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Remarkable strides in computational pathology have been made in the task-agnostic foundation model that advances the performance of a wide array of downstream clinical tasks.
Evaluation of survival data and two new rank order statistics arising in its consideration
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Individual comparisons by ranking methods
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An introduction to the bootstrap
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Mutations in pten are frequent in endometrial carcinoma but rare in other common gynecological malignancies
Hironori Tashiro, Marian S Blazes, Rong Wu, Kathleen R Cho, Shikha Bose, Steven I Wang, Jing Li, Ramon Parsons, and Lora Hedrick Ellenson · 1997
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Age and tp53 mutation frequency in childhood malignant gliomas: results in a multi-institutional cohort
Ian F Pollack, Sydney D Finkelstein, Judith Burnham, Emiko J Holmes, Ronald L Hamilton, Allan J Yates, Jonathan L Finlay, Richard Sposto, and Children’s Cancer Group · 2001
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Gene-expression profiles predict survival of patients with lung adenocarcinoma
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Bleu: a method for automatic evaluation of machine translation
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Rouge: A package for automatic evaluation of summaries
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Breast-cancer stromal cells with tp53 mutations and nodal metastases
Attila Patocs, Li Zhang, Yaomin Xu, Frank Weber, Trinidad Caldes, George L Mutter, Petra Platzer, and Charis Eng · 2007
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Prognostic and therapeutic implications of egfr and kras mutations in resected lung adenocarcinoma
Jenifer L Marks, Stephen Broderick, Qin Zhou, Dhananjay Chitale, Allan R Li, Maureen F Zakowski, Mark G Kris, Valerie W Rusch, Christopher G Azzoli, Venkatraman E Seshan, et al · 2008
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Pten expression in endometrial biopsies as a marker of progression to endometrial carcinoma
James V Lacey Jr, George L Mutter, Brigitte M Ronnett, Olga B Ioffe, Máire A Duggan, Brenda B Rush, Andrew G Glass, Douglas A Richesson, Nilanjan Chatterjee, Bryan Langholz, et al · 2008
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Imagenet: A large-scale hierarchical image database
Jia Deng, Wei Dong, Richard Socher, Li-Jia Li, Kai Li, and Li Fei-Fei · 2009
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Adjuvant trastuzumab in her2-positive breast cancer
Dennis Slamon, Wolfgang Eiermann, Nicholas Robert, Tadeusz Pienkowski, Miguel Martin, Michael Press, John Mackey, John Glaspy, Arlene Chan, Marek Pawlicki, et al · 2011
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Rsem: accurate transcript quantification from rna-seq data with or without a reference genome
Bo Li and Colin N Dewey · 2011
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Meteor 1.3: Automatic metric for reliable optimization and evaluation of machine translation systems
Michael Denkowski and Alon Lavie · 2011
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The cancer genome atlas pan-cancer analysis project
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, and Joshua M Stuart · 2013
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The molecular signatures database hallmark gene set collection
Arthur Liberzon, Chet Birger, Helga Thorvaldsdóttir, Mahmoud Ghandi, Jill P Mesirov, and Pablo Tamayo · 2015
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The cptac data portal: a resource for cancer proteomics research
Nathan J Edwards, Mauricio Oberti, Ratna R Thangudu, Shuang Cai, Peter B McGarvey, Shine Jacob, Subha Madhavan, and Karen A Ketchum · 2015
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Identity mappings in deep residual networks
Kaiming He, Xiangyu Zhang, Shaoqing Ren, and Jian Sun · 2016
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Five-year survival in egfr-mutant metastatic lung adenocarcinoma treated with egfr-tkis
Jessica J Lin, Stephanie Cardarella, Christine A Lydon, Suzanne E Dahlberg, David M Jackman, Pasi A Jänne, and Bruce E Johnson · 2016
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Diagnostic assessment of deep learning algorithms for detection of lymph node metastases in women with breast cancer
Babak Ehteshami Bejnordi, Mitko Veta, Paul Johannes Van Diest, Bram Van Ginneken, Nico Karssemeijer, Geert Litjens, Jeroen AWM Van Der Laak, Meyke Hermsen, Quirine F Manson, Maschenka Balkenhol, et al · 2017
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Oncokb: a precision oncology knowledge base
Debyani Chakravarty, Jianjiong Gao, Sarah Phillips, Ritika Kundra, Hongxin Zhang, Jiaojiao Wang, Julia E Rudolph, Rona Yaeger, Tara Soumerai, Moriah H Nissan, et al · 2017
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Keap1 loss promotes kras-driven lung cancer and results in dependence on glutaminolysis
Rodrigo Romero, Volkan I Sayin, Shawn M Davidson, Matthew R Bauer, Simranjit X Singh, Sarah E LeBoeuf, Triantafyllia R Karakousi, Donald C Ellis, Arjun Bhutkar, Francisco J Sanchez-Rivera, et al · 2017
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A practical guide to single-cell rna-sequencing for biomedical research and clinical applications
Ashraful Haque, Jessica Engel, Sarah A Teichmann, and Tapio Lönnberg · 2017
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In defense of the triplet loss for person re-identification
Alexander Hermans, Lucas Beyer, and Bastian Leibe · 2017
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Attention-based deep multiple instance learning
Maximilian Ilse, Jakub Tomczak, and Max Welling · 2018
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From detection of individual metastases to classification of lymph node status at the patient level: the camelyon17 challenge
Peter Bandi, Oscar Geessink, Quirine Manson, Marcory Van Dijk, Maschenka Balkenhol, Meyke Hermsen, Babak Ehteshami Bejnordi, Byungjae Lee, Kyunghyun Paeng, Aoxiao Zhong, et al · 2018
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Arid1a and pi3-kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion
Mike R Wilson, Jake J Reske, Jeanne Holladay, Genna E Wilber, Mary Rhodes, Julie Koeman, Marie Adams, Ben Johnson, Ren-Wei Su, Niraj R Joshi, et al · 2019
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Targeting the pi3-kinase pathway in triple-negative breast cancer
J Pascual and NC Turner · 2019
A visual–language foundation model for pathology image analysis using medical twitter
Zhi Huang, Federico Bianchi, Mert Yuksekgonul, Thomas J Montine, and James Zou · 2023
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When is a foundation model a foundation model
Saghir Alfasly, Peyman Nejat, Sobhan Hemati, Jibran Khan, Isaiah Lahr, Areej Alsaafin, Abubakr Shafique, Nneka Comfere, Dennis Murphree, Chady Meroueh, et al · 2023
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Gemini: a family of highly capable multimodal models
Gemini Team, Rohan Anil, Sebastian Borgeaud, Yonghui Wu, Jean-Baptiste Alayrac, Jiahui Yu, Radu Soricut, Johan Schalkwyk, Andrew M Dai, Anja Hauth, et al · 2023
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Maple: Multi-modal prompt learning
Muhammad Uzair Khattak, Hanoona Rasheed, Muhammad Maaz, Salman Khan, and Fahad Shahbaz Khan · 2023
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Multimodal optimal transport-based co-attention transformer with global structure consistency for survival prediction
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Cited alongside, same era.
Cic protein instability contributes to tumorigenesis in glioblastoma
Severa Bunda, Pardeep Heir, Julie Metcalf, Annie Si Cong Li, Sameer Agnihotri, Stefan Pusch, Mamatjan Yasin, Mira Li, Kelly Burrell, Sheila Mansouri, et al · 2019
Cited alongside, same era.
Gene2vec: distributed representation of genes based on co-expression
Jingcheng Du, Peilin Jia, Yulin Dai, Cui Tao, Zhongming Zhao, and Degui Zhi · 2019
Cited alongside, same era.
Rna sequencing: new technologies and applications in cancer research
Mingye Hong, Shuang Tao, Ling Zhang, Li-Ting Diao, Xuanmei Huang, Shaohui Huang, Shu-Juan Xie, Zhen-Dong Xiao, and Hua Zhang · 2020
Cited alongside, same era.
Biobert: a pre-trained biomedical language representation model for biomedical text mining
Jinhyuk Lee, Wonjin Yoon, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, and Jaewoo Kang · 2020
Cited alongside, same era.
An image is worth 16x16 words: Transformers for image recognition at scale
Alexey Dosovitskiy, Lucas Beyer, Alexander Kolesnikov, Dirk Weissenborn, Xiaohua Zhai, Thomas Unterthiner, Mostafa Dehghani, Matthias Minderer, Georg Heigold, Sylvain Gelly, et al · 2020
Cited alongside, same era.
Bias in cross-entropy-based training of deep survival networks
Shekoufeh Gorgi Zadeh and Matthias Schmid · 2020
Cited alongside, same era.
Multimodal co-attention transformer for survival prediction in gigapixel whole slide images
Richard J Chen, Ming Y Lu, Wei-Hung Weng, Tiffany Y Chen, Drew FK Williamson, Trevor Manz, Maha Shady, and Faisal Mahmood · 2021
Cited alongside, same era.
Yingxue Xu and Hao Chen · 2023
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Cross-modal translation and alignment for survival analysis
Fengtao Zhou and Hao Chen · 2023
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Molecular markers of metastatic disease in kras-mutant lung adenocarcinoma
D Boiarsky, CA Lydon, ES Chambers, LM Sholl, M Nishino, F Skoulidis, JV Heymach, J Luo, MM Awad, PA Janne, et al · 2023
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Gata3 mediates doxorubicin resistance by inhibiting cyb5r2-catalyzed iron reduction in breast cancer cells
Zhen Zhu, Hongyu Shen, Jialin Xu, Zheng Fang, Guanqun Wo, Ying Ma, Kai Yang, Yalin Wang, Qiang Yu, and Jin-hai Tang · 2023
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Visual language pretrained multiple instance zero-shot transfer for histopathology images
Ming Y Lu, Bowen Chen, Andrew Zhang, Drew FK Williamson, Richard J Chen, Tong Ding, Long Phi Le, Yung-Sung Chuang, and Faisal Mahmood · 2023
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2mo multimodal data fusion enhanced precision neoadjuvant chemotherapy in breast cancer with a multi-task transformer-cnn-mixed learning
Y Yu, Z He, Z Wang, R Lin, Z Zhang, W Ren, L Mao, H Yao, et al · 2023
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Virchow: A million-slide digital pathology foundation model
Eugene Vorontsov, Alican Bozkurt, Adam Casson, George Shaikovski, Michal Zelechowski, Siqi Liu, Philippe Mathieu, Alexander van Eck, Donghun Lee, Julian Viret, et al · 2023
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Mamba: Linear-time sequence modeling with selective state spaces
Albert Gu and Tri Dao · 2023
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Longnet: Scaling transformers to 1,000,000,000 tokens
Jiayu Ding, Shuming Ma, Li Dong, Xingxing Zhang, Shaohan Huang, Wenhui Wang, Nanning Zheng, and Furu Wei · 2023
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Towards a general-purpose foundation model for computational pathology
Richard J Chen, Tong Ding, Ming Y Lu, Drew FK Williamson, Guillaume Jaume, Andrew H Song, Bowen Chen, Andrew Zhang, Daniel Shao, Muhammad Shaban, et al · 2024
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A visual-language foundation model for computational pathology
Ming Y Lu, Bowen Chen, Drew FK Williamson, Richard J Chen, Ivy Liang, Tong Ding, Guillaume Jaume, Igor Odintsov, Long Phi Le, Georg Gerber, et al · 2024
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A whole-slide foundation model for digital pathology from real-world data
Hanwen Xu, Naoto Usuyama, Jaspreet Bagga, Sheng Zhang, Rajesh Rao, Tristan Naumann, Cliff Wong, Zelalem Gero, Javier González, Yu Gu, et al · 2024
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A pathology foundation model for cancer diagnosis and prognosis prediction
Xiyue Wang, Junhan Zhao, Eliana Marostica, Wei Yuan, Jietian Jin, Jiayu Zhang, Ruijiang Li, Hongping Tang, Kanran Wang, Yu Li, et al · 2024
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A multimodal dataset for precision oncology in head and neck cancer
Marion Dörrich, Matthias Balk, Tatjana Heusinger, Sandra Beyer, Hassan Kanso, Christian Matek, Arndt Hartmann, Heinrich Iro, Markus Eckstein, Antoniu-Oreste Gostian, et al · 2024
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A whole-slide foundation model for digital pathology from real-world data
Hanwen Xu, Naoto Usuyama, Jaspreet Bagga, Sheng Zhang, Rajesh Rao, Tristan Naumann, Cliff Wong, Zelalem Gero, Javier González, Yu Gu, et al · 2024
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Zhengrui Guo, Jiabo Ma, Yingxue Xu, Yihui Wang, Liansheng Wang, and Hao Chen · 2024
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Mambamil: Enhancing long sequence modeling with sequence reordering in computational pathology
Shu Yang, Yihui Wang, and Hao Chen · 2024
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scgpt: toward building a foundation model for single-cell multi-omics using generative ai
Haotian Cui, Chloe Wang, Hassaan Maan, Kuan Pang, Fengning Luo, Nan Duan, and Bo Wang · 2024
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Machine learning-driven histotype diagnosis of ovarian carcinoma: Insights from the ocean ai challenge
Maryam Asadi-Aghbolaghi, Hossein Farahani, Allen Zhang, Ardalan Akbari, Sirim Kim, Ashley Chow, Sohier Dane, OCEAN Challenge Consortium, OTTA Consortium, David G Huntsman, et al · 2024
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