Arkadiusz Gertych
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View article: Explainability and uncertainty: Two sides of the same coin for enhancing the interpretability of deep learning models in healthcare
Explainability and uncertainty: Two sides of the same coin for enhancing the interpretability of deep learning models in healthcare Open
Our analysis indicates that integrating UQ with XAI could significantly enhance the reliability of DL models in practice. This approach has the potential to reduce interpretation biases and over-reliance, leading to more cautious and consc…
View article: The Molecular Twin artificial-intelligence platform integrates multi-omic data to predict outcomes for pancreatic adenocarcinoma patients
The Molecular Twin artificial-intelligence platform integrates multi-omic data to predict outcomes for pancreatic adenocarcinoma patients Open
Contemporary analyses focused on a limited number of clinical and molecular biomarkers have been unable to accurately predict clinical outcomes in pancreatic ductal adenocarcinoma. Here we describe a precision medicine platform known as th…
View article: iPSC‐derived tenocytes seeded on microgrooved 3D printed scaffolds for Achilles tendon regeneration
iPSC‐derived tenocytes seeded on microgrooved 3D printed scaffolds for Achilles tendon regeneration Open
Tendons and ligaments have a poor innate healing capacity, yet account for 50% of musculoskeletal injuries in the United States. Full structure and function restoration postinjury remains an unmet clinical need. This study aimed to assess …
View article: Dynamic Changes in the Extracellular Matrix in Primary, Metastatic, and Recurrent Ovarian Cancers
Dynamic Changes in the Extracellular Matrix in Primary, Metastatic, and Recurrent Ovarian Cancers Open
Cancer-associated fibroblasts (CAFs) and their extracellular matrix are active participants in cancer progression. While it is known that functionally different subpopulations of CAFs co-exist in ovarian cancer, it is unclear whether certa…
View article: Directing iPSC differentiation into iTenocytes using combined scleraxis overexpression and cyclic loading
Directing iPSC differentiation into iTenocytes using combined scleraxis overexpression and cyclic loading Open
Regenerative therapies for tendon are falling behind other tissues due to the lack of an appropriate and potent cell therapeutic candidate. This study aimed to induce tenogenesis using stable Scleraxis (Scx) overexpression in combination w…
View article: Computational pathology in ovarian cancer
Computational pathology in ovarian cancer Open
Histopathologic evaluations of tissue sections are key to diagnosing and managing ovarian cancer. Pathologists empirically assess and integrate visual information, such as cellular density, nuclear atypia, mitotic figures, architectural gr…
View article: Efficient automatic 3D segmentation of cell nuclei for high-content screening
Efficient automatic 3D segmentation of cell nuclei for high-content screening Open
Background High-content screening (HCS) is a pre-clinical approach for the assessment of drug efficacy. On modern platforms, it involves fluorescent image capture using three-dimensional (3D) scanning microscopy. Segmentation of cell nucle…
View article: Focal Serous Tubal Intra-Epithelial Carcinoma Lesions Are Associated With Global Changes in the Fallopian Tube Epithelia and Stroma
Focal Serous Tubal Intra-Epithelial Carcinoma Lesions Are Associated With Global Changes in the Fallopian Tube Epithelia and Stroma Open
Objective Serous tubal intra-epithelial carcinoma (STIC) lesions are thought to be precursors to high-grade serous ovarian cancer (HGSOC), but HGSOC is not always accompanied by STIC. Our study was designed to determine if there are global…
View article: Receptor-interacting protein kinase 2 (RIPK2) stabilizes c-Myc and is a therapeutic target in prostate cancer metastasis
Receptor-interacting protein kinase 2 (RIPK2) stabilizes c-Myc and is a therapeutic target in prostate cancer metastasis Open
Despite progress in prostate cancer (PC) therapeutics, distant metastasis remains a major cause of morbidity and mortality from PC. Thus, there is growing recognition that preventing or delaying PC metastasis holds great potential for subs…
View article: Directing iPSC Differentiation into iTenocytes using Combined Scleraxis Overexpression and Cyclic Loading
Directing iPSC Differentiation into iTenocytes using Combined Scleraxis Overexpression and Cyclic Loading Open
Regenerative therapies for tendon are falling behind other tissues due to the lack of an appropriate and potent cell therapeutic candidate. This study aimed to induce cell tenogenesis using stable Scleraxis (Scx) overexpression in combinat…
View article: Predicting Metastasis Risk in Pancreatic Neuroendocrine Tumors Using Deep Learning Image Analysis
Predicting Metastasis Risk in Pancreatic Neuroendocrine Tumors Using Deep Learning Image Analysis Open
Background The prognosis of patients with pancreatic neuroendocrine tumors (PanNET), the second most common type of pancreatic cancer, varies significantly, and up to 15% of patients develop metastasis. Although certain morphological chara…
View article: A U-Net based framework to quantify glomerulosclerosis in digitized PAS and H&E stained human tissues
A U-Net based framework to quantify glomerulosclerosis in digitized PAS and H&E stained human tissues Open
Reliable counting of glomeruli and evaluation of glomerulosclerosis in renal specimens are essential steps to assess morphological changes in kidney and identify individuals requiring treatment. Because microscopic identification of sclero…
View article: Automated Detection of Sleep Stages Using Deep Learning Techniques: A Systematic Review of the Last Decade (2010–2020)
Automated Detection of Sleep Stages Using Deep Learning Techniques: A Systematic Review of the Last Decade (2010–2020) Open
Sleep is vital for one’s general well-being, but it is often neglected, which has led to an increase in sleep disorders worldwide. Indicators of sleep disorders, such as sleep interruptions, extreme daytime drowsiness, or snoring, can be d…
View article: Kidney glomeruli-ROIs extracted from histological slides stained with HE or PAS.
Kidney glomeruli-ROIs extracted from histological slides stained with HE or PAS. Open
Kidney glomeruli-ROIs extracted from histological slides stained with HE or PAS. The multicenter test set of 78 regions of interest together with annotations. ROIs were extracted from 20 WSIs representing various human kidney pathologies. …
View article: Kidney glomeruli-ROIs extracted from histological slides stained with HE or PAS.
Kidney glomeruli-ROIs extracted from histological slides stained with HE or PAS. Open
Kidney glomeruli-ROIs extracted from histological slides stained with HE or PAS. The multicenter test set of 78 regions of interest together with annotations. ROIs were extracted from 20 WSIs representing various human kidney pathologies. …
View article: RIPK2 Stabilizes c-Myc and is an Actionable Target for Inhibiting Prostate Cancer Metastasis
RIPK2 Stabilizes c-Myc and is an Actionable Target for Inhibiting Prostate Cancer Metastasis Open
Despite advances in diagnosis and treatment, metastatic prostate cancer remains incurable and is associated with high mortality rates. Thus, novel actionable drug targets are urgently needed for therapeutic interventions in advanced prosta…
View article: A whole slide image-based machine learning approach to predict ductal carcinoma in situ (DCIS) recurrence risk
A whole slide image-based machine learning approach to predict ductal carcinoma in situ (DCIS) recurrence risk Open
Our machine learning-based model fills an unmet clinical need for accurately predicting the recurrence risk for lumpectomy-treated DCIS patients.
View article: An attention-based multi-resolution model for prostate whole slide imageclassification and localization
An attention-based multi-resolution model for prostate whole slide imageclassification and localization Open
Histology review is often used as the `gold standard' for disease diagnosis. Computer aided diagnosis tools can potentially help improve current pathology workflows by reducing examination time and interobserver variability. Previous work …
View article: PD11-02 DEVELOPMENT AND APPLICATION OF A DIGITAL IMAGE ANALYSIS CLASSIFIER FOR DIAGNOSTIC PROSTATE NEEDLE BIOPSIES TO PREDICT METASTASES
PD11-02 DEVELOPMENT AND APPLICATION OF A DIGITAL IMAGE ANALYSIS CLASSIFIER FOR DIAGNOSTIC PROSTATE NEEDLE BIOPSIES TO PREDICT METASTASES Open
You have accessJournal of UrologyProstate Cancer: Markers I (PD11)1 Apr 2019PD11-02 DEVELOPMENT AND APPLICATION OF A DIGITAL IMAGE ANALYSIS CLASSIFIER FOR DIAGNOSTIC PROSTATE NEEDLE BIOPSIES TO PREDICT METASTASES Nathan Ing, Fangjin Huang,…
View article: Convolutional neural networks can accurately distinguish four histologic growth patterns of lung adenocarcinoma in digital slides
Convolutional neural networks can accurately distinguish four histologic growth patterns of lung adenocarcinoma in digital slides Open
During the diagnostic workup of lung adenocarcinomas (LAC), pathologists evaluate distinct histological tumor growth patterns. The percentage of each pattern on multiple slides bears prognostic significance. To assist with the quantificati…
View article: Spatial Mapping of Myeloid Cells and Macrophages by Multiplexed Tissue Staining
Spatial Mapping of Myeloid Cells and Macrophages by Multiplexed Tissue Staining Open
An array of phenotypically diverse myeloid cells and macrophages (MC&M) resides in the tumor microenvironment, requiring multiplexed detection systems for visualization. Here we report an automated, multiplexed staining approach, named PLE…
View article: Path R-CNN for Prostate Cancer Diagnosis and Gleason Grading of Histological Images
Path R-CNN for Prostate Cancer Diagnosis and Gleason Grading of Histological Images Open
Prostate cancer is the most common and second most deadly form of cancer in men in the United States. The classification of prostate cancers based on Gleason grading using histological images is important in risk assessment and treatment p…
View article: A novel machine learning approach reveals latent vascular phenotypes predictive of renal cancer outcome
A novel machine learning approach reveals latent vascular phenotypes predictive of renal cancer outcome Open
Gene expression signatures are commonly used as predictive biomarkers, but do not capture structural features within the tissue architecture. Here we apply a 2-step machine learning framework for quantitative imaging of tumor vasculature t…
View article: Data integration from pathology slides for quantitative imaging of multiple cell types within the tumor immune cell infiltrate
Data integration from pathology slides for quantitative imaging of multiple cell types within the tumor immune cell infiltrate Open
In summary, we developed a general method to integrate data from IHC stained slides into a single dataset. Because of the transfer error between slides, we recommend applying the antibody for demarcation of the tumor on the same slide as t…
View article: A Multi-scale U-Net for Semantic Segmentation of Histological Images from Radical Prostatectomies.
A Multi-scale U-Net for Semantic Segmentation of Histological Images from Radical Prostatectomies. Open
Gleason grading of histological images is important in risk assessment and treatment planning for prostate cancer patients. Much research has been done in classifying small homogeneous cancer regions within histological images. However, se…
View article: Quantitative imaging for development of companion diagnostics to drugs targeting HGF/MET
Quantitative imaging for development of companion diagnostics to drugs targeting HGF/MET Open
The limited clinical success of anti‐HGF/MET drugs can be attributed to the lack of predictive biomarkers that adequately select patients for treatment. We demonstrate here that quantitative digital imaging of formalin fixed paraffin embed…