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Self-learning for weakly supervised Gleason grading of local patterns

Julio Silva-Rodriguez, Adrian Colomer, Jose Dolz, Valery Naranjo
2021 IEEE journal of biomedical and health informatics  

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2021 pre-print arXiv:2105.10420v1 fatcat:beikgeuaazfb3nptmyqx7kdxom
Prostate cancer is one of the main diseases affecting men worldwide. The gold standard for diagnosis and prognosis is the Gleason grading system.  ...  To evaluate the performance of the proposed method, we perform extensive experiments on three different external datasets for the patch-level Gleason grading, and on two different test sets for global  ...  These works also exploit knowledge distillation by transferring the teacher knowledge to either larger [8] or smaller [9] students.  ... 
doi:10.1109/jbhi.2021.3061457 fatcat:gfaorq25zbegncbwrued6kacim
Multiple Versions
Citation

Julio Silva-Rodriguez, Adrian Colomer, Jose Dolz, Valery Naranjo. "Self-learning for weakly supervised Gleason grading of local patterns." IEEE journal of biomedical and health informatics 25.8 (2021) 1-1

Continual Learning in Medical Image Analysis: A Comprehensive Review of Recent Advancements and Future Prospects [article]

Pratibha Kumari, Joohi Chauhan, Afshin Bozorgpour, Boqiang Huang, Reza Azad, Dorit Merhof
2024 arXiv   pre-print

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2023 pre-print
arXiv:2312.17004v1 fatcat:gwo5hsze5bcafar3uag6ijw5i4
Continual learning techniques enable models to adapt and accumulate knowledge over time, which is essential for maintaining performance on evolving datasets and novel tasks.  ...  environments for various application areas.  ...  to liver tumor segmentation belling based knowledge distillation Ji et al. (2023) CIS for multi-organ segmentation Architecture: organ specific decoder + pseudo labelling based knowledge distillation  ... 
arXiv:2312.17004v2 fatcat:lloikuohcngpph4dklytsrul6i
Open Access Multiple Versions
Citation

Pratibha Kumari, Joohi Chauhan, Afshin Bozorgpour, Boqiang Huang, Reza Azad, Dorit Merhof. "Continual Learning in Medical Image Analysis: A Comprehensive Review of Recent Advancements and Future Prospects." arXiv (2024)

Semi-supervised ViT knowledge distillation network with style transfer normalization for colorectal liver metastases survival prediction [article]

Mohamed El Amine Elforaici, Emmanuel Montagnon, Francisco Perdigon Romero, William Trung Le, Feryel Azzi, Dominique Trudel, Bich Nguyen, Simon Turcotte, An Tang, Samuel Kadoury
2023 arXiv   pre-print

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In parallel, we train a vision Transformer (ViT) in a knowledge distillation framework to replicate and enhance the performance of the prognosis prediction.  ...  Traditional methods like tumor grading scores (e.g., tumor regression grade - TRG) for prognosis suffer from subjectivity, time constraints, and expertise demands.  ...  Bilodeau from the CHUM hepatopancreatobiliary biobank and prospective registry for patients recruitment, biospecimen acquisition, and maintenance of clinicopathological data.  ... 
arXiv:2311.10305v1 fatcat:jkmnkti3gvb4xas23z4uwcjvam
Open Access
Citation

Mohamed El Amine Elforaici, Emmanuel Montagnon, Francisco Perdigon Romero, William Trung Le, Feryel Azzi, Dominique Trudel, Bich Nguyen, Simon Turcotte, An Tang, Samuel Kadoury. "Semi-supervised ViT knowledge distillation network with style transfer normalization for colorectal liver metastases survival prediction." arXiv (2023)

Computational Pathology: A Survey Review and The Way Forward [article]

Mahdi S. Hosseini, Babak Ehteshami Bejnordi, Vincent Quoc-Huy Trinh, Danial Hasan, Xingwen Li, Taehyo Kim, Haochen Zhang, Theodore Wu, Kajanan Chinniah, Sina Maghsoudlou, Ryan Zhang, Stephen Yang (+9 others)
2024 arXiv   pre-print

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2023 pre-print
arXiv:2304.05482v1 fatcat:5wkpmd7vtzcy7c44j4ggoukrgq
2024 pre-print
arXiv:2304.05482v2 fatcat:apb6pwywvnecti3aed4cfyh5mm
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  ...  and treatment of cancer that are mainly address by CPath tools.  ...  Acknowledgment Authors would like to thank Huron Digital Pathology for providing support and insightful discussions related to digital pathology hardware infrastructures.  ... 
arXiv:2304.05482v3 fatcat:orhl2kemibcwrevxew4fygv4pq
Multiple Versions
Citation

Mahdi S. Hosseini, Babak Ehteshami Bejnordi, Vincent Quoc-Huy Trinh, Danial Hasan, Xingwen Li, Taehyo Kim, Haochen Zhang, Theodore Wu, Kajanan Chinniah, Sina Maghsoudlou, Ryan Zhang, Stephen Yang, Jiadai Zhu, Lyndon Chan, Samir Khaki, Andrei Buin, Fatemeh Chaji, Ala Salehi, Bich Ngoc Nguyen, Dimitris Samaras, Konstantinos N. Plataniotis. "Computational Pathology: A Survey Review and The Way Forward." arXiv (2024)

Weakly Supervised AI for Efficient Analysis of 3D Pathology Samples [article]

Andrew H. Song, Mane Williams, Drew F.K. Williamson, Guillaume Jaume, Andrew Zhang, Bowen Chen, Robert Serafin, Jonathan T.C. Liu, Alex Baras, Anil V. Parwani, Faisal Mahmood
2023 arXiv   pre-print

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Archived prostate cancer specimens were imaged with open-top light-sheet microscopy or microcomputed tomography and the resulting 3D datasets were used to train risk-stratification networks based on 5-  ...  Here we present Modality-Agnostic Multiple instance learning for volumetric Block Analysis (MAMBA), a deep-learning-based platform for processing 3D tissue images from diverse imaging modalities and predicting  ...  We choose prostate cancer to validate MAMBA since the important glandular and architectural features for prostate cancer prognosis 39 can reliably be captured at varying spatial resolutions.  ... 
arXiv:2307.14907v1 fatcat:scj7ide7o5akfecihgz33a7emy
Open Access
Citation

Andrew H. Song, Mane Williams, Drew F.K. Williamson, Guillaume Jaume, Andrew Zhang, Bowen Chen, Robert Serafin, Jonathan T.C. Liu, Alex Baras, Anil V. Parwani, Faisal Mahmood. "Weakly Supervised AI for Efficient Analysis of 3D Pathology Samples." arXiv (2023)

Label-Efficient Deep Learning in Medical Image Analysis: Challenges and Future Directions [article]

Cheng Jin, Zhengrui Guo, Yi Lin, Luyang Luo, Hao Chen
2023 arXiv   pre-print

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2023 pre-print
arXiv:2303.12484v1 fatcat:2ivfqb4h25ctzpg2hm3np4w2xm
2023 pre-print
arXiv:2303.12484v2 fatcat:sl4corxay5h7vhamumnki6favu
2023 pre-print
arXiv:2303.12484v3 fatcat:jptsdxvn5beclivh3quvh3mahi
this survey not only elucidates the commonalities and unique features of the surveyed methods but also presents a detailed analysis of the current challenges in the field and suggests potential avenues for  ...  Specifically, we provide an in-depth investigation, covering not only canonical semi-supervised, self-supervised, and multi-instance learning schemes, but also recently emerged active and annotation-efficient  ...  pageId=68550661 PANDA (Bulten et al., 2020) Classification https://www.kaggle.com/c/ Prostate ProMRI (Litjens et al., 2014; prostate-cancer-grade-assessment/data/ Segmentation https://promise12.grand-challenge.org  ... 
arXiv:2303.12484v4 fatcat:hfuzqtc76vfnzl6iunurrtoq4y
Open Access Multiple Versions
Citation

Cheng Jin, Zhengrui Guo, Yi Lin, Luyang Luo, Hao Chen. "Label-Efficient Deep Learning in Medical Image Analysis: Challenges and Future Directions." arXiv (2023)

Data efficient deep learning for medical image analysis: A survey [article]

Suruchi Kumari, Pravendra Singh
2023 arXiv   pre-print

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For example, we categorize inexact supervision into multiple instance learning and learning with weak annotations.  ...  This paper conducts a thorough review of data-efficient deep learning methods for medical image analysis.  ...  repository PANDA (2020) [63] Prostate Whole-slide images Gleason grading of prostate cancer Development set: 10,616 biopsies; Tuning set: 393; Internal validation set: 545; External valida-tion: 1071 https  ... 
arXiv:2310.06557v1 fatcat:544qh54zcvfeze2lg35rvbikwu
Open Access
Citation

Suruchi Kumari, Pravendra Singh. "Data efficient deep learning for medical image analysis: A survey." arXiv (2023)

Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions [article]

Luyang Luo, Xi Wang, Yi Lin, Xiaoqi Ma, Andong Tan, Ronald Chan, Varut Vardhanabhuti, Winnie CW Chu, Kwang-Ting Cheng, Hao Chen
2024 arXiv   pre-print

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2023 pre-print arXiv:2304.06662v3 fatcat:w2bqc2lqunhrfmx456tjqnxguq

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2023 pre-print
arXiv:2304.06662v1 fatcat:gpsgmjkrw5fzzjj2ppfahlov2m
2023 pre-print
arXiv:2304.06662v2 fatcat:agfofbfsbrej5ifjplp2thnpc4
Drawn from the findings of this survey, we present a comprehensive discussion of the challenges and potential avenues for future research in deep learning-based breast cancer imaging.  ...  Breast cancer has reached the highest incidence rate worldwide among all malignancies since 2020.  ...  Wang et al. (2022a) CL IMD, CMMD Prototype learning + knowledge distillation for breast cancer classification.  ... 
arXiv:2304.06662v4 fatcat:t5nvpybawjhfhiw4h2bekozo74
Open Access Multiple Versions
Citation

Luyang Luo, Xi Wang, Yi Lin, Xiaoqi Ma, Andong Tan, Ronald Chan, Varut Vardhanabhuti, Winnie CW Chu, Kwang-Ting Cheng, Hao Chen. "Deep Learning in Breast Cancer Imaging: A Decade of Progress and Future Directions." arXiv (2024)

Computer-Assisted Analysis of Biomedical Images [article]

Leonardo Rundo
2021 arXiv   pre-print

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As a matter of fact, the proposed computer-assisted bioimage analysis methods can be beneficial for the definition of imaging biomarkers, as well as for quantitative medicine and biology.  ...  This thesis aims at proposing novel and advanced computer-assisted methods for biomedical image analysis, also as an instrument in the development of Clinical Decision Support Systems, by always keeping  ...  To the best of our knowledge, we tackle for the first time CNN-based prostate zonal segmentation on T2w MRI alone.  ... 
arXiv:2106.04381v1 fatcat:osqiyd3sbja3zgrby7bf4eljfm
Open Access
Citation

Leonardo Rundo. "Computer-Assisted Analysis of Biomedical Images." arXiv (2021)

A Review of Predictive and Contrastive Self-supervised Learning for Medical Images [article]

Wei-Chien Wang, Euijoon Ahn, Dagan Feng, Jinman Kim
2023 arXiv   pre-print

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2024 accepted
arXiv:2302.05043v2 fatcat:sm6lziegvfcrpfge2c4fdmu7ha
This review investigates several state-of-the-art contrastive SSL algorithms originally on natural images as well as their adaptations for medical images, and concludes by discussing recent advances, current  ...  Chaitanya et al., 2020 [142, 143] (1) ACDC dataset (2) Prostate dataset (3) MMWHS dataset (1) Cardiac multi-structures segmentation (2) Prostate structures segmentation (3) Heart multi-structures segmentation  ...  One was on prostate segmentation of two MRI modalities, and another was liver segmentation of both CT and MRI modalities.  ... 
arXiv:2302.05043v1 fatcat:xxxjlu25r5dbthsfvjdnabc6te
Open Access Multiple Versions
Citation

Wei-Chien Wang, Euijoon Ahn, Dagan Feng, Jinman Kim. "A Review of Predictive and Contrastive Self-supervised Learning for Medical Images." arXiv (2023)

B2 adrenergic receptors and morphological changes of the enteric nervous system in colorectal adenocarcinoma

Raluca Niculina Ciurea, Ion Rogoveanu, Daniel Pirici, Georgică-Costinel Târtea, Costin Teodor Streba, Cristina Florescu, Bogdan Cătălin, Ileana Puiu, Elena-Anca Târtea, Cristin Constantin Vere
2017 World Journal of Gastroenterology  

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This type of receptor was also studied in other types of cancer including for example pancreas cancer [28] , lung cancer [31] , breast cancer [32] and prostate cancer [33] .  ...  There are too few elements to judge a functional association between these factors, but this is to our knowledge the first report of such a correlation for colon cancer.  ...  angiogenesis, but also concerning neurogenesis in colorectal cancer.  ... 
doi:10.3748/wjg.v23.i7.1250 pmid:28275305 pmcid:PMC5323450 fatcat:3mjngnoz6fgfriqzzznurfw45e
Open Access
Citation

Raluca Niculina Ciurea, Ion Rogoveanu, Daniel Pirici, Georgică-Costinel Târtea, Costin Teodor Streba, Cristina Florescu, Bogdan Cătălin, Ileana Puiu, Elena-Anca Târtea, Cristin Constantin Vere. "B2 adrenergic receptors and morphological changes of the enteric nervous system in colorectal adenocarcinoma." World Journal of Gastroenterology 23.7 (2017) 1250

Deep learning in medical imaging and radiation therapy

Berkman Sahiner, Aria Pezeshk, Lubomir M. Hadjiiski, Xiaosong Wang, Karen Drukker, Kenny H. Cha, Ronald M. Summers, Maryellen L. Giger
2018 Medical Physics (Lancaster)  

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summarize what has been achieved to date; (b) identify common and unique challenges, and strategies that researchers have taken to address these challenges; and (c) identify some of the promising avenues for  ...  introduce the general principles of DL and convolutional neural networks, survey five major areas of application of DL in medical imaging and radiation therapy, identify common themes, discuss methods for  ...  Azizi et al. 16 applied an unsupervised domain adaptation method based on DL for the prostate cancer detection problem.  ... 
doi:10.1002/mp.13264 pmid:30367497 pmcid:PMC9560030 fatcat:bottst5mvrbkfedbuocbrstcnm
Citation

Berkman Sahiner, Aria Pezeshk, Lubomir M. Hadjiiski, Xiaosong Wang, Karen Drukker, Kenny H. Cha, Ronald M. Summers, Maryellen L. Giger. "Deep learning in medical imaging and radiation therapy." Medical Physics (Lancaster) 46.1 (2018) e1-e36

Unsupervised Domain Adaptation Using Feature Disentanglement And GCNs For Medical Image Classification [article]

Dwarikanath Mahapatra
2022 arXiv   pre-print

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The success of deep learning has set new benchmarks for many medical image analysis tasks.  ...  One method commonly employed to counter distribution shifts is domain adaptation: using samples from the target domain to learn to account for shifted distributions.  ...  Ju, L., Wang, X., Zhao, X., Lu, H., Mahapatra, D., Bonnington, P., Ge, Z.: Synergic adversarial label learning for grading retinal diseases via knowledge distillation and multi-task learning.  ... 
arXiv:2206.13123v1 fatcat:fjqckpuwczg37gjf2uh2esjj6y
Open Access
Citation

Dwarikanath Mahapatra. "Unsupervised Domain Adaptation Using Feature Disentanglement And GCNs For Medical Image Classification." arXiv (2022)

A comprehensive analysis of coregulator recruitment, androgen receptor function and gene expression in prostate cancer

Song Liu, Sangeeta Kumari, Qiang Hu, Dhirodatta Senapati, Varadha Balaji Venkadakrishnan, Dan Wang, Adam D DePriest, Simon E Schlanger, Salma Ben-Salem, Malyn May Valenzuela, Belinda Willard, Shaila Mudambi (+12 others)
2017 eLife  

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Standard treatment for metastatic prostate cancer (CaP) prevents ligand-activation of androgen receptor (AR). Despite initial remission, CaP progresses while relying on AR.  ...  Isolation of a novel transcriptional mechanism in which WDR77 unites the actions of AR and p53, the major genomic drivers of lethal CaP, to control cell cycle progression provides proof-of-principle for  ...  Cassandra Talerico for helpful discussions and review of the manuscript, and Dr. Natalya Guseva for providing the LNCaP cell line in which expression of p53 has been silenced.  ... 
doi:10.7554/elife.28482 pmid:28826481 pmcid:PMC5608510 fatcat:gifilikqtzeblasc4secj5muli
DOAJ
Citation

Song Liu, Sangeeta Kumari, Qiang Hu, Dhirodatta Senapati, Varadha Balaji Venkadakrishnan, Dan Wang, Adam D DePriest, Simon E Schlanger, Salma Ben-Salem, Malyn May Valenzuela, Belinda Willard, Shaila Mudambi, Wendy M Swetzig, Gokul M Das, Mojgan Shourideh, Shahriah Koochekpour, Sara Moscovita Falzarano, Cristina Magi-Galluzzi, Neelu Yadav, Xiwei Chen, Changshi Lao, Jianmin Wang, Jean-Noel Billaud, Hannelore V Heemers. "A comprehensive analysis of coregulator recruitment, androgen receptor function and gene expression in prostate cancer." eLife (2017)

Decision support systems for personalized and participative radiation oncology

Philippe Lambin, Jaap Zindler, Ben G.L. Vanneste, Lien Van De Voorde, Daniëlle Eekers, Inge Compter, Kranthi Marella Panth, Jurgen Peerlings, Ruben T.H.M. Larue, Timo M. Deist, Arthur Jochems, Tim Lustberg (+27 others)
2017 Advanced Drug Delivery Reviews  

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In the reasonably near future, decision support systems will be fully integrated within the clinic, with data and knowledge being shared in a standardized, dynamic, and potentially global manner enabling  ...  treatment of prostate cancer.  ...  An example and overview of an interactive PDA for prostate cancer (http://www.treatmentchoice.info/).  ... 
doi:10.1016/j.addr.2016.01.006 pmid:26774327 fatcat:rpfktbxw3rf4vewbiuj5alsave
Citation

Philippe Lambin, Jaap Zindler, Ben G.L. Vanneste, Lien Van De Voorde, Daniëlle Eekers, Inge Compter, Kranthi Marella Panth, Jurgen Peerlings, Ruben T.H.M. Larue, Timo M. Deist, Arthur Jochems, Tim Lustberg, Johan van Soest, Evelyn E.C. de Jong, Aniek J.G. Even, Bart Reymen, Nicolle Rekers, Marike van Gisbergen, Erik Roelofs, Sara Carvalho, Ralph T.H. Leijenaar, Catharina M.L. Zegers, Maria Jacobs, Janita van Timmeren, Patricia Brouwers, Jonathan A. Lal, Ludwig Dubois, Ala Yaromina, Evert Jan Van Limbergen, Maaike Berbee, Wouter van Elmpt, Cary Oberije, Bram Ramaekers, Andre Dekker, Liesbeth J. Boersma, Frank Hoebers, Kim M. Smits, Adriana J. Berlanga, Sean Walsh. "Decision support systems for personalized and participative radiation oncology." Advanced Drug Delivery Reviews (2017) 131-153

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