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Spatial proteomics technologies have transformed our understanding of complex tissue architecture in cancer but present unique challenges for computational analysis.
Fibroblasts in cancer
Raghu Kalluri and Michael Zeisberg · 2006
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Extracting and Composing Robust Features with Denoising Autoencoders
Pascal Vincent, Hugo Larochelle, Yoshua Bengio, and Pierre-Antoine Manzagol · 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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Hallmarks of cancer: the next generation
Douglas Hanahan and Robert A Weinberg · 2011
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Scikit-learn: Machine learning in Python
F. Pedregosa, G. Varoquaux, A. Gramfort, V. Michel, B. Thirion, O. Grisel, M. Blondel, P. Prettenhofer, R. Weiss, V. Dubourg, J. Vanderplas, A. Passos, D. Cournapeau, M. Brucher, M. Perrot, and E. Duchesnay · 2011
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The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
Christina Curtis, Sohrab P Shah, Suet-Feung Chin, Gulisa Turashvili, Oscar M Rueda, Mark J Dunning, Doug Speed, Andy G Lynch, Shamith Samarajiwa, Yinyin Yuan, et al · 2012
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Sinkhorn Distances: Lightspeed Computation of Optimal Transport
Marco Cuturi · 2013
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scikit-image: image processing in Python
Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu, and the scikit-image contributors · 2014
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Cancer-associated fibroblasts connect metastasis-promoting communication in colorectal cancer
Joke Tommelein, Laurine Verset, Tom Boterberg, Pieter Demetter, Marc Bracke, and Olivier De Wever · 2015
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Sliced and Radon Wasserstein Barycenters of Measures
Nicolas Bonneel, Julien Rabin, Gabriel Peyré, and Hanspeter Pfister · 2015
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Adam: A Method for Stochastic Optimization
Diederik P Kingma and Jimmy Ba · 2015
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Identifying cancer origin using circulating tumor cells
Si-Hong Lu, Wen-Sy Tsai, Ying-Hsu Chang, Teh-Ying Chou, See-Tong Pang, Po-Hung Lin, Chun-Ming Tsai, and Ying-Chih Chang · 2016
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Deep Residual Learning for Image Recognition
Kaiming He, Xiangyu Zhang, Shaoqing Ren, and Jian Sun · 2016
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Attention is All you Need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin · 2017
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Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA
Yuan Tian, Mariana Babor, Jerome Lane, Veronique Schulten, Veena S Patil, Grégory Seumois, Sandy L Rosales, Zheng Fu, Gaelle Picarda, Julie Burel, et al · 2017
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Attention-based Deep Multiple Instance Learning
Maximilian Ilse, Jakub Tomczak, and Max Welling · 2018
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Stromal CD10 expression in breast cancer correlates with tumor invasion and cancer stem cell phenotype
Tahani Louhichi, Hanene Saad, Myriam Ben Dhiab, Sonia Ziadi, and Mounir Trimeche · 2018
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Simultaneous multiplexed imaging of mrna and proteins with subcellular resolution in breast cancer tissue samples by mass cytometry
Daniel Schulz, Vito Riccardo Tomaso Zanotelli, Jana Raja Fischer, Denis Schapiro, Stefanie Engler, Xiao-Kang Lun, Hartland Warren Jackson, and Bernd Bodenmiller · 2018
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Computational Optimal Transport
Gabriel Peyré, Marco Cuturi, et al · 2019
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A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry
Nicolas Damond, Stefanie Engler, Vito RT Zanotelli, Denis Schapiro, Clive H Wasserfall, Irina Kusmartseva, Harry S Nick, Fabrizio Thorel, Pedro L Herrera, Mark A Atkinson, et al · 2019
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lifelines: survival analysis in python
Cameron Davidson-Pilon · 2019
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Language Models are Few-Shot Learners
Tom B Brown, Benjamin Mann, Nick Ryder, Melanie Subbiah, Jared Kaplan, Prafulla Dhariwal, Arvind Neelakantan, Pranav Shyam, Girish Sastry, Amanda Askell, et al · 2020
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The single-cell pathology landscape of breast cancer
Hartland W Jackson, Jana R Fischer, Vito RT Zanotelli, H Raza Ali, Robert Mechera, Savas D Soysal, Holger Moch, Simone Muenst, Zsuzsanna Varga, Walter P Weber, et al · 2020
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Relationship between tumor-infiltrating lymphocytes (tils) and outcomes in the keynote-119 study of pembrolizumab vs chemotherapy for previously treated metastatic triple-negative breast cancer (mtnbc)
Sherene Loi, Eric Winer, Oleg Lipatov, Seock-Ah Im, Anthony Goncalves, Javier Cortes, Keun S Lee, Peter Schmid, Laura Testa, Isabell Witzel, et al · 2020
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On Layer Normalization in the Transformer Architecture
Ruibin Xiong, Yunchang Yang, Di He, Kai Zheng, Shuxin Zheng, Chen Xing, Huishuai Zhang, Yanyan Lan, Liwei Wang, and Tieyan Liu · 2020
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scikit-survival: A library for time-to-event analysis built on top of scikit-learn
Sebastian Pölsterl · 2020
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Machine learning in python: Main developments and technology trends in data science, machine learning, and artificial intelligence
Sebastian Raschka, Joshua Patterson, and Corey Nolet · 2020
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Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma
Darci Phillips, Magdalena Matusiak, Belén Rivero Gutierrez, Salil S Bhate, Graham L Barlow, Sizun Jiang, Janos Demeter, Kimberly S Smythe, Robert H Pierce, Steven P Fling, et al · 2021
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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, Jakob Uszkoreit, and Neil Houlsby · 2021
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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, Gretchen Krueger, and Ilya Sutskever · 2021
Cited alongside, same era.
Is Space-Time Attention All You Need for Video Understanding?
Gedas Bertasius, Heng Wang, and Lorenzo Torresani · 2021
Cited alongside, same era.
The paradoxical role of matrix metalloproteinase-11 in cancer
Bing Ma, Rui Ran, Hai-Yang Liao, and Hai-Hong Zhang · 2021
Cited alongside, same era.
Hallmarks of cancer: new dimensions
Douglas Hanahan · 2022
Cited alongside, same era.
Breast tumor microenvironment structures are associated with genomic features and clinical outcome
Esther Danenberg, Helen Bardwell, Vito RT Zanotelli, Elena Provenzano, Suet-Feung Chin, Oscar M Rueda, Andrew Green, Emad Rakha, Samuel Aparicio, Ian O Ellis, et al · 2022
Cited alongside, same era.
Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients
Andrea J Radtke, Ekaterina Postovalova, Arina Varlamova, Alexander Bagaev, Maria Sorokina, Olga Kudryashova, Mark Meerson, Margarita Polyakova, Ilia Galkin, Viktor Svekolkin, et al · 2024
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Masked Autoencoders for Microscopy are Scalable Learners of Cellular Biology
Oren Kraus, Kian Kenyon-Dean, Saber Saberian, Maryam Fallah, Peter McLean, Jess Leung, Vasudev Sharma, Ayla Khan, Jia Balakrishnan, Safiye Celik, et al · 2024
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Integrating AI-Powered Digital Pathology and Imaging Mass Cytometry Identifies Key Classifiers of Tumor Cells, Stroma, and Immune Cells in Non–Small Cell Lung Cancer
Alessandra Rigamonti, Marika Viatore, Rebecca Polidori, Daoud Rahal, Marco Erreni, Maria Rita Fumagalli, Damiano Zanini, Andrea Doni, Anna Rita Putignano, Paola Bossi, et al · 2024
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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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Kaiming He, Xinlei Chen, Saining Xie, Yanghao Li, Piotr Dollár, and Ross Girshick · 2022
Cited alongside, same era.
MultiMAE: Multi-modal Multi-task Masked Autoencoders
Roman Bachmann, David Mizrahi, Andrei Atanov, and Amir Zamir · 2022
Cited alongside, same era.
Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy
Tobias Hoch, Daniel Schulz, Nils Eling, Julia Martínez Gómez, Mitchell P Levesque, and Bernd Bodenmiller · 2022
Cited alongside, same era.
Pathologic complete response (pcr) to neoadjuvant treatment with or without atezolizumab in triple-negative, early high-risk and locally advanced breast cancer: Neotrip michelangelo randomized study
Luca Gianni, CS Huang, D Egle, B Bermejo, C Zamagni, M Thill, A Anton, S Zambelli, G Bianchini, S Russo, et al · 2022
Cited alongside, same era.
Spatially variant immune infiltration scoring in human cancer tissues
Mayar Allam, Thomas Hu, Jeongjin Lee, Jeffrey Aldrich, Sunil S Badve, Yesim Gökmen-Polar, Manali Bhave, Suresh S Ramalingam, Frank Schneider, and Ahmet F Coskun · 2022
Cited alongside, same era.
Spatially mapping the immune landscape of melanoma using imaging mass cytometry
Dan Moldoveanu, LeeAnn Ramsay, Mathieu Lajoie, Luke Anderson-Trocme, Marine Lingrand, Diana Berry, Lucas JM Perus, Yuhong Wei, Cleber Moraes, Rached Alkallas, et al · 2022
Cited alongside, same era.
FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness
Tri Dao, Daniel Y. Fu, Stefano Ermon, Atri Rudra, and Christopher Ré · 2022
Cited alongside, same era.
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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SubCell: Vision foundation models for microscopy capture single-cell biology
Ankit Gupta, Zoe Wefers, Konstantin Kahnert, Jan N Hansen, William D Leineweber, Anthony Cesnik, Dan Lu, Ulrika Axelsson, Frederic Ballllosera Navarro, Theofanis Karaletsos, et al · 2024
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How to build the virtual cell with artificial intelligence: Priorities and opportunities
Charlotte Bunne, Yusuf Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Marcel Roed, Theo Alexandrov, Mohammed AlQuraishi, Patricia Brennan, Daniel B Burkhardt, et al · 2024
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Cancer-associated fibroblast phenotypes are associated with patient outcome in non-small cell lung cancer
Lena Cords, Stefanie Engler, Martina Haberecker, Jan Hendrik Rüschoff, Holger Moch, Natalie de Souza, and Bernd Bodenmiller · 2024
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Neoadjuvant nivolumab or nivolumab plus ipilimumab in early-stage triple-negative breast cancer: a phase 2 adaptive trial
Iris Nederlof, Olga I Isaeva, Manon de Graaf, Robbert CAM Gielen, Noor AM Bakker, Adrianne L Rolfes, Hannah Garner, Bram Boeckx, Joleen JH Traets, Ingrid AM Mandjes, et al · 2024
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Accelerating histopathology workflows with generative AI-based virtually multiplexed tumour profiling
Pushpak Pati, Sofia Karkampouna, Francesco Bonollo, Eva Compérat, Martina Radić, Martin Spahn, Adriano Martinelli, Martin Wartenberg, Marianna Kruithof-de Julio, and Marianna Rapsomaniki · 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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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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Roformer: Enhanced transformer with rotary position embedding
Jianlin Su, Murtadha Ahmed, Yu Lu, Shengfeng Pan, Wen Bo, and Yunfeng Liu · 2024
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FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning
Tri Dao · 2024
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Immucan panel 1 cell type classification, 2024
Daniel Schulz, Nils Eling, Bruno Palau Fernandez, Michelle Daniel, and Bernd Bodenmiller · 2024
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ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy
Kian Kenyon-Dean, Zitong Jerry Wang, John Urbanik, Konstantin Donhauser, Jason Hartford, Saber Saberian, Nil Sahin, Ihab Bendidi, Safiye Celik, Marta Fay, et al · 2025
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A foundation model for spatial proteomics
Muhammad Shaban, Yuzhou Chang, Huaying Qiu, Yao Yu Yeo, Andrew H Song, Guillaume Jaume, Yuchen Wang, Luca L Weishaupt, Tong Ding, Anurag Vaidya, et al · 2025
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Self-Supervised AI Reveals a Hidden Landscape of Prognostic Spatial Patterns in Multiplex Immunofluorescence Images
Lucas Farndale, Kai Rakovic, Phimmada Hatthakarnkul, Sona Szalma, Leonor Patricia Schubert Santana, Silvia Martinelli, Fiona Ballantyne, Rachel L Baird, Ian R Powley, Leah Officer-Jones, et al · 2025
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A stratification system for breast cancer based on basoluminal tumor cells and spatial tumor architecture
Lasse Meyer, Hartland W Jackson, Nils Eling, Shan Zhao, Genki Usui, Haithem Dakhli, Peter Schraml, Susanne Dettwiler, Constanze Elfgen, Zsuzsanna Varga, et al · 2025
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Test-Time View Selection for Multi-Modal Decision Making
Eeshaan Jain, Johann Wenckstern, Benedikt von Querfurth, and Charlotte Bunne · 2025
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MTBBench: A Multimodal Sequential Clinical Decision-Making Benchmark in Oncology
Kiril Vasilev, Alexandre Misrahi, Eeshaan Jain, Phil F Cheng, Petros Liakopoulos, Olivier Michielin, Michael Moor, and Charlotte Bunne · 2025
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A cell atlas foundation model for scalable search of similar human cells
Graham Heimberg, Tony Kuo, Daryle J DePianto, Omar Salem, Tobias Heigl, Nathaniel Diamant, Gabriele Scalia, Tommaso Biancalani, Shannon J Turley, Jason R Rock, et al · 2025
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A cross-species generative cell atlas across 1.5 billion years of evolution: The transcriptformer single-cell model
James D Pearce, Sara E Simmonds, Gita Mahmoudabadi, Lakshmi Krishnan, Giovanni Palla, Ana-Maria Istrate, Alexander Tarashansky, Benjamin Nelson, Omar Valenzuela, Donghui Li, et al · 2025
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A visual–omics foundation model to bridge histopathology with spatial transcriptomics
Weiqing Chen, Pengzhi Zhang, Tu N Tran, Yiwei Xiao, Shengyu Li, Vrutant V Shah, Hao Cheng, Kristopher W Brannan, Keith Youker, Li Lai, et al · 2025
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The lipidomic architecture of the mouse brain
Luca Fusar Bassini, Halima Hannah Schede, Laura Capolupo, Leila Haj Abdullah Alieh, Francesca Venturi, Alessandro Valente, Colas Droin, Daniel Trejo Banos, Irina Khven, Ece Z Asirim, et al · 2025
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Rosie: Ai generation of multiplex immunofluorescence staining from histopathology images
Eric Wu, Matthew Bieniosek, Zhenqin Wu, Nitya Thakkar, Gregory W Charville, Ahmad Makky, Christian M Schürch, Jeroen R Huyghe, Ulrike Peters, Christopher I Li, et al · 2025
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Histopathology-based protein multiplex generation using deep learning
Sonali Andani, Boqi Chen, Joanna Ficek-Pascual, Simon Heinke, Ruben Casanova, Bernard Friedrich Hild, Bettina Sobottka, Bernd Bodenmiller, Viktor H Koelzer, et al · 2025
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Spatial and multiomics analysis of human and mouse lung adenocarcinoma precursors reveals tim-3 as a putative target for precancer interception
Bo Zhu, Pingjun Chen, Muhammad Aminu, Jian-Rong Li, Junya Fujimoto, Yanhua Tian, Lingzhi Hong, Hong Chen, Xin Hu, Chenyang Li, et al · 2025
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