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Cerny Oliveira L, Chauhan J, Chaudhari A, Cheung SCS, Patel V, Villablanca AC, Jin LW, DeCarli C, Chuah CN, Dugger BN. A machine learning approach to automate microinfarct and microhemorrhage screening in hematoxylin and eosin-stained human brain tissues. J Neuropathol Exp Neurol 2025; 84:114-125. [PMID: 39724914 PMCID: PMC11747222 DOI: 10.1093/jnen/nlae120] [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] [Indexed: 12/28/2024] Open
Abstract
Microinfarcts and microhemorrhages are characteristic lesions of cerebrovascular disease. Although multiple studies have been published, there is no one universal standard criteria for the neuropathological assessment of cerebrovascular disease. In this study, we propose a novel application of machine learning in the automated screening of microinfarcts and microhemorrhages. Utilizing whole slide images (WSIs) from postmortem human brain samples, we adapted a patch-based pipeline with convolutional neural networks. Our cohort consisted of 22 cases from the University of California Davis Alzheimer's Disease Research Center brain bank with hematoxylin and eosin-stained formalin-fixed, paraffin-embedded sections across 3 anatomical areas: frontal, parietal, and occipital lobes (40 WSIs with microinfarcts and/or microhemorrhages, 26 without). We propose a multiple field-of-view prediction step to mitigate false positives. We report screening performance (ie, the ability to distinguish microinfarct/microhemorrhage-positive from microinfarct/microhemorrhage-negative WSIs), and detection performance (ie, the ability to localize the affected regions within a WSI). Our proposed approach improved detection precision and screening accuracy by reducing false positives thereby achieving 100% screening accuracy. Although this sample size is small, this pipeline provides a proof-of-concept for high efficacy in screening for characteristic brain changes of cerebrovascular disease to aid in screening of microinfarcts/microhemorrhages at the WSI level.
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Affiliation(s)
- Luca Cerny Oliveira
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA, United States
| | - Joohi Chauhan
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA, United States
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, United States
| | - Ajinkya Chaudhari
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA, United States
| | - Sen-ching S Cheung
- Department of Electrical and Computer Engineering, University of Kentucky, Lexington, KY, United States
| | - Viharkumar Patel
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, United States
| | - Amparo C Villablanca
- Department of Internal Medicine, University of California Davis, Davis, CA, United States
| | - Lee-Way Jin
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, United States
| | - Charles DeCarli
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, United States
| | - Chen-Nee Chuah
- Department of Electrical and Computer Engineering, University of California Davis, Davis, CA, United States
| | - Brittany N Dugger
- Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, CA, United States
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Bajaj S, Bala M, Angurala M. A comparative analysis of different augmentations for brain images. Med Biol Eng Comput 2024; 62:3123-3150. [PMID: 38782880 DOI: 10.1007/s11517-024-03127-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Deep learning (DL) requires a large amount of training data to improve performance and prevent overfitting. To overcome these difficulties, we need to increase the size of the training dataset. This can be done by augmentation on a small dataset. The augmentation approaches must enhance the model's performance during the learning period. There are several types of transformations that can be applied to medical images. These transformations can be applied to the entire dataset or to a subset of the data, depending on the desired outcome. In this study, we categorize data augmentation methods into four groups: Absent augmentation, where no modifications are made; basic augmentation, which includes brightness and contrast adjustments; intermediate augmentation, encompassing a wider array of transformations like rotation, flipping, and shifting in addition to brightness and contrast adjustments; and advanced augmentation, where all transformation layers are employed. We plan to conduct a comprehensive analysis to determine which group performs best when applied to brain CT images. This evaluation aims to identify the augmentation group that produces the most favorable results in terms of improving model accuracy, minimizing diagnostic errors, and ensuring the robustness of the model in the context of brain CT image analysis.
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Affiliation(s)
- Shilpa Bajaj
- Applied Sciences (Computer Applications), I.K. Gujral Punjab Technical University, Jalandhar, Kapurthala, India.
| | - Manju Bala
- Department of Computer Science and Engineering, Khalsa College of Engineering and Technology, Amritsar, India
| | - Mohit Angurala
- Apex Institute of Technology (CSE), Chandigarh University, Gharuan, Mohali, Punjab, India
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Hamamoto R, Koyama T, Kouno N, Yasuda T, Yui S, Sudo K, Hirata M, Sunami K, Kubo T, Takasawa K, Takahashi S, Machino H, Kobayashi K, Asada K, Komatsu M, Kaneko S, Yatabe Y, Yamamoto N. Introducing AI to the molecular tumor board: one direction toward the establishment of precision medicine using large-scale cancer clinical and biological information. Exp Hematol Oncol 2022; 11:82. [PMID: 36316731 PMCID: PMC9620610 DOI: 10.1186/s40164-022-00333-7] [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: 08/31/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
Since U.S. President Barack Obama announced the Precision Medicine Initiative in his New Year's State of the Union address in 2015, the establishment of a precision medicine system has been emphasized worldwide, particularly in the field of oncology. With the advent of next-generation sequencers specifically, genome analysis technology has made remarkable progress, and there are active efforts to apply genome information to diagnosis and treatment. Generally, in the process of feeding back the results of next-generation sequencing analysis to patients, a molecular tumor board (MTB), consisting of experts in clinical oncology, genetic medicine, etc., is established to discuss the results. On the other hand, an MTB currently involves a large amount of work, with humans searching through vast databases and literature, selecting the best drug candidates, and manually confirming the status of available clinical trials. In addition, as personalized medicine advances, the burden on MTB members is expected to increase in the future. Under these circumstances, introducing cutting-edge artificial intelligence (AI) technology and information and communication technology to MTBs while reducing the burden on MTB members and building a platform that enables more accurate and personalized medical care would be of great benefit to patients. In this review, we introduced the latest status of elemental technologies that have potential for AI utilization in MTB, and discussed issues that may arise in the future as we progress with AI implementation.
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Affiliation(s)
- Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.
| | - Takafumi Koyama
- Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Nobuji Kouno
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8303, Japan
| | - Tomohiro Yasuda
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Research and Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Shuntaro Yui
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Research and Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Kazuki Sudo
- Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Medical Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Makoto Hirata
- Department of Genetic Medicine and Services, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Kuniko Sunami
- Department of Laboratory Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takashi Kubo
- Department of Laboratory Medicine, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Ken Takasawa
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Satoshi Takahashi
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Hidenori Machino
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Kazuma Kobayashi
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Ken Asada
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Masaaki Komatsu
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Syuzo Kaneko
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Division of Molecular Pathology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Noboru Yamamoto
- Department of Experimental Therapeutics, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
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