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Tafavvoghi M, Bongo LA, Shvetsov N, Busund LTR, Møllersen K. Publicly available datasets of breast histopathology H&E whole-slide images: A scoping review. J Pathol Inform 2024; 15:100363. [PMID: 38405160 PMCID: PMC10884505 DOI: 10.1016/j.jpi.2024.100363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/24/2023] [Accepted: 01/23/2024] [Indexed: 02/27/2024] Open
Abstract
Advancements in digital pathology and computing resources have made a significant impact in the field of computational pathology for breast cancer diagnosis and treatment. However, access to high-quality labeled histopathological images of breast cancer is a big challenge that limits the development of accurate and robust deep learning models. In this scoping review, we identified the publicly available datasets of breast H&E-stained whole-slide images (WSIs) that can be used to develop deep learning algorithms. We systematically searched 9 scientific literature databases and 9 research data repositories and found 17 publicly available datasets containing 10 385 H&E WSIs of breast cancer. Moreover, we reported image metadata and characteristics for each dataset to assist researchers in selecting proper datasets for specific tasks in breast cancer computational pathology. In addition, we compiled 2 lists of breast H&E patches and private datasets as supplementary resources for researchers. Notably, only 28% of the included articles utilized multiple datasets, and only 14% used an external validation set, suggesting that the performance of other developed models may be susceptible to overestimation. The TCGA-BRCA was used in 52% of the selected studies. This dataset has a considerable selection bias that can impact the robustness and generalizability of the trained algorithms. There is also a lack of consistent metadata reporting of breast WSI datasets that can be an issue in developing accurate deep learning models, indicating the necessity of establishing explicit guidelines for documenting breast WSI dataset characteristics and metadata.
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Affiliation(s)
- Masoud Tafavvoghi
- Department of Community Medicine, Uit The Arctic University of Norway, Tromsø, Norway
| | - Lars Ailo Bongo
- Department of Computer Science, Uit The Arctic University of Norway, Tromsø, Norway
| | - Nikita Shvetsov
- Department of Computer Science, Uit The Arctic University of Norway, Tromsø, Norway
| | | | - Kajsa Møllersen
- Department of Community Medicine, Uit The Arctic University of Norway, Tromsø, Norway
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Wang Y, Liu L, Wang C. Trends in using deep learning algorithms in biomedical prediction systems. Front Neurosci 2023; 17:1256351. [PMID: 38027475 PMCID: PMC10665494 DOI: 10.3389/fnins.2023.1256351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
In the domain of using DL-based methods in medical and healthcare prediction systems, the utilization of state-of-the-art deep learning (DL) methodologies assumes paramount significance. DL has attained remarkable achievements across diverse domains, rendering its efficacy particularly noteworthy in this context. The integration of DL with health and medical prediction systems enables real-time analysis of vast and intricate datasets, yielding insights that significantly enhance healthcare outcomes and operational efficiency in the industry. This comprehensive literature review systematically investigates the latest DL solutions for the challenges encountered in medical healthcare, with a specific emphasis on DL applications in the medical domain. By categorizing cutting-edge DL approaches into distinct categories, including convolutional neural networks (CNNs), recurrent neural networks (RNNs), generative adversarial networks (GANs), long short-term memory (LSTM) models, support vector machine (SVM), and hybrid models, this study delves into their underlying principles, merits, limitations, methodologies, simulation environments, and datasets. Notably, the majority of the scrutinized articles were published in 2022, underscoring the contemporaneous nature of the research. Moreover, this review accentuates the forefront advancements in DL techniques and their practical applications within the realm of medical prediction systems, while simultaneously addressing the challenges that hinder the widespread implementation of DL in image segmentation within the medical healthcare domains. These discerned insights serve as compelling impetuses for future studies aimed at the progressive advancement of using DL-based methods in medical and health prediction systems. The evaluation metrics employed across the reviewed articles encompass a broad spectrum of features, encompassing accuracy, precision, specificity, F-score, adoptability, adaptability, and scalability.
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Affiliation(s)
- Yanbu Wang
- School of Strength and Conditioning, Beijing Sport University, Beijing, China
| | - Linqing Liu
- Department of Physical Education, Peking University, Beijing, China
| | - Chao Wang
- Institute of Competitive Sports, Beijing Sport University, Beijing, China
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3
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Computational intelligence in eye disease diagnosis: a comparative study. Med Biol Eng Comput 2023; 61:593-615. [PMID: 36595155 DOI: 10.1007/s11517-022-02737-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 12/09/2022] [Indexed: 01/04/2023]
Abstract
In recent years, eye disorders are an important health issue among older people. Generally, individuals with eye diseases are unaware of the gradual growth of symptoms. Therefore, routine eye examinations are required for early diagnosis. Usually, eye disorders are identified by an ophthalmologist via a slit-lamp investigation. Slit-lamp interpretations are inadequate due to the differences in the analytical skills of the ophthalmologist, inconsistency in eye disorder analysis, and record maintenance issues. Therefore, digital images of an eye and computational intelligence (CI)-based approaches are preferred as assistive methods for eye disease diagnosis. A comparative study of CI-based decision support models for eye disorder diagnosis is presented in this paper. The CI-based decision support systems used for eye abnormalities diagnosis were grouped as anterior and retinal eye abnormalities diagnostic systems, and numerous algorithms used for diagnosing the eye abnormalities were also briefed. Various eye imaging modalities, pre-processing methods such as reflection removal, contrast enhancement, region of interest segmentation methods, and public eye image databases used for CI-based eye disease diagnosis system development were also discussed in this paper. In this comparative study, the reliability of various CI-based systems used for anterior eye and retinal disorder diagnosis was compared based on the precision, sensitivity, and specificity in eye disease diagnosis. The outcomes of the comparative analysis indicate that the CI-based anterior and retinal disease diagnosis systems attained significant prediction accuracy. Hence, these CI-based diagnosis systems can be used in clinics to reduce the burden on physicians, minimize fatigue-related misdetection, and take precise clinical decisions.
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Hrebik R, Kukal J. Concept of hidden classes in pattern classification. Artif Intell Rev 2023. [DOI: 10.1007/s10462-023-10430-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
AbstractOur paper presents a novel approach to pattern classification. The general disadvantage of a traditional classifier is in too different behaviour and optimal parameter settings during training on a given pattern set and the following cross-validation. We describe the term critical sensitivity, which means the lowest reached sensitivity for an individual class. This approach ensures a uniform classification quality for individual class classification. Therefore, it prevents outlier classes with terrible results. We focus on the evaluation of critical sensitivity, as a quality criterion. Our proposed classifier eliminates this disadvantage in many cases. Our aim is to present that easily formed hidden classes can significantly contribute to improving the quality of a classifier. Therefore, we decided to propose classifier will have a relatively simple structure. The proposed classifier structure consists of three layers. The first is linear, used for dimensionality reduction. The second layer serves for clustering and forms hidden classes. The third one is the output layer for optimal cluster unioning. For verification of the proposed system results, we use standard datasets. Cross-validation performed on standard datasets showed that our critical sensitivity-based classifier provides comparable sensitivity to reference classifiers.
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Said S, Bouloiz H, Gallab M. Contributions of Industry 4.0 to resilience achievement in the context of COVID-19 pandemic. IFAC-PAPERSONLINE 2022; 55:3226-3231. [PMID: 38620797 PMCID: PMC9605721 DOI: 10.1016/j.ifacol.2022.10.144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the totally unprecedented context of the COVID-19 health crisis, the widespread adoption of Industry 4.0 technologies, and the great interest in resilience, have been stronger than ever. Within this framework, the present paper outlines the involvement of technologies emerging from the fourth industrial revolution in the fight against the epidemic expansion, and the results of this implication in terms of strengthening and achieving resilience in diverse fields. In order to gain a fuller understanding of these points, fourteen resilience domains related to the COVID-19 pandemic are defined. On the other hand, the third section of this paper digs into the literature to expose a variety of Industry 4.0 solutions developed to cope with the sanitary crisis. Afterwards, a fuzzy cognitive map is elaborated, using mental modeler, in order to emphasize the causal links between Industry 4.0 technologies and resilience domains. Subsequently, a simulation of this model is performed to evaluate the contribution of an optimized joint use of Industry 4.0 core technologies in the achievement of resilience in its different dimensions during the COVID-19 pandemic, and to discuss how the identified gaps or weaknesses can be addressed.
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Affiliation(s)
- Saloua Said
- Systems engineering and decision support laboratory, Ibn Zohr University, ENSA Agadir, Morocco
| | - Hafida Bouloiz
- Systems engineering and decision support laboratory, Ibn Zohr University, ENSA Agadir, Morocco
| | - Maryam Gallab
- MIS-LISTD Laboratory, Computer Science Department, Mines-Rabat School (ENSMR), Rabat, Morocco
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Wei L, Hou S, Liu Q. Clinical Care of Hyperthyroidism Using Wearable Medical Devices in a Medical IoT Scenario. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:5951326. [PMID: 35251571 PMCID: PMC8890839 DOI: 10.1155/2022/5951326] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 01/30/2023]
Abstract
This paper presents an in-depth study and analysis of clinical care of patients with hyperthyroidism using wearable medical devices in the context of medical IoT scenarios. According to the use scenario of the gateway and the connectivity of the equipment, the hardware architecture, hardware interfaces, functionality, and performance of the gateway were briefly designed, so as to monitor patients with hyperthyroidism more comprehensively and save labor costs. The gateway can provide access to different devices and adaptation functions to different hardware interfaces and provide hardware support for the subsequent deployment of the proposed new medical communication protocols and related information systems. A medical data convergence information system based on multidevice management and multiprotocol parsing was designed and implemented. The system enables the management and configuration of different medical devices and access to data through the targeted parsing of the underlying medical device communication protocols. The system also provides the automatic adaptation of multiple types of underlying medical device communication protocols and automatic parsing of multiple versions and can provide multiple devices to process fused data streams or device information and data from a single device. The use of event-driven asynchronous communication eliminates the tight dependency on service invocation in the synchronous communication approach. The use of a metadata-based data model structure enables model extensions to accommodate the impact of iterative business requirements on the database structure. Real-time patient physiological data transmission for intraoperative monitoring based on the MQTT protocol and video transmission for intraoperative patient monitoring based on the RTMP protocol were implemented. The development of the intelligent medical monitoring service system was completed, and the system was tested, optimized, and deployed. The functionality and performance of the system were tested, the performance issue of slow query speed was optimized, and the deployment of the project using Docker containers was automated.
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Affiliation(s)
- Lili Wei
- Department of Radiology, Tangshan Gongren Hospital, Tangshan, Hebei 063000, China
| | - Sujuan Hou
- Department of Radiology, Tangshan Gongren Hospital, Tangshan, Hebei 063000, China
| | - Qiuxia Liu
- Department of Radiology, Tangshan Gongren Hospital, Tangshan, Hebei 063000, China
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Reska D, Czajkowski M, Jurczuk K, Boldak C, Kwedlo W, Bauer W, Koszelew J, Kretowski M. Integration of solutions and services for multi-omics data analysis towards personalized medicine. Biocybern Biomed Eng 2021. [DOI: 10.1016/j.bbe.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Qian X, Zhou Z, Hu J, Zhu J, Huang H, Dai Y. A comparative study of kernel-based vector machines with probabilistic outputs for medical diagnosis. Biocybern Biomed Eng 2021. [DOI: 10.1016/j.bbe.2021.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Nagy M, Radakovich N, Nazha A. Machine Learning in Oncology: What Should Clinicians Know? JCO Clin Cancer Inform 2021; 4:799-810. [PMID: 32926637 DOI: 10.1200/cci.20.00049] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The volume and complexity of scientific and clinical data in oncology have grown markedly over recent years, including but not limited to the realms of electronic health data, radiographic and histologic data, and genomics. This growth holds promise for a deeper understanding of malignancy and, accordingly, more personalized and effective oncologic care. Such goals require, however, the development of new methods to fully make use of the wealth of available data. Improvements in computer processing power and algorithm development have positioned machine learning, a branch of artificial intelligence, to play a prominent role in oncology research and practice. This review provides an overview of the basics of machine learning and highlights current progress and challenges in applying this technology to cancer diagnosis, prognosis, and treatment recommendations, including a discussion of current takeaways for clinicians.
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Affiliation(s)
- Matthew Nagy
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH
| | - Nathan Radakovich
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH
| | - Aziz Nazha
- Center for Clinical Artificial Intelligence, Cleveland Clinic, Cleveland, OH.,Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, OH
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Pawar SD, Sharma KK, Sapate SG, Yadav GY. Segmentation of pectoral muscle from digital mammograms with depth-first search algorithm towards breast density classification. Biocybern Biomed Eng 2021. [DOI: 10.1016/j.bbe.2021.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Salau AO, Jain S. Adaptive diagnostic machine learning technique for classification of cell decisions for AKT protein. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Atif AUR, Su J. Review of gesture recognition technique using cloud-assisted wearable devices for real-time healthcare. 2020 5TH INTERNATIONAL CONFERENCE ON INNOVATIVE TECHNOLOGIES IN INTELLIGENT SYSTEMS AND INDUSTRIAL APPLICATIONS (CITISIA) 2020. [DOI: 10.1109/citisia50690.2020.9371838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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A Novel Approach for Coronary Artery Disease Diagnosis using Hybrid Particle Swarm Optimization based Emotional Neural Network. Biocybern Biomed Eng 2020. [DOI: 10.1016/j.bbe.2020.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Machine learning in haematological malignancies. LANCET HAEMATOLOGY 2020; 7:e541-e550. [PMID: 32589980 DOI: 10.1016/s2352-3026(20)30121-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/02/2020] [Accepted: 04/14/2020] [Indexed: 02/06/2023]
Abstract
Machine learning is a branch of computer science and statistics that generates predictive or descriptive models by learning from training data rather than by being rigidly programmed. It has attracted substantial attention for its many applications in medicine, both as a catalyst for research and as a means of improving clinical care across the cycle of diagnosis, prognosis, and treatment of disease. These applications include the management of haematological malignancy, in which machine learning has created inroads in pathology, radiology, genomics, and the analysis of electronic health record data. As computational power becomes cheaper and the tools for implementing machine learning become increasingly democratised, it is likely to become increasingly integrated into the research and practice landscape of haematology. As such, machine learning merits understanding and attention from researchers and clinicians alike. This narrative Review describes important concepts in machine learning for unfamiliar readers, details machine learning's current applications in haematological malignancy, and summarises important concepts for clinicians to be aware of when appraising research that uses machine learning.
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Human Tongue Thermography Could Be a Prognostic Tool for Prescreening the Type II Diabetes Mellitus. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:3186208. [PMID: 32419801 PMCID: PMC7201785 DOI: 10.1155/2020/3186208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/28/2019] [Accepted: 11/27/2019] [Indexed: 12/26/2022]
Abstract
Diabetes mellitus is one of the life threatening diseases over the globe, and an early prediction of diabetes is of utmost importance in this current scenario. International Diabetes Federation (IDF) reported nearly half of the world's population was undiagnosed and unaware of being developed into diabetes. In 2017, around 84 million individuals were living with diabetes, and it might increase to 156 million by the end of 2045 stated by IDF. Generally, the diagnosis of diabetes relies on the biochemical method that may cause uneasiness and probability of infections to the subjects. To overcome such difficulties, a noninvasive method is much needed around the globe for primary screening. A change in body temperature is an indication of various diseases. Infrared thermal imaging is relatively a novel technique for skin temperature measurement and turned out to be well known in the medical field due to being noninvasive, risk-free, and repeatable. According to traditional Chinese medicine, the human tongue is a sensitive mirror that reflects the body's pathophysiological condition. So, we have (i) analysed and classified diabetes based on thermal variations at human tongue, (ii) segmented the hot spot regions from tongue thermogram by RGB (red, green, blue) based color histogram image segmentation method and extracted the features using gray level co-occurrence matrix algorithm, (iii) classified normal and diabetes using various machine learning algorithms, and (iv) developed computer aided diagnostic system to classify diabetes mellitus. The baseline measurements and tongue thermograms were obtained from 140 subjects. The measured tongue surface temperature of the diabetic group was found to be greater than normal. The statistical correlation between the HbA1c and the thermal distribution in the tongue region was found to be r2 = 0.5688. The Convolutional Neural Network has outperformed the other classifiers with 94.28% accuracy rate. Thus, tongue thermograms could be used as a preliminary screening approach for diabetes prognosis.
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