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The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning (SSL).
Bleu: a method for automatic evaluation of machine translation
Papineni, K., Roukos, S., Ward, T. & Zhu, W.-J · 2002
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Rouge: A package for automatic evaluation of summaries
Lin, C.-Y · 2004
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METEOR: An automatic metric for MT evaluation with improved correlation with human judgments
Banerjee, S. & Lavie, A · 2005
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Content-based multimedia information retrieval: State of the art and challenges
Lew, M. S., Sebe, N., Djeraba, C. & Jain, R · 2006
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Histopathology image classification using bag of features and kernel functions
Caicedo, J. C., Cruz, A. & Gonzalez, F. A · 2009
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Visual pattern mining in histology image collections using bag of features
Cruz-Roa, A., Caicedo, J. C. & González, F. A · 2011
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The cancer genome atlas pan-cancer analysis project
Weinstein, J. N. et al · 2013
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Content-based image retrieval of digitized histopathology in boosted spectrally embedded spaces
Sridhar, A., Doyle, S. & Madabhushi, A · 2015
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The CPTAC Data Portal: A Resource for Cancer Proteomics Research
Edwards, N. J. et al · 2015
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The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans
Consortium, G. et al · 2015
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Predicting non-small cell lung cancer prognosis by fully automated microscopic pathology image features
Yu, K.-H. et al · 2016
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Clear cell renal cell carcinoma subtypes identified by BAP1 and PBRM1 expression
Joseph, R. W. et al · 2016
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Diagnostic assessment of deep learning algorithms for detection of lymph node metastases in women with breast cancer
Bejnordi, B. E. et al · 2017
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Burden and centralised treatment in europe of rare tumours: results of rarecarenet—a population-based study
Gatta, G. et al · 2017
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Mdnet: A semantically and visually interpretable medical image diagnosis network
Zhang, Z., Xie, Y., Xing, F., McGough, M. & Yang, L · 2017
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Prototypical networks for few-shot learning
Snell, J., Swersky, K. & Zemel, R · 2017
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Classification and mutation prediction from non–small cell lung cancer histopathology images using deep learning
Coudray, N. et al · 2018
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Artificial intelligence in healthcare
Yu, K.-H., Beam, A. L. & Kohane, I. S · 2018
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Histopathological whole slide image analysis using context-based cbir
Zheng, Y. et al · 2018
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Attention-based deep multiple instance learning
Ilse, M., Tomczak, J. & Welling, M · 2018
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An integrated TCGA pan-cancer clinical data resource to drive high-quality survival outcome analytics
Liu, J. et al · 2018
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Machine learning methods for histopathological image analysis
Komura, D. & Ishikawa, S · 2018
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Artificial intelligence in digital pathology—new tools for diagnosis and precision oncology
Bera, K., Schalper, K. A., Rimm, D. L., Velcheti, V. & Madabhushi, A · 2019
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Clinical-grade computational pathology using weakly supervised deep learning on whole slide images
Campanella, G. et al · 2019
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Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer
Kather, J. N. et al · 2019
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Deep learning-based classification of mesothelioma improves prediction of patient outcome
Courtiol, P. et al · 2019
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Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks
Wei, J. W. et al · 2019
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Simpleshot: Revisiting nearest-neighbor classification for few-shot learning
Wang, Y., Chao, W.-L., Weinberger, K. Q. & Van Der Maaten, L · 2019
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Similar image search for histopathology: SMILY
Hegde, N. et al · 2019
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Pheochromocytoma and paraganglioma
Neumann, H. P., Young Jr, W. F. & Eng, C · 2019
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Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks
Wei, J. W. et al · 2019
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Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis
Fu, Y. et al · 2020
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Deep learning for prediction of colorectal cancer outcome: a discovery and validation study
Skrede, O.-J. et al · 2020
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Yottixel–an image search engine for large archives of histopathology whole slide images
Kalra, S. et al · 2020
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An image is worth 16x16 words: Transformers for image recognition at scale
Dosovitskiy, A. et al · 2020
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Abstract LB-242: Proteomic Data Commons: A resource for proteogenomic analysis
Thangudu, R. R. et al · 2020
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Scaling laws for neural language models
Kaplan, J. et al · 2020
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Bias in cross-entropy-based training of deep survival networks
Zadeh, S. G. & Schmid, M · 2020
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Fine-tuning and training of densenet for histopathology image representation using tcga diagnostic slides
Riasatian, A. et al · 2021
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Deep learning in cancer pathology: a new generation of clinical biomarkers
Echle, A. et al · 2021
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AI-based pathology predicts origins for cancers of unknown primary
Lu, M. Y. et al · 2021
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Deep learning in histopathology: the path to the clinic
Van der Laak, J., Litjens, G. & Ciompi, F · 2021
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Data-efficient and weakly supervised computational pathology on whole-slide images
Lu, M. Y. et al · 2021
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Dual-stream multiple instance learning network for whole slide image classification with self-supervised contrastive learning
Li, B., Li, Y. & Eliceiri, K. W · 2021
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Whole slide images are 2d point clouds: Context-aware survival prediction using patch-based graph convolutional networks
Chen, R. J. et al · 2021
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Transmil: Transformer based correlated multiple instance learning for whole slide image classification
Shao, Z. et al · 2021
Cited alongside, same era.
On the opportunities and risks of foundation models
Bommasani, R. et al · 2021
Cited alongside, same era.
ibot: Image bert pre-training with online tokenizer
Zhou, J. et al · 2021
Cited alongside, same era.
Synthetic data in machine learning for medicine and healthcare
Chen, R. J., Lu, M. Y., Chen, T. Y., Williamson, D. F. & Mahmood, F · 2021
Cited alongside, same era.
Development and evaluation of a deep neural network for histologic classification of renal cell carcinoma on biopsy and surgical resection slides
Zhu, M. et al · 2021
Cited alongside, same era.
Giga-ssl: Self-supervised learning for gigapixel images
Lazard, T., Lerousseau, M., Decencière, E. & Walter, T · 2023
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Exploring Low-Rank Property in Multiple Instance Learning for Whole Slide Image Classification
Xiang, J. & Zhang, J · 2023
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Foundation models for generalist medical artificial intelligence
Moor, M. et al · 2023
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Dinov2: Learning robust visual features without supervision
Oquab, M. et al · 2023
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Leakage and the reproducibility crisis in machine-learning-based science
Kapoor, S. & Narayanan, A · 2023
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Embedding space augmentation for weakly supervised learning in whole-slide images
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Oncotree: a cancer classification system for precision oncology
Kundra, R. et al · 2021
Cited alongside, same era.
Learning transferable visual models from natural language supervision
Radford, A. et al · 2021
Cited alongside, same era.
Perceiver: General perception with iterative attention
Jaegle, A. et al · 2021
Cited alongside, same era.
Swin transformer: Hierarchical vision transformer using shifted windows
Liu, Z. et al · 2021
Cited alongside, same era.
Emerging properties in self-supervised vision transformers
Caron, M. et al · 2021
Cited alongside, same era.
The impact of site-specific digital histology signatures on deep learning model accuracy and bias
Howard, F. M. et al · 2021
Cited alongside, same era.
Predicting axillary lymph node metastasis in early breast cancer using deep learning on primary tumor biopsy slides
Xu, F. et al · 2021
Cited alongside, same era.
Zaffar, I., Jaume, G., Rajpoot, N. & Mahmood, F · 2023
Later among the works it cites.
Augdiff: Diffusion based feature augmentation for multiple instance learning in whole slide image
Shao, Z., Dai, L., Wang, Y., Wang, H. & Zhang, Y · 2023
Later among the works it cites.
Weakly supervised joint whole-slide segmentation and classification in prostate cancer
Pati, P. et al · 2023
Later among the works it cites.
Towards a general-purpose foundation model for computational pathology
Chen, R. J. et al · 2024
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A visual-language foundation model for computational pathology
Lu, M. Y. et al · 2024
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A foundation model for clinical-grade computational pathology and rare cancers detection
Vorontsov, E. et al · 2024
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Virchow 2: Scaling self-supervised mixed magnification models in pathology
Zimmermann, E. et al · 2024
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H-optimus-0 (2024)
Saillard, C. et al · 2024
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Phikon-v2, a large and public feature extractor for biomarker prediction (2024)
Filiot, A., Jacob, P., Kain, A. M. & Saillard, C · 2024
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Pluto: Pathology-universal transformer
Juyal, D. et al · 2024
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Rudolfv: A foundation model by pathologists for pathologists
Dippel, J. et al · 2024
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A clinical benchmark of public self-supervised pathology foundation models
Campanella, G. et al · 2024
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Benchmarking foundation models as feature extractors for weakly-supervised computational pathology
Neidlinger, P. et al · 2024
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National Cancer Institute Accessed: 2024-11-20
NCI Dictionary of Cancer Terms. Rare cancer · 2024
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National Cancer Institute Accessed: 2024-11-21
Surveillance, Epidemiology, an End Results Program. Rare cancer classification · 2024
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Histopathology slide indexing and search—are we there yet?
Shang, H. H. et al · 2024
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Quilt-1m: One million image-text pairs for histopathology
Ikezogwo, W. et al · 2024
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A whole-slide foundation model for digital pathology from real-world data
Xu, H. et al · 2024
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A self-supervised framework for learning whole slide representations (2024)
Hou, X. et al · 2024
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Generating clinical-grade pathology reports from gigapixel whole slide images with HistoGPT
Tran, M. et al · 2024
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PRISM: A Multi-Modal Generative Foundation Model for Slide-Level Histopathology
Shaikovski, G. et al · 2024
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A multimodal knowledge-enhanced whole-slide pathology foundation model
Xu, Y. et al · 2024
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Transcriptomics-guided slide representation learning in computational pathology
Jaume, G. et al · 2024
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Morphological prototyping for unsupervised slide representation learning in computational pathology
Song, A. H. et al · 2024
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Multistain pretraining for slide representation learning in pathology
Jaume, G. et al · 2024
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Foundation models for fast, label-free detection of glioma infiltration
Kondepudi, A. et al · 2024
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PathAlign: A vision-language model for whole slide images in histopathology (2024)
Ahmed, F. et al · 2024
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A pathology foundation model for cancer diagnosis and prognosis prediction
Wang, X. et al · 2024
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A Multimodal Generative AI Copilot for Human Pathology
Lu, M. Y. et al · 2024
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Generation of synthetic whole-slide image tiles of tumours from RNA-sequencing data via cascaded diffusion models
Carrillo-Perez, F. et al · 2024
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Frozen feature augmentation for few-shot image classification
Bär, A., Houlsby, N., Dehghani, M. & Kumar, M · 2024
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Yang, A. et al · 2024
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Stablerep: Synthetic images from text-to-image models make strong visual representation learners
Tian, Y., Fan, L., Isola, P., Chang, H. & Krishnan, D · 2024
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Roformer: Enhanced transformer with rotary position embedding
Su, J. et al · 2024
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Rotary position embedding for vision transformer
Heo, B., Park, S., Han, D. & Yun, S · 2024
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TCGA-Reports: A machine-readable pathology report resource for benchmarking text-based AI models
Kefeli, J. & Tatonetti, N · 2024
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Hibou: A Family of Foundational Vision Transformers for Pathology (2024)
Nechaev, D., Pchelnikov, A. & Ivanova, E · 2024
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PaliGemma: A versatile 3B VLM for transfer
Beyer, L. et al · 2024
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An interpretable machine learning system for colorectal cancer diagnosis from pathology slides
Neto, P. C. et al · 2024
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Demographic bias in misdiagnosis by computational pathology models
Vaidya, A. et al · 2024
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