Umay Kiraz
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View article: Validation of an Artificial Intelligence Model for Breast Cancer Molecular Subtyping Using Hematoxylin and Eosin-Stained Whole-Slide Images in a Population-Based Cohort
Validation of an Artificial Intelligence Model for Breast Cancer Molecular Subtyping Using Hematoxylin and Eosin-Stained Whole-Slide Images in a Population-Based Cohort Open
Background/Objectives: Breast cancer (BC) is the most commonly diagnosed cancer in women and the leading cause of cancer-related deaths globally. Molecular subtyping is crucial for prognosis and treatment planning, with immunohistochemistr…
View article: Self-contrastive weakly supervised learning framework for prognostic prediction using whole slide images
Self-contrastive weakly supervised learning framework for prognostic prediction using whole slide images Open
We present a pioneering investigation into the application of deep learning techniques to analyze histopathological images for addressing the substantial challenge of automated prognostic prediction. Prognostic prediction poses a unique ch…
View article: In triple-negative breast cancer, fibrotic focus, the mitotic activity index and tumour-infiltrating lymphocytes have independent prognostic value: an observational population-based cohort study with very long follow-up
In triple-negative breast cancer, fibrotic focus, the mitotic activity index and tumour-infiltrating lymphocytes have independent prognostic value: an observational population-based cohort study with very long follow-up Open
Aims Triple-negative breast cancer (TNBC) is prognostically and therapeutically heterogeneous. The mitotic activity index (MAI) and fibrotic focus (FF) have been established as predictors in non-TNBC but not in TNBC. Late distant metastase…
View article: Dual Functions of Androgen Receptor Overexpression in Triple-Negative Breast Cancer: A Complex Prognostic Marker
Dual Functions of Androgen Receptor Overexpression in Triple-Negative Breast Cancer: A Complex Prognostic Marker Open
A subset of triple-negative breast cancer (TNBC) expresses the androgen receptor (AR), but thresholds for AR positivity and its clinical significance vary. We hypothesize that objective assessment outperforms subjective methods, and that h…
View article: Equipping computational pathology systems with artifact processing pipelines: a showcase for computation and performance trade-offs
Equipping computational pathology systems with artifact processing pipelines: a showcase for computation and performance trade-offs Open
Background Histopathology is a gold standard for cancer diagnosis. It involves extracting tissue specimens from suspicious areas to prepare a glass slide for a microscopic examination. However, histological tissue processing procedures res…
View article: NMGrad: Advancing Histopathological Bladder Cancer Grading with Weakly Supervised Deep Learning
NMGrad: Advancing Histopathological Bladder Cancer Grading with Weakly Supervised Deep Learning Open
The most prevalent form of bladder cancer is urothelial carcinoma, characterized by a high recurrence rate and substantial lifetime treatment costs for patients. Grading is a prime factor for patient risk stratification, although it suffer…
View article: Nottingham prognostic x (<scp>NPx</scp>): a risk stratification tool in <scp>ER</scp>‐positive <scp>HER2</scp>‐negative breast cancer: a validation study
Nottingham prognostic x (<span>NPx</span>): a risk stratification tool in <span>ER</span>‐positive <span>HER2</span>‐negative breast cancer: a validation study Open
Aims In this study, we validate the use of Nottingham Prognostic x (NPx), consisting of tumour size, tumour grade, progesterone receptor (PR) and Ki67 in luminal BC. Materials and methods Two large cohorts of luminal early‐stage BC ( n = 2…
View article: NMGrad: Advancing Histopathological Bladder Cancer Grading with Weakly Supervised Deep Learning
NMGrad: Advancing Histopathological Bladder Cancer Grading with Weakly Supervised Deep Learning Open
The most prevalent form of bladder cancer is urothelial carcinoma, characterized by a high recurrence rate and substantial lifetime treatment costs for patients. Grading is a prime factor for patient risk stratification, although it suffer…
View article: Self-Contrastive Weakly Supervised Learning Framework for Prognostic Prediction Using Whole Slide Images
Self-Contrastive Weakly Supervised Learning Framework for Prognostic Prediction Using Whole Slide Images Open
We present a pioneering investigation into the application of deep learning techniques to analyze histopathological images for addressing the substantial challenge of automated prognostic prediction. Prognostic prediction poses a unique ch…
View article: Equipping Computational Pathology Systems with Artifact Processing Pipelines: A Showcase for Computation and Performance Trade-offs
Equipping Computational Pathology Systems with Artifact Processing Pipelines: A Showcase for Computation and Performance Trade-offs Open
Background: Histopathology is a gold standard for cancer diagnosis. It involves extracting tissue specimens from suspicious areas to prepare a glass slide for a microscopic examination. However, histological tissue processing procedures re…
View article: Equipping Computational Pathology Systems with Artifact Processing Pipelines: A Showcase for Computation and Performance Trade-offs
Equipping Computational Pathology Systems with Artifact Processing Pipelines: A Showcase for Computation and Performance Trade-offs Open
Background Histopathology is a gold standard for cancer diagnosis. It involves extracting tissue specimens from suspicious areas to prepare a glass slide for a microscopic examination. However, histological tissue processing procedures res…
View article: HistoArtifacts
HistoArtifacts Open
This dataset contains five notable histological artifacts: blur, blood (hemorrhage), air bubbles, folded tissue, and damaged tissue. This dataset is used in the following works, and a description of the dataset can be found at https://arxi…
View article: Image‐based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno‐oncology Biomarker Working Group on Breast Cancer
Image‐based multiplex immune profiling of cancer tissues: translational implications. A report of the International Immuno‐oncology Biomarker Working Group on Breast Cancer Open
Recent advances in the field of immuno‐oncology have brought transformative changes in the management of cancer patients. The immune profile of tumours has been found to have key value in predicting disease prognosis and treatment response…
View article: Uninformed Teacher-Student for hard-samples distillation in weakly supervised mitosis localization
Uninformed Teacher-Student for hard-samples distillation in weakly supervised mitosis localization Open
The proposed Uninformed Teacher-Student pipeline leverages strong augmentations to distill uncertain samples and measure dissimilarities between predicted and annotated mitosis. Results demonstrate the feasibility of the weakly supervised …
View article: Predicting Neoadjuvant Treatment Response in Triple-Negative Breast Cancer Using Machine Learning
Predicting Neoadjuvant Treatment Response in Triple-Negative Breast Cancer Using Machine Learning Open
Background: Neoadjuvant chemotherapy (NAC) is the standard treatment for early-stage triple negative breast cancer (TNBC). The primary endpoint of NAC is a pathological complete response (pCR). NAC results in pCR in only 30–40% of TNBC pat…
View article: Are you sure it’s an artifact? Artifact detection and uncertainty quantification in histological images
Are you sure it’s an artifact? Artifact detection and uncertainty quantification in histological images Open
Modern cancer diagnostics involves extracting tissue specimens from suspicious areas and conducting histotechnical procedures to prepare a digitized glass slide, called Whole Slide Image (WSI), for further examination. These procedures fre…
View article: Whole-Exome Sequencing Reveals High Mutational Concordance between Primary and Matched Recurrent Triple-Negative Breast Cancers
Whole-Exome Sequencing Reveals High Mutational Concordance between Primary and Matched Recurrent Triple-Negative Breast Cancers Open
Purpose: Triple-negative breast cancer (TNBC) is a molecularly complex and heterogeneous breast cancer subtype with distinct biological features and clinical behavior. Although TNBC is associated with an increased risk of metastasis and re…
View article: Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer
Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer Open
Modern histologic imaging platforms coupled with machine learning methods have provided new opportunities to map the spatial distribution of immune cells in the tumor microenvironment. However, there exists no standardized method for descr…
View article: Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer
Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer Open
The clinical significance of the tumor‐immune interaction in breast cancer is now established, and tumor‐infiltrating lymphocytes (TILs) have emerged as predictive and prognostic biomarkers for patients with triple‐negative (estrogen recep…
View article: Predicting neoadjuvant treatment response in triple-negative breast cancer using machine learning
Predicting neoadjuvant treatment response in triple-negative breast cancer using machine learning Open
Background Neoadjuvant chemotherapy (NAC) is the standard treatment for early-stage triple negative breast cancer (TNBC). The primary endpoint of NAC is a pathological complete response (pCR). NAC results in pCR in only 30%–40% of TNBC pat…
View article: Is decreased tissue elasticity more important than histopathological changes in ruptures of ascending aortic aneurysms?
Is decreased tissue elasticity more important than histopathological changes in ruptures of ascending aortic aneurysms? Open
Background: In this study, we aimed to investigate the natural properties of ascending aortic aneurysms and to compare dilated aortic tissues of patients with ascending aortic aneurysms and the non-pathological aortic tissues of cadavers. …
View article: A spatial attention guided deep learning system for prediction of pathological complete response using breast cancer histopathology images
A spatial attention guided deep learning system for prediction of pathological complete response using breast cancer histopathology images Open
Motivation Predicting pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC) patients accurately is direly needed for clinical decision making. pCR is also regarded as a strong predic…
View article: Invasive Cancerous Area Detection in Non-Muscle Invasive Bladder Cancer Whole Slide Images
Invasive Cancerous Area Detection in Non-Muscle Invasive Bladder Cancer Whole Slide Images Open
Bladder cancer patients’ stratification into risk groups relies on grade, stage and clinical factors. For non-muscle invasive bladder cancer, T1 tumours that invade the subepithelial tissue are high-risk lesions with a high probability to …
View article: A Spatial Attention Guided Deep Learning System for Prediction of Pathological Complete Response Using Breast Cancer Histopathology Images
A Spatial Attention Guided Deep Learning System for Prediction of Pathological Complete Response Using Breast Cancer Histopathology Images Open
Predicting pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC) patients accurately is direly needed for clinical decision making. pCR is also regarded as a strong predictor of over…
View article: Distinct Gene Expression Profiles of Matched Primary and Metastatic Triple-Negative Breast Cancers
Distinct Gene Expression Profiles of Matched Primary and Metastatic Triple-Negative Breast Cancers Open
Background: Although triple-negative breast cancer (TNBC) is associated with an increased risk of recurrence and metastasis, the molecular mechanisms underlying metastasis in TNBC remain unknown. To identify transcriptional changes and gen…
View article: Challenging Mitosis Detection Algorithms: Global Labels Allow Centroid Localization
Challenging Mitosis Detection Algorithms: Global Labels Allow Centroid Localization Open
View article: Az Diferansiye Tiroid Karsinomlarının Turin ve “Memorial Sloan Kettering Kanser Merkezi” Kriterlerine Göre Retrospektif Değerlendirilmesi
Az Diferansiye Tiroid Karsinomlarının Turin ve “Memorial Sloan Kettering Kanser Merkezi” Kriterlerine Göre Retrospektif Değerlendirilmesi Open
Amaç: Az diferansiye tiroid karsinomları (ADTK), biyolojik davranışlarına göre, iyi diferansiye tiroid karsinomlarla anaplastik karsinomlar arasında yeralır. ADTK tanısını koymak için, Turin tanı kriterleri 2017 Dünya Sağlık Örgütü (DSÖ) s…
View article: Infiltration of thyroid papillary cancer tissue with myeloid leukemic cells: a case report
Infiltration of thyroid papillary cancer tissue with myeloid leukemic cells: a case report Open
View article: Breast Recurrence of Acute Myeloid Leukemia After Bone Marrow Transplantation: A Case Report About Myeloid Sarcoma of the Breast
Breast Recurrence of Acute Myeloid Leukemia After Bone Marrow Transplantation: A Case Report About Myeloid Sarcoma of the Breast Open
Myeloid sarcoma of the breast is a rare malignancy, can be seen after bone marrow transplantation. Although there are no specific features for this malignancy which is difficult to diagnose, some common features draw attention in the publi…
View article: Endobronchial Lymphoma: A Case Report
Endobronchial Lymphoma: A Case Report Open