentation, and (iv) Performance evaluation and validation. In this work, the merit of pre-trained CNN segmentation schemes is verified using (i) One-fold training and (ii) Two-fold training methods. The test images for this study are collected from The Cancer Imaging Archive (TCIA) database. The experimental investigation is executed using Python®, and the outcome of this study confirms that the VGG-SegNet helps to get better values of Jaccard (>88%), Dice (>93%), and Accuracy (>96%) compared to other CNN methods.

关键词： Lung nodule CT scan CNN segmentation VGG-SegNet Accuracy Detection

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Evaluating explainability for graph neural networks

arXiv

引用

arXiv 2022年

作者： Agarwal, Chirag Queen, Owen Lakkaraju, Himabindu Zitnik, Marinka Media and Data Science Research Lab Adobe Noida201304 India Department of Computer Science University of Tennessee KnoxvilleTN37996 United States Harvard Business School BostonMA02163 United States Department of Biomedical Informatics Harvard University BostonMA02115 United States Broad Institute of MIT Harvard CambridgeMA02142 United States Harvard Data Science Initiative CambridgeMA02138 United States Department of Computer Science Harvard University BostonMA02134 United States

As explanations are increasingly used to understand the behavior of graph neural networks (GNNs), evaluating the quality and reliability of GNN explanations is crucial. However, assessing the quality of GNN explanations is challenging as existing graph datasets have no or unreliable ground-truth explanations. Here, we introduce a synthetic graph data generator, SHAPEGGEN, which can generate a variety of benchmark datasets (e.g., varying graph sizes, degree distributions, homophilic vs. heterophilic graphs) accompanied by ground-truth explanations. The flexibility to generate diverse synthetic datasets and corresponding ground-truth explanations allows SHAPEGGEN to mimic the data in various real-world areas. We include SHAPEGGEN and several real-world graph datasets in a graph explainability library, GRAPHXAI. In addition to synthetic and real-world graph datasets with ground-truth explanations, GRAPHXAI provides data loaders, data processing functions, visualizers, GNN model implementations, and evaluation metrics to benchmark GNN explainability methods. © 2022, CC BY.

关键词： Data handling

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