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Williams DKA, Graifman G, Hussain N, Amiel M, Tran P, Reddy A, Haider A, Kavitesh BK, Li A, Alishahian L, Perera N, Efros C, Babu M, Tharakan M, Etienne M, Babu BA. Digital pathology, deep learning, and cancer: a narrative review. Transl Cancer Res 2024; 13:2544-2560. [PMID: 38881914 PMCID: PMC11170525 DOI: 10.21037/tcr-23-964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/24/2024] [Indexed: 06/18/2024]
Abstract
Background and Objective Cancer is a leading cause of morbidity and mortality worldwide. The emergence of digital pathology and deep learning technologies signifies a transformative era in healthcare. These technologies can enhance cancer detection, streamline operations, and bolster patient care. A substantial gap exists between the development phase of deep learning models in controlled laboratory environments and their translations into clinical practice. This narrative review evaluates the current landscape of deep learning and digital pathology, analyzing the factors influencing model development and implementation into clinical practice. Methods We searched multiple databases, including Web of Science, Arxiv, MedRxiv, BioRxiv, Embase, PubMed, DBLP, Google Scholar, IEEE Xplore, Semantic Scholar, and Cochrane, targeting articles on whole slide imaging and deep learning published from 2014 and 2023. Out of 776 articles identified based on inclusion criteria, we selected 36 papers for the analysis. Key Content and Findings Most articles in this review focus on the in-laboratory phase of deep learning model development, a critical stage in the deep learning lifecycle. Challenges arise during model development and their integration into clinical practice. Notably, lab performance metrics may not always match real-world clinical outcomes. As technology advances and regulations evolve, we expect more clinical trials to bridge this performance gap and validate deep learning models' effectiveness in clinical care. High clinical accuracy is vital for informed decision-making throughout a patient's cancer care. Conclusions Deep learning technology can enhance cancer detection, clinical workflows, and patient care. Challenges may arise during model development. The deep learning lifecycle involves data preprocessing, model development, and clinical implementation. Achieving health equity requires including diverse patient groups and eliminating bias during implementation. While model development is integral, most articles focus on the pre-deployment phase. Future longitudinal studies are crucial for validating models in real-world settings post-deployment. A collaborative approach among computational pathologists, technologists, industry, and healthcare providers is essential for driving adoption in clinical settings.
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Affiliation(s)
| | | | - Nowair Hussain
- Department of Internal Medicine, Overlook Medical Center, Summit, NJ, USA
| | | | | | - Arjun Reddy
- Applied Mathematics & Statistics Stony Brook University, Stony Brook, NY, USA
| | - Ali Haider
- Department of Artificial Intelligence, Yeshiva University, New York, NY, USA
| | - Bali Kumar Kavitesh
- Centre for Frontier AI Research (CFAR), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Austin Li
- New York Medical College, Valhalla, NY, USA
| | | | | | | | - Myoungmee Babu
- Artificial Intelligence and Mathematics, New York City Department of Education, New York, NY, USA
| | | | - Mill Etienne
- Department of Neurology, New York Medical College, Valhalla, NY, USA
| | - Benson A Babu
- New York Medical College, Valhalla, NY, USA
- Department of Hospital Medicine, Wyckoff, Medical Center, New York, NY, USA
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Shu W, Song Y, Lin Z, Yang M, Pan B, Su R, Yang M, Lu Z, Zheng S, Xu X, Yang Z, Wei X. Evaluation of liver regeneration after hemi-hepatectomy by combining computed tomography and post-operative liver function. Heliyon 2024; 10:e30964. [PMID: 38803961 PMCID: PMC11128876 DOI: 10.1016/j.heliyon.2024.e30964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024] Open
Abstract
Background Accurate evaluation of postoperative liver regeneration is essential to prevent postoperative liver failure. Aims To analyze the predictors that affect liver regeneration after hemi-hepatectomy. Method Patients who underwent hemi-hepatectomy in Hangzhou First People's Hospital and Hangzhou Shulan Hospital from January 2016 to December 2021 were enrolled in this study. The regeneration index (RI) was calculated by the following equation: RI = [(postoperative total liver volume {TLVpost} - future liver remnant volume {FLRV}/FLRV] × 100 %. Hepatic dysfunction was defined according to the "TBilpeak>7" standard, which was interpreted as (peak) total bilirubin (TBil) >7.0 mg/dL. Good liver regeneration was defined solely when the RI surpassed the median with hepatic dysfunction. Logistic regression analyses were performed to estimate prognostic factors affecting liver regeneration. Result A total of 153 patients were enrolled, with 33 in the benign group and 120 patients in the malignant group. In the entire study population, FLRV% [OR 4.087 (1.405-11.889), P = 0.010], international normalized ratio (INR) [OR 2.763 (95%CI, 1.008-7.577), P = 0.048] and TBil [OR 2.592 (95%CI, 1.177-5.710), P = 0.018] were independent prognostic factors associated with liver regeneration. In the benign group, only the computed tomography (CT) parameter FLRV% [OR, 11.700 (95%CI, 1.265-108.200), P = 0.030] predicted regeneration. In the malignant group, parenchymal hepatic resection rate (PHRR%) [OR 0.141 (95%CI, 0.040-0.499), P = 0.002] and TBil [OR 3.384 (95%CI, 1.377-8.319), P = 0.008] were independent prognostic factors. Conclusion FLRV%, PHRR%, TBil and INR were predictive factors associated with liver regeneration.
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Affiliation(s)
- Wenzhi Shu
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou, 310006, China
- Zhejiang University School of Medicine, Hangzhou, 310058, China
- Department of Hepatobiliary and Pancreatic Surgery, Hangzhou First People's Hospital, Hangzhou, 310006, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Yisu Song
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou, 310006, China
- Zhejiang University School of Medicine, Hangzhou, 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Zuyuan Lin
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou, 310006, China
- Zhejiang University School of Medicine, Hangzhou, 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Mengfan Yang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Binhua Pan
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou, 310006, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Renyi Su
- Zhejiang University School of Medicine, Hangzhou First People's Hospital, Hangzhou, 310006, China
- Zhejiang University School of Medicine, Hangzhou, 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Modan Yang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Zhengyang Lu
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Shusen Zheng
- Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, 310022, China
| | - Xiao Xu
- Zhejiang University School of Medicine, Hangzhou, 310058, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
| | - Zhe Yang
- Shulan (Hangzhou) Hospital, Zhejiang Shuren University School of Medicine, Hangzhou, 310022, China
| | - Xuyong Wei
- Department of Hepatobiliary and Pancreatic Surgery, Hangzhou First People's Hospital, Hangzhou, 310006, China
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou, 310006, China
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Li T, Li Y, Zhu X, He Y, Wu Y, Ying T, Xie Z. Artificial intelligence in cancer immunotherapy: Applications in neoantigen recognition, antibody design and immunotherapy response prediction. Semin Cancer Biol 2023; 91:50-69. [PMID: 36870459 DOI: 10.1016/j.semcancer.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Cancer immunotherapy is a method of controlling and eliminating tumors by reactivating the body's cancer-immunity cycle and restoring its antitumor immune response. The increased availability of data, combined with advancements in high-performance computing and innovative artificial intelligence (AI) technology, has resulted in a rise in the use of AI in oncology research. State-of-the-art AI models for functional classification and prediction in immunotherapy research are increasingly used to support laboratory-based experiments. This review offers a glimpse of the current AI applications in immunotherapy, including neoantigen recognition, antibody design, and prediction of immunotherapy response. Advancing in this direction will result in more robust predictive models for developing better targets, drugs, and treatments, and these advancements will eventually make their way into the clinical setting, pushing AI forward in the field of precision oncology.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yupeng Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyi Zhu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanling Wu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Tianlei Ying
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China.
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China; Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China.
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Manuel C, Zehnder P, Kaya S, Sullivan R, Hu F. Impact of color augmentation and tissue type in deep learning for hematoxylin and eosin image super resolution. J Pathol Inform 2022; 13:100148. [PMID: 36268062 PMCID: PMC9577134 DOI: 10.1016/j.jpi.2022.100148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/23/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
| | | | | | | | - Fangyao Hu
- Corresponding author at: Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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Deng Y, Feng M, Jiang Y, Zhou Y, Qin H, Xiang F, Wang Y, Bu H, Bao J. Development of pathological reconstructed high-resolution images using artificial intelligence based on whole slide image. MedComm (Beijing) 2021; 1:410-417. [PMID: 34766132 PMCID: PMC8491245 DOI: 10.1002/mco2.39] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/12/2020] [Accepted: 10/19/2020] [Indexed: 02/05/2023] Open
Abstract
Pathology plays a very important role in cancer diagnosis. The rapid development of digital pathology (DP) based on whole slide image (WSI) has led to many improvements in computer‐assisted diagnosis by artificial intelligence. The common digitization strategy is to scan the pathology slice with 20× or 40× objective, and the 40× objective requires excessive storage space and transmission time, which are significant negative factors in the popularization of DP. In this article, we present a novel reconstructed high‐resolution (HR) process based on deep learning to switch 20 × WSI to 40 × without the loss of whole and local features. Furthermore, we collected the WSI data of 100 uterine leiomyosarcomas and 100 adult granulosa cell tumors to test our reconstructed HR process. We tested the reconstructed HR WSI by the peak signal‐to‐noise ratio, structural similarity, and the blind/reject image spatial quality evaluator, which were 42.03, 0.99, and 49.22, respectively. Subsequently, we confirmed the consistency between the actual and our reconstructed HR images. The testing results indicate that the reconstructed HR imaging is a reliable method for the digital slides of a variety of tumors and can be available on a large scale in clinical pathology as an innovative technique.
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Affiliation(s)
- Yang Deng
- Laboratory of Pathology Key Laboratory of Transplant Engineering and Immunology NHC, West China Hospital Sichuan University Chengdu China
| | - Min Feng
- Laboratory of Pathology Key Laboratory of Transplant Engineering and Immunology NHC, West China Hospital Sichuan University Chengdu China.,Department of Pathology West China Second University Hospital Sichuan University China & key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University) Ministry of Education Chengdu China.,Department of Pathology West China Hospital Sichuan University Chengdu China
| | - Yong Jiang
- Department of Pathology West China Hospital Sichuan University Chengdu China
| | - Yanyan Zhou
- Laboratory of Pathology Key Laboratory of Transplant Engineering and Immunology NHC, West China Hospital Sichuan University Chengdu China
| | - Hangyu Qin
- Laboratory of Pathology Key Laboratory of Transplant Engineering and Immunology NHC, West China Hospital Sichuan University Chengdu China
| | - Fei Xiang
- Chengdu Knowledge Vision Science and Technology Co., Ltd. Chengdu China
| | - Yizhe Wang
- Chengdu Knowledge Vision Science and Technology Co., Ltd. Chengdu China
| | - Hong Bu
- Laboratory of Pathology Key Laboratory of Transplant Engineering and Immunology NHC, West China Hospital Sichuan University Chengdu China.,Department of Pathology West China Hospital Sichuan University Chengdu China
| | - Ji Bao
- Laboratory of Pathology Key Laboratory of Transplant Engineering and Immunology NHC, West China Hospital Sichuan University Chengdu China.,Frontiers Science Center for Disease-related Molecular Network West China Hospital Sichuan University Chengdu China
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