l4proj.bib

@article{Srinidhi2021,
   author = {Chetan L. Srinidhi and Ozan Ciga and Anne L. Martel},
   doi = {10.1016/j.media.2020.101813},
   issn = {13618423},
   journal = {Medical Image Analysis},
   keywords = {Computational histopathology,Convolutional neural networks,Deep learning,Digital pathology,Histology image analysis,Review,Survey},
   month = {1},
   pmid = {33049577},
   publisher = {Elsevier B.V.},
   title = {Deep neural network models for computational histopathology: A survey},
   volume = {67},
   year = {2021},
}
@article{Montazeri2016,
   author = {Mitra Montazeri and Mohadeseh Montazeri and Mahdieh Montazeri and Amin Beigzadeh},
   doi = {10.3233/THC-151071},
   issn = {09287329},
   issue = {1},
   journal = {Technology and Health Care},
   month = {1},
   pages = {31-42},
   title = {Machine learning models in breast cancer survival prediction},
   volume = {24},
   url = {https://pubmed.ncbi.nlm.nih.gov/26409558/#:~:text=Background%3A%20Breast%20cancer%20is%20one,%25%20to%20more%20than%2086%25.},
   year = {2016},
}
@article{Couture2018,
   author = {Heather D Couture and Lindsay A Williams and Joseph Geradts and Sarah J Nyante and Ebonee N Butler and J S Marron and Charles M Perou and Melissa A Troester and Marc Niethammer},
   doi = {10.1038/s41523-018-0079-1},
   issn = {2374-4677},
   journal = {NPJ breast cancer},
   pages = {30},
   pmid = {30182055},
   title = {Image analysis with deep learning to predict breast cancer grade, ER status, histologic subtype, and intrinsic subtype.},
   volume = {4},
   year = {2018},
}
@article{Arya2021,
   author = {Nikhilanand Arya and Sriparna Saha},
   doi = {10.1016/j.knosys.2021.106965},
   issn = {09507051},
   journal = {Knowledge-Based Systems},
   keywords = {Bi-Attention,Breast cancer prognosis prediction,Cross-modality attention,Random forest (RF),Sigmoid gated attention convolutional neural network (SiGaAtCNN),Stacked features,Uni-modal and multi-modal architecture},
   month = {6},
   publisher = {Elsevier B.V.},
   title = {Multi-modal advanced deep learning architectures for breast cancer survival prediction[Formula presented]},
   volume = {221},
   year = {2021},
}
@article{Kather2019,
   author = {Jakob Nikolas Kather and Johannes Krisam and Pornpimol Charoentong and Tom Luedde and Esther Herpel and Cleo Aron Weis and Timo Gaiser and Alexander Marx and Nektarios A. Valous and Dyke Ferber and Lina Jansen and Constantino Carlos Reyes-Aldasoro and Inka Zörnig and Dirk Jäger and Hermann Brenner and Jenny Chang-Claude and Michael Hoffmeister and Niels Halama},
   doi = {10.1371/journal.pmed.1002730},
   issn = {15491676},
   issue = {1},
   journal = {PLoS Medicine},
   pmid = {30677016},
   publisher = {Public Library of Science},
   title = {Predicting survival from colorectal cancer histology slides using deep learning: A retrospective multicenter study},
   volume = {16},
   year = {2019},
}
@article{TreeckDeepMed,
   doi = {10.1101/2021.12.19.473344},
   issue = {1},
   journal = {Tobias Paul Seraphin},
   pages = {6},
   title = {DeepMed: A unified, modular pipeline for end-to-end deep learning in computational pathology) * equal contribution},
   volume = {1},
   url = {https://doi.org/10.1101/2021.12.19.473344},
}

@article{van2021deepmed,
  title={DeepMed: A unified, modular pipeline for end-to-end deep learning in computational pathology},
  author={van Treeck, Marko and Cifci, Didem and Laleh, Narmin Ghaffari and Saldanha, Oliver Lester and Loeffler, Chiara ML and Hewitt, Katherine J and Muti, Hannah Sophie and Echle, Amelie and Seibel, Tobias and Seraphin, Tobias Paul and others},
  journal={BioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}

@book{,
   abstract = {Title from PDF title page (IEEE Xplore, viewed on Dec. 3, 2009). "IEEE Catalog Number: CFP09BIS"--PDF copyright page.},
   author = {Institute of Electrical and Electronics Engineers. and IEEE Engineering in Medicine and Biology Society. and IEEE Signal Processing Society.},
   isbn = {9781424439324},
   publisher = {IEEE},
   title = {2009 6th IEEE International Symposium on Biomedical Imaging : from nano to macro : proceedings : June 28-July 1, 2009, Boston Park Plaza Hotel, Boston, Massachusetts, U.S.A.},
   year = {2009},
}
@article{Liu2022,
   author = {Huidong Liu and Tahsin Kurc},
   doi = {10.1093/bioinformatics/btac381},
   issn = {14602059},
   issue = {14},
   journal = {Bioinformatics},
   month = {7},
   pages = {3629-3637},
   publisher = {Oxford University Press},
   title = {Deep learning for survival analysis in breast cancer with whole slide image data},
   volume = {38},
   year = {2022},
}
@article{Wetstein2022,
   doi = {10.1038/s41598-022-19112-9},
   issn = {20452322},
   issue = {1},
   author={Wetstein, Suzanne C and de Jong, Vincent MT and Stathonikos, Nikolas and Opdam, Mark and Dackus, Gwen MHE and Pluim, Josien PW and van Diest, Paul J and Veta, Mitko},
   journal = {Scientific Reports},
   month = {12},
   pmid = {36068311},
   title = {Deep learning-based breast cancer grading and survival analysis on whole-slide histopathology images},
   volume = {12},
   year = {2022},
   publisher = {Nature Publishing Group UK London},
}

@article{Shao2021,
   author = {Wei Shao and Tongxin Wang and Zhi Huang and Zhi Han and Jie Zhang and Kun Huang},
   doi = {10.1109/TMI.2021.3097319},
   issn = {0278-0062},
   issue = {12},
   journal = {IEEE Transactions on Medical Imaging},
   month = {12},
   pages = {3739-3747},
   title = {Weakly Supervised Deep Ordinal Cox Model for Survival Prediction From Whole-Slide Pathological Images},
   volume = {40},
   year = {2021},
}
@article{,
   author = {Angel Cruz-Roa and Hannah Gilmore and Ajay Basavanhally and Michael Feldman and Shridar Ganesan and Natalie N.C. Shih and John Tomaszewski and Fabio A. González and Anant Madabhushi},
   doi = {10.1038/srep46450},
   issn = {20452322},
   journal = {Scientific Reports},
   month = {4},
   pmid = {28418027},
   publisher = {Nature Publishing Group},
   title = {Accurate and reproducible invasive breast cancer detection in whole-slide images: A Deep Learning approach for quantifying tumor extent},
   volume = {7},
   year = {2017},
}
@article{Khened2021,
   author = {Mahendra Khened and Avinash Kori and Haran Rajkumar and Ganapathy Krishnamurthi and Balaji Srinivasan},
   doi = {10.1038/s41598-021-90444-8},
   issn = {20452322},
   issue = {1},
   journal = {Scientific Reports},
   month = {12},
   pmid = {34078928},
   publisher = {Nature Research},
   title = {A generalized deep learning framework for whole-slide image segmentation and analysis},
   volume = {11},
   year = {2021},
}
@article{Yao2020,
   issn = {13618423},
   journal = {Medical Image Analysis},
   keywords = {Deep learning,Multiple instance learning,Survival prediction,Whole slide images},
   month = {10},
   pmid = {32739769},
   publisher = {Elsevier B.V.},
   title = {Whole slide images based cancer survival prediction using attention guided deep multiple instance learning networks},
   volume = {65},
   year = {2020},
}
@article{Takada2020,
   author = {Koji Takada and Shinichiro Kashiwagi and Yuka Asano and Wataru Goto and Rika Kouhashi and Akimichi Yabumoto and Tamami Morisaki and Masatsune Shibutani and Tsutomu Takashima and Hisakazu Fujita and Kosei Hirakawa and Kosei Hirakawa and Masaichi Ohira and Masaichi Ohira},
   doi = {10.1186/s12885-020-07101-y},
   issn = {14712407},
   issue = {1},
   journal = {BMC Cancer},
   keywords = {Breast cancer,Lymph node metastasis,Sentinel lymph node,Tumor immune-microenvironment,Tumor-infiltrating lymphocytes},
   month = {6},
   pmid = {32590956},
   publisher = {BioMed Central},
   title = {Prediction of lymph node metastasis by tumor-infiltrating lymphocytes in T1 breast cancer},
   volume = {20},
   year = {2020},
}
@book{Bancroft2013,
   author = {John D. Bancroft and Christopher Layton},
   doi = {10.1016/B978-0-7020-4226-3.00010-X},
   journal = {Bancroft's Theory and Practice of Histological Techniques},
   pages = {173-186},
   publisher = {Elsevier},
   title = {The hematoxylins and eosin},
   year = {2013},
}

@article{chan2014wonderful,
  title={The wonderful colors of the hematoxylin--eosin stain in diagnostic surgical pathology},
  author={Chan, John KC},
  journal={International journal of surgical pathology},
  volume={22},
  number={1},
  pages={12--32},
  year={2014},
  publisher={SAGE Publications Sage CA: Los Angeles, CA}
}

@article{provenzano2008collagen,
  title={Collagen density promotes mammary tumor initiation and progression},
  author={Provenzano, Paolo P and Inman, David R and Eliceiri, Kevin W and Knittel, Justin G and Yan, Long and Rueden, Curtis T and White, John G and Keely, Patricia J},
  journal={BMC medicine},
  volume={6},
  number={1},
  pages={1--15},
  year={2008},
  publisher={BioMed Central}
}

@article{ghaznavi2013digital,
  title={Digital imaging in pathology: whole-slide imaging and beyond},
  author={Ghaznavi, Farzad and Evans, Andrew and Madabhushi, Anant and Feldman, Michael},
  journal={Annu Rev Pathol},
  volume={8},
  number={1},
  pages={331--359},
  year={2013}
}

@inbook{kino1996confocal,
  title={Confocal scanning optical microscopy and related imaging systems},
  author={Kino, Gordon S and Corle, Timothy R},
  year={1996},
  publisher={Academic Press},
  pages={1-66}
}

@inproceedings{wang2012managing,
  title={Managing and querying whole slide images},
  author={Wang, Fusheng and Oh, Tae W and Vergara-Niedermayr, Cristobal and Kurc, Tahsin and Saltz, Joel},
  booktitle={Medical Imaging 2012: Advanced PACS-Based Imaging Informatics and Therapeutic Applications},
  volume={8319},
  pages={137--148},
  year={2012},
  organization={SPIE}
}

@article{aeffner2019introduction,
  title={Introduction to digital image analysis in whole-slide imaging: a white paper from the digital pathology association},
  author={Aeffner, Famke and Zarella, Mark D and Buchbinder, Nathan and Bui, Marilyn M and Goodman, Matthew R and Hartman, Douglas J and Lujan, Giovanni M and Molani, Mariam A and Parwani, Anil V and Lillard, Kate and others},
  journal={Journal of pathology informatics},
  volume={10},
  number={1},
  pages={9},
  year={2019},
  publisher={Elsevier}
}

@article{anghel2019high,
  title={A high-performance system for robust stain normalization of whole-slide images in histopathology},
  author={Anghel, Andreea and Stanisavljevic, Milos and Andani, Sonali and Papandreou, Nikolaos and R{\"u}schoff, Jan Hendrick and Wild, Peter and Gabrani, Maria and Pozidis, Haralampos},
  journal={Frontiers in medicine},
  volume={6},
  pages={193},
  year={2019},
  publisher={Frontiers Media SA}
}

@article{li2015complete,
  title={A complete color normalization approach to histopathology images using color cues computed from saturation-weighted statistics},
  author={Li, Xingyu and Plataniotis, Konstantinos N},
  journal={IEEE Transactions on Biomedical Engineering},
  volume={62},
  number={7},
  pages={1862--1873},
  year={2015},
  publisher={IEEE}
}

@article{gorelick2013prostate,
  title={Prostate histopathology: Learning tissue component histograms for cancer detection and classification},
  author={Gorelick, Lena and Veksler, Olga and Gaed, Mena and G{\'o}mez, Jos{\'e} A and Moussa, Madeleine and Bauman, Glenn and Fenster, Aaron and Ward, Aaron D},
  journal={IEEE transactions on medical imaging},
  volume={32},
  number={10},
  pages={1804--1818},
  year={2013},
  publisher={IEEE}
}

@inproceedings{macenko2009method,
  title={A method for normalizing histology slides for quantitative analysis},
  author={Macenko, Marc and Niethammer, Marc and Marron, James S and Borland, David and Woosley, John T and Guan, Xiaojun and Schmitt, Charles and Thomas, Nancy E},
  booktitle={2009 IEEE international symposium on biomedical imaging: from nano to macro},
  pages={1107--1110},
  year={2009},
  organization={IEEE}
}

@article{gurcan2009histopathological,
  title={Histopathological image analysis: A review},
  author={Gurcan, Metin N and Boucheron, Laura E and Can, Ali and Madabhushi, Anant and Rajpoot, Nasir M and Yener, Bulent},
  journal={IEEE reviews in biomedical engineering},
  volume={2},
  pages={147--171},
  year={2009},
  publisher={IEEE}
}

@article{alexe2007high,
  title={High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates},
  author={Alexe, Gabriela and Dalgin, Gul S and Scanfeld, Daniel and Tamayo, Pablo and Mesirov, Jill P and DeLisi, Charles and Harris, Lyndsay and Barnard, Nicola and Martel, Maritza and Levine, Arnold J and others},
  journal={Cancer research},
  volume={67},
  number={22},
  pages={10669--10676},
  year={2007},
  publisher={AACR}
}

@inproceedings{cruz2014automatic,
  title={Automatic detection of invasive ductal carcinoma in whole slide images with convolutional neural networks},
  author={Cruz-Roa, Angel and Basavanhally, Ajay and Gonz{\'a}lez, Fabio and Gilmore, Hannah and Feldman, Michael and Ganesan, Shridar and Shih, Natalie and Tomaszewski, John and Madabhushi, Anant},
  booktitle={Medical Imaging 2014: Digital Pathology},
  volume={9041},
  pages={904103},
  year={2014},
  organization={SPIE}
}

@article{qin2018large,
  title={Large-scale tissue histopathology image segmentation based on feature pyramid},
  author={Qin, Pinle and Chen, Jun and Zeng, Jianchao and Chai, Rui and Wang, Lifang},
  journal={EURASIP Journal on Image and Video Processing},
  volume={2018},
  number={1},
  pages={1--9},
  year={2018},
  publisher={Springer}
}

@article{bandi2018detection,
  title={From detection of individual metastases to classification of lymph node status at the patient level: the camelyon17 challenge},
  author={Bandi, Peter and Geessink, Oscar and Manson, Quirine and Van Dijk, Marcory and Balkenhol, Maschenka and Hermsen, Meyke and Bejnordi, Babak Ehteshami and Lee, Byungjae and Paeng, Kyunghyun and Zhong, Aoxiao and others},
  journal={IEEE transactions on medical imaging},
  volume={38},
  number={2},
  pages={550--560},
  year={2018},
  publisher={IEEE}
}

@article{bankhead2017qupath,
  title={QuPath: Open source software for digital pathology image analysis},
  author={Bankhead, Peter and Loughrey, Maurice B and Fern{\'a}ndez, Jos{\'e} A and Dombrowski, Yvonne and McArt, Darragh G and Dunne, Philip D and McQuaid, Stephen and Gray, Ronan T and Murray, Liam J and Coleman, Helen G and others},
  journal={Scientific reports},
  volume={7},
  number={1},
  pages={1--7},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{goode2013openslide,
  title={OpenSlide: A vendor-neutral software foundation for digital pathology},
  author={Goode, Adam and Gilbert, Benjamin and Harkes, Jan and Jukic, Drazen and Satyanarayanan, Mahadev},
  journal={Journal of pathology informatics},
  volume={4},
  number={1},
  pages={27},
  year={2013},
  publisher={Elsevier}
}

@article{pedersen2021fastpathology,
  title={Fastpathology: an open-source platform for deep learning-based research and decision support in digital pathology},
  author={Pedersen, Andr{\'e} and Valla, Marit and Bofin, Anna M and De Frutos, Javier P{\'e}rez and Reinertsen, Ingerid and Smistad, Erik},
  journal={Ieee Access},
  volume={9},
  pages={58216--58229},
  year={2021},
  publisher={IEEE}
}

@article{priego2020automatic,
  title={Automatic segmentation of whole-slide H\&E stained breast histopathology images using a deep convolutional neural network architecture},
  author={Priego-Torres, Blanca Maria and Sanchez-Morillo, Daniel and Fernandez-Granero, Miguel Angel and Garcia-Rojo, Marcial},
  journal={Expert Systems With Applications},
  volume={151},
  pages={113387},
  year={2020},
  publisher={Elsevier}
}

@article{bejnordi2017diagnostic,
  title={Diagnostic assessment of deep learning algorithms for detection of lymph node metastases in women with breast cancer},
  author={Bejnordi, Babak Ehteshami and Veta, Mitko and Van Diest, Paul Johannes and Van Ginneken, Bram and Karssemeijer, Nico and Litjens, Geert and Van Der Laak, Jeroen AWM and Hermsen, Meyke and Manson, Quirine F and Balkenhol, Maschenka and others},
  journal={Jama},
  volume={318},
  number={22},
  pages={2199--2210},
  year={2017},
  publisher={American Medical Association}
}

@book{sobin2011tnm,
  title={TNM classification of malignant tumours},
  author={Sobin, Leslie H and Gospodarowicz, Mary K and Wittekind, Christian},
  year={2011},
  publisher={John Wiley \& Sons}
}

@article{katzman2018deepsurv,
  title={DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network},
  author={Katzman, Jared L and Shaham, Uri and Cloninger, Alexander and Bates, Jonathan and Jiang, Tingting and Kluger, Yuval},
  journal={BMC medical research methodology},
  volume={18},
  number={1},
  pages={1--12},
  year={2018},
  publisher={BioMed Central}
}

@article{wulczyn2020deep,
  title={Deep learning-based survival prediction for multiple cancer types using histopathology images},
  author={Wulczyn, Ellery and Steiner, David F and Xu, Zhaoyang and Sadhwani, Apaar and Wang, Hongwu and Flament-Auvigne, Isabelle and Mermel, Craig H and Chen, Po-Hsuan Cameron and Liu, Yun and Stumpe, Martin C},
  journal={PloS one},
  volume={15},
  number={6},
  pages={e0233678},
  year={2020},
  publisher={Public Library of Science San Francisco, CA USA}
}

@article{cox1972regression,
  title={Regression models and life-tables},
  author={Cox, David R},
  journal={Journal of the Royal Statistical Society: Series B (Methodological)},
  volume={34},
  number={2},
  pages={187--202},
  year={1972},
  publisher={Wiley Online Library}
}

@article{schober2021kaplan,
  title={Kaplan-meier curves, log-rank tests, and cox regression for time-to-event data},
  author={Schober, Patrick and Vetter, Thomas R},
  journal={Anesthesia \& Analgesia},
  volume={132},
  number={4},
  pages={969--970},
  year={2021},
  publisher={LWW}
}

@article{bewick2004statistics,
  title={Statistics review 12: survival analysis},
  author={Bewick, Viv and Cheek, Liz and Ball, Jonathan},
  journal={Critical care},
  volume={8},
  number={5},
  pages={1--6},
  year={2004},
  publisher={Springer}
}

@ARTICLE{Veeling2018-qh,
  title         = "Rotation Equivariant {CNNs} for Digital Pathology",
  author        = "Veeling, Bastiaan S and Linmans, Jasper and Winkens, Jim and
                   Cohen, Taco and Welling, Max",
  month         =  jun,
  year          =  2018,
  archivePrefix = "arXiv",
  primaryClass  = "cs.CV",
  eprint        = "1806.03962"
}

@article{stevenson2009introduction,
  title={An introduction to survival analysis},
  author={Stevenson, Mark and EpiCentre, IVABS},
  journal={EpiCentre, IVABS, Massey University},
  year={2009}
}

@article{sung2021global,
  title={Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries},
  author={Sung, Hyuna and Ferlay, Jacques and Siegel, Rebecca L and Laversanne, Mathieu and Soerjomataram, Isabelle and Jemal, Ahmedin and Bray, Freddie},
  journal={CA: a cancer journal for clinicians},
  volume={71},
  number={3},
  pages={209--249},
  year={2021},
  publisher={Wiley Online Library}
}

@book{klein2014handbook,
  title={Handbook of survival analysis},
  author={Klein, John P and Van Houwelingen, Hans C and Ibrahim, Joseph G and Scheike, Thomas H},
  year={2014},
  publisher={CRC Press Boca Raton, FL:}
}