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  TITLE = {Foundations of Machine Learning},
  AUTHOR = {Mehryar Mohri, Afshin rostamizadeh, Amett Talwalkar},
  YEAR = {2018},
  edition = {2nd},
  PUBLISHER = {MIT Press},
  address = {Cambridge, Massachusetts}
}

@article{histo_gnn_survey,
author = {Brussee, Siemen and Buzzanca, Giorgio and Schrader, Anne and Kers, Jesper},
year = {2025},
OPTvolume={101},
OPTpages={103444},
title = {Graph Neural Networks in Histopathology: Emerging Trends and Future Directions},
journal = {Medical Image Analysis}
}

@article{glomerular_gnn,
author = {He, Qiming and Ge, Shuang and Zeng, Siqi and Wang, Yanxia and Ye, Jing and He, Yonghong and Li, Jing and Wang, Zhe and Guan, Tian},
year = {2024},
OPTpages = {108369},
title = {Global attention based {GNN} with {B}ayesian collaborative learning for glomerular lesion recognition},
OPTvolume = {173},
journal = {Computers in Biology and Medicine}
}

@article{kidney_disease_chronic,
author = {Kovesdy, Csaba},
year = {2022},
OPTpages = {7-11},
title = {Epidemiology of chronic kidney disease: An update 2022},
OPTvolume = {12},
journal = {Kidney international supplements}
}

@article{histo_gnn_survey2,
author = {Ahmedt-Aristizabal, David and Armin, Ali and Denman, Simon and Fookes, Clinton and Petersson, Lars},
year = {2021},
OPTpages = {102027},
title = {A Survey on Graph-Based Deep Learning for Computational Histopathology},
OPTvolume = {95},
journal = {Computerized Medical Imaging and Graphics}
}

@inproceedings{image_net,
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}

@article{histo_survey_path,
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  journal   = {Nature Medicine},
  year      = {2021},
  OPTvolume    = {27},
  OPTnumber    = {5},
  OPTpages     = {775--784}
}

@article{histo_dl_survey,
    author = {Banerji, Sugata and Mitra, Sushmita},
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    year = {2022}
}

@BOOK{gnn_book,
author={Hamilton, William L.},
title={Graph Representation Learning},
edition={14th},
year={2022},
OPTnumber={3},
OPTpages={1---59},
publisher={Morgan and Claypool}
} 

@inproceedings{gcn,
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booktitle={International Conference on Learning Representations},
year={2017}
}

@inproceedings{gat_v2,
title={How Attentive are Graph Attention Networks?},
author={Shaked Brody and Uri Alon and Eran Yahav},
booktitle={International Conference on Learning Representations},
year={2022}
}

@article{gin,
author = {Peng, Yuzhong and Lin, Yanmei and Jing, Xiao-Yuan and Zhang, Hao and Huang, Yiran and Luo, Guang},
year = {2020},
OPTpages = {168344--168360},
title = {Enhanced Graph Isomorphism Network for Molecular ADMET Properties Prediction},
OPTvolume = {8},
journal = {IEEE Access},
}

@inproceedings{gine,
title={Strategies for Pre-training Graph Neural Networks},
author={Weihua Hu and Bowen Liu and Joseph Gomes and Marinka Zitnik and Percy Liang and Vijay Pande and Jure Leskovec},
booktitle={International Conference on Learning Representations},
year={2020}
}

@inproceedings{gat,
      title={Graph Attention Networks}, 
      author={Petar Veličković and Guillem Cucurull and Arantxa Casanova and Adriana Romero and Pietro Liò and Yoshua Bengio},
      year={2018},
      booktitle = {International Conference on Learning Representations}
}


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@book{cnn_book,
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    edition={1st}
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@misc{batchnorm,
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      year={2015}
}

@article{layer_norm,
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@inproceedings{resnet,
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  OPTpages={770--778}
}

@inproceedings{imagenet,
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year = {2009},
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title = {ImageNet: A Large-Scale Hierarchical Image Database},
booktitle = {IEEE Conference on Computer Vision and Pattern Recognition}
}

@article{glom_cnn_oxford,
title = {Performance and limitations of a supervised deep learning approach for the histopathological {O}xford Classification of glomeruli with {I}g{A} nephropathy},
journal = {Computer Methods and Programs in Biomedicine},
volume = {242},
OPTpages = {107814},
year = {2023},
author = {Nicola Altini and others}
}

@INPROCEEDINGS{glomerular_ai,
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  year={2018},
  OPTpages={17--20}
  }

@article{oxford1,
title = {The {O}xford classification of {I}g{A} nephropathy: Rationale, clinicopathological correlations, and classification},
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OPTvolume = {76},
OPTnumber = {5},
OPTpages = {534--545},
year = {2009},
author = {Daniel C. Cattran and others}
}

@article{oxford2,
title = {The {O}xford classification of {I}g{A} nephropathy: Pathology definitions, correlations, and reproducibility},
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OPTvolume = {76},
OPTnumber = {5},
OPTpages = {546--556},
year = {2009},
author = {Ian S.D. Roberts and others}
}

@article{oxford3,
title = {{O}xford Classification of {I}g{A} nephropathy 2016: An update from the {I}g{A} Nephropathy Classification Working Group},
journal = {Kidney International},
OPTvolume = {91},
OPTnumber = {5},
OPTpages = {1014--1021},
year = {2017},
author = {Hernán Trimarchi and others}
}

@unknown{efficient_net,
author = {Tan, Mingxing and Le, Quoc},
year = {2019},
title = {EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks}
}

@inproceedings{efficient_net_v2,
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  author={Mingxing Tan and Quoc V. Le},
  booktitle={International Conference on Machine Learning},
  year={2021}
}

@article {cellpose,
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	journal = {Nat Methods}
}


@unknown{slic,
author = {Khorasgani, Salar and Chen, Yuxuan and Shkurti, Florian},
year = {2022},
title = {SLIC: Self-Supervised Learning with Iterative Clustering for Human Action Videos}
}

@INPROCEEDINGS{inception_v3,
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  year={2016},
  OPTpages={2818--2826}
}

@inproceedings{unet,
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      year={2015},
  booktitle={Medical Image Computing and Computer-Assisted Intervention}
}

@misc{pytorch_resnet,
  author = {Kaiming He and X. Zhang and Shaoqing Ren and Jian Sun},
  title = {ResNet Model},
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}

@article{stain_deconvolution,
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year = {2001},
OPTmonth = {08},
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}

@misc{skimage_stain_deconv,
    author = {Ruifrok, Arnout and Johnston, Dennis},
    year = {2001},
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@article {cellpose2,
	author = {Stringer, Carsen and Pachitariu, Marius},
	title = {Cellpose 2.0: {H}ow to train your own model},
	year = {2022},
	OPTdoi = {https://doi.org/10.1038/s41592-022-01663-4},
	OPTeprint = {https://www.biorxiv.org/content/early/2022/04/05/2022.04.01.486764.full.pdf},
	journal = {Nat Methods}
}

@misc{cellpose_package,
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    year = {2020},
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@misc{find_contour_function,
book = {OpenCV API reference},
year = {2020},
title = {findContours},
url = {https://docs.opencv.org/3.4/d3/dc0/group__imgproc__shape.html#ga17ed9f5d79ae97bd4c7cf18403e1689a},
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}

@INPROCEEDINGS{lbp,
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@misc{fit_ellipse_function,
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    year = {2020},
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}

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  year={1995}
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@article{vonluxburg,
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@book{delaunay_book,
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@article{sysmifta,
author = {Merveille, Odyssee and Lampert, Thomas and Schmitz, Jessica and Forestier, Germain and Feuerhake, Friedrich and Wemmert, Cédric},
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OPTpages = {106157},
year = {2021}
}


@article{minmaxscaling,
title = {The choice of scaling technique matters for classification performance},
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OPTpages = {109924},
year = {2023},
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@inbook{receptive_field,
author = {Richter, Mats and Schöning, Julius and Wiedenroth, Anna and Krumnack, Ulf},
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year = {2022},
OPTmonth = {11},
OPTpages = {235--261},
title = {Receptive Field Analysis for Optimizing Convolutional Neural Network Architectures Without Training},
OPTisbn = {978-981-19-6152-6},
edition={1st}
}


@InProceedings{jumping_knowledge,
  title = 	 {Representation Learning on Graphs with Jumping Knowledge Networks},
  author =       {Xu, Keyulu and Li, Chengtao and Tian, Yonglong and Sonobe, Tomohiro and Kawarabayashi, Ken-ichi and Jegelka, Stefanie},
  booktitle = 	 {International Conference on Machine Learning},
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  year = 	 {2018},
  OPTvolume = 	 {80},
  OPTpublisher =    {PMLR}
}

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@article{renal_fib,
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@article{fsgs,
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year = {2021},
OPTmonth = {12},
OPTpages = {93},
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@article{ckd,
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@book{sabotta,
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@book{histo_book,
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    edition={7th}
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@incollection{Jackson,
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year = {2016},
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year = {2010},
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@article{chen,
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}

@article{Wynn_macro_fib,
  title={Macrophages: {M}aster Regulators of Inflammation and Fibrosis},
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  year={2010},
  OPTvolume={30},
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@article{xu_tcell8_sclero,
author = {Xu, Xiaodong and Qu, Shuang and Zhang, Changming and Zhang, Mingchao and Qin, Weisong and Ren, Guisheng and Bao, Hao and Li, Limin and Zen, Ke and Liu, Hehe},
year = {2023},
title = {CD8 T Cell‐Derived Exosomal miR‐186‐5p Elicits Renal Inflammation via Activating Tubular TLR7/8 Signal Axis},
OPTvolume = {10},
journal = {Advanced Science}
}

@article{braun_tcell_sclero,
author = {Braun, Fabian and Homeyer, Inka and Alachkar, Nada and Huber, Tobias},
year = {2021},
OPTmonth = {08},
OPTpages = {1--12},
title = {Immune-mediated entities of (primary) focal segmental glomerulosclerosis},
OPTvolume = {385},
journal = {Cell and Tissue Research}
}

@article{braese_marco_tranplant,
title = {Macrophage density in early surveillance biopsies predicts future renal transplant function},
journal = {Kidney International},
OPTvolume = {92},
OPTnumber = {2},
OPTpages = {479--489},
year = {2017},
OPTissn = {0085-2538},
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@inproceedings{byol,
author = {Grill, Jean-Bastien and Strub, Florian and Altché, Florent and Tallec, Corentin and Richemond, Pierre and Buchatskaya, Elena and Doersch, Carl and Pires, Bernardo and Guo, Zhaohan and Azar, Mohammad and Piot, Bilal and Kavukcuoglu, Koray and Munos, Remi and Valko, Michal},
booktitle = {Conference on Neural Information Processing Systems},
year = {2020},
OPTvolume = {21271-21284},
OPTpages = {479-489},
title = {Bootstrap Your Own Latent: {A} New Approach to Self-Supervised Learning}
}

@article{zeeshan,
      title={Maximising Histopathology Segmentation using Minimal Labels via Self-Supervision}, 
      author={Zeeshan Nisar and Thomas Lampert},
      year={2024},
      journal={arXiv:2412.15389},
      OPTdoi={10.48550/arXiv.2412.15389},
}

@inproceedings{schnet,
author = {Schütt, Kristof and Kindermans, Pieter-Jan and Sauceda, Huziel E. and Chmiela, Stefan and Tkatchenko, Alexandre and Müller, Klaus-Robert},
year = {2017},
booktitle = {Neural Information Processing Systems},
title = {SchNet: A continuous-filter convolutional neural network for modeling quantum interactions}
}

@InProceedings{rgcn,
author="Schlichtkrull, Michael
and Kipf, Thomas N.
and Bloem, Peter
and van den Berg, Rianne
and Titov, Ivan
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title="Modeling Relational Data with Graph Convolutional Networks",
booktitle="The Semantic Web",
year="2018",
OPTpublisher = {Springer-Verlag},
OPTaddress = {Berlin, Heidelberg},
OPTaddress="Cham",
OPTpages="593--607"
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@inproceedings{gilmer,
  title={Neural Message Passing for Quantum Chemistry},
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  year={2017}
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@misc{biopsy_german,
  title = {Biopsie},
  howpublished = {\url{https://flexikon.doccheck.com/de/Biopsie}},
  author = {Frank Antwerpes},
  year={2024},
  note = {Accessed: 2025-01-07}
}

@misc{biopsy_nhs,
  title = {Biopsie},
  howpublished = {\url{https://www.nhs.uk/conditions/biopsy/}},
  year={2021},
  publisher = {National Health Service},
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@article{fibrosis_curcuit,
author = {Adler, Miri and Mayo, Avi and Zhou, Xu and Franklin, Ruth and Meizlish, Matthew and Medzhitov, Ruslan and Kallenberger, Stefan and Alon, Uri},
year = {2019},
journal={iScience},
title = {Principles of Cell Circuits for Tissue Repair and Fibrosis}
}

@article{colour_histo,
  title={Color indexing},
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@book{tcells,
	Title = {Histology, T-Cell Lymphocyte},
	Author = {Sauls, Ryan S. and McCausland, Cassidy and Taylor, Bryce N.},
	Publisher = {StatPearls Publishing, Treasure Island (FL)},
	Year = {2023}
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@article{domain_shifts_tom,
author = {Vasiljevic, Jelica and Feuerhake, Friedrich and Wemmert, Cédric and Lampert, Thomas},
year = {2021},
OPTmonth = {07},
OPTpages = {277--291},
title = {Towards Histopathological Stain Invariance by Unsupervised Domain Augmentation using Generative Adversarial Networks},
OPTvolume = {460},
journal = {Neurocomputing}
}

@article{HistoStarGan,
author = {Vasiljevic, Jelica and Feuerhake, Friedrich and Wemmert, Cédric and Lampert, Thomas},
year = {2022},
 journal={Knowledge-Based Systems},
OPTmonth = {10},
OPTpages = {},
title = {HistoStarGAN: A Unified Approach to Stain Normalisation, Stain Transfer and Stain Invariant Segmentation in Renal Histopathology}
}

@book{Jarrell,
    author = {Jarrell, Bruce E., and Strauch, Eric D.,},
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    edition = {2nd}
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@misc{GiGL,
      title={GiGL: Large-Scale Graph Neural Networks at Snapchat}, 
      author={Tong Zhao and Yozen Liu and Matthew Kolodner and Kyle Montemayor and Elham Ghazizadeh and Ankit Batra and Zihao Fan and Xiaobin Gao and Xuan Guo and Jiwen Ren and Serim Park and Peicheng Yu and Jun Yu and Shubham Vij and Neil Shah},
      year={2025}
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@article{stain_augmentation,
  author={Tellez, David and Balkenhol, Maschenka and Otte-Höller, Irene and van de Loo, Rob and Vogels, Rob and Bult, Peter and Wauters, Carla and Vreuls, Willem and Mol, Suzanne and Karssemeijer, Nico and Litjens, Geert and van der Laak, Jeroen and Ciompi, Francesco},
  journal={IEEE Transactions on Medical Imaging}, 
  title={Whole-Slide Mitosis Detection in {H}\&{E} Breast Histology Using {PHH}3 as a Reference to Train Distilled Stain-Invariant Convolutional Networks}, 
  year={2018}}
