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Elangovan K, Lim G, Ting D. A comparative study of an on premise AutoML solution for medical image classification. Sci Rep 2024; 14:10483. [PMID: 38714764 PMCID: PMC11076477 DOI: 10.1038/s41598-024-60429-4] [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: 07/15/2023] [Accepted: 04/23/2024] [Indexed: 05/10/2024] Open
Abstract
Automated machine learning (AutoML) allows for the simplified application of machine learning to real-world problems, by the implicit handling of necessary steps such as data pre-processing, feature engineering, model selection and hyperparameter optimization. This has encouraged its use in medical applications such as imaging. However, the impact of common parameter choices such as the number of trials allowed, and the resolution of the input images, has not been comprehensively explored in existing literature. We therefore benchmark AutoKeras (AK), an open-source AutoML framework, against several bespoke deep learning architectures, on five public medical datasets representing a wide range of imaging modalities. It was found that AK could outperform the bespoke models in general, although at the cost of increased training time. Moreover, our experiments suggest that a large number of trials and higher resolutions may not be necessary for optimal performance to be achieved.
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Affiliation(s)
- Kabilan Elangovan
- Artificial Intelligence and Digital Health Research Group, Singapore Eye Research Institute, Singapore, Singapore
- Artificial Intelligence Office, Singapore Health Service, Singapore, Singapore
| | - Gilbert Lim
- Artificial Intelligence and Digital Health Research Group, Singapore Eye Research Institute, Singapore, Singapore
- Artificial Intelligence Office, Singapore Health Service, Singapore, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore
| | - Daniel Ting
- Artificial Intelligence and Digital Health Research Group, Singapore Eye Research Institute, Singapore, Singapore.
- Artificial Intelligence Office, Singapore Health Service, Singapore, Singapore.
- Duke-NUS Medical School, National University of Singapore, Singapore, Singapore.
- Singapore National Eye Centre, Singapore General Hospital, 11 Third Hospital Avenue, Singapore, 168751, Singapore.
- Byers Eye Institute, Stanford University, Stanford, USA.
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Ferrero A, Ghelichkhan E, Manoochehri H, Ho MM, Albertson DJ, Brintz BJ, Tasdizen T, Whitaker RT, Knudsen BS. HistoEM: A Pathologist-Guided and Explainable Workflow Using Histogram Embedding for Gland Classification. Mod Pathol 2024; 37:100447. [PMID: 38369187 DOI: 10.1016/j.modpat.2024.100447] [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: 04/05/2023] [Revised: 01/06/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
Pathologists have, over several decades, developed criteria for diagnosing and grading prostate cancer. However, this knowledge has not, so far, been included in the design of convolutional neural networks (CNN) for prostate cancer detection and grading. Further, it is not known whether the features learned by machine-learning algorithms coincide with diagnostic features used by pathologists. We propose a framework that enforces algorithms to learn the cellular and subcellular differences between benign and cancerous prostate glands in digital slides from hematoxylin and eosin-stained tissue sections. After accurate gland segmentation and exclusion of the stroma, the central component of the pipeline, named HistoEM, utilizes a histogram embedding of features from the latent space of the CNN encoder. Each gland is represented by 128 feature-wise histograms that provide the input into a second network for benign vs cancer classification of the whole gland. Cancer glands are further processed by a U-Net structured network to separate low-grade from high-grade cancer. Our model demonstrates similar performance compared with other state-of-the-art prostate cancer grading models with gland-level resolution. To understand the features learned by HistoEM, we first rank features based on the distance between benign and cancer histograms and visualize the tissue origins of the 2 most important features. A heatmap of pixel activation by each feature is generated using Grad-CAM and overlaid on nuclear segmentation outlines. We conclude that HistoEM, similar to pathologists, uses nuclear features for the detection of prostate cancer. Altogether, this novel approach can be broadly deployed to visualize computer-learned features in histopathology images.
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Affiliation(s)
- Alessandro Ferrero
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah
| | - Elham Ghelichkhan
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah
| | - Hamid Manoochehri
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah
| | - Man Minh Ho
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah
| | | | | | - Tolga Tasdizen
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah
| | - Ross T Whitaker
- Scientific Computing and Imaging Institute, University of Utah, Salt Lake City, Utah
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Ramacciotti LS, Hershenhouse JS, Mokhtar D, Paralkar D, Kaneko M, Eppler M, Gill K, Mogoulianitis V, Duddalwar V, Abreu AL, Gill I, Cacciamani GE. Comprehensive Assessment of MRI-based Artificial Intelligence Frameworks Performance in the Detection, Segmentation, and Classification of Prostate Lesions Using Open-Source Databases. Urol Clin North Am 2024; 51:131-161. [PMID: 37945098 DOI: 10.1016/j.ucl.2023.08.003] [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: 11/12/2023]
Abstract
Numerous MRI-based artificial intelligence (AI) frameworks have been designed for prostate cancer lesion detection, segmentation, and classification via MRI as a result of intrareader and interreader variability that is inherent to traditional interpretation. Open-source data sets have been released with the intention of providing freely available MRIs for the testing of diverse AI frameworks in automated or semiautomated tasks. Here, an in-depth assessment of the performance of MRI-based AI frameworks for detecting, segmenting, and classifying prostate lesions using open-source databases was performed. Among 17 data sets, 12 were specific to prostate cancer detection/classification, with 52 studies meeting the inclusion criteria.
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Affiliation(s)
- Lorenzo Storino Ramacciotti
- USC Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Artificial Intelligence Center at USC Urology, USC Institute of Urology, University of Southern California, Los Angeles, CA, USA; Center for Image-Guided and Focal Therapy for Prostate Cancer, Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jacob S Hershenhouse
- USC Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Artificial Intelligence Center at USC Urology, USC Institute of Urology, University of Southern California, Los Angeles, CA, USA; Center for Image-Guided and Focal Therapy for Prostate Cancer, Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daniel Mokhtar
- USC Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Artificial Intelligence Center at USC Urology, USC Institute of Urology, University of Southern California, Los Angeles, CA, USA; Center for Image-Guided and Focal Therapy for Prostate Cancer, Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Divyangi Paralkar
- USC Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Artificial Intelligence Center at USC Urology, USC Institute of Urology, University of Southern California, Los Angeles, CA, USA; Center for Image-Guided and Focal Therapy for Prostate Cancer, Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Masatomo Kaneko
- USC Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Artificial Intelligence Center at USC Urology, USC Institute of Urology, University of Southern California, Los Angeles, CA, USA; Center for Image-Guided and Focal Therapy for Prostate Cancer, Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Urology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Michael Eppler
- USC Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Artificial Intelligence Center at USC Urology, USC Institute of Urology, University of Southern California, Los Angeles, CA, USA; Center for Image-Guided and Focal Therapy for Prostate Cancer, Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Karanvir Gill
- USC Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Artificial Intelligence Center at USC Urology, USC Institute of Urology, University of Southern California, Los Angeles, CA, USA; Center for Image-Guided and Focal Therapy for Prostate Cancer, Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Vasileios Mogoulianitis
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, USA
| | - Vinay Duddalwar
- Department of Radiology, University of Southern California, Los Angeles, CA, USA
| | - Andre L Abreu
- USC Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Artificial Intelligence Center at USC Urology, USC Institute of Urology, University of Southern California, Los Angeles, CA, USA; Center for Image-Guided and Focal Therapy for Prostate Cancer, Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Radiology, University of Southern California, Los Angeles, CA, USA
| | - Inderbir Gill
- USC Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Artificial Intelligence Center at USC Urology, USC Institute of Urology, University of Southern California, Los Angeles, CA, USA; Center for Image-Guided and Focal Therapy for Prostate Cancer, Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Giovanni E Cacciamani
- USC Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Artificial Intelligence Center at USC Urology, USC Institute of Urology, University of Southern California, Los Angeles, CA, USA; Center for Image-Guided and Focal Therapy for Prostate Cancer, Institute of Urology and Catherine and Joseph Aresty Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Radiology, University of Southern California, Los Angeles, CA, USA.
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Currie C, Bjerknes C, Myklebust TÅ, Framroze B. Assessing the Potential of Small Peptides for Altering Expression Levels of the Iron-Regulatory Genes FTH1 and TFRC and Enhancing Androgen Receptor Inhibitor Activity in In Vitro Prostate Cancer Models. Int J Mol Sci 2023; 24:15231. [PMID: 37894914 PMCID: PMC10607736 DOI: 10.3390/ijms242015231] [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: 08/30/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Recent research highlights the key role of iron dyshomeostasis in the pathogenesis of prostate cancer (PCa). PCa cells are heavily dependent on bioavailable iron, which frequently results in the reprogramming of iron uptake and storage pathways. Although advanced-stage PCa is currently incurable, bioactive peptides capable of modulating key iron-regulatory genes may constitute a means of exploiting a metabolic adaptation necessary for tumor growth. Recent annual increases in PCa incidence have been reported, highlighting the urgent need for novel treatments. We examined the ability of LNCaP, PC3, VCaP, and VCaP-EnzR cells to form colonies in the presence of androgen receptor inhibitors (ARI) and a series of iron-gene modulating oligopeptides (FT-001-FT-008). The viability of colonies following treatment was determined with clonogenic assays, and the expression levels of FTH1 (ferritin heavy chain 1) and TFRC (transferrin receptor) were determined with quantitative polymerase chain reaction (PCR). Peptides and ARIs combined significantly reduced PCa cell growth across all phenotypes, of which two peptides were the most effective. Colony growth suppression generally correlated with the magnitude of concurrent increases in FTH1 and decreases in TFRC expression for all cells. The results of this study provide preliminary insight into a novel approach at targeting iron dysmetabolism and sensitizing PCa cells to established cancer treatments.
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Affiliation(s)
- Crawford Currie
- HBC Immunology Inc., 1455 Adams Drive, Suite, Menlo Park, CA 2043, USA;
- Hofseth Biocare, Keiser Wilhelmsgate 24, 6003 Ålesund, Norway;
| | - Christian Bjerknes
- Hofseth Biocare, Keiser Wilhelmsgate 24, 6003 Ålesund, Norway;
- Department for Health Sciences, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 6025 Ålesund, Norway
| | - Tor Åge Myklebust
- Department of Registration, Cancer Registry of Norway, 0379 Oslo, Norway;
- Department of Research and Innovation, Møre og Romsdal Hospital Trust, 6026 Ålesund, Norway
| | - Bomi Framroze
- HBC Immunology Inc., 1455 Adams Drive, Suite, Menlo Park, CA 2043, USA;
- GPH Biotech LLC, 1455 Adams Drive, Menlo Park, CA 94025, USA
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