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Diagnostics
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Artificial Intelligence in Histopathology: Biomarkers, Diagnosis and Prognosis
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Artificial Intelligence in Histopathology: Biomarkers, Diagnosis and Prognosis

A special issue of Diagnostics (ISSN 2075-4418). This special issue belongs to the section "Machine Learning and Artificial Intelligence in Diagnostics".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 3999

Special Issue Editor

Dr. Muhammad Shaban

E-Mail Website
Guest Editor
Harvard Medical School, Boston, MA, USA
Interests: artificial intelligence; deep learning; computational pathology; histopathology

Special Issue Information

Dear Colleagues, 

This Special Issue, entitled "Artificial Intelligence in Histopathology: Biomarkers, Diagnosis and Prognosis", aims to highlight recent advances in the application of artificial intelligence (AI) for improving the diagnosis, prognosis, and treatment of various diseases based on histopathological images. The Special Issue will cover a broad range of topics related to AI in histopathology, including, but not limited to image analysis, feature extraction, pattern recognition and machine learning algorithms. The Issue will also focus on the development of new AI-based tools and techniques for identifying biomarkers, predicting disease outcomes and assessing treatment responses. Ultimately, this Special Issue aims to provide insights into the current state of the art in AI-based histopathology research and its potential impact on clinical practice.

Dr. Muhammad Shaban
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diagnostics is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • artificial intelligence
  • histopathology
  • computational pathology
  • digital biomarkers
  • automated diagnosis
  • automated prognosis
  • machine learning
  • deep learning
  • treatment response

Published Papers (3 papers)

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Research

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10 pages, 1356 KiB  
Article
The Diagnosis of Malignant Pleural Effusion Using Tumor-Marker Combinations: A Cost-Effectiveness Analysis Based on a Stacking Model
by Jingyuan Wang, Jiangjie Zhou, Hanyu Wu, Yangyu Chen and Baosheng Liang
Diagnostics 2023, 13(19), 3136; https://doi.org/10.3390/diagnostics13193136 - 05 Oct 2023
Viewed by 729
Abstract
Purpose: By incorporating the cost of multiple tumor-marker tests, this work aims to comprehensively evaluate the financial burden of patients and the accuracy of machine learning models in diagnosing malignant pleural effusion (MPE) using tumor-marker combinations. Methods: Carcinoembryonic antigen (CEA), carbohydrate antigen (CA)19-9, [...] Read more.
Purpose: By incorporating the cost of multiple tumor-marker tests, this work aims to comprehensively evaluate the financial burden of patients and the accuracy of machine learning models in diagnosing malignant pleural effusion (MPE) using tumor-marker combinations. Methods: Carcinoembryonic antigen (CEA), carbohydrate antigen (CA)19-9, CA125, and CA15-3 were collected from pleural effusion (PE) and peripheral blood (PB) of 319 patients with pleural effusion. A stacked ensemble (stacking) model based on five machine learning models was utilized to evaluate the diagnostic accuracy of tumor markers. We evaluated the discriminatory accuracy of various tumor-marker combinations using the area under the curve (AUC), sensitivity, and specificity. To evaluate the cost-effectiveness of different tumor-marker combinations, a comprehensive score (C-score) with a tuning parameter w was proposed. Results: In most scenarios, the stacking model outperformed the five individual machine learning models in terms of AUC. Among the eight tumor markers, the CEA in PE (PE.CEA) showed the best AUC of 0.902. Among all tumor-marker combinations, the PE.CA19-9 + PE.CA15-3 + PE.CEA + PB.CEA combination (C9 combination) achieved the highest AUC of 0.946. When w puts more weight on the cost, the highest C-score was achieved with the single PE.CEA marker. As w puts over 0.8 weight on AUC, the C-score favored diagnostic models with more expensive tumor-marker combinations. Specifically, when w was set to 0.99, the C9 combination achieved the best C-score. Conclusion: The stacking diagnostic model using PE.CEA is a relatively accurate and affordable choice in diagnosing MPE for patients without medical insurance or in a low economic level. The stacking model using the combination PE.CA19-9 + PE.CA15-3 + PE.CEA + PB.CEA is the most accurate diagnostic model and the best choice for patients without an economic burden. From a cost-effectiveness perspective, the stacking diagnostic model with PE.CA19-9 + PE.CA15-3 + PE.CEA combination is particularly recommended, as it gains the best trade-off between the low cost and high effectiveness. Full article
(This article belongs to the Special Issue Artificial Intelligence in Histopathology: Biomarkers, Diagnosis and Prognosis)
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13 pages, 2579 KiB  
Article
Use of a Novel Deep Learning Open-Source Model for Quantification of Ki-67 in Breast Cancer Patients in Pakistan: A Comparative Study between the Manual and Automated Methods
by Talat Zehra, Nazish Jaffar, Mahin Shams, Qurratulain Chundriger, Arsalan Ahmed, Fariha Anum, Najah Alsubaie and Zubair Ahmad
Diagnostics 2023, 13(19), 3105; https://doi.org/10.3390/diagnostics13193105 - 30 Sep 2023
Cited by 2 | Viewed by 1225
Abstract
Introduction: Breast cancer is the most common cancer in women; its early detection plays a crucial role in improving patient outcomes. Ki-67 is a biomarker commonly used for evaluating the proliferation of cancer cells in breast cancer patients. The quantification of Ki-67 has [...] Read more.
Introduction: Breast cancer is the most common cancer in women; its early detection plays a crucial role in improving patient outcomes. Ki-67 is a biomarker commonly used for evaluating the proliferation of cancer cells in breast cancer patients. The quantification of Ki-67 has traditionally been performed by pathologists through a manual examination of tissue samples, which can be time-consuming and subject to inter- and intra-observer variability. In this study, we used a novel deep learning model to quantify Ki-67 in breast cancer in digital images prepared by a microscope-attached camera. Objective: To compare the automated detection of Ki-67 with the manual eyeball/hotspot method. Place and duration of study: This descriptive, cross-sectional study was conducted at the Jinnah Sindh Medical University. Glass slides of diagnosed cases of breast cancer were obtained from the Aga Khan University Hospital after receiving ethical approval. The duration of the study was one month. Methodology: We prepared 140 digital images stained with the Ki-67 antibody using a microscope-attached camera at 10×. An expert pathologist (P1) evaluated the Ki-67 index of the hotspot fields using the eyeball method. The images were uploaded to the DeepLiif software to detect the exact percentage of Ki-67 positive cells. SPSS version 24 was used for data analysis. Diagnostic accuracy was also calculated by other pathologists (P2, P3) and by AI using a Ki-67 cut-off score of 20 and taking P1 as the gold standard. Results: The manual and automated scoring methods showed a strong positive correlation as the kappa coefficient was significant. The p value was <0.001. The highest diagnostic accuracy, i.e., 95%, taking P1 as gold standard, was found for AI, compared to pathologists P2 and P3. Conclusions: Use of quantification-based deep learning models can make the work of pathologists easier and more reproducible. Our study is one of the earliest studies in this field. More studies with larger sample sizes are needed in future to develop a cohort. Full article
(This article belongs to the Special Issue Artificial Intelligence in Histopathology: Biomarkers, Diagnosis and Prognosis)
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Other

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18 pages, 1131 KiB  
Systematic Review
Artificial Intelligence in Predicting Microsatellite Instability and KRAS, BRAF Mutations from Whole-Slide Images in Colorectal Cancer: A Systematic Review
by Theo Guitton, Pierre Allaume, Noémie Rabilloud, Nathalie Rioux-Leclercq, Sébastien Henno, Bruno Turlin, Marie-Dominique Galibert-Anne, Astrid Lièvre, Alexandra Lespagnol, Thierry Pécot and Solène-Florence Kammerer-Jacquet
Diagnostics 2024, 14(1), 99; https://doi.org/10.3390/diagnostics14010099 - 31 Dec 2023
Cited by 1 | Viewed by 1528
Abstract
Mismatch repair deficiency (d-MMR)/microsatellite instability (MSI), KRAS, and BRAF mutational status are crucial for treating advanced colorectal cancer patients. Traditional methods like immunohistochemistry or polymerase chain reaction (PCR) can be challenged by artificial intelligence (AI) based on whole slide images (WSI) to [...] Read more.
Mismatch repair deficiency (d-MMR)/microsatellite instability (MSI), KRAS, and BRAF mutational status are crucial for treating advanced colorectal cancer patients. Traditional methods like immunohistochemistry or polymerase chain reaction (PCR) can be challenged by artificial intelligence (AI) based on whole slide images (WSI) to predict tumor status. In this systematic review, we evaluated the role of AI in predicting MSI status, KRAS, and BRAF mutations in colorectal cancer. Studies published in PubMed up to June 2023 were included (n = 17), and we reported the risk of bias and the performance for each study. Some studies were impacted by the reduced number of slides included in the data set and the lack of external validation cohorts. Deep learning models for the d-MMR/MSI status showed a good performance in training cohorts (mean AUC = 0.89, [0.74–0.97]) but slightly less than expected in the validation cohort when available (mean AUC = 0.82, [0.63–0.98]). Contrary to the MSI status, the prediction of KRAS and BRAF mutations was less explored with a less robust methodology. The performance was lower, with a maximum of 0.77 in the training cohort, 0.58 in the validation cohort for KRAS, and 0.82 AUC in the training cohort for BRAF. Full article
(This article belongs to the Special Issue Artificial Intelligence in Histopathology: Biomarkers, Diagnosis and Prognosis)
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