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Marra A, Morganti S, Pareja F, Campanella G, Bibeau F, Fuchs T, Loda M, Parwani A, Scarpa A, Reis-Filho JS, Curigliano G, Marchiò C, Kather JN. Artificial intelligence entering the pathology arena in oncology: current applications and future perspectives. Ann Oncol 2025; 36:712-725. [PMID: 40307127 DOI: 10.1016/j.annonc.2025.03.006] [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: 12/18/2024] [Revised: 02/19/2025] [Accepted: 03/07/2025] [Indexed: 05/02/2025] Open
Abstract
BACKGROUND Artificial intelligence (AI) is rapidly transforming the fields of pathology and oncology, offering novel opportunities for advancing diagnosis, prognosis, and treatment of cancer. METHODS Through a systematic review-based approach, the representatives from the European Society for Medical Oncology (ESMO) Precision Oncology Working Group (POWG) and international experts identified studies in pathology and oncology that applied AI-based algorithms for tumour diagnosis, molecular biomarker detection, and cancer prognosis assessment. These findings were synthesised to provide a comprehensive overview of current AI applications and future directions in cancer pathology. RESULTS The integration of AI tools in digital pathology is markedly improving the accuracy and efficiency of image analysis, allowing for automated tumour detection and classification, identification of prognostic molecular biomarkers, and prediction of treatment response and patient outcomes. Several barriers for the adoption of AI in clinical workflows, such as data availability, explainability, and regulatory considerations, still persist. There are currently no prognostic or predictive AI-based biomarkers supported by level IA or IB evidence. The ongoing advancements in AI algorithms, particularly foundation models, generalist models and transformer-based deep learning, offer immense promise for the future of cancer research and care. AI is also facilitating the integration of multi-omics data, leading to more precise patient stratification and personalised treatment strategies. CONCLUSIONS The application of AI in pathology is poised to not only enhance the accuracy and efficiency of cancer diagnosis and prognosis but also facilitate the development of personalised treatment strategies. Although barriers to implementation remain, ongoing research and development in this field coupled with addressing ethical and regulatory considerations will likely lead to a future where AI plays an integral role in cancer management and precision medicine. The continued evolution and adoption of AI in pathology and oncology are anticipated to reshape the landscape of cancer care, heralding a new era of precision medicine and improved patient outcomes.
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Affiliation(s)
- A Marra
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
| | - S Morganti
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA; Department of Medicine, Harvard Medical School, Boston, USA; Gerstner Center for Cancer Diagnostics, Broad Institute of MIT and Harvard, Boston, USA
| | - F Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - G Campanella
- Hasso Plattner Institute for Digital Health, Mount Sinai Medical School, New York, USA; Department of AI and Human Health, Icahn School of Medicine at Mount Sinai, New York, USA
| | - F Bibeau
- Department of Pathology, University Hospital of Besançon, Besancon, France
| | - T Fuchs
- Hasso Plattner Institute for Digital Health, Mount Sinai Medical School, New York, USA; Department of AI and Human Health, Icahn School of Medicine at Mount Sinai, New York, USA
| | - M Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA; Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK; Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - A Parwani
- Department of Pathology, Wexner Medical Center, Ohio State University, Columbus, USA
| | - A Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Center, University of Verona, Verona, Italy
| | - J S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - G Curigliano
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - C Marchiò
- Candiolo Cancer Institute, FPO IRCCS, Candiolo, Italy; Department of Medical Sciences, University of Turin, Turin, Italy
| | - J N Kather
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany; Department of Medicine I, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany.
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Klein V, Büttner M, Göstemeyer G, Rolle S, Tichy A, Schwendicke F, Nordblom NF. From inconsistent annotations to ground truth: Aggregation strategies for annotations of proximal carious lesions in dental imagery. J Dent 2025; 157:105728. [PMID: 40169067 DOI: 10.1016/j.jdent.2025.105728] [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: 02/07/2025] [Revised: 03/26/2025] [Accepted: 03/29/2025] [Indexed: 04/03/2025] Open
Abstract
OBJECTIVES Annotating carious lesions on images is challenging. For artificial intelligence (AI) applications, the aggregation of heterogeneous multi-examiner annotations into one single annotation (e.g. via majority voting, MV) is usually needed. We assessed different aggregation strategies for multi-examiner annotations of primary proximal carious lesions on orthoradial radiographs and Near-Infrared Light Transillumination (NILT) images. METHODS A total of 1007 proximal surfaces from 522 extracted posterior teeth were assessed by five dentists. Histological analysis provided the gold standard. Surfaces were classified as (1) sound, (2) enamel lesion or (3) dentin lesion. Four label aggregation strategies - MV, Weighted Majority Voting (WMV), Dawid-Skene (DS), and multi-annotator competence estimation (MACE) - were applied to unimodal (radiographs, NILT) and multimodal (combined) datasets. The area under the receiver operating characteristic curve (AUROC) was the primary outcome metric. RESULTS According to the gold standard, 637 (63 %) surfaces were sound, 280 (28 %) showed carious lesions limited to the enamel, and 90 (9 %) showed lesions extending into the dentin. For radiographs, aggregation using MACE outperformed MV, WMV and DS significantly across all lesion depths (p < 0.002). For NILT, MACE significantly outperformed MV across all lesion depths (p < 0.001) and DS for enamel and dentin lesions (p ≤ 0.002). In the multimodal dataset, DS outperformed the other label aggregation strategies across all lesion depths significantly (p < 0.05). CONCLUSIONS The commonly applied MV may be suboptimal. There is a need for informed application of specific aggregation strategies, depending on the dataset characteristics. CLINICAL SIGNIFICANCE Most AI applications for dental image analysis are trained on a single annotation, usually resulting from aggregated multi-examiner annotations of each image. However, since these annotations are usually aggregated in an in vivo setting where no definitive ground truth is available, the choice of aggregation strategy plays a crucial role.
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Affiliation(s)
- Vanessa Klein
- Department of Oral Diagnostics, Digital Health and Health Services Research, Charité - Universitätsmedizin Berlin, Berlin, Germany; Conservative Dentistry and Periodontology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Martha Büttner
- Department of Oral Diagnostics, Digital Health and Health Services Research, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gerd Göstemeyer
- Department of Operative and Preventive Dentistry, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sarina Rolle
- Department of Oral Diagnostics, Digital Health and Health Services Research, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Antonin Tichy
- Conservative Dentistry and Periodontology, LMU University Hospital, LMU Munich, Munich, Germany; Institute of Dental Medicine, First Faculty of Medicine of the Charles University, Prague, Czech Republic
| | - Falk Schwendicke
- Department of Oral Diagnostics, Digital Health and Health Services Research, Charité - Universitätsmedizin Berlin, Berlin, Germany; Conservative Dentistry and Periodontology, LMU University Hospital, LMU Munich, Munich, Germany.
| | - Noah F Nordblom
- Department of Oral Diagnostics, Digital Health and Health Services Research, Charité - Universitätsmedizin Berlin, Berlin, Germany.
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Chadha S, Mukherjee S, Sanyal S. Advancements and implications of artificial intelligence for early detection, diagnosis and tailored treatment of cancer. Semin Oncol 2025; 52:152349. [PMID: 40345002 DOI: 10.1016/j.seminoncol.2025.152349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 03/20/2025] [Accepted: 04/04/2025] [Indexed: 05/11/2025]
Abstract
The complexity and heterogeneity of cancer makes early detection and effective treatment crucial to enhance patient survival and quality of life. The intrinsic creative ability of artificial intelligence (AI) offers improvements in patient screening, diagnosis, and individualized care. Advanced technologies, like computer vision, machine learning, deep learning, and natural language processing, can analyze large datasets and identify patterns that permit early cancer detection, diagnosis, management and incorporation of conclusive treatment plans, ensuring improved quality of life for patients by personalizing care and minimizing unnecessary interventions. Genomics, transcriptomics and proteomics data can be combined with AI algorithms to unveil an extensive overview of cancer biology, assisting in its detailed understanding and will help in identifying new drug targets and developing effective therapies. This can also help to identify personalized molecular signatures which can facilitate tailored interventions addressing the unique aspects of each patient. AI-driven transcriptomics, proteomics, and genomes represents a revolutionary strategy to improve patient outcome by offering precise diagnosis and tailored therapy. The inclusion of AI in oncology may boost efficiency, reduce errors, and save costs, but it cannot take the role of medical professionals. While clinicians and doctors have the final say in all matters, it might serve as their faithful assistant.
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Affiliation(s)
- Sonia Chadha
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, Uttar Pradesh, India.
| | - Sayali Mukherjee
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, Uttar Pradesh, India
| | - Somali Sanyal
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, Uttar Pradesh, India
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Zubair M, Owais M, Hassan T, Bendechache M, Hussain M, Hussain I, Werghi N. An interpretable framework for gastric cancer classification using multi-channel attention mechanisms and transfer learning approach on histopathology images. Sci Rep 2025; 15:13087. [PMID: 40240457 PMCID: PMC12003787 DOI: 10.1038/s41598-025-97256-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Accepted: 04/03/2025] [Indexed: 04/18/2025] Open
Abstract
The importance of gastric cancer (GC) and the role of deep learning techniques in categorizing GC histopathology images have recently increased. Identifying the drawbacks of traditional deep learning models, including lack of interpretability, inability to capture complex patterns, lack of adaptability, and sensitivity to noise. A multi-channel attention mechanism-based framework is proposed that can overcome the limitations of conventional deep learning models by dynamically focusing on relevant features, enhancing extraction, and capturing complex relationships in medical data. The proposed framework uses three different attention mechanism channels and convolutional neural networks to extract multichannel features during the classification process. The proposed framework's strong performance is confirmed by competitive experiments conducted on a publicly available Gastric Histopathology Sub-size Image Database, which yielded remarkable classification accuracies of 99.07% and 98.48% on the validation and testing sets, respectively. Additionally, on the HCRF dataset, the framework achieved high classification accuracy of 99.84% and 99.65% on the validation and testing sets, respectively. The effectiveness and interchangeability of the three channels are further confirmed by ablation and interchangeability experiments, highlighting the remarkable performance of the framework in GC histopathological image classification tasks. This offers an advanced and pragmatic artificial intelligence solution that addresses challenges posed by unique medical image characteristics for intricate image analysis. The proposed approach in artificial intelligence medical engineering demonstrates significant potential for enhancing diagnostic precision by achieving high classification accuracy and treatment outcomes.
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Affiliation(s)
- Muhammad Zubair
- Interdisciplinary Research Center for Finance and Digital Economy, King Fahd University of Petroleum and Minerals, 31261, Dhahran, Saudi Arabia
| | - Muhammad Owais
- Department of Mechanical & Nuclear Engineering, Khalifa University, Abu Dhabi, United Arab Emirates.
| | - Taimur Hassan
- Departement of Electrical and Computer Engineering, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Malika Bendechache
- ADAPT Research Centre, School of Computer Science, University of Galway, H91 TK33, Galway, Ireland
| | - Muzammil Hussain
- Department of Software Engineering, Faculty of Information Technology, Al-Ahliyya Amman University, Amman, Jordan
| | - Irfan Hussain
- Department of Mechanical & Nuclear Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Naoufel Werghi
- Department of Computer Science, Khalifa University, Abu Dhabi, United Arab Emirates
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Gao Y, Wen P, Liu Y, Sun Y, Qian H, Zhang X, Peng H, Gao Y, Li C, Gu Z, Zeng H, Hong Z, Wang W, Yan R, Hu Z, Fu H. Application of artificial intelligence in the diagnosis of malignant digestive tract tumors: focusing on opportunities and challenges in endoscopy and pathology. J Transl Med 2025; 23:412. [PMID: 40205603 PMCID: PMC11983949 DOI: 10.1186/s12967-025-06428-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: 11/20/2024] [Accepted: 03/25/2025] [Indexed: 04/11/2025] Open
Abstract
BACKGROUND Malignant digestive tract tumors are highly prevalent and fatal tumor types globally, often diagnosed at advanced stages due to atypical early symptoms, causing patients to miss optimal treatment opportunities. Traditional endoscopic and pathological diagnostic processes are highly dependent on expert experience, facing problems such as high misdiagnosis rates and significant inter-observer variations. With the development of artificial intelligence (AI) technologies such as deep learning, real-time lesion detection with endoscopic assistance and automated pathological image analysis have shown potential in improving diagnostic accuracy and efficiency. However, relevant applications still face challenges including insufficient data standardization, inadequate interpretability, and weak clinical validation. OBJECTIVE This study aims to systematically review the current applications of artificial intelligence in diagnosing malignant digestive tract tumors, focusing on the progress and bottlenecks in two key areas: endoscopic examination and pathological diagnosis, and to provide feasible ideas and suggestions for subsequent research and clinical translation. METHODS A systematic literature search strategy was adopted to screen relevant studies published between 2017 and 2024 from databases including PubMed, Web of Science, Scopus, and IEEE Xplore, supplemented with searches of early classical literature. Inclusion criteria included studies on malignant digestive tract tumors such as esophageal cancer, gastric cancer, or colorectal cancer, involving the application of artificial intelligence technology in endoscopic diagnosis or pathological analysis. The effects and main limitations of AI diagnosis were summarized through comprehensive analysis of research design, algorithmic methods, and experimental results from relevant literature. RESULTS In the field of endoscopy, multiple deep learning models have significantly improved detection rates in real-time polyp detection, early gastric cancer, and esophageal cancer screening, with some commercialized systems successfully entering clinical trials. However, the scale and quality of data across different studies vary widely, and the generalizability of models to multi-center, multi-device environments remains to be verified. In pathological analysis, using convolutional neural networks, multimodal pre-training models, etc., automatic tissue segmentation, tumor grading, and assisted diagnosis can be achieved, showing good scalability in interactive question-answering. Nevertheless, clinical implementation still faces obstacles such as non-uniform data standards, lack of large-scale prospective validation, and insufficient model interpretability and continuous learning mechanisms. CONCLUSION Artificial intelligence provides new technological opportunities for endoscopic and pathological diagnosis of malignant digestive tract tumors, achieving positive results in early lesion identification and assisted decision-making. However, to achieve the transition from research to widespread clinical application, data standardization, model reliability, and interpretability still need to be improved through multi-center joint research, and a complete regulatory and ethical system needs to be established. In the future, artificial intelligence will play a more important role in the standardization and precision management of diagnosis and treatment of digestive tract tumors.
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Affiliation(s)
- Yinhu Gao
- Department of Gastroenterology, Shaanxi Province Rehabilitation Hospital, Xi'an, Shaanxi, China
| | - Peizhen Wen
- Department of General Surgery, Changzheng Hospital, Navy Medical University, 415 Fengyang Road, Shanghai, 200003, China.
| | - Yuan Liu
- Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yahuang Sun
- Division of Colorectal Surgery, Changzheng Hospital, Navy Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Hui Qian
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Xin Zhang
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Huan Peng
- Division of Colorectal Surgery, Changzheng Hospital, Navy Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Yanli Gao
- Infection Control Office, Shaanxi Province Rehabilitation Hospital, Xi'an, Shaanxi, China
| | - Cuiyu Li
- Department of Radiology, The First Hospital of Nanchang, the Third Affiliated Hospital of Nanchang University, Nanchang, 330008, Jiangxi, China
| | - Zhangyuan Gu
- Tongji University School of Medicine, Tongji University, Shanghai, 200092, People's Republic of China
| | - Huajin Zeng
- Department of General Surgery, Changzheng Hospital, Navy Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Zhijun Hong
- Tongji University School of Medicine, Tongji University, Shanghai, 200092, People's Republic of China
| | - Weijun Wang
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, 415 Fengyang Road, Shanghai, 200003, China.
| | - Ronglin Yan
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, 415 Fengyang Road, Shanghai, 200003, China.
| | - Zunqi Hu
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, 415 Fengyang Road, Shanghai, 200003, China.
| | - Hongbing Fu
- Department of Gastrointestinal Surgery, Changzheng Hospital, Navy Medical University, 415 Fengyang Road, Shanghai, 200003, China.
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El Zoghbi M, Malhotra A, Bilal M, Shaukat A. Impact of Artificial Intelligence on Clinical Research. Gastrointest Endosc Clin N Am 2025; 35:445-455. [PMID: 40021240 DOI: 10.1016/j.giec.2024.10.002] [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] [Indexed: 03/03/2025]
Abstract
Artificial intelligence (AI) has potential to significantly impact clinical research when it comes to research preparation and data interpretation. Development of AI tools that can help in performing literature searches, synthesizing and streamlining data collection and analysis, and formatting of study could make the clinical research process more efficient. Several of these tools have been developed and trialed and many more are being rapidly developed. This article highlights the AI applications in clinical research in gastroenterology including its impact on drug discovery and explores areas where further guidance is needed to supplement the current understanding and enhance its use.
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Affiliation(s)
- Maysaa El Zoghbi
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Ashish Malhotra
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Mohammad Bilal
- University of Minnesota, Minneapolis VA Medical Center, Minneapolis, MN, USA
| | - Aasma Shaukat
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA.
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Ye Z, Wu X, Wei Z, Sun Q, Wang Y, Li T, Yuan Y, Jing J. Microsatellite-Stable Gastric Cancer Can be Classified into 2 Molecular Subtypes with Different Immunotherapy Response and Prognosis Based on Gene Sequencing and Computational Pathology. J Transl Med 2025; 105:104101. [PMID: 39894411 DOI: 10.1016/j.labinv.2025.104101] [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: 08/01/2024] [Revised: 01/07/2025] [Accepted: 01/27/2025] [Indexed: 02/04/2025] Open
Abstract
Most patients with gastric cancer (GC) exhibit microsatellite stability, yet comprehensive subtyping for prognostic prediction and clinical treatment decisions for microsatellite-stable GC is lacking. In this work, RNA-sequencing gene expression data and clinical information of patients with microsatellite-stable GC were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. We employed several machine learning methods to develop and validate a signature based on immune-related genes (IRGs) for subtyping patients with microsatellite-stable GC. Moreover, 2 deep learning models based on the Vision Transformer (ViT) architecture were developed to predict GC tumor tiles and identify microsatellite-stable GC subtypes from digital pathology slides. Microsatellite status was evaluated by immunohistochemistry, and prognostic data as well as hematoxylin and eosin whole-slide images were collected from 105 patients with microsatellite-stable GC to serve as an independent validation cohort. A signature comprising 5 IRGs was established and validated, stratifying patients with microsatellite-stable GC into high-risk (microsatellite-stable-HR) and low-risk (microsatellite-stable-LR) groups. This signature demonstrated consistent performance, with areas under the receiver operating characteristic curve (AUC) of 0.65, 0.70, and 0.70 at 1, 3, and 5 years in the TCGA cohort, and 0.70, 0.60, and 0.62 in the GEO cohort, respectively. The microsatellite-stable-HR subtype exhibited higher levels of tumor immune dysfunction and exclusion, suggesting a greater potential for immune escape compared with the microsatellite-stable-LR subtype. Moreover, the microsatellite-stable-HR/LR subtypes showed differential sensitivities to various therapeutic drugs. Leveraging morphologic differences, the tumor recognition segmentation model achieved an impressive AUC of 0.97, whereas the microsatellite-stable-HR/LR identification model effectively classified microsatellite-stable-HR/LR subtypes with an AUC of 0.94. Both models demonstrated promising results in classifying patients with microsatellite-stable GC in the external validation cohort, highlighting the strong ability to accurately differentiate between microsatellite-stable GC subtypes. The IRG-related microsatellite-stable-HR/LR subtypes had the potential to enhance outcome prediction accuracy and guide treatment strategies. This research may optimize precision treatment and improve the prognosis for patients with microsatellite-stable GC.
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Affiliation(s)
- Zhiyi Ye
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Xiaoyang Wu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Zheng Wei
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Qiuyan Sun
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Yanli Wang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Tan Li
- Department of Cardiovascular Ultrasound, the First Hospital of China Medical University, Shenyang, China.
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China; Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.
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8
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Shanmugam K, Rajaguru H. Enhanced Superpixel-Guided ResNet Framework with Optimized Deep-Weighted Averaging-Based Feature Fusion for Lung Cancer Detection in Histopathological Images. Diagnostics (Basel) 2025; 15:805. [PMID: 40218155 PMCID: PMC11989018 DOI: 10.3390/diagnostics15070805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2025] [Revised: 03/06/2025] [Accepted: 03/11/2025] [Indexed: 04/14/2025] Open
Abstract
Background/Objectives: Lung cancer is a leading cause of cancer-related mortalities, with early diagnosis crucial for survival. While biopsy is the gold standard, manual histopathological analysis is time-consuming. This research enhances lung cancer diagnosis through deep learning-based feature extraction, fusion, optimization, and classification for improved accuracy and efficiency. Methods: The study begins with image preprocessing using an adaptive fuzzy filter, followed by segmentation with a modified simple linear iterative clustering (SLIC) algorithm. The segmented images are input into deep learning architectures, specifically ResNet-50 (RN-50), ResNet-101 (RN-101), and ResNet-152 (RN-152), for feature extraction. The extracted features are fused using a deep-weighted averaging-based feature fusion (DWAFF) technique, producing ResNet-X (RN-X)-fused features. To further refine these features, particle swarm optimization (PSO) and red deer optimization (RDO) techniques are employed within the selective feature pooling layer. The optimized features are classified using various machine learning classifiers, including support vector machine (SVM), decision tree (DT), random forest (RF), K-nearest neighbor (KNN), SoftMax discriminant classifier (SDC), Bayesian linear discriminant analysis classifier (BLDC), and multilayer perceptron (MLP). A performance evaluation is performed using K-fold cross-validation with K values of 2, 4, 5, 8, and 10. Results: The proposed DWAFF technique, combined with feature selection using RDO and classification with MLP, achieved the highest classification accuracy of 98.68% when using K = 10 for cross-validation. The RN-X features demonstrated superior performance compared to individual ResNet variants, and the integration of segmentation and optimization significantly enhanced classification accuracy. Conclusions: The proposed methodology automates lung cancer classification using deep learning, feature fusion, optimization, and advanced classification techniques. Segmentation and feature selection enhance performance, improving diagnostic accuracy. Future work may explore further optimizations and hybrid models.
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Xia Y, Jia J, Ma H, Tang S, Zhai S, Zhang T, Zhao Y, Shi J, Liu L. Impact of PSMD2 on Gastric Cancer Tissue Stiffness Investigated via Motor-Piezoceramic Coupled Atomic Force Microscopy. NANO LETTERS 2025; 25:3931-3938. [PMID: 40016166 DOI: 10.1021/acs.nanolett.4c06514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2025]
Abstract
Gastric cancer is one of the deadliest malignant tumors of the digestive tract, and its development and metastasis are regulated by various factors. Some studies have shown that PSMD2 is involved in cancer development by regulating the tumor microenvironment stiffness. However, the exact mechanism is unclear, and effective means to quantify the effect of PSMD2 on gastric cancer tissue hardness are lacking. Herein, we revealed the mechanical heterogeneity of tumor tissues in gastric cancer patients using a large-scale AFM-based in situ method. Gastric cancer cryosections were probed by this method under aqueous condition. The in situ fluorescence images were measured to correlate tissue stiffness with PSMD2 expression. Experimental results clearly revealed the specific distribution of mechanics in gastric cancer tissues under differences in PSMD2 expression. The study unveils the effect of PSMD2 expression levels on cancer invasion and increased matrix stiffness, providing a novel insight into gastric cancer research.
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Affiliation(s)
- Yixiao Xia
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junkai Jia
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Hongying Ma
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Si Tang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shenghang Zhai
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianbiao Zhang
- Department of Biochemistry & Molecular Biology, China Medical University, Shenyang 110122, China
| | - Ying Zhao
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Jialin Shi
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
| | - Lianqing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China
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10
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Ebigbo A, Messmann H, Lee SH. Artificial Intelligence Applications in Image-Based Diagnosis of Early Esophageal and Gastric Neoplasms. Gastroenterology 2025:S0016-5085(25)00471-8. [PMID: 40043857 DOI: 10.1053/j.gastro.2025.01.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Revised: 01/14/2025] [Accepted: 01/22/2025] [Indexed: 04/03/2025]
Abstract
Artificial intelligence (AI) holds the potential to transform the management of upper gastrointestinal (GI) conditions, such as Barrett's esophagus, esophageal squamous cell cancer, and early gastric cancer. Advancements in deep learning and convolutional neural networks offer improved diagnostic accuracy and reduced diagnostic variability across different clinical settings, particularly where human error or fatigue may impair diagnostic precision. Deep learning models have shown the potential to improve early cancer detection and lesion characterization, predict invasion depth, and delineate lesion margins with remarkable accuracy, all contributing to effective treatment planning. Several challenges, however, limit the broad application of AI in GI endoscopy, particularly in the upper GI tract. Subtle lesion morphology and restricted diversity in training datasets, which are often sourced from specialized centers, may constrain the generalizability of AI models in various clinical settings. Furthermore, the "black box" nature of some AI systems can impede explainability and clinician trust. To address these issues, efforts are underway to incorporate multimodal data, such as combining endoscopic and histopathologic imaging, to bolster model robustness and transparency. In the future, AI promises substantial advancements in automated real-time endoscopic guidance, personalized risk assessment, and optimized biopsy decision making. As it evolves, it would substantially impact not only early diagnosis and prognosis, but also the cost-effectiveness of managing upper GI diseases, ultimately leading to improved patient outcomes and more efficient health care delivery.
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Affiliation(s)
- Alanna Ebigbo
- Department of Gastroenterology, University Hospital Augsburg, Augsburg, Germany.
| | - Helmut Messmann
- Department of Gastroenterology, University Hospital Augsburg, Augsburg, Germany.
| | - Sung Hak Lee
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul, South Korea; Seoul St. Mary's Hospital, Seoul, South Korea.
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11
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Ke Q, Yap WS, Tee YK, Hum YC, Zheng H, Gan YJ. Advanced deep learning for multi-class colorectal cancer histopathology: integrating transfer learning and ensemble methods. Quant Imaging Med Surg 2025; 15:2329-2346. [PMID: 40160652 PMCID: PMC11948397 DOI: 10.21037/qims-24-1641] [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: 08/14/2024] [Accepted: 01/21/2025] [Indexed: 04/02/2025]
Abstract
Background Cancer is a major global health threat, constantly endangering people's well-being and lives. The application of deep learning in the diagnosis of colorectal cancer can improve early detection rates, thereby significantly reducing the incidence and mortality of colorectal cancer patients. Our study aims to optimize the performance of deep learning model in the classification of colorectal cancer histopathological images to assist pathologists in improving diagnostic accuracy. Methods In this study, we developed ensemble models based on deep convolutional neural networks (CNNs) for the classification of colorectal cancer histopathology images. The method first involved data preprocessing techniques such as patch cropping, stain normalization, data augmentation and data balancing on histopathology images with different magnifications. Subsequently, the CNN models were fine-tuned and pre-trained using transfer learning methods, and models with superior performance were then selected as the base classifiers to build the ensemble models. Finally, the ensemble models were used to predict the final classification outcomes. To evaluate the effectiveness of the proposed models, we tested their performance on a publicly available colorectal cancer dataset, Enteroscope Biopsy Histopathological Hematoxylin and Eosin Image (EBHI) dataset. Results Experimental results show that the proposed ensemble model, composed of the top five classifiers, achieved the promising classification accuracy across sub-databases with four different magnification factors. Specifically, on the 40× magnification subset, the highest classification accuracy reached 99.11%; on the 100× magnification subset, it reached 99.36%; on the 200× magnification subset, it was 99.29%; and on the 400× magnification subset, it was 98.96%. Additionally, the proposed ensemble model achieved exceptional results in recall, precision, and F1 score. Conclusions The proposed ensemble models obtained good classification performance on the EBHI dataset of histopathological images for colorectal cancer. The findings of this study may contribute to the early detection and accurate classification of colorectal cancer, thereby aiding in more precise diagnostic analysis of colorectal cancer.
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Affiliation(s)
- Qi Ke
- School of Big Data and Artificial Intelligence, Guangxi University of Finance and Economics, Nanning, China
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Selangor, Malaysia
| | - Wun-She Yap
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Selangor, Malaysia
| | - Yee Kai Tee
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Selangor, Malaysia
| | - Yan Chai Hum
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Selangor, Malaysia
| | - Hua Zheng
- Guangxi Key Laboratory of Seaward Economic Intelligent System Analysis and Decision-making, Guangxi University of Finance and Economics, Nanning, China
| | - Yu-Jian Gan
- Department of Information Studies, University College London, London, UK
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12
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Faa G, Fraschini M, Didaci L, Saba L, Scartozzi M, Orvieto E, Rugge M. "Artificial histology" in colonic Neoplasia: A critical approach. Dig Liver Dis 2025; 57:663-668. [PMID: 39616091 DOI: 10.1016/j.dld.2024.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 11/01/2024] [Accepted: 11/06/2024] [Indexed: 03/01/2025]
Abstract
BACKGROUND The histological assessment of colorectal precancer and cancer lesions is challenging and primarily impacts the clinical strategies of secondary colon cancer prevention. Artificial intelligence (AI) models may potentially assist in the histological diagnosis of this spectrum of phenotypical changes. OBJECTIVES To provide a current overview of the evidence on AI-based methods for histologically assessing colonic precancer and cancer lesions. METHODS Based on the available studies, this review focuses on the reliability of AI-driven models in ranking the histological phenotypes included in colonic oncogenesis. RESULTS This review acknowledges the efforts to shift from subjective pathologists-based to more objective AI-based histological phenotyping. However, it also points out significant limitations and areas that require improvement. CONCLUSIONS Current AI-driven methods have not yet achieved the expected level of clinical effectiveness, and there are still significant ethical concerns that need careful consideration. The integration of "artificial histology" into diagnostic practice requires further efforts to combine advancements in engineering techniques with the expertise of pathologists.
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Affiliation(s)
- Gavino Faa
- Department of Medical Sciences and Public Health, Università degli Studi di Cagliari, 09123 Cagliari, Italy; Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, 19122 USA.
| | - Matteo Fraschini
- Department of Electrical and Electronic Engineering, Università degli Studi di Cagliari, 09123 Cagliari, Italy.
| | - Luca Didaci
- Department of Electrical and Electronic Engineering, Università degli Studi di Cagliari, 09123 Cagliari, Italy.
| | - Luca Saba
- Department of Radiology, University Hospital, Università degli Studi di Cagliari, 40138 Cagliari, Italy.
| | - Mario Scartozzi
- Medical Oncology Unit, University Hospital of Cagliari, Università degli Studi di Cagliari, 09123 Cagliari, Italy.
| | - Enrico Orvieto
- Department of Pathology, ULSS 8 Berica, San Bortolo Hospital, 36100 Vicenza, Italy.
| | - Massimo Rugge
- Department of Medicine - DIMED; General Anatomic Pathology and Cytopathology Unit, Università degli Studi di Padova, 35121 Padova, Italy.
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13
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Zehnder P, Feng J, Nguyen T, Shen P, Sullivan R, Fuji RN, Hu F. Diagnostic classification in toxicologic pathology using attention-guided weak supervision and whole slide image features: a pilot study in rat livers. Sci Rep 2025; 15:4202. [PMID: 39905121 PMCID: PMC11794696 DOI: 10.1038/s41598-025-86615-6] [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: 12/07/2023] [Accepted: 01/13/2025] [Indexed: 02/06/2025] Open
Abstract
The diagnostic classification of digitized tissue images based on histopathologic lesions present in whole slide images (WSI) is a significant task that eludes modern image classification techniques. Even with advanced methods designed for digital histopathology, the domain of toxicologic pathology presents challenges in that histopathologic features may be at times complex, subtle, and/or rare. We propose an innovative weakly supervised learning method that leverages minimal annotations, a state-of-the-art self-supervised vision transformer for embedding extraction, and a novel guided attention mechanism that is better suited for heavily imbalanced datasets typical in toxicologic pathology. Our model demonstrates improvements in diagnostic classification and attention heatmap quality over the previously described clustering-constrained-attention multiple-instance learning method on several lesion classes in rat livers (38% improvement in AUC). We also demonstrate how an ensemble of binary classifiers improves interpretability and allows for multiclass classification and the classification of diagnostic regions of interest in each slide. The improved classification performance and higher contrast heatmaps better support toxicologic pathologists' histopathology analysis and will enable more efficient workflows as they are further refined and integrated into routine use.
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Affiliation(s)
- Philip Zehnder
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jeffrey Feng
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Trung Nguyen
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Philip Shen
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ruth Sullivan
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Reina N Fuji
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Fangyao Hu
- Department of Safety Assessment, Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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14
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White CD, Chetty R, Weldon J, Morrissey ME, Sykes R, Gîrleanu C, Colleuori M, Fitzgerald J, Power A, Ahmad A, Carmody S, Moulin P, O'Shea D, Aslam M, Dada MA, Loughrey MB, McManus MC, Nowak KM, McCombe K, Hutton S, Rafferty M, Mulligan N. A deep learning approach to case prioritisation of colorectal biopsies. Histopathology 2025; 86:373-384. [PMID: 39360579 DOI: 10.1111/his.15331] [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: 05/13/2024] [Revised: 07/29/2024] [Accepted: 09/15/2024] [Indexed: 10/04/2024]
Abstract
AIMS To create and validate a weakly supervised artificial intelligence (AI) model for detection of abnormal colorectal histology, including dysplasia and cancer, and prioritise biopsies according to clinical significance (severity of diagnosis). MATERIALS AND METHODS Triagnexia Colorectal, a weakly supervised deep learning model, was developed for the classification of colorectal samples from haematoxylin and eosin (H&E)-stained whole slide images. The model was trained on 24 983 digitised images and assessed by multiple pathologists in a simulated digital pathology environment. The AI application was implemented as part of a point and click graphical user interface to streamline decision-making. Pathologists assessed the accuracy of the AI tool, its value, ease of use and integration into the digital pathology workflow. RESULTS Validation of the model was conducted on two cohorts: the first, on 100 single-slide cases, achieved micro-average model specificity of 0.984, micro-average model sensitivity of 0.949 and micro-average model F1 score of 0.949 across all classes. A secondary multi-institutional validation cohort, of 101 single-slide cases, achieved micro-average model specificity of 0.978, micro-average model sensitivity of 0.931 and micro-average model F1 score of 0.931 across all classes. Pathologists reflected their positive impressions on the overall accuracy of the AI in detecting colorectal pathology abnormalities. CONCLUSIONS We have developed a high-performing colorectal biopsy AI triage model that can be integrated into a routine digital pathology workflow to assist pathologists in prioritising cases and identifying cases with dysplasia/cancer versus non-neoplastic biopsies.
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Affiliation(s)
- Ciara D White
- Department of Histopathology, Mater Misericordiae University Hospital, Dublin, Ireland
- Deciphex, DCU Alpha Innovation Campus, Dublin, Ireland
| | - Runjan Chetty
- Deciphex, DCU Alpha Innovation Campus, Dublin, Ireland
| | - John Weldon
- Deciphex, DCU Alpha Innovation Campus, Dublin, Ireland
| | | | - Rob Sykes
- Deciphex, DCU Alpha Innovation Campus, Dublin, Ireland
| | - Corina Gîrleanu
- Department of Histopathology, Mater Misericordiae University Hospital, Dublin, Ireland
| | | | | | - Adam Power
- Deciphex, DCU Alpha Innovation Campus, Dublin, Ireland
| | - Ajaz Ahmad
- Deciphex, DCU Alpha Innovation Campus, Dublin, Ireland
| | - Seán Carmody
- Deciphex, DCU Alpha Innovation Campus, Dublin, Ireland
| | - Pierre Moulin
- Deciphex, DCU Alpha Innovation Campus, Dublin, Ireland
| | - Donal O'Shea
- Deciphex, DCU Alpha Innovation Campus, Dublin, Ireland
| | - Muhammad Aslam
- Diagnexia, Exeter, UK
- Betsi Calawaladar NHS Health Board, Wales, UK
| | | | - Maurice B Loughrey
- Diagnexia, Exeter, UK
- Centre for Public Health, Department of Cellular Pathology, Queens University Belfast, Belfast Health and Social Care Trust, Belfast, UK
| | | | - Klaudia M Nowak
- Diagnexia, Exeter, UK
- University Health Network, Toronto, Canada
| | | | - Sinead Hutton
- Department of Histopathology, Mater Misericordiae University Hospital, Dublin, Ireland
| | | | - Niall Mulligan
- Department of Histopathology, Mater Misericordiae University Hospital, Dublin, Ireland
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15
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Yang T, Li P, Liu B, Lv Y, Fan D, Fan Y, Liu P, Ni Y. Multi-Class Segmentation Network Based on Tumor Tissue in Endometrial Cancer Pathology Images: ECMTrans-net. THE AMERICAN JOURNAL OF PATHOLOGY 2025; 195:232-246. [PMID: 39476956 DOI: 10.1016/j.ajpath.2024.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 10/02/2024] [Accepted: 10/10/2024] [Indexed: 11/15/2024]
Abstract
Endometrial cancer has the second highest incidence of malignant tumors in the female reproductive system. Accurate and efficient analysis of endometrial cancer pathology images is one of the important research components of computer-aided diagnosis. However, endometrial cancer pathology images have challenges such as smaller solid tumors, lesion areas varying in morphology, and difficulty distinguishing solid and nonsolid tumors, which would affect the accuracy of subsequent pathologic analyses. An Endometrial Cancer Multi-class Transformer Network (ECMTrans-net) is therefore proposed herein to improve the segmentation accuracy of endometrial cancer pathology images. An ECM-Attention module can sequentially infer attention maps along three separate dimensions (channel, local spatial, and global spatial) and multiply the attention maps and the input feature map for adaptive feature refinement. This approach may solve the problems of the small size of solid tumors and similar characteristics of solid tumors to nonsolid tumors and further improve the accuracy of segmentation of solid tumors. In addition, an ECM-Transformer module is proposed, which can fuse multi-class feature information and dynamically adjust the receptive field, solving the issue of complex tumor features. Experiments on the Solid Tumor Endometrial Cancer Pathological (ST-ECP) data set found that performance of the ECMTrans-net was superior to state-of-the-art image segmentation methods, and the average values of accuracy, Mean Intersection over Union, precision, and Dice coefficients were 0.952, 0.927, 0.931, and 0.901, respectively.
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Affiliation(s)
- Tong Yang
- School of Medicine, Huaqiao University, Quanzhou, China
| | - Ping Li
- Department of Gynecology and Obstetrics, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, China
| | - Bo Liu
- School of Medicine, Huaqiao University, Quanzhou, China
| | - Yuchun Lv
- Department of Gynecology and Obstetrics, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, China
| | - Dage Fan
- Department of Pathology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
| | - Yuling Fan
- College of Engineering, Huaqiao University, Quanzhou, China
| | - Peizhong Liu
- School of Medicine, Huaqiao University, Quanzhou, China; College of Engineering, Huaqiao University, Quanzhou, China.
| | - Yaping Ni
- Department of Pathology, The First Hospital of Quanzhou Affiliated to Fujian Medical University, Quanzhou, China.
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16
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Nguyen MH, Tran ND, Le NQK. Big Data and Artificial Intelligence in Drug Discovery for Gastric Cancer: Current Applications and Future Perspectives. Curr Med Chem 2025; 32:1968-1986. [PMID: 37711014 DOI: 10.2174/0929867331666230913105829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/04/2023] [Accepted: 08/04/2023] [Indexed: 09/16/2023]
Abstract
Gastric cancer (GC) represents a significant global health burden, ranking as the fifth most common malignancy and the fourth leading cause of cancer-related death worldwide. Despite recent advancements in GC treatment, the five-year survival rate for advanced-stage GC patients remains low. Consequently, there is an urgent need to identify novel drug targets and develop effective therapies. However, traditional drug discovery approaches are associated with high costs, time-consuming processes, and a high failure rate, posing challenges in meeting this critical need. In recent years, there has been a rapid increase in the utilization of artificial intelligence (AI) algorithms and big data in drug discovery, particularly in cancer research. AI has the potential to improve the drug discovery process by analyzing vast and complex datasets from multiple sources, enabling the prediction of compound efficacy and toxicity, as well as the optimization of drug candidates. This review provides an overview of the latest AI algorithms and big data employed in drug discovery for GC. Additionally, we examine the various applications of AI in this field, with a specific focus on therapeutic discovery. Moreover, we discuss the challenges, limitations, and prospects of emerging AI methods, which hold significant promise for advancing GC research in the future.
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Affiliation(s)
- Mai Hanh Nguyen
- International Ph.D. Program in Cell Therapy and Regenerative Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- AIBioMed Research Group, Taipei Medical University, Taipei 110, Taiwan
- Pathology and Forensic Medicine Department, 103 Military Hospital, Hanoi, Vietnam
| | - Ngoc Dung Tran
- Pathology and Forensic Medicine Department, 103 Military Hospital, Hanoi, Vietnam
| | - Nguyen Quoc Khanh Le
- AIBioMed Research Group, Taipei Medical University, Taipei 110, Taiwan
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 106, Taiwan
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei 106, Taiwan
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei 110, Taiwan
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17
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Wang C, Du X, Yan X, Teng X, Wang X, Yang Z, Chang H, Fan Y, Ran C, Lian J, Li C, Li H, Cui L, Jiang Y. Weakly supervised learning in thymoma histopathology classification: an interpretable approach. Front Med (Lausanne) 2024; 11:1501875. [PMID: 39722817 PMCID: PMC11668976 DOI: 10.3389/fmed.2024.1501875] [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: 09/25/2024] [Accepted: 11/25/2024] [Indexed: 12/28/2024] Open
Abstract
Introduction Thymoma classification is challenging due to its diverse morphology. Accurate classification is crucial for diagnosis, but current methods often struggle with complex tumor subtypes. This study presents an AI-assisted diagnostic model that combines weakly supervised learning with a divide-and-conquer multi-instance learning (MIL) approach to improve classification accuracy and interpretability. Methods We applied the model to 222 thymoma slides, simplifying the five-class classification into binary and ternary steps. The model features an attention-based mechanism that generates heatmaps, enabling visual interpretation of decisions. These heatmaps align with clinically validated morphological differences between thymoma subtypes. Additionally, we embedded domain-specific pathological knowledge into the interpretability framework. Results The model achieved a classification AUC of 0.9172. The generated heatmaps accurately reflected the morphological distinctions among thymoma subtypes, as confirmed by pathologists. The model's transparency allows pathologists to visually verify AI decisions, enhancing diagnostic reliability. Discussion This model offers a significant advancement in thymoma classification, combining high accuracy with interpretability. By integrating weakly supervised learning, MIL, and attention mechanisms, it provides an interpretable AI framework that is applicable in clinical settings. The model reduces the diagnostic burden on pathologists and has the potential to improve patient outcomes by making AI tools more transparent and clinically relevant.
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Affiliation(s)
- Chunbao Wang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xianglong Du
- School of Information Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Xiaoyu Yan
- School of Information Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Xiali Teng
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaolin Wang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhe Yang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hongyun Chang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yangyang Fan
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Caihong Ran
- Department of Pathology, Ngari Prefecture People's Hospital, Ngari, Tibet, China
| | - Jie Lian
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Chen Li
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hansheng Li
- School of Information Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Lei Cui
- School of Information Science and Technology, Northwest University, Xi'an, Shaanxi, China
| | - Yina Jiang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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18
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Akram F, de Bruyn DP, van den Bosch QCC, Trandafir TE, van den Bosch TPP, Verdijk RM, de Klein A, Kiliç E, Stubbs AP, Brosens E, von der Thüsen JH. Prediction of molecular subclasses of uveal melanoma by deep learning using routine haematoxylin-eosin-stained tissue slides. Histopathology 2024; 85:909-919. [PMID: 38952117 DOI: 10.1111/his.15271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/09/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
AIMS Uveal melanoma has a high propensity to metastasize. Prognosis is associated with specific driver mutations and copy number variations, and these can only be obtained after genetic testing. In this study we evaluated the efficacy of patient outcome prediction using deep learning on haematoxylin and eosin (HE)-stained primary uveal melanoma slides in comparison to molecular testing. METHODS In this retrospective study of patients with uveal melanoma, 113 patients from the Erasmus Medical Centre who underwent enucleation had tumour tissue analysed for molecular classification between 1993 and 2020. Routine HE-stained slides were scanned to obtain whole-slide images (WSI). After annotation of regions of interest, tiles of 1024 × 1024 pixels were extracted at a magnification of 40×. An ablation study to select the best-performing deep-learning model was carried out using three state-of-the-art deep-learning models (EfficientNet, Vision Transformer, and Swin Transformer). RESULTS Deep-learning models were subjected to a training cohort (n = 40), followed by a validation cohort (n = 20), and finally underwent a test cohort (n = 48). A k-fold cross-validation (k = 3) of validation and test cohorts (n = 113 of three classes: BAP1, SF3B1, EIF1AX) demonstrated Swin Transformer as the best-performing deep-learning model to predict molecular subclasses based on HE stains. The model achieved an accuracy of 0.83 ± 0.09 on the validation cohort and 0.75 ± 0.04 on the test cohort. Within the subclasses, this model correctly predicted 70% BAP1-mutated, 61% SF3B1-mutated and 80% EIF1AX-mutated UM in the test set. CONCLUSIONS This study showcases the potential of the deep-learning methodology for predicting molecular subclasses in a multiclass manner using HE-stained WSI. This development holds promise for advanced prognostication of UM patients without the need of molecular or immunohistochemical testing. Additionally, this study suggests there are distinct histopathological features per subclass; mainly utilizing epithelioid cellular morphology for BAP1-classification, but an unknown feature distinguishes EIF1AX and SF3B1.
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Affiliation(s)
- Farhan Akram
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Daniël P de Bruyn
- Ophthalmology, Erasmus MC Rotterdam, Rotterdam, the Netherlands
- Clinical Genetics, Erasmus MC Rotterdam, Rotterdam, the Netherlands
- Cancer Institute, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Quincy C C van den Bosch
- Ophthalmology, Erasmus MC Rotterdam, Rotterdam, the Netherlands
- Clinical Genetics, Erasmus MC Rotterdam, Rotterdam, the Netherlands
- Cancer Institute, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Teodora E Trandafir
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Thierry P P van den Bosch
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Rob M Verdijk
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Annelies de Klein
- Ophthalmology, Erasmus MC Rotterdam, Rotterdam, the Netherlands
- Cancer Institute, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Emine Kiliç
- Ophthalmology, Erasmus MC Rotterdam, Rotterdam, the Netherlands
- Cancer Institute, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Andrew P Stubbs
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Erwin Brosens
- Clinical Genetics, Erasmus MC Rotterdam, Rotterdam, the Netherlands
- Cancer Institute, Erasmus MC Rotterdam, Rotterdam, the Netherlands
| | - Jan H von der Thüsen
- Department of Pathology and Clinical Bioinformatics, Erasmus MC Rotterdam, Rotterdam, the Netherlands
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19
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Khosravi M, Jasemi SK, Hayati P, Javar HA, Izadi S, Izadi Z. Transformative artificial intelligence in gastric cancer: Advancements in diagnostic techniques. Comput Biol Med 2024; 183:109261. [PMID: 39488054 DOI: 10.1016/j.compbiomed.2024.109261] [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: 06/25/2024] [Revised: 09/30/2024] [Accepted: 10/07/2024] [Indexed: 11/04/2024]
Abstract
Gastric cancer represents a significant global health challenge with elevated incidence and mortality rates, highlighting the need for advancements in diagnostic and therapeutic strategies. This review paper addresses the critical need for a thorough synthesis of the role of artificial intelligence (AI) in the management of gastric cancer. It provides an in-depth analysis of current AI applications, focusing on their contributions to early diagnosis, treatment planning, and outcome prediction. The review identifies key gaps and limitations in the existing literature by examining recent studies and technological developments. It aims to clarify the evolution of AI-driven methods and their impact on enhancing diagnostic accuracy, personalizing treatment strategies, and improving patient outcomes. The paper emphasizes the transformative potential of AI in overcoming the challenges associated with gastric cancer management and proposes future research directions to further harness AI's capabilities. Through this synthesis, the review underscores the importance of integrating AI technologies into clinical practice to revolutionize gastric cancer management.
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Affiliation(s)
- Mobina Khosravi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Seyedeh Kimia Jasemi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Parsa Hayati
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Hamid Akbari Javar
- Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Saadat Izadi
- Department of Computer Engineering and Information Technology, Razi University, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Zhila Izadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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20
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Cannarozzi AL, Massimino L, Latiano A, Parigi TL, Giuliani F, Bossa F, Di Brina AL, Ungaro F, Biscaglia G, Danese S, Perri F, Palmieri O. Artificial intelligence: A new tool in the pathologist's armamentarium for the diagnosis of IBD. Comput Struct Biotechnol J 2024; 23:3407-3417. [PMID: 39345902 PMCID: PMC11437746 DOI: 10.1016/j.csbj.2024.09.003] [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: 07/20/2024] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 10/01/2024] Open
Abstract
Inflammatory bowel diseases (IBD) are classified into two entities, namely Crohn's disease (CD) and ulcerative colitis (UC), which differ in disease trajectories, genetics, epidemiological, clinical, endoscopic, and histopathological aspects. As no single golden standard modality for diagnosing IBD exists, the differential diagnosis among UC, CD, and non-IBD involves a multidisciplinary approach, considering professional groups that include gastroenterologists, endoscopists, radiologists, and pathologists. In this context, histological examination of endoscopic or surgical specimens plays a fundamental role. Nevertheless, in differentiating IBD from non-IBD colitis, the histopathological evaluation of the morphological lesions is limited by sampling and subjective human judgment, leading to potential diagnostic discrepancies. To overcome these limitations, artificial intelligence (AI) techniques are emerging to enable automated analysis of medical images with advantages in accuracy, precision, and speed of investigation, increasing interest in the histological analysis of gastrointestinal inflammation. This review aims to provide an overview of the most recent knowledge and advances in AI methods, summarizing its applications in the histopathological analysis of endoscopic biopsies from IBD patients, and discussing its strengths and limitations in daily clinical practice.
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Affiliation(s)
- Anna Lucia Cannarozzi
- Division of Gastroenterology, Fondazione IRCCS - Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Luca Massimino
- Gastroenterology and Digestive Endoscopy Department, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Anna Latiano
- Division of Gastroenterology, Fondazione IRCCS - Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Lorenzo Parigi
- Gastroenterology and Digestive Endoscopy Department, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Francesco Giuliani
- Innovation & Research Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Fabrizio Bossa
- Division of Gastroenterology, Fondazione IRCCS - Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Anna Laura Di Brina
- Division of Gastroenterology, Fondazione IRCCS - Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Federica Ungaro
- Gastroenterology and Digestive Endoscopy Department, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Giuseppe Biscaglia
- Division of Gastroenterology, Fondazione IRCCS - Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Silvio Danese
- Faculty of Medicine, Università Vita-Salute San Raffaele, Milan, Italy
| | - Francesco Perri
- Division of Gastroenterology, Fondazione IRCCS - Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Orazio Palmieri
- Division of Gastroenterology, Fondazione IRCCS - Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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21
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Wang Z, Peng H, Wan J, Song A. Identification of histopathological classification and establishment of prognostic indicators of gastric adenocarcinoma based on deep learning algorithm. Med Mol Morphol 2024; 57:286-298. [PMID: 39088070 PMCID: PMC11543764 DOI: 10.1007/s00795-024-00399-8] [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: 03/11/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024]
Abstract
The aim of this study is to establish a deep learning (DL) model to predict the pathological type of gastric adenocarcinoma cancer based on whole-slide images(WSIs). We downloaded 356 histopathological images of gastric adenocarcinoma (STAD) patients from The Cancer Genome Atlas database and randomly divided them into the training set, validation set and test set (8:1:1). Additionally, 80 H&E-stained WSIs of STAD were collected for external validation. The CLAM tool was used to cut the WSIs and further construct the model by DL algorithm, achieving an accuracy of over 90% in identifying and predicting histopathological subtypes. External validation results demonstrated the model had a certain generalization ability. Moreover, DL features were extracted from the model to further investigate the differences in immune infiltration and patient prognosis between the two subtypes. The DL model can accurately predict the pathological classification of STAD patients, and provide certain reference value for clinical diagnosis. The nomogram combining DL-signature, gene-signature and clinical features can be used as a prognostic classifier for clinical decision-making and treatment.
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Affiliation(s)
- Zhihui Wang
- Department of Ultrasound Imaging, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430101, Hubei, China
| | - Hui Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430101, Hubei, China
| | - Jie Wan
- Department of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430101, Hubei, China
| | - Anping Song
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430101, Hubei, China.
- Department of Oncology, Tongji Hospital Sino-French New City Branch, Caidian District, No.288 Xintian Avenue, Wuhan, 430101, Hubei, China.
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22
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Hosseini MS, Bejnordi BE, Trinh VQH, Chan L, Hasan D, Li X, Yang S, Kim T, Zhang H, Wu T, Chinniah K, Maghsoudlou S, Zhang R, Zhu J, Khaki S, Buin A, Chaji F, Salehi A, Nguyen BN, Samaras D, Plataniotis KN. Computational pathology: A survey review and the way forward. J Pathol Inform 2024; 15:100357. [PMID: 38420608 PMCID: PMC10900832 DOI: 10.1016/j.jpi.2023.100357] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 03/02/2024] Open
Abstract
Computational Pathology (CPath) is an interdisciplinary science that augments developments of computational approaches to analyze and model medical histopathology images. The main objective for CPath is to develop infrastructure and workflows of digital diagnostics as an assistive CAD system for clinical pathology, facilitating transformational changes in the diagnosis and treatment of cancer that are mainly address by CPath tools. With evergrowing developments in deep learning and computer vision algorithms, and the ease of the data flow from digital pathology, currently CPath is witnessing a paradigm shift. Despite the sheer volume of engineering and scientific works being introduced for cancer image analysis, there is still a considerable gap of adopting and integrating these algorithms in clinical practice. This raises a significant question regarding the direction and trends that are undertaken in CPath. In this article we provide a comprehensive review of more than 800 papers to address the challenges faced in problem design all-the-way to the application and implementation viewpoints. We have catalogued each paper into a model-card by examining the key works and challenges faced to layout the current landscape in CPath. We hope this helps the community to locate relevant works and facilitate understanding of the field's future directions. In a nutshell, we oversee the CPath developments in cycle of stages which are required to be cohesively linked together to address the challenges associated with such multidisciplinary science. We overview this cycle from different perspectives of data-centric, model-centric, and application-centric problems. We finally sketch remaining challenges and provide directions for future technical developments and clinical integration of CPath. For updated information on this survey review paper and accessing to the original model cards repository, please refer to GitHub. Updated version of this draft can also be found from arXiv.
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Affiliation(s)
- Mahdi S. Hosseini
- Department of Computer Science and Software Engineering (CSSE), Concordia Univeristy, Montreal, QC H3H 2R9, Canada
| | | | - Vincent Quoc-Huy Trinh
- Institute for Research in Immunology and Cancer of the University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Lyndon Chan
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Danial Hasan
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Xingwen Li
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Stephen Yang
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Taehyo Kim
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Haochen Zhang
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Theodore Wu
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Kajanan Chinniah
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Sina Maghsoudlou
- Department of Computer Science and Software Engineering (CSSE), Concordia Univeristy, Montreal, QC H3H 2R9, Canada
| | - Ryan Zhang
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Jiadai Zhu
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Samir Khaki
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
| | - Andrei Buin
- Huron Digitial Pathology, St. Jacobs, ON N0B 2N0, Canada
| | - Fatemeh Chaji
- Department of Computer Science and Software Engineering (CSSE), Concordia Univeristy, Montreal, QC H3H 2R9, Canada
| | - Ala Salehi
- Department of Electrical and Computer Engineering, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Bich Ngoc Nguyen
- University of Montreal Hospital Center, Montreal, QC H2X 0C2, Canada
| | - Dimitris Samaras
- Department of Computer Science, Stony Brook University, Stony Brook, NY 11794, United States
| | - Konstantinos N. Plataniotis
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering (ECE), University of Toronto, Toronto, ON M5S 3G4, Canada
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23
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Shahadat N, Lama R, Nguyen A. Lung and Colon Cancer Detection Using a Deep AI Model. Cancers (Basel) 2024; 16:3879. [PMID: 39594834 PMCID: PMC11592951 DOI: 10.3390/cancers16223879] [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: 09/11/2024] [Revised: 10/31/2024] [Accepted: 11/10/2024] [Indexed: 11/28/2024] Open
Abstract
Lung and colon cancers are among the leading causes of cancer-related mortality worldwide. Early and accurate detection of these cancers is crucial for effective treatment and improved patient outcomes. False or incorrect detection is harmful. Accurately detecting cancer in a patient's tissue is crucial to their effective treatment. While analyzing tissue samples is complicated and time-consuming, deep learning techniques have made it possible to complete this process more efficiently and accurately. As a result, researchers can study more patients in a shorter amount of time and at a lower cost. Much research has been conducted to investigate deep learning models that require great computational ability and resources. However, none of these have had a 100% accurate detection rate for these life-threatening malignancies. Misclassified or falsely detecting cancer can have very harmful consequences. This research proposes a new lightweight, parameter-efficient, and mobile-embedded deep learning model based on a 1D convolutional neural network with squeeze-and-excitation layers for efficient lung and colon cancer detection. This proposed model diagnoses and classifies lung squamous cell carcinomas and adenocarcinoma of the lung and colon from digital pathology images. Extensive experiment demonstrates that our proposed model achieves 100% accuracy for detecting lung, colon, and lung and colon cancers from the histopathological (LC25000) lung and colon datasets, which is considered the best accuracy for around 0.35 million trainable parameters and around 6.4 million flops. Compared with the existing results, our proposed architecture shows state-of-the-art performance in lung, colon, and lung and colon cancer detection.
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Affiliation(s)
- Nazmul Shahadat
- Department of Computer and Data Sciences, Truman State University, Kirksville, MO 63501, USA; (R.L.); (A.N.)
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24
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Shen M, Jiang Z. Artificial Intelligence Applications in Lymphoma Diagnosis and Management: Opportunities, Challenges, and Future Directions. J Multidiscip Healthc 2024; 17:5329-5339. [PMID: 39582879 PMCID: PMC11583773 DOI: 10.2147/jmdh.s485724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Accepted: 10/09/2024] [Indexed: 11/26/2024] Open
Abstract
Lymphoma, a heterogeneous group of blood cancers, presents significant diagnostic and therapeutic challenges due to its complex subtypes and variable clinical outcomes. Artificial intelligence (AI) has emerged as a promising tool to enhance the accuracy and efficiency of lymphoma pathology. This review explores the potential of AI in lymphoma diagnosis, classification, prognosis prediction, and treatment planning, as well as addressing the challenges and future directions in this rapidly evolving field.
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Affiliation(s)
- Miao Shen
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, 310000, People’s Republic of China
- Department of Pathology, Deqing People’s Hospital, Huzhou City, Zhejiang Province, 313200, People’s Republic of China
| | - Zhinong Jiang
- Department of Pathology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou City, Zhejiang Province, 310000, People’s Republic of China
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25
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Rahaman MM, Millar EKA, Meijering E. Generalized deep learning for histopathology image classification using supervised contrastive learning. J Adv Res 2024:S2090-1232(24)00532-0. [PMID: 39551131 DOI: 10.1016/j.jare.2024.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 10/07/2024] [Accepted: 11/10/2024] [Indexed: 11/19/2024] Open
Abstract
INTRODUCTION Cancer is a leading cause of death worldwide, necessitating effective diagnostic tools for early detection and treatment. Histopathological image analysis is crucial for cancer diagnosis but is often hindered by human error and variability. This study introduces HistopathAI, a hybrid network designed for histopathology image classification, aimed at enhancing diagnostic precision and efficiency in clinical pathology. OBJECTIVES The primary goal of this study is to demonstrate that HistopathAI, leveraging supervised contrastive learning (SCL) and hybrid deep feature fusion (HDFF), can significantly improve the accuracy of histopathological image classification, including scenarios involving imbalanced datasets. METHODS HistopathAI integrates features from EfficientNetB3 and ResNet50, using HDFF to provide a rich representation of histopathology images. The framework employs a sequential methodology, transitioning from feature learning to classifier learning, mirroring the essence of contrastive learning with the aim of producing superior feature representations. The model combines SCL for feature representation with cross-entropy (CE) loss for classification. We evaluated HistopathAI across seven publicly available datasets and one private dataset, covering various histopathology domains. RESULTS HistopathAI achieved state-of-the-art classification accuracy across all datasets, demonstrating superior performance in both binary and multiclass classification tasks. Statistical testing confirmed that HistopathAI's performance is significantly better than baseline models, ensuring robust and reliable improvements. CONCLUSION HistopathAI offers a robust tool for histopathology image classification, enhancing diagnostic accuracy and supporting the transition to digital pathology. This framework has the potential to improve cancer diagnosis and patient outcomes, paving the way for broader clinical application. The code is available on https://github.com/Mamunur-20/HistopathAI.
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Affiliation(s)
- Md Mamunur Rahaman
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Ewan K A Millar
- Department of Anatomical Pathology, NSW Health Pathology, St. George Hospital, Sydney NSW 2217, Australia; St. George and Sutherland Clinical School, University of New South Wales, Sydney NSW 2052, Australia; Faculty of Medicine & Health Sciences, Western Sydney University, Sydney NSW 2560, Australia.
| | - Erik Meijering
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia.
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26
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Chen S, Ding P, Guo H, Meng L, Zhao Q, Li C. Applications of artificial intelligence in digital pathology for gastric cancer. Front Oncol 2024; 14:1437252. [PMID: 39529836 PMCID: PMC11551048 DOI: 10.3389/fonc.2024.1437252] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 10/07/2024] [Indexed: 11/16/2024] Open
Abstract
Gastric cancer is one of the most common cancers and is one of the leading causes of cancer-related deaths in worldwide. Early diagnosis and treatment are essential for a positive outcome. The integration of artificial intelligence in the pathology field is increasingly widespread, including histopathological images analysis. In recent years, the application of digital pathology technology emerged as a potential solution to enhance the understanding and management of gastric cancer. Through sophisticated image analysis algorithms, artificial intelligence technologies facilitate the accuracy and sensitivity of gastric cancer diagnosis and treatment and personalized therapeutic strategies. This review aims to evaluate the current landscape and future potential of artificial intelligence in transforming gastric cancer pathology, so as to provide ideas for future research.
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Affiliation(s)
- Sheng Chen
- School of Clinical Medicine, Hebei University, Affiliated Hospital of Hebei University, Baoding, China
| | - Ping’an Ding
- The Third Department of Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Big Data Analysis and Mining Application for Precise Diagnosis and Treatment of Gastric Cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Honghai Guo
- The Third Department of Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Big Data Analysis and Mining Application for Precise Diagnosis and Treatment of Gastric Cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Lingjiao Meng
- The Third Department of Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Big Data Analysis and Mining Application for Precise Diagnosis and Treatment of Gastric Cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Qun Zhao
- The Third Department of Surgery, the Fourth Hospital of Hebei Medical University, Shijiazhuang Hebei, China
- Hebei Key Laboratory of Precision Diagnosis and Comprehensive Treatment of Gastric Cancer, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Big Data Analysis and Mining Application for Precise Diagnosis and Treatment of Gastric Cancer Hebei Provincial Engineering Research Center, Shijiazhuang, Hebei, China
| | - Cong Li
- School of Clinical Medicine, Hebei University, Affiliated Hospital of Hebei University, Baoding, China
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, China
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27
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Wang J. Deep Learning in Hematology: From Molecules to Patients. Clin Hematol Int 2024; 6:19-42. [PMID: 39417017 PMCID: PMC11477942 DOI: 10.46989/001c.124131] [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: 05/31/2024] [Accepted: 06/29/2024] [Indexed: 10/19/2024] Open
Abstract
Deep learning (DL), a subfield of machine learning, has made remarkable strides across various aspects of medicine. This review examines DL's applications in hematology, spanning from molecular insights to patient care. The review begins by providing a straightforward introduction to the basics of DL tailored for those without prior knowledge, touching on essential concepts, principal architectures, and prevalent training methods. It then discusses the applications of DL in hematology, concentrating on elucidating the models' architecture, their applications, performance metrics, and inherent limitations. For example, at the molecular level, DL has improved the analysis of multi-omics data and protein structure prediction. For cells and tissues, DL enables the automation of cytomorphology analysis, interpretation of flow cytometry data, and diagnosis from whole slide images. At the patient level, DL's utility extends to analyzing curated clinical data, electronic health records, and clinical notes through large language models. While DL has shown promising results in various hematology applications, challenges remain in model generalizability and explainability. Moreover, the integration of novel DL architectures into hematology has been relatively slow in comparison to that in other medical fields.
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Affiliation(s)
- Jiasheng Wang
- Division of Hematology, Department of MedicineThe Ohio State University Comprehensive Cancer Center
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28
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Alsaafin A, Nejat P, Shafique A, Khan J, Alfasly S, Alabtah G, Tizhoosh HR. Sequential Patching Lattice for Image Classification and Enquiry: Streamlining Digital Pathology Image Processing. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:1898-1912. [PMID: 39032601 DOI: 10.1016/j.ajpath.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/06/2024] [Accepted: 06/18/2024] [Indexed: 07/23/2024]
Abstract
Digital pathology and the integration of artificial intelligence (AI) models have revolutionized histopathology, opening new opportunities. With the increasing availability of whole-slide images (WSIs), demand is growing for efficient retrieval, processing, and analysis of relevant images from vast biomedical archives. However, processing WSIs presents challenges due to their large size and content complexity. Full computer digestion of WSIs is impractical, and processing all patches individually is prohibitively expensive. In this article, we propose an unsupervised patching algorithm, Sequential Patching Lattice for Image Classification and Enquiry (SPLICE). This novel approach condenses a histopathology WSI into a compact set of representative patches, forming a collage of WSI while minimizing redundancy. SPLICE prioritizes patch quality and uniqueness by sequentially analyzing a WSI and selecting nonredundant representative features. In search and match applications, SPLICE showed improved accuracy, reduced computation time, and storage requirements compared with existing state-of-the-art methods. As an unsupervised method, SPLICE effectively reduced storage requirements for representing tissue images by 50%. This reduction can enable numerous algorithms in computational pathology to operate much more efficiently, paving the way for accelerated adoption of digital pathology.
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Affiliation(s)
- Areej Alsaafin
- KIMIA Lab, Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Peyman Nejat
- KIMIA Lab, Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Abubakr Shafique
- KIMIA Lab, Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Jibran Khan
- KIMIA Lab, Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Saghir Alfasly
- KIMIA Lab, Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Ghazal Alabtah
- KIMIA Lab, Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Hamid R Tizhoosh
- KIMIA Lab, Department of Artificial Intelligence and Informatics, Mayo Clinic, Rochester, Minnesota.
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29
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Mubarak M, Rashid R, Sapna F, Shakeel S. Expanding role and scope of artificial intelligence in the field of gastrointestinal pathology. Artif Intell Gastroenterol 2024; 5:91550. [DOI: 10.35712/aig.v5.i2.91550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 07/06/2024] [Accepted: 07/29/2024] [Indexed: 08/08/2024] Open
Abstract
Digital pathology (DP) and its subsidiaries including artificial intelligence (AI) are rapidly making inroads into the area of diagnostic anatomic pathology (AP) including gastrointestinal (GI) pathology. It is poised to revolutionize the field of diagnostic AP. Historically, AP has been slow to adopt digital technology, but this is changing rapidly, with many centers worldwide transitioning to DP. Coupled with advanced techniques of AI such as deep learning and machine learning, DP is likely to transform histopathology from a subjective field to an objective, efficient, and transparent discipline. AI is increasingly integrated into GI pathology, offering numerous advancements and improvements in overall diagnostic accuracy, efficiency, and patient care. Specifically, AI in GI pathology enhances diagnostic accuracy, streamlines workflows, provides predictive insights, integrates multimodal data, supports research, and aids in education and training, ultimately improving patient care and outcomes. This review summarized the latest developments in the role and scope of AI in AP with a focus on GI pathology. The main aim was to provide updates and create awareness among the pathology community.
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Affiliation(s)
- Muhammed Mubarak
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Rahma Rashid
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
| | - Fnu Sapna
- Department of Pathology, Montefiore Medical Center, The University Hospital for Albert Einstein School of Medicine, Bronx, NY 10461, United States
| | - Shaheera Shakeel
- Department of Histopathology, Sindh Institute of Urology and Transplantation, Karachi 74200, Sindh, Pakistan
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30
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Khayatian D, Maleki A, Nasiri H, Dorrigiv M. Histopathology image analysis for gastric cancer detection: a hybrid deep learning and catboost approach. MULTIMEDIA TOOLS AND APPLICATIONS 2024. [DOI: 10.1007/s11042-024-19816-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/04/2024] [Accepted: 06/25/2024] [Indexed: 01/03/2025]
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31
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Huang J, Saw SN, He T, Yang R, Qin Y, Chen Y, Kiong LC. DCNNLFS: A Dilated Convolutional Neural Network With Late Fusion Strategy for Intelligent Classification of Gastric Histopathology Images. IEEE J Biomed Health Inform 2024; 28:4534-4543. [PMID: 37983160 DOI: 10.1109/jbhi.2023.3334709] [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: 11/22/2023]
Abstract
Gastric cancer has a high incidence rate, significantly threatening patients' health. Gastric histopathology images can reliably diagnose related diseases. Still, the data volume of histopathology images is too large, making misdiagnosis or missed diagnosis easy. The classification model based on deep learning has made some progress on gastric histopathology images. However, traditional convolutional neural networks (CNNs) generally use pooling operations, which will reduce the spatial resolution of the image, resulting in poor prediction results. The image feature in previous CNN has a poor perception of details. Therefore, we design a dilated CNN with a late fusion strategy (DCNNLFS) for gastric histopathology image classification. The DCNNLFS model utilizes dilated convolutions, enabling it to expand the receptive field. The dilated convolutions can learn the different contextual information by adjusting the dilation rate. The DCNNLFS model uses a late fusion strategy to enhance the classification ability of DCNNLFS. We run related experiments on a gastric histopathology image dataset to verify the excellence of the DCNNLFS model, where the three metrics Precision, Accuracy, and F1-Score are 0.938, 0.935, and 0.959.
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Hu J, Li Y, Lin L, Chen YW. UPMatch: Enhancing Semi-Supervised Medical Image Classification through Contrastive Learning with Unreliable Pseudo Labels. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2024; 2024:1-5. [PMID: 40031450 DOI: 10.1109/embc53108.2024.10782507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Pseudo-labeling based semi-supervised learning (SSL) framework has proven highly successful in medical image analysis (MIA) by addressing the problem of a shortage of labeled samples. However, the existing SSL methods use a fixed or flexible confidence threshold to filter reliable samples, leaving large number of unlabeled samples unused. This is a more serious issue in MIA because of the low inter-class distance and imbalanced categories. We argue that effectively mining useful information hidden in ambiguous unlabeled sample is the key to improve model performance, so we propose UPmatch, a new pseudo labeling-based SSL framework. Our framework introduces a contrastive unreliable pseudo label learning module (CUPM) that incorporates unreliable pseudo label samples into the training process. Additionally, we propose an informative sample selection strategy (ISSS) that selects samples used in contrastive learning iteratively in each mini-batch. Our experiments on TissueMNIST and ISIC2019 dataset with various training settings demonstrate the effectiveness of our proposed strategy.
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Chen J, Yang J, Wang J, Zhao Z, Wang M, Sun C, Song N, Feng S. Study on an Automatic Classification Method for Determining the Malignancy Grade of Glioma Pathological Sections Based on Hyperspectral Multi-Scale Spatial-Spectral Fusion Features. SENSORS (BASEL, SWITZERLAND) 2024; 24:3803. [PMID: 38931588 PMCID: PMC11207485 DOI: 10.3390/s24123803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
This study describes a novel method for grading pathological sections of gliomas. Our own integrated hyperspectral imaging system was employed to characterize 270 bands of cancerous tissue samples from microarray slides of gliomas. These samples were then classified according to the guidelines developed by the World Health Organization, which define the subtypes and grades of diffuse gliomas. We explored a hyperspectral feature extraction model called SMLMER-ResNet using microscopic hyperspectral images of brain gliomas of different malignancy grades. The model combines the channel attention mechanism and multi-scale image features to automatically learn the pathological organization of gliomas and obtain hierarchical feature representations, effectively removing the interference of redundant information. It also completes multi-modal, multi-scale spatial-spectral feature extraction to improve the automatic classification of glioma subtypes. The proposed classification method demonstrated high average classification accuracy (>97.3%) and a Kappa coefficient (0.954), indicating its effectiveness in improving the automatic classification of hyperspectral gliomas. The method is readily applicable in a wide range of clinical settings, offering valuable assistance in alleviating the workload of clinical pathologists. Furthermore, the study contributes to the development of more personalized and refined treatment plans, as well as subsequent follow-up and treatment adjustment, by providing physicians with insights into the underlying pathological organization of gliomas.
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Affiliation(s)
- Jiaqi Chen
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China; (J.C.)
- University of Chinese Academy of Sciences, Beijing 130033, China
| | - Jin Yang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China; (J.C.)
| | - Jinyu Wang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China; (J.C.)
- University of Chinese Academy of Sciences, Beijing 130033, China
| | - Zitong Zhao
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China; (J.C.)
- University of Chinese Academy of Sciences, Beijing 130033, China
| | - Mingjia Wang
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China; (J.C.)
| | - Ci Sun
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China; (J.C.)
| | - Nan Song
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China; (J.C.)
| | - Shulong Feng
- Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, China; (J.C.)
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Norose T, Ohike N, Nakaya D, Kamiya K, Sugiura Y, Takatsuki M, Koizumi H, Okawa C, Ohya A, Sasaki M, Aoki R, Nakahara K, Kobayashi S, Tateishi K, Koike J. Investigation of the usefulness of a bile duct biopsy and bile cytology using a hyperspectral camera and machine learning. Pathol Int 2024; 74:337-345. [PMID: 38787324 DOI: 10.1111/pin.13438] [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: 12/24/2023] [Revised: 04/15/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
To improve the efficiency of pathological diagnoses, the development of automatic pathological diagnostic systems using artificial intelligence (AI) is progressing; however, problems include the low interpretability of AI technology and the need for large amounts of data. We herein report the usefulness of a general-purpose method that combines a hyperspectral camera with machine learning. As a result of analyzing bile duct biopsy and bile cytology specimens, which are especially difficult to determine as benign or malignant, using multiple machine learning models, both were able to identify benign or malignant cells with an accuracy rate of more than 80% (93.3% for bile duct biopsy specimens and 83.2% for bile cytology specimens). This method has the potential to contribute to the diagnosis and treatment of bile duct cancer and is expected to be widely applied and utilized in general pathological diagnoses.
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Affiliation(s)
- Tomoko Norose
- Division of Molecular Pathology, Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Nobuyuki Ohike
- Division of Molecular Pathology, Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | | | | | - Yoshiya Sugiura
- Division of Molecular Pathology, Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Misato Takatsuki
- Division of Molecular Pathology, Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hirotaka Koizumi
- Division of Molecular Pathology, Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Chie Okawa
- Division of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Aya Ohya
- Division of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Miyu Sasaki
- Division of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Ruka Aoki
- Division of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Kazunari Nakahara
- Department of Gastroenterology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Shinjiro Kobayashi
- Department of Gastroenterological and General Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Keisuke Tateishi
- Department of Gastroenterology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Junki Koike
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
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Zhang S, Yuan Z, Zhou X, Wang H, Chen B, Wang Y. VENet: Variational energy network for gland segmentation of pathological images and early gastric cancer diagnosis of whole slide images. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 250:108178. [PMID: 38652995 DOI: 10.1016/j.cmpb.2024.108178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/08/2024] [Accepted: 04/13/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND AND OBJECTIVE Gland segmentation of pathological images is an essential but challenging step for adenocarcinoma diagnosis. Although deep learning methods have recently made tremendous progress in gland segmentation, they have not given satisfactory boundary and region segmentation results of adjacent glands. These glands usually have a large difference in glandular appearance, and the statistical distribution between the training and test sets in deep learning is inconsistent. These problems make networks not generalize well in the test dataset, bringing difficulties to gland segmentation and early cancer diagnosis. METHODS To address these problems, we propose a Variational Energy Network named VENet with a traditional variational energy Lv loss for gland segmentation of pathological images and early gastric cancer detection in whole slide images (WSIs). It effectively integrates the variational mathematical model and the data-adaptability of deep learning methods to balance boundary and region segmentation. Furthermore, it can effectively segment and classify glands in large-size WSIs with reliable nucleus width and nucleus-to-cytoplasm ratio features. RESULTS The VENet was evaluated on the 2015 MICCAI Gland Segmentation challenge (GlaS) dataset, the Colorectal Adenocarcinoma Glands (CRAG) dataset, and the self-collected Nanfang Hospital dataset. Compared with state-of-the-art methods, our method achieved excellent performance for GlaS Test A (object dice 0.9562, object F1 0.9271, object Hausdorff distance 73.13), GlaS Test B (object dice 94.95, object F1 95.60, object Hausdorff distance 59.63), and CRAG (object dice 95.08, object F1 92.94, object Hausdorff distance 28.01). For the Nanfang Hospital dataset, our method achieved a kappa of 0.78, an accuracy of 0.9, a sensitivity of 0.98, and a specificity of 0.80 on the classification task of test 69 WSIs. CONCLUSIONS The experimental results show that the proposed model accurately predicts boundaries and outperforms state-of-the-art methods. It can be applied to the early diagnosis of gastric cancer by detecting regions of high-grade gastric intraepithelial neoplasia in WSI, which can assist pathologists in analyzing large WSI and making accurate diagnostic decisions.
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Affiliation(s)
- Shuchang Zhang
- Department of Mathematics, National University of Defense Technology, Changsha, China.
| | - Ziyang Yuan
- Academy of Military Sciences of the People's Liberation Army, Beijing, China.
| | - Xianchen Zhou
- Department of Mathematics, National University of Defense Technology, Changsha, China
| | - Hongxia Wang
- Department of Mathematics, National University of Defense Technology, Changsha, China.
| | - Bo Chen
- Suzhou Research Center, Institute of Automation, Chinese Academy of Sciences, Suzhou, China
| | - Yadong Wang
- Department of Laboratory Pathology, Baiyun Branch, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Zhou CM, Zhao SH. Evaluation of the value of combined detection of tumor markers CA724, carcinoembryonic antigen, CA242, and CA19-9 in gastric cancer. World J Gastrointest Oncol 2024; 16:1737-1744. [PMID: 38764828 PMCID: PMC11099441 DOI: 10.4251/wjgo.v16.i5.1737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/08/2024] [Accepted: 03/20/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND Gastric cancer is a global health concern that poses a significant threat to human well-being. AIM To detecting serum changes in carcinoembryonic antigen (CEA), carbohydrate antigens (CA) 724, CA242, and CA19-9 expression among patients with gastric cancer. METHODS Eighty patients diagnosed with gastric cancer between January 2020 and January 2023 were included in the observation group, while 80 patients with benign gastric diseases were included in the control group. Both groups were tested for tumor markers (CA724, CEA, CA242, and CA19-9]. Tumor marker indicators (CA724, CEA, CA242, and CA19-9) were compared between the two groups, assessing positive rates of tumor markers across various stages in the observation group. Additionally, single and combined detection of various tumor markers were examined. RESULTS The sensitivity, specificity, accuracy, positive predictive value, and negative predictive value observed for the combined detection of CA724, CEA, CA242, and CA19-9 were higher than those of CA724, CEA, CA242, and CA19-9 individually. Therefore, the combined detection of CA724, CEA, CA242, and CA19-9 has a high diagnostic accuracy and could reduce the occurrence of missed or misdiagnosed cases, facilitating the early diagnosis and treatment of patients. CONCLUSION CA724, CEA, CA242, and CA19-9 serum levels in gastric cancer patients significantly surpassed those in non-gastric cancer patients (P < 0.05). Their combined detection can improve the diagnostic accuracy for gastric cancer, warranting clinical promotion.
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Affiliation(s)
- Chong-Mei Zhou
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Zhengzhou 450003, Henan Province, China
| | - Shao-Hua Zhao
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Zhengzhou 450003, Henan Province, China
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McGenity C, Clarke EL, Jennings C, Matthews G, Cartlidge C, Freduah-Agyemang H, Stocken DD, Treanor D. Artificial intelligence in digital pathology: a systematic review and meta-analysis of diagnostic test accuracy. NPJ Digit Med 2024; 7:114. [PMID: 38704465 PMCID: PMC11069583 DOI: 10.1038/s41746-024-01106-8] [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: 06/17/2023] [Accepted: 04/12/2024] [Indexed: 05/06/2024] Open
Abstract
Ensuring diagnostic performance of artificial intelligence (AI) before introduction into clinical practice is essential. Growing numbers of studies using AI for digital pathology have been reported over recent years. The aim of this work is to examine the diagnostic accuracy of AI in digital pathology images for any disease. This systematic review and meta-analysis included diagnostic accuracy studies using any type of AI applied to whole slide images (WSIs) for any disease. The reference standard was diagnosis by histopathological assessment and/or immunohistochemistry. Searches were conducted in PubMed, EMBASE and CENTRAL in June 2022. Risk of bias and concerns of applicability were assessed using the QUADAS-2 tool. Data extraction was conducted by two investigators and meta-analysis was performed using a bivariate random effects model, with additional subgroup analyses also performed. Of 2976 identified studies, 100 were included in the review and 48 in the meta-analysis. Studies were from a range of countries, including over 152,000 whole slide images (WSIs), representing many diseases. These studies reported a mean sensitivity of 96.3% (CI 94.1-97.7) and mean specificity of 93.3% (CI 90.5-95.4). There was heterogeneity in study design and 99% of studies identified for inclusion had at least one area at high or unclear risk of bias or applicability concerns. Details on selection of cases, division of model development and validation data and raw performance data were frequently ambiguous or missing. AI is reported as having high diagnostic accuracy in the reported areas but requires more rigorous evaluation of its performance.
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Affiliation(s)
- Clare McGenity
- University of Leeds, Leeds, UK.
- Leeds Teaching Hospitals NHS Trust, Leeds, UK.
| | - Emily L Clarke
- University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Charlotte Jennings
- University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | | | | | | | - Darren Treanor
- University of Leeds, Leeds, UK
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Department of Clinical Pathology and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Centre for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
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Yilmaz F, Brickman A, Najdawi F, Yakirevich E, Egger R, Resnick MB. Advancing Artificial Intelligence Integration Into the Pathology Workflow: Exploring Opportunities in Gastrointestinal Tract Biopsies. J Transl Med 2024; 104:102043. [PMID: 38431118 DOI: 10.1016/j.labinv.2024.102043] [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: 10/30/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024] Open
Abstract
This review aims to present a comprehensive overview of the current landscape of artificial intelligence (AI) applications in the analysis of tubular gastrointestinal biopsies. These publications cover a spectrum of conditions, ranging from inflammatory ailments to malignancies. Moving beyond the conventional diagnosis based on hematoxylin and eosin-stained whole-slide images, the review explores additional implications of AI, including its involvement in interpreting immunohistochemical results, molecular subtyping, and the identification of cellular spatial biomarkers. Furthermore, the review examines how AI can contribute to enhancing the quality and control of diagnostic processes, introducing new workflow options, and addressing the limitations and caveats associated with current AI platforms in this context.
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Affiliation(s)
- Fazilet Yilmaz
- The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island
| | - Arlen Brickman
- The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island
| | - Fedaa Najdawi
- The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island
| | - Evgeny Yakirevich
- The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island
| | | | - Murray B Resnick
- The Warren Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island.
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Yuan L, Zhou H, Xiao X, Zhang X, Chen F, Liu L, Liu J, Bao S, Tao K. Development and external validation of a transfer learning-based system for the pathological diagnosis of colorectal cancer: a large emulated prospective study. Front Oncol 2024; 14:1365364. [PMID: 38725622 PMCID: PMC11079287 DOI: 10.3389/fonc.2024.1365364] [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: 01/19/2024] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Abstract
Background The progress in Colorectal cancer (CRC) screening and management has resulted in an unprecedented caseload for histopathological diagnosis. While artificial intelligence (AI) presents a potential solution, the predominant emphasis on slide-level aggregation performance without thorough verification of cancer in each location, impedes both explainability and transparency. Effectively addressing these challenges is crucial to ensuring the reliability and efficacy of AI in histology applications. Method In this study, we created an innovative AI algorithm using transfer learning from a polyp segmentation model in endoscopy. The algorithm precisely localized CRC targets within 0.25 mm² grids from whole slide imaging (WSI). We assessed the CRC detection capabilities at this fine granularity and examined the influence of AI on the diagnostic behavior of pathologists. The evaluation utilized an extensive dataset comprising 858 consecutive patient cases with 1418 WSIs obtained from an external center. Results Our results underscore a notable sensitivity of 90.25% and specificity of 96.60% at the grid level, accompanied by a commendable area under the curve (AUC) of 0.962. This translates to an impressive 99.39% sensitivity at the slide level, coupled with a negative likelihood ratio of <0.01, signifying the dependability of the AI system to preclude diagnostic considerations. The positive likelihood ratio of 26.54, surpassing 10 at the grid level, underscores the imperative for meticulous scrutiny of any AI-generated highlights. Consequently, all four participating pathologists demonstrated statistically significant diagnostic improvements with AI assistance. Conclusion Our transfer learning approach has successfully yielded an algorithm that can be validated for CRC histological localizations in whole slide imaging. The outcome advocates for the integration of the AI system into histopathological diagnosis, serving either as a diagnostic exclusion application or a computer-aided detection (CADe) tool. This integration has the potential to alleviate the workload of pathologists and ultimately benefit patients.
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Affiliation(s)
- Liuhong Yuan
- Department of Pathology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Pathology, Tongren Hospital, School of Medicine Shanghai Jiaotong University, Shanghai, China
| | - Henghua Zhou
- Department of Pathology, Tongren Hospital, School of Medicine Shanghai Jiaotong University, Shanghai, China
| | | | - Xiuqin Zhang
- Department of Pathology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Pathology, Tongren Hospital, School of Medicine Shanghai Jiaotong University, Shanghai, China
| | - Feier Chen
- Department of Pathology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Pathology, Tongren Hospital, School of Medicine Shanghai Jiaotong University, Shanghai, China
| | - Lin Liu
- Institute of Natural Sciences, MOE-LSC, School of Mathematical Sciences, CMA-Shanghai, SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | | | - Shisan Bao
- Department of Pathology, Tongren Hospital, School of Medicine Shanghai Jiaotong University, Shanghai, China
| | - Kun Tao
- Department of Pathology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Pathology, Tongren Hospital, School of Medicine Shanghai Jiaotong University, Shanghai, China
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Wang BS, Zhang CL, Cui X, Li Q, Yang L, He ZY, Yang Z, Zeng MM, Cao N. Curcumin inhibits the growth and invasion of gastric cancer by regulating long noncoding RNA AC022424.2. World J Gastrointest Oncol 2024; 16:1437-1452. [PMID: 38660661 PMCID: PMC11037052 DOI: 10.4251/wjgo.v16.i4.1437] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/19/2023] [Accepted: 01/17/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Gastric cancer, characterized by a multifactorial etiology and high heterogeneity, continues to confound researchers in terms of its pathogenesis. Curcumin, a natural anticancer agent, exhibits therapeutic promise in gastric cancer. Its effects include promoting cell apoptosis, curtailing tumor angiogenesis, and enhancing sensitivity to radiation and chemotherapy. Long noncoding RNAs (lncRNAs) have garnered significant attention as biomarkers for early screening, diagnosis, treatment, and drug response because of their remarkable specificity and sensitivity. Recent investigations have revealed an association between aberrant lncRNA expression and early diagnosis, clinical staging, metastasis, drug sensitivity, and prognosis in gastric cancer. A profound understanding of the intricate mechanisms through which lncRNAs influence gastric cancer development can provide novel insights for precision treatment and tailored management of patients with gastric cancer. This study aimed to unravel the potential of curcumin in suppressing the malignant behavior of gastric cancer cells by upregulating specific lncRNAs and modulating gastric cancer onset and progression. AIM To identify lncRNAs associated with curcumin treatment and investigate the role of lncRNA AC022424.2 in the effects of curcumin on gastric cancer cell apoptosis, proliferation, and invasion. Furthermore, these findings were validated in clinical samples. METHODS The study employed CCK-8 assays to assess the impact of curcumin on gastric cancer cell proliferation, flow cytometry to investigate its effects on apoptosis, and scratch and Transwell assays to evaluate its influence on the migration and invasion of BGC-823 and MGC-803 cells. Western blotting was used to gauge changes in the protein expression levels of CDK6, CDK4, Bax, Bcl-2, caspase-3, P65, and the PI3K/Akt/mTOR pathway in gastric cancer cell lines after curcumin treatment. Differential expression of lncRNAs before and after curcumin treatment was assessed using lncRNA sequencing and validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR) in BGC-823 and MGC-803 cells. AC022424.2-1 knockdown BGC-823 and MGC-803 cells were generated to scrutinize the impact of lncRNA AC022424.2 on apoptosis, proliferation, migration, and invasion of gastric cancer cells. Western blotting was performed to ascertain changes in the expression of proteins implicated in the PI3K/Akt/mTOR and NF-κB signaling pathways. RT-PCR was employed to measure lncRNA AC022424.2 expression in clinical gastric cancer tissues and to correlate its expression with clinical pathological characteristics. RESULTS Curcumin induced apoptosis and hindered proliferation, migration, and invasion of gastric cancer cells in a dose- and time-dependent manner. LncRNA AC022424.2 was upregulated after curcumin treatment, and its knockdown enhanced cancer cell aggressiveness. LncRNA AC022424.2 may have affected cancer cells via the PI3K/Akt/mTOR and NF-κB signaling pathways. LncRNA AC022424.2 downregulation was correlated with lymph node metastasis, making it a potential diagnostic and prognostic marker. CONCLUSION Curcumin has potential anticancer effects on gastric cancer cells by regulating lncRNA AC022424.2. This lncRNA plays a significant role in cancer cell behavior and may have clinical implications in diagnosis and prognosis evaluation. The results of this study enhance our understanding of gastric cancer development and precision treatment.
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Affiliation(s)
- Bin-Sheng Wang
- Department of General Surgery, First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Chen-Li Zhang
- School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Xiang Cui
- Department of General Surgery, First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Qiang Li
- Third Department of General Surgery, First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Lei Yang
- Department of General Surgery, First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Zhi-Yun He
- Department of General Surgery, First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Ze Yang
- Department of General Surgery, First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Miao-Miao Zeng
- Department of General Surgery, First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Nong Cao
- Department of General Surgery, First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
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Tam KH, Soares MF, Kers J, Sharples EJ, Ploeg RJ, Kaisar M, Rittscher J. Predicting clinical endpoints and visual changes with quality-weighted tissue-based renal histological features. FRONTIERS IN TRANSPLANTATION 2024; 3:1305468. [PMID: 38993786 PMCID: PMC11235227 DOI: 10.3389/frtra.2024.1305468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 03/15/2024] [Indexed: 07/13/2024]
Abstract
Two common obstacles limiting the performance of data-driven algorithms in digital histopathology classification tasks are the lack of expert annotations and the narrow diversity of datasets. Multi-instance learning (MIL) can address the former challenge for the analysis of whole slide images (WSI), but performance is often inferior to full supervision. We show that the inclusion of weak annotations can significantly enhance the effectiveness of MIL while keeping the approach scalable. An analysis framework was developed to process periodic acid-Schiff (PAS) and Sirius Red (SR) slides of renal biopsies. The workflow segments tissues into coarse tissue classes. Handcrafted and deep features were extracted from these tissues and combined using a soft attention model to predict several slide-level labels: delayed graft function (DGF), acute tubular injury (ATI), and Remuzzi grade components. A tissue segmentation quality metric was also developed to reduce the adverse impact of poorly segmented instances. The soft attention model was trained using 5-fold cross-validation on a mixed dataset and tested on the QUOD dataset containing n = 373 PAS and n = 195 SR biopsies. The average ROC-AUC over different prediction tasks was found to be 0.598 ± 0.011 , significantly higher than using only ResNet50 ( 0.545 ± 0.012 ), only handcrafted features ( 0.542 ± 0.011 ), and the baseline ( 0.532 ± 0.012 ) of state-of-the-art performance. In conjunction with soft attention, weighting tissues by segmentation quality has led to further improvement ( A U C = 0.618 ± 0.010 ) . Using an intuitive visualisation scheme, we show that our approach may also be used to support clinical decision making as it allows pinpointing individual tissues relevant to the predictions.
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Affiliation(s)
- Ka Ho Tam
- Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Maria F. Soares
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jesper Kers
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
- Department of Pathology, Leiden Transplant Center, Leiden University Medical Center, Leiden, Netherlands
- Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Edward J. Sharples
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Rutger J. Ploeg
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Research and Development, NHS Blood and Transplant Filton and Oxford, Oxford, United Kingdom
| | - Maria Kaisar
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Research and Development, NHS Blood and Transplant Filton and Oxford, Oxford, United Kingdom
| | - Jens Rittscher
- Institute of Biomedical Engineering, University of Oxford, Oxford, United Kingdom
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42
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Yengec-Tasdemir SB, Aydin Z, Akay E, Dogan S, Yilmaz B. An effective colorectal polyp classification for histopathological images based on supervised contrastive learning. Comput Biol Med 2024; 172:108267. [PMID: 38479197 DOI: 10.1016/j.compbiomed.2024.108267] [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: 10/09/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Early detection of colon adenomatous polyps is pivotal in reducing colon cancer risk. In this context, accurately distinguishing between adenomatous polyp subtypes, especially tubular and tubulovillous, from hyperplastic variants is crucial. This study introduces a cutting-edge computer-aided diagnosis system optimized for this task. Our system employs advanced Supervised Contrastive learning to ensure precise classification of colon histopathology images. Significantly, we have integrated the Big Transfer model, which has gained prominence for its exemplary adaptability to visual tasks in medical imaging. Our novel approach discerns between in-class and out-of-class images, thereby elevating its discriminatory power for polyp subtypes. We validated our system using two datasets: a specially curated one and the publicly accessible UniToPatho dataset. The results reveal that our model markedly surpasses traditional deep convolutional neural networks, registering classification accuracies of 87.1% and 70.3% for the custom and UniToPatho datasets, respectively. Such results emphasize the transformative potential of our model in polyp classification endeavors.
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Affiliation(s)
- Sena Busra Yengec-Tasdemir
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, BT39DT, United Kingdom.
| | - Zafer Aydin
- Department of Electrical and Computer Engineering, Abdullah Gul University, Kayseri, 38080, Turkey; Department of Computer Engineering, Abdullah Gul University, Kayseri, 38080, Turkey
| | - Ebru Akay
- Pathology Clinic, Kayseri City Hospital, Kayseri, 38080, Turkey
| | - Serkan Dogan
- Gastroenterology Clinic, Kayseri City Hospital, Kayseri, 38080, Turkey
| | - Bulent Yilmaz
- Department of Electrical and Computer Engineering, Abdullah Gul University, Kayseri, 38080, Turkey; Department of Electrical Engineering, Gulf University for Science and Technology, Mishref, 40005, Kuwait
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43
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Wu D, Lu J, Zheng N, Elsehrawy MG, Alfaiz FA, Zhao H, Alqahtani MS, Xu H. Utilizing nanotechnology and advanced machine learning for early detection of gastric cancer surgery. ENVIRONMENTAL RESEARCH 2024; 245:117784. [PMID: 38065392 DOI: 10.1016/j.envres.2023.117784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 01/06/2024]
Abstract
Nanotechnology has emerged as a promising frontier in revolutionizing the early diagnosis and surgical management of gastric cancers. The primary factors influencing curative efficacy in GIC patients are drug inefficacy and high surgical and pharmacological therapy recurrence rates. Due to its unique optical features, good biocompatibility, surface effects, and small size effects, nanotechnology is a developing and advanced area of study for detecting and treating cancer. Considering the limitations of GIC MRI and endoscopy and the complexity of gastric surgery, the early diagnosis and prompt treatment of gastric illnesses by nanotechnology has been a promising development. Nanoparticles directly target tumor cells, allowing their detection and removal. It also can be engineered to carry specific payloads, such as drugs or contrast agents, and enhance the efficacy and precision of cancer treatment. In this research, the boosting technique of machine learning was utilized to capture nonlinear interactions between a large number of input variables and outputs by using XGBoost and RNN-CNN as a classification method. The research sample included 350 patients, comprising 200 males and 150 females. The patients' mean ± SD was 50.34 ± 13.04 with a mean age of 50.34 ± 13.04. High-risk behaviors (P = 0.070), age at diagnosis (P = 0.034), distant metastasis (P = 0.004), and tumor stage (P = 0.014) were shown to have a statistically significant link with GC patient survival. AUC was 93.54%, Accuracy 93.54%, F1-score 93.57%, Precision 93.65%, and Recall 93.87% when analyzing stomach pictures. Integrating nanotechnology with advanced machine learning techniques holds promise for improving the diagnosis and treatment of gastric cancer, providing new avenues for precision medicine and better patient outcomes.
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Affiliation(s)
- Dan Wu
- Department of Gastrointestinal Surgery, Lishui Municipal Central Hospital, Lishui, 323000, Zhejiang, China
| | - Jianhua Lu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Nan Zheng
- School of Pharmacy, Wenzhou Medicine University, Wenzhou, 325000, China
| | - Mohamed Gamal Elsehrawy
- Prince Sattam Bin Abdulaziz University, College of Applied Medical Sciences, Kingdom of Saudi Arabia; Nursing Faculty, Port-Said University, Egypt.
| | - Faiz Abdulaziz Alfaiz
- Department of Biology, College of Science, Majmaah University, Al-Majmaah, 11952, Saudi Arabia.
| | - Huajun Zhao
- School of Pharmacy, Wenzhou Medicine University, Wenzhou, 325000, China.
| | - Mohammed S Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha, 61421, Saudi Arabia; BioImaging Unit, Space Research Centre, Michael Atiyah Building, University of Leicester, Leicester, LE1 7RH, UK
| | - Hongtao Xu
- Department of Gastrointestinal Surgery, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, 323000, Zhejiang, China.
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44
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Bouzid K, Sharma H, Killcoyne S, Castro DC, Schwaighofer A, Ilse M, Salvatelli V, Oktay O, Murthy S, Bordeaux L, Moore L, O'Donovan M, Thieme A, Nori A, Gehrung M, Alvarez-Valle J. Enabling large-scale screening of Barrett's esophagus using weakly supervised deep learning in histopathology. Nat Commun 2024; 15:2026. [PMID: 38467600 PMCID: PMC10928093 DOI: 10.1038/s41467-024-46174-2] [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: 09/01/2023] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
Timely detection of Barrett's esophagus, the pre-malignant condition of esophageal adenocarcinoma, can improve patient survival rates. The Cytosponge-TFF3 test, a non-endoscopic minimally invasive procedure, has been used for diagnosing intestinal metaplasia in Barrett's. However, it depends on pathologist's assessment of two slides stained with H&E and the immunohistochemical biomarker TFF3. This resource-intensive clinical workflow limits large-scale screening in the at-risk population. To improve screening capacity, we propose a deep learning approach for detecting Barrett's from routinely stained H&E slides. The approach solely relies on diagnostic labels, eliminating the need for expensive localized expert annotations. We train and independently validate our approach on two clinical trial datasets, totaling 1866 patients. We achieve 91.4% and 87.3% AUROCs on discovery and external test datasets for the H&E model, comparable to the TFF3 model. Our proposed semi-automated clinical workflow can reduce pathologists' workload to 48% without sacrificing diagnostic performance, enabling pathologists to prioritize high risk cases.
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Affiliation(s)
| | | | | | | | | | - Max Ilse
- Microsoft Health Futures, Cambridge, UK
| | | | | | | | | | - Luiza Moore
- Department of Histopathology, Addenbrookes Hospital, Cambridge University NHS Foundation Trust, Cambridge, UK
| | - Maria O'Donovan
- Cyted Ltd, Cambridge, UK
- Department of Histopathology, Addenbrookes Hospital, Cambridge University NHS Foundation Trust, Cambridge, UK
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45
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Neto PC, Montezuma D, Oliveira SP, Oliveira D, Fraga J, Monteiro A, Monteiro J, Ribeiro L, Gonçalves S, Reinhard S, Zlobec I, Pinto IM, Cardoso JS. An interpretable machine learning system for colorectal cancer diagnosis from pathology slides. NPJ Precis Oncol 2024; 8:56. [PMID: 38443695 PMCID: PMC10914836 DOI: 10.1038/s41698-024-00539-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/08/2024] [Indexed: 03/07/2024] Open
Abstract
Considering the profound transformation affecting pathology practice, we aimed to develop a scalable artificial intelligence (AI) system to diagnose colorectal cancer from whole-slide images (WSI). For this, we propose a deep learning (DL) system that learns from weak labels, a sampling strategy that reduces the number of training samples by a factor of six without compromising performance, an approach to leverage a small subset of fully annotated samples, and a prototype with explainable predictions, active learning features and parallelisation. Noting some problems in the literature, this study is conducted with one of the largest WSI colorectal samples dataset with approximately 10,500 WSIs. Of these samples, 900 are testing samples. Furthermore, the robustness of the proposed method is assessed with two additional external datasets (TCGA and PAIP) and a dataset of samples collected directly from the proposed prototype. Our proposed method predicts, for the patch-based tiles, a class based on the severity of the dysplasia and uses that information to classify the whole slide. It is trained with an interpretable mixed-supervision scheme to leverage the domain knowledge introduced by pathologists through spatial annotations. The mixed-supervision scheme allowed for an intelligent sampling strategy effectively evaluated in several different scenarios without compromising the performance. On the internal dataset, the method shows an accuracy of 93.44% and a sensitivity between positive (low-grade and high-grade dysplasia) and non-neoplastic samples of 0.996. On the external test samples varied with TCGA being the most challenging dataset with an overall accuracy of 84.91% and a sensitivity of 0.996.
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Affiliation(s)
- Pedro C Neto
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), R. Dr. Roberto Frias, Porto, 4200-465, Porto, Portugal.
- Faculty of Engineering, University of Porto (FEUP), R. Dr. Roberto Frias, Porto, 4200-465, Porto, Portugal.
| | - Diana Montezuma
- IMP Diagnostics, Praça do Bom Sucesso, 61, sala 808, Porto, 4150-146, Porto, Portugal.
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida 865, Porto, 4200-072, Porto, Portugal.
- Doctoral Programme in Medical Sciences, School of Medicine and Biomedical Sciences - University of Porto (ICBAS-UP), R. Jorge de Viterbo Ferreira 228, Porto, 4050-313, Porto, Portugal.
| | - Sara P Oliveira
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), R. Dr. Roberto Frias, Porto, 4200-465, Porto, Portugal.
- Faculty of Engineering, University of Porto (FEUP), R. Dr. Roberto Frias, Porto, 4200-465, Porto, Portugal.
| | - Domingos Oliveira
- IMP Diagnostics, Praça do Bom Sucesso, 61, sala 808, Porto, 4150-146, Porto, Portugal
| | - João Fraga
- Department of Pathology, IPO-Porto, R. Dr. António Bernardino de Almeida 865, Porto, 4200-072, Porto, Portugal
| | - Ana Monteiro
- IMP Diagnostics, Praça do Bom Sucesso, 61, sala 808, Porto, 4150-146, Porto, Portugal
| | - João Monteiro
- IMP Diagnostics, Praça do Bom Sucesso, 61, sala 808, Porto, 4150-146, Porto, Portugal
| | - Liliana Ribeiro
- IMP Diagnostics, Praça do Bom Sucesso, 61, sala 808, Porto, 4150-146, Porto, Portugal
| | - Sofia Gonçalves
- IMP Diagnostics, Praça do Bom Sucesso, 61, sala 808, Porto, 4150-146, Porto, Portugal
| | - Stefan Reinhard
- Institute of Pathology, University of Bern, Uni Bern, Murtenstrasse 31, Bern, 3008, Bern, Switzerland
| | - Inti Zlobec
- Institute of Pathology, University of Bern, Uni Bern, Murtenstrasse 31, Bern, 3008, Bern, Switzerland
| | - Isabel M Pinto
- IMP Diagnostics, Praça do Bom Sucesso, 61, sala 808, Porto, 4150-146, Porto, Portugal
| | - Jaime S Cardoso
- Institute for Systems and Computer Engineering, Technology and Science (INESC TEC), R. Dr. Roberto Frias, Porto, 4200-465, Porto, Portugal
- Faculty of Engineering, University of Porto (FEUP), R. Dr. Roberto Frias, Porto, 4200-465, Porto, Portugal
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46
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Yong MP, Hum YC, Lai KW, Lee YL, Goh CH, Yap WS, Tee YK. Histopathological Cancer Detection Using Intra-Domain Transfer Learning and Ensemble Learning. IEEE ACCESS 2024; 12:1434-1457. [DOI: 10.1109/access.2023.3343465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2024]
Affiliation(s)
- Ming Ping Yong
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
| | - Yan Chai Hum
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
| | - Khin Wee Lai
- Department of Biomedical Engineering, Faculty of Engineering, University of Malaya, Kuala Lumpur, Malaysia
| | - Ying Loong Lee
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
| | - Choon-Hian Goh
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
| | - Wun-She Yap
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
| | - Yee Kai Tee
- Lee Kong Chian Faculty of Engineering and Science, Universiti Tunku Abdul Rahman, Kajang, Malaysia
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47
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Ushakov E, Naumov A, Fomberg V, Vishnyakova P, Asaturova A, Badlaeva A, Tregubova A, Karpulevich E, Sukhikh G, Fatkhudinov T. EndoNet: A Model for the Automatic Calculation of H-Score on Histological Slides. INFORMATICS 2023; 10:90. [DOI: 10.3390/informatics10040090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2025] Open
Abstract
H-score is a semi-quantitative method used to assess the presence and distribution of proteins in tissue samples by combining the intensity of staining and the percentage of stained nuclei. It is widely used but time-consuming and can be limited in terms of accuracy and precision. Computer-aided methods may help overcome these limitations and improve the efficiency of pathologists’ workflows. In this work, we developed a model EndoNet for automatic H-score calculation on histological slides. Our proposed method uses neural networks and consists of two main parts. The first is a detection model which predicts the keypoints of centers of nuclei. The second is an H-score module that calculates the value of the H-score using mean pixel values of predicted keypoints. Our model was trained and validated on 1780 annotated tiles with a shape of 100 × 100 µm and we achieved 0.77 mAP on a test dataset. We obtained our best results in H-score calculation; these results proved superior to QuPath predictions. Moreover, the model can be adjusted to a specific specialist or whole laboratory to reproduce the manner of calculating the H-score. Thus, EndoNet is effective and robust in the analysis of histology slides, which can improve and significantly accelerate the work of pathologists.
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Affiliation(s)
- Egor Ushakov
- Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences (ISP RAS), 109004 Moscow, Russia
| | - Anton Naumov
- Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences (ISP RAS), 109004 Moscow, Russia
| | - Vladislav Fomberg
- Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences (ISP RAS), 109004 Moscow, Russia
| | - Polina Vishnyakova
- FSBI “National Medical Research Centre for Obstetrics, Gynecology and Perinatology Named after Academician V.I.Kulakov”, Ministry of Health of the Russian Federation, 4, Oparina Street, 117997 Moscow, Russia
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya Street 6, 117198 Moscow, Russia
| | - Aleksandra Asaturova
- FSBI “National Medical Research Centre for Obstetrics, Gynecology and Perinatology Named after Academician V.I.Kulakov”, Ministry of Health of the Russian Federation, 4, Oparina Street, 117997 Moscow, Russia
| | - Alina Badlaeva
- FSBI “National Medical Research Centre for Obstetrics, Gynecology and Perinatology Named after Academician V.I.Kulakov”, Ministry of Health of the Russian Federation, 4, Oparina Street, 117997 Moscow, Russia
| | - Anna Tregubova
- FSBI “National Medical Research Centre for Obstetrics, Gynecology and Perinatology Named after Academician V.I.Kulakov”, Ministry of Health of the Russian Federation, 4, Oparina Street, 117997 Moscow, Russia
| | - Evgeny Karpulevich
- Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences (ISP RAS), 109004 Moscow, Russia
| | - Gennady Sukhikh
- FSBI “National Medical Research Centre for Obstetrics, Gynecology and Perinatology Named after Academician V.I.Kulakov”, Ministry of Health of the Russian Federation, 4, Oparina Street, 117997 Moscow, Russia
| | - Timur Fatkhudinov
- Research Institute of Molecular and Cellular Medicine, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya Street 6, 117198 Moscow, Russia
- Avtsyn Research Institute of Human Morphology, Federal State Budgetary Scientific Institution “Petrovsky National Research Centre of Surgery”, 3 Tsurupa Street, 117418 Moscow, Russia
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48
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Schacherer DP, Herrmann MD, Clunie DA, Höfener H, Clifford W, Longabaugh WJR, Pieper S, Kikinis R, Fedorov A, Homeyer A. The NCI Imaging Data Commons as a platform for reproducible research in computational pathology. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 242:107839. [PMID: 37832430 PMCID: PMC10841477 DOI: 10.1016/j.cmpb.2023.107839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 09/20/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND AND OBJECTIVES Reproducibility is a major challenge in developing machine learning (ML)-based solutions in computational pathology (CompPath). The NCI Imaging Data Commons (IDC) provides >120 cancer image collections according to the FAIR principles and is designed to be used with cloud ML services. Here, we explore its potential to facilitate reproducibility in CompPath research. METHODS Using the IDC, we implemented two experiments in which a representative ML-based method for classifying lung tumor tissue was trained and/or evaluated on different datasets. To assess reproducibility, the experiments were run multiple times with separate but identically configured instances of common ML services. RESULTS The results of different runs of the same experiment were reproducible to a large extent. However, we observed occasional, small variations in AUC values, indicating a practical limit to reproducibility. CONCLUSIONS We conclude that the IDC facilitates approaching the reproducibility limit of CompPath research (i) by enabling researchers to reuse exactly the same datasets and (ii) by integrating with cloud ML services so that experiments can be run in identically configured computing environments.
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Affiliation(s)
- Daniela P Schacherer
- Fraunhofer Institute for Digital Medicine MEVIS, Max-von-Laue-Straße 2, 28359 Bremen, Germany
| | - Markus D Herrmann
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Henning Höfener
- Fraunhofer Institute for Digital Medicine MEVIS, Max-von-Laue-Straße 2, 28359 Bremen, Germany
| | | | | | | | - Ron Kikinis
- Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Andrey Fedorov
- Department of Radiology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - André Homeyer
- Fraunhofer Institute for Digital Medicine MEVIS, Max-von-Laue-Straße 2, 28359 Bremen, Germany.
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49
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Shi J, Tang L, Gao Z, Li Y, Wang C, Gong T, Li C, Fu H. MG-Trans: Multi-Scale Graph Transformer With Information Bottleneck for Whole Slide Image Classification. IEEE TRANSACTIONS ON MEDICAL IMAGING 2023; 42:3871-3883. [PMID: 37682644 DOI: 10.1109/tmi.2023.3313252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
Multiple instance learning (MIL)-based methods have become the mainstream for processing the megapixel-sized whole slide image (WSI) with pyramid structure in the field of digital pathology. The current MIL-based methods usually crop a large number of patches from WSI at the highest magnification, resulting in a lot of redundancy in the input and feature space. Moreover, the spatial relations between patches can not be sufficiently modeled, which may weaken the model's discriminative ability on fine-grained features. To solve the above limitations, we propose a Multi-scale Graph Transformer (MG-Trans) with information bottleneck for whole slide image classification. MG-Trans is composed of three modules: patch anchoring module (PAM), dynamic structure information learning module (SILM), and multi-scale information bottleneck module (MIBM). Specifically, PAM utilizes the class attention map generated from the multi-head self-attention of vision Transformer to identify and sample the informative patches. SILM explicitly introduces the local tissue structure information into the Transformer block to sufficiently model the spatial relations between patches. MIBM effectively fuses the multi-scale patch features by utilizing the principle of information bottleneck to generate a robust and compact bag-level representation. Besides, we also propose a semantic consistency loss to stabilize the training of the whole model. Extensive studies on three subtyping datasets and seven gene mutation detection datasets demonstrate the superiority of MG-Trans.
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50
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Yousif M, Pantanowitz L. Artificial Intelligence-Enabled Gastric Cancer Interpretations: Are We There yet? Surg Pathol Clin 2023; 16:673-686. [PMID: 37863559 DOI: 10.1016/j.path.2023.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
The integration of digital pathology and artificial intelligence (AI) is revolutionizing pathology by providing pathologists with new tools to improve workflow, enhance diagnostic accuracy, and undertake novel discovery. The capability of AI to recognize patterns and features in digital images beyond human perception is particularly valuable, thereby providing additional information for prognostic and predictive purposes. AI-based tools diagnose gastric carcinoma in digital images, detect gastric carcinoma metastases in lymph nodes, automate Ki-67 scoring in gastric neuroendocrine tumors, and quantify tumor-infiltrating lymphocytes. This article provides an overview of all of these applications of AI pertaining to gastric cancer.
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Affiliation(s)
- Mustafa Yousif
- Department of Pathology, University of Michigan, NCRC Building 35, 2800 Plymouth Road, Ann Arbor, MI 48109, USA.
| | - Liron Pantanowitz
- Department of Pathology, UPMC Shadyside Hospital, 5150 Centre Avenue Cancer Pavilion, POB2, Suite 3B, Room 347, Pittsburgh, PA 15232, USA
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