@misc{ellipse,
  author = {Yinzhu Jin},
  title = {ellipse},
  year = {2022},
  url = {https://pypi.org/project/ellipse/},
  note = {Accessed: 2025-01-31}
}

@inproceedings{wang2021explanations,
  title={Are explanations helpful? a comparative study of the effects of explanations in ai-assisted decision-making},
  author={Wang, Xinru and Yin, Ming},
  booktitle={Proceedings of the 26th International Conference on Intelligent User Interfaces},
  pages={318--328},
  year={2021}
}

@article{lamontagne2019oasis,
  title={OASIS-3: longitudinal neuroimaging, clinical, and cognitive dataset for normal aging and Alzheimer disease},
  author={LaMontagne, Pamela J and Benzinger, Tammie LS and Morris, John C and Keefe, Sarah and Hornbeck, Russ and Xiong, Chengjie and Grant, Elizabeth and Hassenstab, Jason and Moulder, Krista and Vlassenko, Andrei G and others},
  journal={medrxiv},
  pages={2019--12},
  year={2019},
  publisher={Cold Spring Harbor Laboratory Press}
}

@article{paszke2017automatic,
  title={Automatic differentiation in PyTorch},
  author={Paszke, Adam and Gross, Sam and Chintala, Soumith and Chanan, Gregory and Yang, Edward and DeVito, Zachary and Lin, Zeming and Desmaison, Alban and Antiga, Luca and Lerer, Adam},
  year={2017}
}

@inproceedings{song2020score,
  title={Score-Based Generative Modeling through Stochastic Differential Equations},
  author={Song, Yang and Sohl-Dickstein, Jascha and Kingma, Diederik P and Kumar, Abhishek and Ermon, Stefano and Poole, Ben},
  booktitle={International Conference on Learning Representations},
  year={2021}
}

@inproceedings{pinaya2022brain,
  title={Brain imaging generation with latent diffusion models},
  author={Pinaya, Walter HL and Tudosiu, Petru-Daniel and Dafflon, Jessica and Da Costa, Pedro F and Fernandez, Virginia and Nachev, Parashkev and Ourselin, Sebastien and Cardoso, M Jorge},
  booktitle={MICCAI Workshop on Deep Generative Models},
  pages={117--126},
  year={2022},
  organization={Springer}
}

@article{dhariwal2021diffusion,
  title={Diffusion models beat gans on image synthesis},
  author={Dhariwal, Prafulla and Nichol, Alexander},
  journal={Advances in neural information processing systems},
  volume={34},
  pages={8780--8794},
  year={2021}
}

@article{ho2020denoising,
  title={Denoising diffusion probabilistic models},
  author={Ho, Jonathan and Jain, Ajay and Abbeel, Pieter},
  journal={Advances in neural information processing systems},
  volume={33},
  pages={6840--6851},
  year={2020}
}

@inproceedings{sohl2015deep,
  title={Deep unsupervised learning using nonequilibrium thermodynamics},
  author={Sohl-Dickstein, Jascha and Weiss, Eric and Maheswaranathan, Niru and Ganguli, Surya},
  booktitle={International conference on machine learning},
  pages={2256--2265},
  year={2015},
  organization={PMLR}
}

@inproceedings{chung2023diffusion,
  title={Diffusion Posterior Sampling for General Noisy Inverse Problems},
  author={Chung, Hyungjin and Kim, Jeongsol and Mccann, Michael T and Klasky, Marc L and Ye, Jong Chul},
  booktitle={The Eleventh International Conference on Learning Representations, ICLR 2023},
  year={2023},
  organization={The International Conference on Learning Representations}
}

@article{fontanella2023diffusion,
  title={Diffusion models for counterfactual generation and anomaly detection in brain images},
  author={Fontanella, Alessandro and Mair, Grant and Wardlaw, Joanna and Trucco, Emanuele and Storkey, Amos},
  journal={arXiv preprint arXiv:2308.02062},
  year={2023}
}

@book{fox2015applied,
  title={Applied regression analysis and generalized linear models},
  author={Fox, John},
  year={2015},
  publisher={Sage publications}
}

@article{augustin2022diffusion,
  title={Diffusion visual counterfactual explanations},
  author={Augustin, Maximilian and Boreiko, Valentyn and Croce, Francesco and Hein, Matthias},
  journal={Advances in Neural Information Processing Systems},
  volume={35},
  pages={364--377},
  year={2022}
}

@article{pearson1901liii,
  title={LIII. On lines and planes of closest fit to systems of points in space},
  author={Pearson, Karl},
  journal={The London, Edinburgh, and Dublin philosophical magazine and journal of science},
  volume={2},
  number={11},
  pages={559--572},
  year={1901},
  publisher={Taylor \& Francis}
}

@inproceedings{selvaraju2017grad,
  title={Grad-cam: Visual explanations from deep networks via gradient-based localization},
  author={Selvaraju, Ramprasaath R and Cogswell, Michael and Das, Abhishek and Vedantam, Ramakrishna and Parikh, Devi and Batra, Dhruv},
  booktitle={Proceedings of the IEEE international conference on computer vision},
  pages={618--626},
  year={2017}
}

@inproceedings{sundararajan2017axiomatic,
  title={Axiomatic attribution for deep networks},
  author={Sundararajan, Mukund and Taly, Ankur and Yan, Qiqi},
  booktitle={International conference on machine learning},
  pages={3319--3328},
  year={2017},
  organization={PMLR}
}

@inproceedings{schulzrestricting,
  title={Restricting the Flow: Information Bottlenecks for Attribution},
  author={Schulz, Karl and Sixt, Leon and Tombari, Federico and Landgraf, Tim},
  booktitle={International Conference on Learning Representations},
  year={202}
}

@article{wachter2017counterfactual,
  title={Counterfactual explanations without opening the black box: Automated decisions and the GDPR},
  author={Wachter, Sandra and Mittelstadt, Brent and Russell, Chris},
  journal={Harv. JL \& Tech.},
  volume={31},
  pages={841},
  year={2017},
  publisher={HeinOnline}
}

@inproceedings{goyal2019counterfactual,
  title={Counterfactual visual explanations},
  author={Goyal, Yash and Wu, Ziyan and Ernst, Jan and Batra, Dhruv and Parikh, Devi and Lee, Stefan},
  booktitle={International Conference on Machine Learning},
  pages={2376--2384},
  year={2019},
  organization={PMLR}
}

@inproceedings{jeanneret2022diffusion,
  title={Diffusion models for counterfactual explanations},
  author={Jeanneret, Guillaume and Simon, Lo{\"\i}c and Jurie, Fr{\'e}d{\'e}ric},
  booktitle={Proceedings of the Asian Conference on Computer Vision},
  pages={858--876},
  year={2022}
}

@article{goyal2019explaining,
  title={Explaining classifiers with causal concept effect (cace)},
  author={Goyal, Yash and Feder, Amir and Shalit, Uri and Kim, Been},
  journal={arXiv preprint arXiv:1907.07165},
  year={2019}
}

@INPROCEEDINGS{jin2024measuring,
  author={Jin, Yinzhu and Dwyer, Matthew B. and Fletcher, P. Thomas},
  booktitle={2024 IEEE International Symposium on Biomedical Imaging (ISBI)}, 
  title={Measuring Feature Dependency of Neural Networks by Collapsing Feature Dimensions in The Data Manifold}, 
  year={2024},
  volume={},
  number={},
  pages={1-5},
  keywords={Manifolds;Solid modeling;Image texture;Image segmentation;Shape;Magnetic resonance imaging;Biomedical measurement},
  doi={10.1109/ISBI56570.2024.10635874}}

@inproceedings{ribeiro2016should,
  title={" Why should i trust you?" Explaining the predictions of any classifier},
  author={Ribeiro, Marco Tulio and Singh, Sameer and Guestrin, Carlos},
  booktitle={Proceedings of the 22nd ACM SIGKDD international conference on knowledge discovery and data mining},
  pages={1135--1144},
  year={2016}
}

@inproceedings{jin2022feature,
  title={Feature Gradient Flow for Interpreting Deep Neural Networks in Head and Neck Cancer Prediction},
  author={Jin, Yinzhu and Garneau, Jonathan C and Fletcher, P Thomas},
  booktitle={2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI)},
  pages={1--5},
  year={2022},
  organization={IEEE}
}

@article{kingma2013auto,
  title={Auto-encoding variational bayes},
  author={Kingma, Diederik P},
  journal={arXiv preprint arXiv:1312.6114},
  year={2013}
}

@inproceedings{liu2015faceattributes,
  title = {Deep Learning Face Attributes in the Wild},
  author = {Liu, Ziwei and Luo, Ping and Wang, Xiaogang and Tang, Xiaoou},
  booktitle = {Proceedings of International Conference on Computer Vision (ICCV)},
  month = {December},
  year = {2015} 
}

@article{lecun1998gradient,
  title={Gradient-based learning applied to document recognition},
  author={LeCun, Yann and Bottou, L{\'e}on and Bengio, Yoshua and Haffner, Patrick},
  journal={Proceedings of the IEEE},
  volume={86},
  number={11},
  pages={2278--2324},
  year={1998},
  publisher={IEEE}
}

@inproceedings{he2016deep,
  title={Deep residual learning for image recognition},
  author={He, Kaiming and Zhang, Xiangyu and Ren, Shaoqing and Sun, Jian},
  booktitle={Proceedings of the IEEE conference on computer vision and pattern recognition},
  pages={770--778},
  year={2016}
}

@misc{rw2019timm,
  author = {Ross Wightman},
  title = {PyTorch Image Models},
  year = {2019},
  publisher = {GitHub},
  journal = {GitHub repository},
  doi = {10.5281/zenodo.4414861},
  howpublished = {\url{https://github.com/rwightman/pytorch-image-models}}
}

@inproceedings{ronneberger2015u,
  title={U-net: Convolutional networks for biomedical image segmentation},
  author={Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
  booktitle={Medical image computing and computer-assisted intervention--MICCAI 2015: 18th international conference, Munich, Germany, October 5-9, 2015, proceedings, part III 18},
  pages={234--241},
  year={2015},
  organization={Springer}
}

@article{solovyev20223d,
  title={3D convolutional neural networks for stalled brain capillary detection},
  author={Solovyev, Roman and Kalinin, Alexandr A and Gabruseva, Tatiana},
  journal={Computers in Biology and Medicine},
  volume={141},
  pages={105089},
  year={2022},
  publisher={Elsevier},
  doi={10.1016/j.compbiomed.2021.105089}
}

@inproceedings{rombach2022high,
  title={High-resolution image synthesis with latent diffusion models},
  author={Rombach, Robin and Blattmann, Andreas and Lorenz, Dominik and Esser, Patrick and Ommer, Bj{\"o}rn},
  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
  pages={10684--10695},
  year={2022}
}

@article{pinaya2023generative,
  title={Generative ai for medical imaging: extending the monai framework},
  author={Pinaya, Walter HL and Graham, Mark S and Kerfoot, Eric and Tudosiu, Petru-Daniel and Dafflon, Jessica and Fernandez, Virginia and Sanchez, Pedro and Wolleb, Julia and Da Costa, Pedro F and Patel, Ashay and others},
  journal={arXiv preprint arXiv:2307.15208},
  year={2023}
}

@inproceedings{zhu2024quantifying,
  title={Quantifying Hippocampal Shape Asymmetry in Alzheimer’s Disease Using Optimal Shape Correspondences},
  author={Zhu, Shen and Zawar, Ifrah and Kapur, Jaideep and Fletcher, P Thomas},
  booktitle={2024 IEEE International Symposium on Biomedical Imaging (ISBI)},
  pages={1--4},
  year={2024},
  organization={IEEE}
}

@article{sarica2018mri,
  title={MRI asymmetry index of hippocampal subfields increases through the continuum from the mild cognitive impairment to the Alzheimer's disease},
  author={Sarica, Alessia and Vasta, Roberta and Novellino, Fabiana and Vaccaro, Maria Grazia and Cerasa, Antonio and Quattrone, Aldo and Alzheimer's Disease Neuroimaging Initiative},
  journal={Frontiers in neuroscience},
  volume={12},
  pages={576},
  year={2018},
  publisher={Frontiers Media SA}
}

@article{fischi2002whole,
  title={Whole brain segmentation: Automated labeling of neuroanatomical structures in the human brain},
  author={fischi, Bruce and Salat, David H and Busa, Evelina and Albert, Marilyn and Dieterich, Megan and Haselgrove, Christian and Van Der Kouwe, Andre and killiany, Ron and kennedy, David and Klaveness, Shuna and others},
  journal={Neuron},
  volume={33},
  number={3},
  pages={341--355},
  year={2002},
  publisher={Cell Press}
}

@inproceedings{naeem2020reliable,
  title={Reliable fidelity and diversity metrics for generative models},
  author={Naeem, Muhammad Ferjad and Oh, Seong Joon and Uh, Youngjung and Choi, Yunjey and Yoo, Jaejun},
  booktitle={International Conference on Machine Learning},
  pages={7176--7185},
  year={2020},
  organization={PMLR}
}

@inproceedings{simonyan2015very,
  title={Very deep convolutional networks for large-scale image recognition},
  author={Simonyan, K and Zisserman, A},
  booktitle={3rd International Conference on Learning Representations (ICLR 2015)},
  year={2015},
  organization={Computational and Biological Learning Society}
}

@inproceedings{deng2009imagenet,
  title={Imagenet: A large-scale hierarchical image database},
  author={Deng, Jia and Dong, Wei and Socher, Richard and Li, Li-Jia and Li, Kai and Fei-Fei, Li},
  booktitle={2009 IEEE conference on computer vision and pattern recognition},
  pages={248--255},
  year={2009},
  organization={IEEE}
}

@incollection{efron1992bootstrap,
  title={Bootstrap methods: another look at the jackknife},
  author={Efron, Bradley},
  booktitle={Breakthroughs in statistics: Methodology and distribution},
  pages={569--593},
  year={1992},
  publisher={Springer}
}
