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Behara K, Bhero E, Agee JT. AI in dermatology: a comprehensive review into skin cancer detection. PeerJ Comput Sci 2024; 10:e2530. [PMID: 39896358 PMCID: PMC11784784 DOI: 10.7717/peerj-cs.2530] [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: 07/04/2024] [Accepted: 10/28/2024] [Indexed: 02/04/2025]
Abstract
Background Artificial Intelligence (AI) is significantly transforming dermatology, particularly in early skin cancer detection and diagnosis. This technological advancement addresses a crucial public health issue by enhancing diagnostic accuracy, efficiency, and accessibility. AI integration in medical imaging and diagnostic procedures offers promising solutions to the limitations of traditional methods, which often rely on subjective clinical evaluations and histopathological analyses. This study systematically reviews current AI applications in skin cancer classification, providing a comprehensive overview of their advantages, challenges, methodologies, and functionalities. Methodology In this study, we conducted a comprehensive analysis of artificial intelligence (AI) applications in the classification of skin cancer. We evaluated publications from three prominent journal databases: Scopus, IEEE, and MDPI. We conducted a thorough selection process using the PRISMA guidelines, collecting 1,156 scientific articles. Our methodology included evaluating the titles and abstracts and thoroughly examining the full text to determine their relevance and quality. Consequently, we included a total of 95 publications in the final study. We analyzed and categorized the articles based on four key dimensions: advantages, difficulties, methodologies, and functionalities. Results AI-based models exhibit remarkable performance in skin cancer detection by leveraging advanced deep learning algorithms, image processing techniques, and feature extraction methods. The advantages of AI integration include significantly improved diagnostic accuracy, faster turnaround times, and increased accessibility to dermatological expertise, particularly benefiting underserved areas. However, several challenges remain, such as concerns over data privacy, complexities in integrating AI systems into existing workflows, and the need for large, high-quality datasets. AI-based methods for skin cancer detection, including CNNs, SVMs, and ensemble learning techniques, aim to improve lesion classification accuracy and increase early detection. AI systems enhance healthcare by enabling remote consultations, continuous patient monitoring, and supporting clinical decision-making, leading to more efficient care and better patient outcomes. Conclusions This comprehensive review highlights the transformative potential of AI in dermatology, particularly in skin cancer detection and diagnosis. While AI technologies have significantly improved diagnostic accuracy, efficiency, and accessibility, several challenges remain. Future research should focus on ensuring data privacy, developing robust AI systems that can generalize across diverse populations, and creating large, high-quality datasets. Integrating AI tools into clinical workflows is critical to maximizing their utility and effectiveness. Continuous innovation and interdisciplinary collaboration will be essential for fully realizing the benefits of AI in skin cancer detection and diagnosis.
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Affiliation(s)
- Kavita Behara
- Department of Electrical Engineering, Mangosuthu University of Technology, Durban, Kwazulu- Natal, South Africa
| | - Ernest Bhero
- Discipline of Computer Engineering, University of KwaZulu Natal, Durban, KwaZulu-Natal, South Africa
| | - John Terhile Agee
- Discipline of Computer Engineering, University of KwaZulu Natal, Durban, KwaZulu-Natal, South Africa
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Gagna CE, Yodice AN, D'Amico J, Elkoulily L, Gill SM, DeOcampo FG, Rabbani M, Kaur J, Shah A, Ahmad Z, Lambert MW, Clark Lambert W. Novel B-DNA dermatophyte assay for demonstration of canonical DNA in dermatophytes: Histopathologic characterization by artificial intelligence. Clin Dermatol 2024; 42:233-258. [PMID: 38185195 DOI: 10.1016/j.clindermatol.2023.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
We describe a novel assay and artificial intelligence-driven histopathologic approach identifying dermatophytes in human skin tissue sections (ie, B-DNA dermatophyte assay) and demonstrate, for the first time, the presence of dermatophytes in tissue using immunohistochemistry to detect canonical right-handed double-stranded (ds) B-DNA. Immunohistochemistry was performed using anti-ds-B-DNA monoclonal antibodies with formalin-fixed paraffin-embedded tissues to determine the presence of dermatophytes. The B-DNA assay resulted in a more accurate identification of dermatophytes, nuclear morphology, dimensions, and gene expression of dermatophytes (ie, optical density values) than periodic acid-Schiff (PAS), Grocott methenamine silver (GMS), or hematoxylin and eosin (H&E) stains. The novel assay guided by artificial intelligence allowed for efficient identification of different types of dermatophytes (eg, hyphae, microconidia, macroconidia, and arthroconidia). Using the B-DNA dermatophyte assay as a clinical tool for diagnosing dermatophytes is an alternative to PAS, GMS, and H&E as a fast and inexpensive way to accurately detect dermatophytosis and reduce the number of false negatives. Our assay resulted in superior identification, sensitivity, life cycle stages, and morphology compared to H&E, PAS, and GMS stains. This method detects a specific structural marker (ie, ds-B-DNA), which can assist with diagnosis of dermatophytes. It represents a significant advantage over methods currently in use.
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Affiliation(s)
- Claude E Gagna
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA; Department of Pathology and Laboratory Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, USA; Department of Dermatology, Rutgers-New Jersey Medical School, Newark, New Jersey, USA; Department of Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, USA.
| | - Anthony N Yodice
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Juliana D'Amico
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Lina Elkoulily
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Shaheryar M Gill
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Francis G DeOcampo
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Maryam Rabbani
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Jai Kaur
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Aangi Shah
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Zainab Ahmad
- Department of Biological and Chemical Sciences, College of Arts and Sciences, New York Institute of Technology, Old Westbury, New York, USA
| | - Muriel W Lambert
- Department of Pathology and Laboratory Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, USA; Department of Dermatology, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
| | - W Clark Lambert
- Department of Pathology and Laboratory Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, USA; Department of Dermatology, Rutgers-New Jersey Medical School, Newark, New Jersey, USA; Department of Medicine, Rutgers-New Jersey Medical School, Newark, New Jersey, USA
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3
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Eliwa EHI, El Koshiry AM, Abd El-Hafeez T, Farghaly HM. Utilizing convolutional neural networks to classify monkeypox skin lesions. Sci Rep 2023; 13:14495. [PMID: 37661211 PMCID: PMC10475460 DOI: 10.1038/s41598-023-41545-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023] Open
Abstract
Monkeypox is a rare viral disease that can cause severe illness in humans, presenting with skin lesions and rashes. However, accurately diagnosing monkeypox based on visual inspection of the lesions can be challenging and time-consuming, especially in resource-limited settings where laboratory tests may not be available. In recent years, deep learning methods, particularly Convolutional Neural Networks (CNNs), have shown great potential in image recognition and classification tasks. To this end, this study proposes an approach using CNNs to classify monkeypox skin lesions. Additionally, the study optimized the CNN model using the Grey Wolf Optimizer (GWO) algorithm, resulting in a significant improvement in accuracy, precision, recall, F1-score, and AUC compared to the non-optimized model. The GWO optimization strategy can enhance the performance of CNN models on similar tasks. The optimized model achieved an impressive accuracy of 95.3%, indicating that the GWO optimizer has improved the model's ability to discriminate between positive and negative classes. The proposed approach has several potential benefits for improving the accuracy and efficiency of monkeypox diagnosis and surveillance. It could enable faster and more accurate diagnosis of monkeypox skin lesions, leading to earlier detection and better patient outcomes. Furthermore, the approach could have crucial public health implications for controlling and preventing monkeypox outbreaks. Overall, this study offers a novel and highly effective approach for diagnosing monkeypox, which could have significant real-world applications.
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Affiliation(s)
- Entesar Hamed I Eliwa
- Department of Mathematics and Statistics, College of Science, King Faisal University, P.O. Box: 400, 31982, Al-Ahsa, Saudi Arabia.
- Department of Computer Science, Faculty of Science, Minia University, Minya, Egypt.
| | - Amr Mohamed El Koshiry
- Department of Curricula and Teaching Methods, College of Education, King Faisal University, P.O. Box: 400, 31982, Al-Ahsa, Saudi Arabia.
- Faculty of Specific Education, Minia University, Minya, Egypt.
| | - Tarek Abd El-Hafeez
- Department of Computer Science, Faculty of Science, Minia University, Minya, Egypt.
- Computer Science Unit, Deraya University, New Minya, Egypt.
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Alharbi AH, Towfek SK, Abdelhamid AA, Ibrahim A, Eid MM, Khafaga DS, Khodadadi N, Abualigah L, Saber M. Diagnosis of Monkeypox Disease Using Transfer Learning and Binary Advanced Dipper Throated Optimization Algorithm. Biomimetics (Basel) 2023; 8:313. [PMID: 37504202 PMCID: PMC10807651 DOI: 10.3390/biomimetics8030313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/03/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
The virus that causes monkeypox has been observed in Africa for several years, and it has been linked to the development of skin lesions. Public panic and anxiety have resulted from the deadly repercussions of virus infections following the COVID-19 pandemic. Rapid detection approaches are crucial since COVID-19 has reached a pandemic level. This study's overarching goal is to use metaheuristic optimization to boost the performance of feature selection and classification methods to identify skin lesions as indicators of monkeypox in the event of a pandemic. Deep learning and transfer learning approaches are used to extract the necessary features. The GoogLeNet network is the deep learning framework used for feature extraction. In addition, a binary implementation of the dipper throated optimization (DTO) algorithm is used for feature selection. The decision tree classifier is then used to label the selected set of features. The decision tree classifier is optimized using the continuous version of the DTO algorithm to improve the classification accuracy. Various evaluation methods are used to compare and contrast the proposed approach and the other competing methods using the following metrics: accuracy, sensitivity, specificity, p-Value, N-Value, and F1-score. Through feature selection and a decision tree classifier, the following results are achieved using the proposed approach; F1-score of 0.92, sensitivity of 0.95, specificity of 0.61, p-Value of 0.89, and N-Value of 0.79. The overall accuracy of the proposed methodology after optimizing the parameters of the decision tree classifier is 94.35%. Furthermore, the analysis of variation (ANOVA) and Wilcoxon signed rank test have been applied to the results to investigate the statistical distinction between the proposed methodology and the alternatives. This comparison verified the uniqueness and importance of the proposed approach to Monkeypox case detection.
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Affiliation(s)
- Amal H. Alharbi
- Department of Computer Sciences, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - S. K. Towfek
- Computer Science and Intelligent Systems Research Center, Blacksburg, VA 24060, USA
- Department of Communications and Electronics, Delta Higher Institute of Engineering and Technology, Mansoura 35111, Egypt
| | - Abdelaziz A. Abdelhamid
- Department of Computer Science, College of Computing and Information Technology, Shaqra University, Shaqra 11961, Saudi Arabia
- Department of Computer Science, Faculty of Computer and Information Sciences, Ain Shams University, Cairo 11566, Egypt
| | - Abdelhameed Ibrahim
- Computer Engineering and Control Systems Department, Faculty of Engineering, Mansoura University, Mansoura 35516, Egypt
| | - Marwa M. Eid
- Faculty of Artificial Intelligence, Delta University for Science and Technology, Mansoura P.O. Box 11152, Egypt
| | - Doaa Sami Khafaga
- Department of Computer Sciences, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Nima Khodadadi
- Department of Civil and Architectural Engineering, University of Miami, Coral Gables, FL 33146, USA
| | - Laith Abualigah
- Computer Science Department, Prince Hussein Bin Abdullah Faculty for Information Technology, Al al-Bayt University, Mafraq 25113, Jordan
- Department of Electrical and Computer Engineering, Lebanese American University, Byblos 13-5053, Lebanon
- Hourani Center for Applied Scientific Research, Al-Ahliyya Amman University, Amman 19328, Jordan
- MEU Research Unit, Middle East University, Amman 11831, Jordan
- Applied Science Research Center, Applied Science Private University, Amman 11931, Jordan
- School of Computer Sciences, Universiti Sains Malaysia, Gelugor 11800, Malaysia
- School of Engineering and Technology, Sunway University Malaysia, Petaling Jaya 27500, Malaysia
| | - Mohamed Saber
- Electronics and Communications Engineering Department, Faculty of Engineering, Delta University for Science and Technology, Mansoura P.O. Box 11152, Egypt
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Altun M, Gürüler H, Özkaraca O, Khan F, Khan J, Lee Y. Monkeypox Detection Using CNN with Transfer Learning. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23041783. [PMID: 36850381 PMCID: PMC9964526 DOI: 10.3390/s23041783] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 06/01/2023]
Abstract
Monkeypox disease is caused by a virus that causes lesions on the skin and has been observed on the African continent in the past years. The fatal consequences caused by virus infections after the COVID pandemic have caused fear and panic among the public. As a result of COVID reaching the pandemic dimension, the development and implementation of rapid detection methods have become important. In this context, our study aims to detect monkeypox disease in case of a possible pandemic through skin lesions with deep-learning methods in a fast and safe way. Deep-learning methods were supported with transfer learning tools and hyperparameter optimization was provided. In the CNN structure, a hybrid function learning model was developed by customizing the transfer learning model together with hyperparameters. Implemented on the custom model MobileNetV3-s, EfficientNetV2, ResNET50, Vgg19, DenseNet121, and Xception models. In our study, AUC, accuracy, recall, loss, and F1-score metrics were used for evaluation and comparison. The optimized hybrid MobileNetV3-s model achieved the best score, with an average F1-score of 0.98, AUC of 0.99, accuracy of 0.96, and recall of 0.97. In this study, convolutional neural networks were used in conjunction with optimization of hyperparameters and a customized hybrid function transfer learning model to achieve striking results when a custom CNN model was developed. The custom CNN model design we have proposed is proof of how successfully and quickly the deep learning methods can achieve results in classification and discrimination.
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Affiliation(s)
- Murat Altun
- Department of Information Systems Engineering, Faculty of Technology, Mugla Sitki Kocman University, Mugla 48000, Turkey
| | - Hüseyin Gürüler
- Department of Information Systems Engineering, Faculty of Technology, Mugla Sitki Kocman University, Mugla 48000, Turkey
| | - Osman Özkaraca
- Department of Information Systems Engineering, Faculty of Technology, Mugla Sitki Kocman University, Mugla 48000, Turkey
| | - Faheem Khan
- Department of Computer Engineering, Gachon University, Seongnam-si 13120, Republic of Korea
| | - Jawad Khan
- Department of Robotics, Hanyang University, Ansan 15588, Republic of Korea
| | - Youngmoon Lee
- Department of Robotics, Hanyang University, Ansan 15588, Republic of Korea
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Jalaboi R, Faye F, Orbes-Arteaga M, Jørgensen D, Winther O, Galimzianova A. DermX: An end-to-end framework for explainable automated dermatological diagnosis. Med Image Anal 2023; 83:102647. [PMID: 36272237 DOI: 10.1016/j.media.2022.102647] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 08/17/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Dermatological diagnosis automation is essential in addressing the high prevalence of skin diseases and critical shortage of dermatologists. Despite approaching expert-level diagnosis performance, convolutional neural network (ConvNet) adoption in clinical practice is impeded by their limited explainability, and by subjective, expensive explainability validations. We introduce DermX, an end-to-end framework for explainable automated dermatological diagnosis. DermX is a clinically-inspired explainable dermatological diagnosis ConvNet, trained using DermXDB, a 554 image dataset annotated by eight dermatologists with diagnoses, supporting explanations, and explanation attention maps. DermX+ extends DermX with guided attention training for explanation attention maps. Both methods achieve near-expert diagnosis performance, with DermX, DermX+, and dermatologist F1 scores of 0.79, 0.79, and 0.87, respectively. We assess the explanation performance in terms of identification and localization by comparing model-selected with dermatologist-selected explanations, and gradient-weighted class-activation maps with dermatologist explanation maps, respectively. DermX obtained an identification F1 score of 0.77, while DermX+ obtained 0.79. The localization F1 score is 0.39 for DermX and 0.35 for DermX+. These results show that explainability does not necessarily come at the expense of predictive power, as our high-performance models provide expert-inspired explanations for their diagnoses without lowering their diagnosis performance.
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Affiliation(s)
- Raluca Jalaboi
- Department of Applied Mathematics and Computer Science at the Technical University of Denmark, Richard Petersens Plads, Building 324, DK-2800 Kongens Lyngby, Denmark; Omhu A/S, Silkegade 8 st, DK-1113 Copenhagen C, Denmark.
| | - Frederik Faye
- Omhu A/S, Silkegade 8 st, DK-1113 Copenhagen C, Denmark
| | | | - Dan Jørgensen
- Omhu A/S, Silkegade 8 st, DK-1113 Copenhagen C, Denmark
| | - Ole Winther
- Department of Applied Mathematics and Computer Science at the Technical University of Denmark, Richard Petersens Plads, Building 324, DK-2800 Kongens Lyngby, Denmark; Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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7
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Can images crowdsourced from the internet be used to train generalizable joint dislocation deep learning algorithms? Skeletal Radiol 2022; 51:2121-2128. [PMID: 35624310 DOI: 10.1007/s00256-022-04077-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Deep learning has the potential to automatically triage orthopedic emergencies, such as joint dislocations. However, due to the rarity of these injuries, collecting large numbers of images to train algorithms may be infeasible for many centers. We evaluated if the Internet could be used as a source of images to train convolutional neural networks (CNNs) for joint dislocations that would generalize well to real-world clinical cases. METHODS We collected datasets from online radiology repositories of 100 radiographs each (50 dislocated, 50 located) for four joints: native shoulder, elbow, hip, and total hip arthroplasty (THA). We trained a variety of CNN binary classifiers using both on-the-fly and static data augmentation to identify the various joint dislocations. The best-performing classifier for each joint was evaluated on an external test set of 100 corresponding radiographs (50 dislocations) from three hospitals. CNN performance was evaluated using area under the ROC curve (AUROC). To determine areas emphasized by the CNN for decision-making, class activation map (CAM) heatmaps were generated for test images. RESULTS The best-performing CNNs for elbow, hip, shoulder, and THA dislocation achieved high AUROCs on both internal and external test sets (internal/external AUC): elbow (1.0/0.998), hip (0.993/0.880), shoulder (1.0/0.993), THA (1.0/0.950). Heatmaps demonstrated appropriate emphasis of joints for both located and dislocated joints. CONCLUSION With modest numbers of images, radiographs from the Internet can be used to train clinically-generalizable CNNs for joint dislocations. Given the rarity of joint dislocations at many centers, online repositories may be a viable source for CNN-training data.
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Paul W, Hadzic A, Joshi N, Alajaji F, Burlina P. TARA: Training and Representation Alteration for AI Fairness and Domain Generalization. Neural Comput 2022; 34:716-753. [PMID: 35016212 DOI: 10.1162/neco_a_01468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/08/2021] [Indexed: 11/04/2022]
Abstract
We propose a novel method for enforcing AI fairness with respect to protected or sensitive factors. This method uses a dual strategy performing training and representation alteration (TARA) for the mitigation of prominent causes of AI bias. It includes the use of representation learning alteration via adversarial independence to suppress the bias-inducing dependence of the data representation from protected factors and training set alteration via intelligent augmentation to address bias-causing data imbalance by using generative models that allow the fine control of sensitive factors related to underrepresented populations via domain adaptation and latent space manipulation. When testing our methods on image analytics, experiments demonstrate that TARA significantly or fully debiases baseline models while outperforming competing debiasing methods that have the same amount of information-for example, with (% overall accuracy, % accuracy gap) = (78.8, 0.5) versus the baseline method's score of (71.8, 10.5) for Eye-PACS, and (73.7, 11.8) versus (69.1, 21.7) for CelebA. Furthermore, recognizing certain limitations in current metrics used for assessing debiasing performance, we propose novel conjunctive debiasing metrics. Our experiments also demonstrate the ability of these novel metrics in assessing the Pareto efficiency of the proposed methods.
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Affiliation(s)
- William Paul
- Johns Hopkins University Applied Physics Laboratory Laurel, MD 20723, U.S.A.
| | - Armin Hadzic
- Johns Hopkins University Applied Physics Laboratory Laurel, MD 20723, U.S.A.
| | - Neil Joshi
- Johns Hopkins University Applied Physics Laboratory Laurel, MD 20723, U.S.A.
| | - Fady Alajaji
- Department of Mathematics and Statistics, Queens University, ON K7L 3N6, Canada
| | - Philippe Burlina
- Johns Hopkins University Applied Physics Laboratory Laurel, MD 20723, U.S.A., and Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, U.S.A.
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Justen L, Carlsmith D, Paskewitz SM, Bartholomay LC, Bron GM. Identification of public submitted tick images: A neural network approach. PLoS One 2021; 16:e0260622. [PMID: 34855822 PMCID: PMC8638930 DOI: 10.1371/journal.pone.0260622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 11/13/2021] [Indexed: 11/19/2022] Open
Abstract
Ticks and tick-borne diseases represent a growing public health threat in North America and Europe. The number of ticks, their geographical distribution, and the incidence of tick-borne diseases, like Lyme disease, are all on the rise. Accurate, real-time tick-image identification through a smartphone app or similar platform could help mitigate this threat by informing users of the risks associated with encountered ticks and by providing researchers and public health agencies with additional data on tick activity and geographic range. Here we outline the requirements for such a system, present a model that meets those requirements, and discuss remaining challenges and frontiers in automated tick identification. We compiled a user-generated dataset of more than 12,000 images of the three most common tick species found on humans in the U.S.: Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis. We used image augmentation to further increase the size of our dataset to more than 90,000 images. Here we report the development and validation of a convolutional neural network which we call "TickIDNet," that scores an 87.8% identification accuracy across all three species, outperforming the accuracy of identifications done by a member of the general public or healthcare professionals. However, the model fails to match the performance of experts with formal entomological training. We find that image quality, particularly the size of the tick in the image (measured in pixels), plays a significant role in the network's ability to correctly identify an image: images where the tick is small are less likely to be correctly identified because of the small object detection problem in deep learning. TickIDNet's performance can be increased by using confidence thresholds to introduce an "unsure" class and building image submission pipelines that encourage better quality photos. Our findings suggest that deep learning represents a promising frontier for tick identification that should be further explored and deployed as part of the toolkit for addressing the public health consequences of tick-borne diseases.
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Affiliation(s)
- Lennart Justen
- Department of Physics, College of Liberal Arts and Sciences, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Duncan Carlsmith
- Department of Physics, College of Liberal Arts and Sciences, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Susan M. Paskewitz
- Department of Entomology, College of Agricultural and Life Sciences, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Lyric C. Bartholomay
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin—Madison, Madison, WI, United States of America
| | - Gebbiena M. Bron
- Department of Entomology, College of Agricultural and Life Sciences, University of Wisconsin—Madison, Madison, WI, United States of America
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Daneshjou R, Smith MP, Sun MD, Rotemberg V, Zou J. Lack of Transparency and Potential Bias in Artificial Intelligence Data Sets and Algorithms: A Scoping Review. JAMA Dermatol 2021; 157:1362-1369. [PMID: 34550305 PMCID: PMC9379852 DOI: 10.1001/jamadermatol.2021.3129] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Clinical artificial intelligence (AI) algorithms have the potential to improve clinical care, but fair, generalizable algorithms depend on the clinical data on which they are trained and tested. OBJECTIVE To assess whether data sets used for training diagnostic AI algorithms addressing skin disease are adequately described and to identify potential sources of bias in these data sets. DATA SOURCES In this scoping review, PubMed was used to search for peer-reviewed research articles published between January 1, 2015, and November 1, 2020, with the following paired search terms: deep learning and dermatology, artificial intelligence and dermatology, deep learning and dermatologist, and artificial intelligence and dermatologist. STUDY SELECTION Studies that developed or tested an existing deep learning algorithm for triage, diagnosis, or monitoring using clinical or dermoscopic images of skin disease were selected, and the articles were independently reviewed by 2 investigators to verify that they met selection criteria. CONSENSUS PROCESS Data set audit criteria were determined by consensus of all authors after reviewing existing literature to highlight data set transparency and sources of bias. RESULTS A total of 70 unique studies were included. Among these studies, 1 065 291 images were used to develop or test AI algorithms, of which only 257 372 (24.2%) were publicly available. Only 14 studies (20.0%) included descriptions of patient ethnicity or race in at least 1 data set used. Only 7 studies (10.0%) included any information about skin tone in at least 1 data set used. Thirty-six of the 56 studies developing new AI algorithms for cutaneous malignant neoplasms (64.3%) met the gold standard criteria for disease labeling. Public data sets were cited more often than private data sets, suggesting that public data sets contribute more to new development and benchmarks. CONCLUSIONS AND RELEVANCE This scoping review identified 3 issues in data sets that are used to develop and test clinical AI algorithms for skin disease that should be addressed before clinical translation: (1) sparsity of data set characterization and lack of transparency, (2) nonstandard and unverified disease labels, and (3) inability to fully assess patient diversity used for algorithm development and testing.
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Affiliation(s)
- Roxana Daneshjou
- Stanford Department of Dermatology, Stanford School of Medicine, Redwood City, California
- Stanford Department of Biomedical Data Science, Stanford School of Medicine, Stanford, California
| | - Mary P Smith
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mary D Sun
- currently a medical student at Icahn School of Medicine at Mount Sinai, New York, New York
| | - Veronica Rotemberg
- Dermatology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James Zou
- Department of Electrical Engineering, Stanford University, Stanford, California
- Department of Biomedical Data Science, Stanford University, Stanford, California
- Chan Zuckerberg Biohub, San Francisco, California
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Bobe JR, Jutras BL, Horn EJ, Embers ME, Bailey A, Moritz RL, Zhang Y, Soloski MJ, Ostfeld RS, Marconi RT, Aucott J, Ma'ayan A, Keesing F, Lewis K, Ben Mamoun C, Rebman AW, McClune ME, Breitschwerdt EB, Reddy PJ, Maggi R, Yang F, Nemser B, Ozcan A, Garner O, Di Carlo D, Ballard Z, Joung HA, Garcia-Romeu A, Griffiths RR, Baumgarth N, Fallon BA. Recent Progress in Lyme Disease and Remaining Challenges. Front Med (Lausanne) 2021; 8:666554. [PMID: 34485323 PMCID: PMC8416313 DOI: 10.3389/fmed.2021.666554] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Lyme disease (also known as Lyme borreliosis) is the most common vector-borne disease in the United States with an estimated 476,000 cases per year. While historically, the long-term impact of Lyme disease on patients has been controversial, mounting evidence supports the idea that a substantial number of patients experience persistent symptoms following treatment. The research community has largely lacked the necessary funding to properly advance the scientific and clinical understanding of the disease, or to develop and evaluate innovative approaches for prevention, diagnosis, and treatment. Given the many outstanding questions raised into the diagnosis, clinical presentation and treatment of Lyme disease, and the underlying molecular mechanisms that trigger persistent disease, there is an urgent need for more support. This review article summarizes progress over the past 5 years in our understanding of Lyme and tick-borne diseases in the United States and highlights remaining challenges.
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Affiliation(s)
- Jason R. Bobe
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Brandon L. Jutras
- Department of Biochemistry, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, United States
| | | | - Monica E. Embers
- Tulane University Health Sciences, New Orleans, LA, United States
| | - Allison Bailey
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mark J. Soloski
- Division of Rheumatology, Department of Medicine, Lyme Disease Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | | | - Richard T. Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, Richmond, VA, United States
| | - John Aucott
- Division of Rheumatology, Department of Medicine, Lyme Disease Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Avi Ma'ayan
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Kim Lewis
- Department of Biology, Northeastern University, Boston, MA, United States
| | | | - Alison W. Rebman
- Division of Rheumatology, Department of Medicine, Lyme Disease Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Mecaila E. McClune
- Department of Biochemistry, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, United States
| | - Edward B. Breitschwerdt
- Department of Clinical Sciences, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | | | - Ricardo Maggi
- Department of Clinical Sciences, Comparative Medicine Institute, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Bennett Nemser
- Steven & Alexandra Cohen Foundation, Stamford, CT, United States
| | - Aydogan Ozcan
- University of California, Los Angeles, Los Angeles, CA, United States
| | - Omai Garner
- University of California, Los Angeles, Los Angeles, CA, United States
| | - Dino Di Carlo
- University of California, Los Angeles, Los Angeles, CA, United States
| | - Zachary Ballard
- University of California, Los Angeles, Los Angeles, CA, United States
| | - Hyou-Arm Joung
- University of California, Los Angeles, Los Angeles, CA, United States
| | - Albert Garcia-Romeu
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Roland R. Griffiths
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Nicole Baumgarth
- Center for Immunology and Infectious Diseases and the Department of Pathology, Microbiology & Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Brian A. Fallon
- Columbia University Irving Medical Center, New York, NY, United States
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12
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Kassem MA, Hosny KM, Damaševičius R, Eltoukhy MM. Machine Learning and Deep Learning Methods for Skin Lesion Classification and Diagnosis: A Systematic Review. Diagnostics (Basel) 2021; 11:1390. [PMID: 34441324 PMCID: PMC8391467 DOI: 10.3390/diagnostics11081390] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 12/04/2022] Open
Abstract
Computer-aided systems for skin lesion diagnosis is a growing area of research. Recently, researchers have shown an increasing interest in developing computer-aided diagnosis systems. This paper aims to review, synthesize and evaluate the quality of evidence for the diagnostic accuracy of computer-aided systems. This study discusses the papers published in the last five years in ScienceDirect, IEEE, and SpringerLink databases. It includes 53 articles using traditional machine learning methods and 49 articles using deep learning methods. The studies are compared based on their contributions, the methods used and the achieved results. The work identified the main challenges of evaluating skin lesion segmentation and classification methods such as small datasets, ad hoc image selection and racial bias.
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Affiliation(s)
- Mohamed A. Kassem
- Department of Robotics and Intelligent Machines, Faculty of Artificial Intelligence, Kaferelshiekh University, Kaferelshiekh 33511, Egypt;
| | - Khalid M. Hosny
- Department of Information Technology, Faculty of Computers and Informatics, Zagazig University, Zagazig 44519, Egypt
| | - Robertas Damaševičius
- Department of Applied Informatics, Vytautas Magnus University, 44404 Kaunas, Lithuania
| | - Mohamed Meselhy Eltoukhy
- Computer Science Department, Faculty of Computers and Informatics, Suez Canal University, Ismailia 41522, Egypt;
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13
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Turki T, Taguchi YH. Discriminating the single-cell gene regulatory networks of human pancreatic islets: A novel deep learning application. Comput Biol Med 2021; 132:104257. [PMID: 33740535 DOI: 10.1016/j.compbiomed.2021.104257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/24/2022]
Abstract
Analysis of single-cell pancreatic data can play an important role in understanding various metabolic diseases and health conditions. Due to the sparsity and noise present in such single-cell gene expression data, inference of single-cell gene regulatory networks remains a challenge. Since recent studies have reported the reliable inference of single-cell gene regulatory networks (SCGRNs), the current study focused on discriminating the SCGRNs of T2D patients from those of healthy controls. By accurately distinguishing SCGRNs of healthy pancreas from those of T2D pancreas, it would be possible to annotate, organize, visualize, and identify common patterns of SCGRNs in metabolic diseases. Such annotated SCGRNs could play an important role in accelerating the process of building large data repositories. This study aimed to contribute to the development of a novel deep learning (DL) application. First, we generated a dataset consisting of 224 SCGRNs belonging to both T2D and healthy pancreas and made it freely available. Next, we chose seven DL architectures, including VGG16, VGG19, Xception, ResNet50, ResNet101, DenseNet121, and DenseNet169, trained each of them on the dataset, and checked their prediction based on a test set. Of note, we evaluated the DL architectures on a single NVIDIA GeForce RTX 2080Ti GPU. Experimental results on the whole dataset, using several performance measures, demonstrated the superiority of VGG19 DL model in the automatic classification of SCGRNs, derived from the single-cell pancreatic data.
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Affiliation(s)
- Turki Turki
- Department of Computer Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Y-H Taguchi
- Department of Physics, Chuo University, Tokyo, 112-8551, Japan.
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14
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Lantos PM, Rumbaugh J, Bockenstedt LK, Falck-Ytter YT, Aguero-Rosenfeld ME, Auwaerter PG, Baldwin K, Bannuru RR, Belani KK, Bowie WR, Branda JA, Clifford DB, DiMario FJ, Halperin JJ, Krause PJ, Lavergne V, Liang MH, Meissner HC, Nigrovic LE, Nocton JJJ, Osani MC, Pruitt AA, Rips J, Rosenfeld LE, Savoy ML, Sood SK, Steere AC, Strle F, Sundel R, Tsao J, Vaysbrot EE, Wormser GP, Zemel LS. Clinical Practice Guidelines by the Infectious Diseases Society of America (IDSA), American Academy of Neurology (AAN), and American College of Rheumatology (ACR): 2020 Guidelines for the Prevention, Diagnosis and Treatment of Lyme Disease. Clin Infect Dis 2021; 72:e1-e48. [PMID: 33417672 DOI: 10.1093/cid/ciaa1215] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
This evidence-based clinical practice guideline for the prevention, diagnosis, and treatment of Lyme disease was developed by a multidisciplinary panel representing the Infectious Diseases Society of America (IDSA), the American Academy of Neurology (AAN), and the American College of Rheumatology (ACR). The scope of this guideline includes prevention of Lyme disease, and the diagnosis and treatment of Lyme disease presenting as erythema migrans, Lyme disease complicated by neurologic, cardiac, and rheumatologic manifestations, Eurasian manifestations of Lyme disease, and Lyme disease complicated by coinfection with other tick-borne pathogens. This guideline does not include comprehensive recommendations for babesiosis and tick-borne rickettsial infections, which are published in separate guidelines. The target audience for this guideline includes primary care physicians and specialists caring for this condition such as infectious diseases specialists, emergency physicians, internists, pediatricians, family physicians, neurologists, rheumatologists, cardiologists and dermatologists in North America.
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Affiliation(s)
- Paul M Lantos
- Duke University School of Medicine, Durham, North Carolina, USA
| | | | | | - Yngve T Falck-Ytter
- Case Western Reserve University, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | | | - Paul G Auwaerter
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kelly Baldwin
- Geisinger Medical Center, Danville, Pennsylvania, USA
| | | | - Kiran K Belani
- Childrens Hospital and Clinical of Minnesota, Minneapolis, Minnesota, USA
| | - William R Bowie
- University of British Columbia, Vancouver, British Columbia, Canada
| | - John A Branda
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David B Clifford
- Washington University School of Medicine, St. Louis, Missouri, USA
| | | | | | - Peter J Krause
- Yale School of Public Health, New Haven, Connecticut, USA
| | | | | | | | | | | | | | - Amy A Pruitt
- University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jane Rips
- Consumer Representative, Omaha, Nebraska, USA
| | | | | | | | - Allen C Steere
- Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Franc Strle
- University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Robert Sundel
- Boston Children's Hospital Boston, Massachusetts, USA
| | - Jean Tsao
- Michigan State University, East Lansing, Michigan, USA
| | | | | | - Lawrence S Zemel
- Connecticut Children's Medical Center, Hartford, Connecticut, USA
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15
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Cohen AB, Nahed BV. The Digital Neurologic Examination. Digit Biomark 2021; 5:114-126. [PMID: 34056521 DOI: 10.1159/000515577] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/01/2021] [Indexed: 11/19/2022] Open
Abstract
Digital health has been rapidly thrust into the forefront of care delivery. Poised to extend the clinician's reach, a new set of examination tools will redefine neurologic and neurosurgical care, serving as the basis for the digital neurologic examination. We describe its components and review specific technologies, which move beyond traditional video-based telemedicine encounters and include separate digital tools. A future suite of these clinical assessment technologies will blur the lines between history taking, examination, and remote monitoring. Prior to full-scale implementation, however, much more investigation is needed. Because of the nascent state of the technologies, researchers, clinicians, and developers should establish digital neurologic examination requirements in order to maximize its impact.
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Affiliation(s)
- Adam B Cohen
- Department of Neurology, The Johns Hopkins Hospital, Baltimore, Maryland, USA.,Health Technologies, Army Medical Response, National Health Mission Area, The Johns Hopkins University Applied Physics Lab, Laurel, Maryland, USA
| | - Brain V Nahed
- Department of Neurosurgery, The Massachusetts General Hospital, Boston, Massachusetts, USA
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16
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Novak CB, Scheeler VM, Aucott JN. Lyme Disease in the Era of COVID-19: A Delayed Diagnosis and Risk for Complications. Case Rep Infect Dis 2021; 2021:6699536. [PMID: 33628543 PMCID: PMC7883710 DOI: 10.1155/2021/6699536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/19/2021] [Accepted: 02/04/2021] [Indexed: 11/18/2022] Open
Abstract
We describe a patient with fever and myalgia who did not have COVID-19 but instead had Lyme disease. We propose that the co-occurrence of COVID-19 and Lyme disease during the spring of 2020 resulted in a delayed diagnosis of Lyme disease due to COVID-19 pandemic-related changes in healthcare workflow and diagnostic reasoning. This delayed diagnosis of Lyme disease in the patient we describe resulted in disseminated infection and sixth nerve palsy. We present the use of telemedicine to aid in the diagnosis of Lyme disease and to provide prompt access to diagnosis and care during the ongoing COVID-19 pandemic and in the future.
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Affiliation(s)
- Cheryl B. Novak
- Lyme Disease Research Center, Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Verna M. Scheeler
- Lyme Disease Research Center, Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John N. Aucott
- Lyme Disease Research Center, Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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17
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Zahia S, Garcia-Zapirain B, Saralegui I, Fernandez-Ruanova B. Dyslexia detection using 3D convolutional neural networks and functional magnetic resonance imaging. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 197:105726. [PMID: 32916543 DOI: 10.1016/j.cmpb.2020.105726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND OBJECTIVES Dyslexia is a disorder of neurological origin which affects the learning of those who suffer from it, mainly children, and causes difficulty in reading and writing. When undiagnosed, dyslexia leads to intimidation and frustration of the affected children and also of their family circles. In case no early intervention is given, children may reach high school with serious achievement gaps. Hence, early detection and intervention services for dyslexic students are highly important and recommended in order to support children in developing a positive self-esteem and reaching their maximum academic capacities. This paper presents a new approach for automatic recognition of children with dyslexia using functional magnetic resonance Imaging. METHODS Our proposed system is composed of a sequence of preprocessing steps to retrieve the brain activation areas during three different reading tasks. Conversion to Nifti volumes, adjustment of head motion, normalization and smoothing transformations were performed on the fMRI scans in order to bring all the subject brains into one single model which will enable voxels comparison between each subject. Subsequently, using Statistical Parametric Maps (SPMs), a total of 165 3D volumes containing brain activation of 55 children were created. The classification of these volumes was handled using three parallel 3D Convolutional Neural Network (3D CNN), each corresponding to a brain activation during one reading task, and concatenated in the last two dense layers, forming a single architecture devoted to performing optimized detection of dyslexic brain activation. Additionally, we used 4-fold cross validation method in order to assess the generalizability of our model and control overfitting. RESULTS Our approach has achieved an overall average classification accuracy of 72.73%, sensitivity of 75%, specificity of 71.43%, precision of 60% and an F1-score of 67% in dyslexia detection. CONCLUSIONS The proposed system has demonstrated that the recognition of dyslexic children is feasible using deep learning and functional magnetic resonance Imaging when performing phonological and orthographic reading tasks.
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Affiliation(s)
- Sofia Zahia
- eVida research laboratory, University of Deusto, Bilbao 48007, Spain.
| | | | - Ibone Saralegui
- Department of Neuroradiology, Osatek, Biocruces-Bizkaia; Galdakao-Usansolo Hospital / Osakidetza, Galdakao 48960, Spain
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18
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Fu J, Li W, Du J, Xiao B. Multimodal medical image fusion via laplacian pyramid and convolutional neural network reconstruction with local gradient energy strategy. Comput Biol Med 2020; 126:104048. [PMID: 33068809 DOI: 10.1016/j.compbiomed.2020.104048] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND In recent years, numerous fusion algorithms have been proposed for multimodal medical images. The Laplacian pyramid is one type of multiscale fusion method. Although the pyramid-based fusion algorithm can fuse images well, it has the disadvantages of edge degradation, detail loss and image smoothing as the number of decomposition layers increase, which is harmful for medical diagnosis and analysis. METHOD This paper proposes a medical image fusion algorithm based on the Laplacian pyramid and convolutional neural network reconstruction with local gradient energy strategy, which can greatly improve the edge quality. First, multimodal medical images are reconstructed through convolutional neural network. Then, the Laplacian pyramid is applied in the decomposition and fusion process. The optimal number of decomposition layers is determined by experiments. In addition, a local gradient energy fusion strategy is utilized to fuse the coefficients in each layer. Finally, the fused image is output through Laplacian inverse transformation. RESULTS Compared with existing algorithms, our fusion results represent better vision quality performance. Furthermore, our algorithm is considerably superior to the compared algorithms in objective indicators. In addition, in our fusion results of Alzheimer and Glioma, the disease details are much clearer than those of compared algorithms, which can provide a reliable basis for doctors to analyze disease and make pathological diagnoses.
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Affiliation(s)
- Jun Fu
- Chongqing Key Laboratory of Image Cognition, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Weisheng Li
- Chongqing Key Laboratory of Image Cognition, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
| | - Jiao Du
- School of Computer Science and Educational Software, Guangzhou University, Guangzhou, 510006, China
| | - Bin Xiao
- Chongqing Key Laboratory of Image Cognition, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
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19
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Burlina PM, Joshi NJ, Mathew PA, Paul W, Rebman AW, Aucott JN. AI-based detection of erythema migrans and disambiguation against other skin lesions. Comput Biol Med 2020; 125:103977. [DOI: 10.1016/j.compbiomed.2020.103977] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 12/28/2022]
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20
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Yi PH, Kim TK, Wei J, Li X, Hager GD, Sair HI, Fritz J. Automated detection and classification of shoulder arthroplasty models using deep learning. Skeletal Radiol 2020; 49:1623-1632. [PMID: 32415371 DOI: 10.1007/s00256-020-03463-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To develop and evaluate the performance of deep convolutional neural networks (DCNN) to detect and identify specific total shoulder arthroplasty (TSA) models. MATERIALS AND METHODS We included 482 radiography studies obtained from publicly available image repositories with native shoulders, reverse TSA (RTSA) implants, and five different TSA models. We trained separate ResNet DCNN-based binary classifiers to (1) detect the presence of shoulder arthroplasty implants, (2) differentiate between TSA and RTSA, and (3) differentiate between the five TSA models, using five individual classifiers for each model, respectively. Datasets were divided into training, validation, and test datasets. Training and validation datasets were 20-fold augmented. Test performances were assessed with area under the receiver-operating characteristic curves (AUC-ROC) analyses. Class activation mapping was used to identify distinguishing imaging features used for DCNN classification decisions. RESULTS The DCNN for the detection of the presence of shoulder arthroplasty implants achieved an AUC-ROC of 1.0, whereas the AUC-ROC for differentiation between TSA and RTSA was 0.97. Class activation map analysis demonstrated the emphasis on the characteristic arthroplasty components in decision-making. DCNNs trained to distinguish between the five TSA models achieved AUC-ROCs ranging from 0.86 for Stryker Solar to 1.0 for Zimmer Bigliani-Flatow with class activation map analysis demonstrating an emphasis on unique implant design features. CONCLUSION DCNNs can accurately identify the presence of and distinguish between TSA & RTSA, and classify five specific TSA models with high accuracy. The proof of concept of these DCNNs may set the foundation for an automated arthroplasty atlas for rapid and comprehensive model identification.
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Affiliation(s)
- Paul H Yi
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Radiology Artificial Intelligence Lab (RAIL), Malone Center for Engineering in Healthcare, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Tae Kyung Kim
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Radiology Artificial Intelligence Lab (RAIL), Malone Center for Engineering in Healthcare, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Jinchi Wei
- Radiology Artificial Intelligence Lab (RAIL), Malone Center for Engineering in Healthcare, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Xinning Li
- Department of Orthopaedic Surgery, Boston University School of Medicine, Boston, MA, USA
| | - Gregory D Hager
- Radiology Artificial Intelligence Lab (RAIL), Malone Center for Engineering in Healthcare, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Haris I Sair
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Radiology Artificial Intelligence Lab (RAIL), Malone Center for Engineering in Healthcare, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - Jan Fritz
- Department of Radiology, Division of Musculoskeletal Radiology, New York University Grossman School of Medicine, 660 1st Ave, 3rd Floor, Rm #313, New York, NY, 10016, USA.
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21
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Moon KA, Pollak J, Poulsen MN, Hirsch AG, DeWalle J, Heaney CD, Aucott JN, Schwartz BS. Peridomestic and community-wide landscape risk factors for Lyme disease across a range of community contexts in Pennsylvania. ENVIRONMENTAL RESEARCH 2019; 178:108649. [PMID: 31465993 DOI: 10.1016/j.envres.2019.108649] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/11/2019] [Accepted: 08/12/2019] [Indexed: 06/10/2023]
Abstract
Land use and forest fragmentation are thought to be major drivers of Lyme disease incidence and its geographic distribution. We examined the association between landscape composition and configuration and Lyme disease in a population-based case control study in the Geisinger health system in Pennsylvania. Lyme disease cases (n = 9657) were identified using a combination of diagnosis codes, laboratory codes, and antibiotic orders from electronic health records (EHRs). Controls (5:1) were randomly selected and frequency matched on year, age, and sex. We measured six landscape variables based on prior literature, derived from the National Land Cover Database and MODIS satellite imagery: greenness (normalized difference vegetation index), percent forest, percent herbaceous, forest edge density, percent forest-herbaceous edge, and mean forest patch size. We assigned landscape variables within two spatial contexts (community and ½-mile [805 m] Euclidian residential buffer). In models stratified by community type, landscape variables were modeled as tertiles and flexible splines and associations were adjusted for demographic and clinical covariates. In general, we observed positive associations between landscape metrics and Lyme disease, except for percent herbaceous, where associations differed by community type. For example, compared to the lowest tertile, individuals with highest tertile of greenness in residential buffers had higher odds of Lyme disease (odds ratio: 95% confidence interval [CI]) in townships (1.73: 1.55, 1.93), boroughs (1.70: 1.40, 2.07), and cities (3.71: 1.74, 7.92). Similarly, corresponding odds ratios (95% CI) for forest edge density were 1.34 (1.22, 1.47), 1.56 (1.33, 1.82), and 1.90 (1.13, 3.18). Associations were generally higher in residential buffers, compared to community, and in cities, compared to boroughs or townships. Our results reinforce the importance of peridomestic landscape in Lyme disease risk, particularly measures that reflect human interaction with tick habitat. Linkage of EHR data to public data on residential and community context may lead to new health system-based approaches for improving Lyme disease diagnosis, treatment, and prevention.
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Affiliation(s)
- Katherine A Moon
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Jonathan Pollak
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Melissa N Poulsen
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology and Health Services Research, Geisinger, Danville, PA, USA.
| | - Annemarie G Hirsch
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology and Health Services Research, Geisinger, Danville, PA, USA.
| | - Joseph DeWalle
- Department of Epidemiology and Health Services Research, Geisinger, Danville, PA, USA.
| | - Christopher D Heaney
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - John N Aucott
- Johns Hopkins School of Medicine, Department of Medicine, Baltimore, MD, USA.
| | - Brian S Schwartz
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology and Health Services Research, Geisinger, Danville, PA, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Johns Hopkins School of Medicine, Department of Medicine, Baltimore, MD, USA.
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