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Recent advancements in multimodal pre-training models have significantly advanced computational pathology.
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Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning
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Jacob Devlin · 2018
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Attention-based deep multiple instance learning
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Scanpy: large-scale single-cell gene expression data analysis
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Language models are few-shot learners
Tom B Brown · 2020
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A simple framework for contrastive learning of visual representations
Ting Chen, Simon Kornblith, Mohammad Norouzi, and Geoffrey Hinton · 2020
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Revealing dynamics of gene expression variability in cell state space
Dominic Grün · 2020
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Flexible experimental designs for valid single-cell rna-sequencing experiments allowing batch effects correction
Fangda Song, Ga Ming Angus Chan, and Yingying Wei · 2020
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Spatial deconvolution of her2-positive breast cancer delineates tumor-associated cell type interactions
Alma Andersson, Ludvig Larsson, Linnea Stenbeck, Fredrik Salmén, Anna Ehinger, Sunny Z Wu, Ghamdan Al-Eryani, Daniel Roden, Alex Swarbrick, Åke Borg, et al · 2021
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Emerging properties in self-supervised vision transformers
Mathilde Caron, Hugo Touvron, Ishan Misra, Hervé Jégou, Julien Mairal, Piotr Bojanowski, and Armand Joulin · 2021
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An empirical study of training self-supervised vision transformers
Xinlei Chen, Saining Xie, and Kaiming He · 2021
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Scaling up visual and vision-language representation learning with noisy text supervision
Chao Jia, Yinfei Yang, Ye Xia, Yi-Ting Chen, Zarana Parekh, Hieu Pham, Quoc Le, Yun-Hsuan Sung, Zhen Li, and Tom Duerig · 2021
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Dual-stream multiple instance learning network for whole slide image classification with self-supervised contrastive learning
Bin Li, Yin Li, and Kevin W Eliceiri · 2021
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From bulk, single-cell to spatial rna sequencing
Xinmin Li and Cun-Yu Wang · 2021
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Data-efficient and weakly supervised computational pathology on whole-slide images
Ming Y Lu, Drew FK Williamson, Tiffany Y Chen, Richard J Chen, Matteo Barbieri, and Faisal Mahmood · 2021
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Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
Kristen R Maynard, Leonardo Collado-Torres, Lukas M Weber, Cedric Uytingco, Brianna K Barry, Stephen R Williams, Joseph L Catallini, Matthew N Tran, Zachary Besich, Madhavi Tippani, et al · 2021
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Leveraging information in spatial transcriptomics to predict super-resolution gene expression from histology images in tumors
Minxing Pang, Kenong Su, and Mingyao Li · 2021
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A structure-aware hierarchical graph-based multiple instance learning framework for pt staging in histopathological image
Jiangbo Shi, Lufei Tang, Yang Li, Xianli Zhang, Zeyu Gao, Yefeng Zheng, Chunbao Wang, Tieliang Gong, and Chen Li · 2023
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Transfer learning enables predictions in network biology
Christina V Theodoris, Ling Xiao, Anant Chopra, Mark D Chaffin, Zeina R Al Sayed, Matthew C Hill, Helene Mantineo, Elizabeth M Brydon, Zexian Zeng, X Shirley Liu, et al · 2023
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The expanding vistas of spatial transcriptomics
Luyi Tian, Fei Chen, and Evan Z Macosko · 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, Kristen Severson, Eric Zimmermann, James Hall, Neil Tenenholtz, et al · 2023
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Batch alignment of single-cell transcriptomics data using deep metric learning
Xiaokang Yu, Xinyi Xu, Jingxiao Zhang, and Xiangjie Li · 2023
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Learning transferable visual models from natural language supervision
Alec Radford, Jong Wook Kim, Chris Hallacy, Aditya Ramesh, Gabriel Goh, Sandhini Agarwal, Girish Sastry, Amanda Askell, Pamela Mishkin, Jack Clark, et al · 2021
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Transmil: Transformer based correlated multiple instance learning for whole slide image classification
Zhuchen Shao, Hao Bian, Yang Chen, Yifeng Wang, Jian Zhang, Xiangyang Ji, et al · 2021
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Cathepsin c promotes breast cancer lung metastasis by modulating neutrophil infiltration and neutrophil extracellular trap formation
Yansen Xiao, Min Cong, Jiatao Li, Dasa He, Qiuyao Wu, Pu Tian, Yuan Wang, Shuaixi Yang, Chenxi Liang, Yajun Liang, et al · 2021
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Spatially resolved clonal copy number alterations in benign and malignant tissue
Andrew Erickson, Mengxiao He, Emelie Berglund, Maja Marklund, Reza Mirzazadeh, Niklas Schultz, Linda Kvastad, Alma Andersson, Ludvig Bergenstråhle, Joseph Bergenstråhle, et al · 2022
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Masked autoencoders are scalable vision learners
Kaiming He, Xinlei Chen, Saining Xie, Yanghao Li, Piotr Dollár, and Ross Girshick · 2022
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Blip: Bootstrapping language-image pre-training for unified vision-language understanding and generation
Junnan Li, Dongxu Li, Caiming Xiong, and Steven Hoi · 2022
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Transformer-based unsupervised contrastive learning for histopathological image classification
Xiyue Wang, Sen Yang, Jun Zhang, Minghui Wang, Jing Zhang, Wei Yang, Junzhou Huang, and Xiao Han · 2022
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Sodb facilitates comprehensive exploration of spatial omics data
Zhiyuan Yuan, Wentao Pan, Xuan Zhao, Fangyuan Zhao, Zhimeng Xu, Xiu Li, Yi Zhao, Michael Q Zhang, and Jianhua Yao · 2023
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Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and psc human liver
Tallulah S Andrews, Diana Nakib, Catia T Perciani, Xue Zhong Ma, Lewis Liu, Erin Winter, Damra Camat, Sai W Chung, Patricia Lumanto, Justin Manuel, et al · 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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Spatial transcriptomics in health and disease
Sanjay Jain and Michael T Eadon · 2024
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Thitogene: a deep learning method for predicting spatial transcriptomics from histological images
Yuran Jia, Junliang Liu, Li Chen, Tianyi Zhao, and Yadong Wang · 2024
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Inferring histology-associated gene expression gradients in spatial transcriptomic studies
Jan Kueckelhaus, Simon Frerich, Jasim Kada-Benotmane, Christina Koupourtidou, Jovica Ninkovic, Martin Dichgans, Juergen Beck, Oliver Schnell, and Dieter Henrik Heiland · 2024
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Pibf1 regulates multiple gene expression via impeding long-range chromatin interaction to drive the malignant transformation of hpv16 integration epithelial cells
Xiaomin Li, Ci Ren, Anni Huang, Yue Zhao, Liming Wang, Hui Shen, Chun Gao, Bingxin Chen, Tong Zhu, Jinfeng Xiong, et al · 2024
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Exploiting geometric features via hierarchical graph pyramid transformer for cancer diagnosis using histopathological images
Mingxin Liu, Yunzan Liu, Pengbo Xu, Hui Cui, Jing Ke, and Jiquan Ma · 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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Multimodal contrastive learning for spatial gene expression prediction using histology images
Wenwen Min, Zhiceng Shi, Jun Zhang, Jun Wan, and Changmiao Wang · 2024
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Caclust: linking genotype to transcriptional heterogeneity of follicular lymphoma using bcr and exomic variants
Kazimierz Oksza-Orzechowski, Edwin Quinten, Shadi Darvish Shafighi, Szymon M Kiełbasa, Hugo van Kessel, Ruben AL de Groen, Joost SP Vermaat, Julieta H Seplúveda-Yáñez, Marcelo A Navarrete, Hendrik Veelken, et al · 2024
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Rethinking multiple instance learning for whole slide image classification: A good instance classifier is all you need
Linhao Qu, Yingfan Ma, Xiaoyuan Luo, Qinhao Guo, Manning Wang, and Zhijian Song · 2024
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H-optimus-0, 2024
Charlie Saillard, Rodolphe Jenatton, Felipe Llinares-López, Zelda Mariet, David Cahané, Eric Durand, and Jean-Philippe Vert · 2024
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Nicheformer: a foundation model for single-cell and spatial omics
Anna Christina Schaar, Alejandro Tejada-Lapuerta, Giovanni Palla, Robert Gutgesell, Lennard Halle, Mariia Minaeva, Larsen Vornholz, Leander Dony, Francesca Drummer, Mojtaba Bahrami, et al · 2024
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Vila-mil: Dual-scale vision-language multiple instance learning for whole slide image classification
Jiangbo Shi, Chen Li, Tieliang Gong, Yefeng Zheng, and Huazhu Fu · 2024
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Multimodal prototyping for cancer survival prediction
Andrew H Song, Richard J Chen, Guillaume Jaume, Anurag Jayant Vaidya, Alexander Baras, and Faisal Mahmood · 2024
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Spatially resolved gene expression prediction from histology images via bi-modal contrastive learning
Ronald Xie, Kuan Pang, Sai Chung, Catia Perciani, Sonya MacParland, Bo Wang, and Gary Bader · 2024
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Heartsvg: a fast and accurate method for identifying spatially variable genes in large-scale spatial transcriptomics
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