
% ------------------ Clinical Refs --------------------------------------------

@article{khoury1994longitudinal,
  title={Longitudinal MRI in multiple sclerosis: correlation between disability and lesion burden},
  author={Khoury, SJ and Guttmann, CRG and Orav, EJ and Hohol, MJ and Ahn, SS and Hsu, L and Kikinis, R and Mackin, GA and Jolesz, FA and Weiner, HL},
  journal={Neurology},
  volume={44},
  number={11},
  pages={2120--2120},
  year={1994},
  publisher={AAN Enterprises}
}

@article{rudick2006significance,
  title={Significance of T2 lesions in multiple sclerosis: a 13-year longitudinal study},
  author={Rudick, Richard A and Lee, Jar-Chi and Simon, Jack and Fisher, Elizabeth},
  journal={Annals of Neurology: Official Journal of the American Neurological Association and the Child Neurology Society},
  volume={60},
  number={2},
  pages={236--242},
  year={2006},
  publisher={Wiley Online Library}
}

% ------------------ Hough Voting Refs --------------------------------------------

@misc{hough1962method,
  title={Method and means for recognizing complex patterns},
  author={Hough, Paul VC},
  year={1962},
  month=dec # "~18",
  publisher={Google Patents},
  note={US Patent 3,069,654}
}

@article{ballard1981generalizing,
  title={Generalizing the Hough transform to detect arbitrary shapes},
  author={Ballard, Dana H},
  journal={Pattern recognition},
  volume={13},
  number={2},
  pages={111--122},
  year={1981},
  publisher={Elsevier}
}

@incollection{leibe2006interleaving,
  title={Interleaving object categorization and segmentation},
  author={Leibe, Bastian and Schiele, Bernt},
  booktitle={Cognitive vision systems},
  pages={145--161},
  year={2006},
  publisher={Springer}
}

@inproceedings{maji2009object,
  title={Object detection using a max-margin hough transform},
  author={Maji, Subhransu and Malik, Jitendra},
  booktitle={2009 IEEE Conference on Computer Vision and Pattern Recognition},
  pages={1038--1045},
  year={2009},
  organization={IEEE}
}

@article{milletari2017hough,
  title={Hough-CNN: deep learning for segmentation of deep brain regions in MRI and ultrasound},
  author={Milletari, Fausto and Ahmadi, Seyed-Ahmad and Kroll, Christine and Plate, Annika and Rozanski, Verena and Maiostre, Juliana and Levin, Johannes and Dietrich, Olaf and Ertl-Wagner, Birgit and B{\"o}tzel, Kai and others},
  journal={Computer Vision and Image Understanding},
  volume={164},
  pages={92--102},
  year={2017},
  publisher={Elsevier}
}

@inproceedings{qi2019deep,
  title={Deep hough voting for 3d object detection in point clouds},
  author={Qi, Charles R and Litany, Or and He, Kaiming and Guibas, Leonidas J},
  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision},
  pages={9277--9286},
  year={2019}
}

@inproceedings{qi2020imvotenet,
  title={Imvotenet: Boosting 3d object detection in point clouds with image votes},
  author={Qi, Charles R and Chen, Xinlei and Litany, Or and Guibas, Leonidas J},
  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
  pages={4404--4413},
  year={2020}
}

% ------------------ Memory Network Refs --------------------------------------------
@inproceedings{sukhbaatar2015end,
  title={End-to-end memory networks},
  author={Sukhbaatar, Sainbayar and Szlam, Arthur and Weston, Jason and Fergus, Rob},
  booktitle={Proceedings of the 28th International Conference on Neural Information Processing Systems-Volume 2},
  pages={2440--2448},
  year={2015}
}

@inproceedings{zhong2019invariance,
  title={Invariance matters: Exemplar memory for domain adaptive person re-identification},
  author={Zhong, Zhun and Zheng, Liang and Luo, Zhiming and Li, Shaozi and Yang, Yi},
  booktitle={Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  pages={598--607},
  year={2019}
}

@inproceedings{gong2019memorizing,
  title={Memorizing normality to detect anomaly: Memory-augmented deep autoencoder for unsupervised anomaly detection},
  author={Gong, Dong and Liu, Lingqiao and Le, Vuong and Saha, Budhaditya and Mansour, Moussa Reda and Venkatesh, Svetha and Hengel, Anton van den},
  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision},
  pages={1705--1714},
  year={2019}
}

@article{he2020learning,
  title={Learning and Memorizing Representative Prototypes for 3D Point Cloud Semantic and Instance Segmentation},
  author={He, Tong and Gong, Dong and Tian, Zhi and Shen, Chunhua},
  journal={arXiv preprint arXiv:2001.01349},
  year={2020},
  publisher={Springer}
}

@article{zhang2020geometric,
  title={Geometric Loss for Deep Multiple Sclerosis lesion Segmentation},
  author={Zhang, Hang and Zhang, Jinwei and Wang, Rongguang and Zhang, Qihao and Gauthier, Susan A and Spincemaille, Pascal and Nguyen, Thanh D and Wang, Yi},
  journal={arXiv preprint arXiv:2009.13755},
  year={2020}
}

@article{zhang2021nerd,
  title={NeRD: Neural Representation of Distribution for Medical Image Segmentation},
  author={Zhang, Hang and Wang, Rongguang and Zhang, Jinwei and Li, Chao and Yang, Gufeng and Spincemaille, Pascal and Nguyen, Thanh and Wang, Yi},
  journal={arXiv preprint arXiv:2103.04020},
  year={2021}
}

% ------------------ Method Refs --------------------------------------------

@article{schmidt2012automated,
  title={An automated tool for detection of FLAIR-hyperintense white-matter lesions in multiple sclerosis},
  author={Schmidt, Paul and Gaser, Christian and Arsic, Milan and Buck, Dorothea and F{\"o}rschler, Annette and Berthele, Achim and Hoshi, Muna and Ilg, R{\"u}diger and Schmid, Volker J and Zimmer, Claus and others},
  journal={Neuroimage},
  volume={59},
  number={4},
  pages={3774--3783},
  year={2012},
  publisher={Elsevier}
}


@inproceedings{zhang2019multiple,
  title={Multiple sclerosis lesion segmentation with tiramisu and 2.5 d stacked slices},
  author={Zhang, Huahong and Valcarcel, Alessandra M and Bakshi, Rohit and Chu, Renxin and Bagnato, Francesca and Shinohara, Russell T and Hett, Kilian and Oguz, Ipek},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={338--346},
  year={2019},
  organization={Springer}
}

@article{zhang2020efficient,
  title={Efficient Folded Attention for 3D Medical Image Reconstruction and Segmentation},
  author={Zhang, Hang and Zhang, Jinwei and Wang, Rongguang and Zhang, Qihao and Spincemaille, Pascal and Nguyen, Thanh D and Wang, Yi},
  journal={arXiv preprint arXiv:2009.05576},
  year={2020}
}

@inproceedings{zhang2019rsanet,
  title={RsaNet: Recurrent slice-wise attention network for multiple sclerosis lesion segmentation},
  author={Zhang, Hang and Zhang, Jinwei and Zhang, Qihao and Kim, Jeremy and Zhang, Shun and Gauthier, Susan A and Spincemaille, Pascal and Nguyen, Thanh D and Sabuncu, Mert and Wang, Yi},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={411--419},
  year={2019},
  organization={Springer}
}

@article{aslani2019multi,
  title={Multi-branch convolutional neural network for multiple sclerosis lesion segmentation},
  author={Aslani, Shahab and Dayan, Michael and Storelli, Loredana and Filippi, Massimo and Murino, Vittorio and Rocca, Maria A and Sona, Diego},
  journal={NeuroImage},
  volume={196},
  pages={1--15},
  year={2019},
  publisher={Elsevier}
}

@article{schmidt2012automated,
  title={An automated tool for detection of FLAIR-hyperintense white-matter lesions in multiple sclerosis},
  author={Schmidt, Paul and Gaser, Christian and Arsic, Milan and Buck, Dorothea and F{\"o}rschler, Annette and Berthele, Achim and Hoshi, Muna and Ilg, R{\"u}diger and Schmid, Volker J and Zimmer, Claus and others},
  journal={Neuroimage},
  volume={59},
  number={4},
  pages={3774--3783},
  year={2012},
  publisher={Elsevier}
}

@article{shiee2010topology,
  title={A topology-preserving approach to the segmentation of brain images with multiple sclerosis lesions},
  author={Shiee, Navid and Bazin, Pierre-Louis and Ozturk, Arzu and Reich, Daniel S and Calabresi, Peter A and Pham, Dzung L},
  journal={NeuroImage},
  volume={49},
  number={2},
  pages={1524--1535},
  year={2010},
  publisher={Elsevier}
}

@inproceedings{ronneberger2015u,
  title={U-net: Convolutional networks for biomedical image segmentation},
  author={Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
  booktitle={International Conference on Medical image computing and computer-assisted intervention},
  pages={234--241},
  year={2015},
  organization={Springer}
}


@article{barquero2020rimnet,
  title={RimNet: A deep 3D multimodal MRI architecture for paramagnetic rim lesion assessment in multiple sclerosis},
  author={Barquero, Germ{\'a}n and La Rosa, Francesco and Kebiri, Hamza and Lu, Po-Jui and Rahmanzadeh, Reza and Weigel, Matthias and Fartaria, M{\'a}rio Jo{\~a}o and Kober, Tobias and Th{\'e}audin, Marie and Du Pasquier, Renaud and others},
  journal={NeuroImage: Clinical},
  volume={28},
  pages={102412},
  year={2020},
  publisher={Elsevier}
}

@article{dworkin2018automated,
  title={An automated statistical technique for counting distinct multiple sclerosis lesions},
  author={Dworkin, Jordan D and Linn, Kristin A and Oguz, Ipek and Fleishman, Greg M and Bakshi, Rohit and Nair, Govind and Calabresi, Peter A and Henry, Roland G and Oh, Jiwon and Papinutto, Nico and others},
  journal={American Journal of Neuroradiology},
  volume={39},
  number={4},
  pages={626--633},
  year={2018},
  publisher={Am Soc Neuroradiology}
}

@article{mckinley2020automatic,
  title={Automatic detection of lesion load change in Multiple Sclerosis using convolutional neural networks with segmentation confidence},
  author={McKinley, Richard and Wepfer, Rik and Grunder, Lorenz and Aschwanden, Fabian and Fischer, Tim and Friedli, Christoph and Muri, Raphaela and Rummel, Christian and Verma, Rajeev and Weisstanner, Christian and others},
  journal={NeuroImage: Clinical},
  volume={25},
  pages={102104},
  year={2020},
  publisher={Elsevier}
}

@inproceedings{zhang2019rsanet,
  title={RSANet: Recurrent Slice-wise Attention Network for Multiple Sclerosis Lesion Segmentation},
  author={Zhang, Hang and Zhang, Jinwei and Zhang, Qihao and Kim, Jeremy and Zhang, Shun and Gauthier, Susan A and Spincemaille, Pascal and Nguyen, Thanh D and Sabuncu, Mert and Wang, Yi},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={411--419},
  year={2019},
  organization={Springer}
}

@article{zhang2020geometric,
  title={Geometric Loss for Deep Multiple Sclerosis lesion Segmentation},
  author={Zhang, Hang and Zhang, Jinwei and Wang, Rongguang and Zhang, Qihao and Gauthier, Susan A and Spincemaille, Pascal and Nguyen, Thanh D and Wang, Yi},
  journal={arXiv preprint arXiv:2009.13755},
  year={2020}
}

@article{zhang2020efficient,
  title={Efficient Folded Attention for 3D Medical Image Reconstruction and Segmentation},
  author={Zhang, Hang and Zhang, Jinwei and Wang, Rongguang and Zhang, Qihao and Spincemaille, Pascal and Nguyen, Thanh D and Wang, Yi},
  journal={arXiv preprint arXiv:2009.05576},
  year={2020}
}

@inproceedings{zhang2019multiple,
  title={Multiple Sclerosis Lesion Segmentation with Tiramisu and 2.5 D Stacked Slices},
  author={Zhang, Huahong and Valcarcel, Alessandra M and Bakshi, Rohit and Chu, Renxin and Bagnato, Francesca and Shinohara, Russell T and Hett, Kilian and Oguz, Ipek},
  booktitle={International Conference on Medical Image Computing and Computer-Assisted Intervention},
  pages={338--346},
  year={2019},
  organization={Springer}
}

@article{aslani2019multi,
  title={Multi-branch convolutional neural network for multiple sclerosis lesion segmentation},
  author={Aslani, Shahab and Dayan, Michael and Storelli, Loredana and Filippi, Massimo and Murino, Vittorio and Rocca, Maria A and Sona, Diego},
  journal={NeuroImage},
  volume={196},
  pages={1--15},
  year={2019},
  publisher={Elsevier}
}

% others

@article{paszke2019pytorch,
  title={Pytorch: An imperative style, high-performance deep learning library},
  author={Paszke, Adam and Gross, Sam and Massa, Francisco and Lerer, Adam and Bradbury, James and Chanan, Gregory and Killeen, Trevor and Lin, Zeming and Gimelshein, Natalia and Antiga, Luca and others},
  journal={arXiv preprint arXiv:1912.01703},
  year={2019}
}

@article{kingma2014adam,
  title={Adam: A method for stochastic optimization},
  author={Kingma, Diederik P and Ba, Jimmy},
  journal={arXiv preprint arXiv:1412.6980},
  year={2014}
}

@inproceedings{pelleg2000x,
  title={X-means: Extending k-means with efficient estimation of the number of clusters.},
  author={Pelleg, Dan and Moore, Andrew W and others},
  booktitle={Icml},
  volume={1},
  pages={727--734},
  year={2000}
}