Curriculum Vitae

@inproceedings{Yu2024PolyOculus,
      title={PolyOculus: Simultaneous Multi-view Image-based Novel View Synthesis}, 
      author={Jason J. Yu and Tristan Aumentado-Armstrong and Fereshteh Forghani and Konstantinos G. Derpanis and Marcus A. Brubaker},
      year={2024},
      booktitle=ECCV,
      eprint={2402.17986},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url={https://arxiv.org/abs/2402.17986}, 
}

@inproceedings{Mirzaei2023WatchYourSteps,
      title={Watch Your Steps: Local Image and Scene Editing by Text Instructions}, 
      author={Ashkan Mirzaei and Tristan Aumentado-Armstrong and Marcus A. Brubaker and Jonathan Kelly and Alex Levinshtein and Konstantinos G. Derpanis and Igor Gilitschenski},
      year={2024},
      booktitle=ECCV,
      eprint={2308.08947},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url={https://arxiv.org/abs/2308.08947}, 
}

@inproceedings{Mosleh2024NonparametricNoise,
      title={Non-parametric Sensor Noise Modeling and Synthesis},
      author={Ali Mosleh and Luxi Zhao and Atin Singh Jaeduk Han and Abhijith Punnappurath and Marcus A. Brubaker and Jihwan Choe and Michael S. Brown},
      year={2024},
      booktitle=ECCV,
}
      

@misc{Shekarforoush2024ImprovingAbinitioCryoEM,
      title={Improving Ab-Initio Cryo-EM Reconstruction with Semi-Amortized Pose Inference}, 
      author={Shayan Shekarforoush and David B. Lindell and Marcus A. Brubaker and David J. Fleet},
      year={2024},
      eprint={2406.10455},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url={https://arxiv.org/abs/2406.10455}, 
}

@article{Flachot2023Can,
  title={Can deep neural networks for intrinsic image decomposition model human lightness constancy?},
  author={Flachot, Alban and Patel, Jaykishan and Patel, Khushbu and Wallis, Tom SA and Brubaker, Marcus A and Brainard, David H and Murray, Richard F},
  journal={Journal of Vision},
  volume={23},
  number={9},
  pages={5467--5467},
  year={2023},
  publisher={The Association for Research in Vision and Ophthalmology}
}

@article{Patel2023Deep,
  title={A deep convolutional neural network trained to infer surface reflectance is deceived by mid-level lightness illusions},
  author={Patel, Jaykishan and Flachot, Alban and Vazquez-Corral, Javier and Brainard, David H and Wallis, Thomas SA and Brubaker, Marcus A and Murray, Richard F},
  journal={Journal of Vision},
  volume={23},
  number={9},
  pages={4817--4817},
  year={2023},
  publisher={The Association for Research in Vision and Ophthalmology}
}

@inproceedings{Yu2023LongTerm,
      title={Long-Term Photometric Consistent Novel View Synthesis with Diffusion Models}, 
      author={Jason J. Yu and Fereshteh Forghani and Konstantinos G. Derpanis and Marcus A. Brubaker},
      year={2023},
      booktitle=ICCV,
      eprint={2304.10700},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url_arXiv = {https://arxiv.org/abs/2304.10700}
}

@inproceedings{Mirzaei2023ReferenceGuided,
      title={Reference-guided Controllable Inpainting of Neural Radiance Fields}, 
      author={Ashkan Mirzaei and Tristan Aumentado-Armstrong and Marcus A. Brubaker and Jonathan Kelly and Alex Levinshtein and Konstantinos G. Derpanis and Igor Gilitschenski},
      year={2023},
      booktitle=ICCV,
      eprint={2304.09677},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url_arXiv = {https://arxiv.org/abs/2304.09677},
      url_Website = {https://ashmrz.github.io/reference-guided-3d/}
}

@misc{Toader2023EfficientCryoEM,
      title={Efficient high-resolution refinement in cryo-EM with stochastic gradient descent}, 
      author={Bogdan Toader and Marcus A. Brubaker and Roy R. Lederman},
      year={2023},
      eprint={2311.16100},
      archivePrefix={arXiv},
      primaryClass={math.NA},
      url={https://arxiv.org/abs/2311.16100}, 
}

@misc{AumentadoArmstrong2023LatentNeRF,
      title={Reconstructive Latent-Space Neural Radiance Fields for Efficient 3D Scene Representations}, 
      author={Tristan Aumentado-Armstrong and Ashkan Mirzaei and Marcus A. Brubaker and Jonathan Kelly and Alex Levinshtein and Konstantinos G. Derpanis and Igor Gilitschenski},
      year={2023},
      eprint={2310.17880},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url={https://arxiv.org/abs/2310.17880}, 
}

@misc{Shekarforoush2023DualCamera,
      title={Dual-Camera Joint Deblurring-Denoising}, 
      author={Shayan Shekarforoush and Amanpreet Walia and Marcus A. Brubaker and Konstantinos G. Derpanis and Alex Levinshtein},
      year={2023},
      eprint={2309.08826},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url={https://arxiv.org/abs/2309.08826}, 
}

@article{Sastry2022Efficient,
      title={{Efficient CDF Approximations for Normalizing Flows}},
      author={Chandramouli Shama Sastry and Andreas Lehrmann and Marcus A. Brubaker and Alexander Radovic},
      journal=TMLR,
      year={2022},
      eprint={2202.11322},
      archivePrefix={arXiv},
      primaryClass={cs.LG},
      url={https://openreview.net/forum?id=LnjclqBl8R},
      url_arXiv={https://arxiv.org/abs/2202.11322}
}

@inproceedings{Shekarforoush2022ResidualMFN,
      title = {Residual Multiplicative Filter Networks for Multiscale Reconstruction},
      author = {Shekarforoush, Shayan and Lindell, David B. and Fleet, David J. and Brubaker, Marcus A.},
      year = {2022},
      booktitle=NeurIPS,
      eprint={2206.00746},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url_arXiv = {https://arxiv.org/abs/2206.00746},
}

@inproceedings{Nam2022Neural,
      title={Neural Image Representations for Multi-Image Fusion and Layer Separation}, 
      author={Seonghyeon Nam and Marcus A. Brubaker and Michael S. Brown},
      year={2022},
      booktitle=ECCV,
      eprint={2108.01199},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url_arXiv = {https://arxiv.org/abs/2108.01199},
      url_Website = {http://snam.ml/research/nir}
}

@inproceedings{Maleky2022Noise2NoiseFlow,
	title={{Noise2NoiseFlow: Realistic Camera Noise Modeling without Clean Images}},
	author={Ali Maleky and Shayan Kousha and Michael S. Brown and Marcus A. Brubaker},
	year={2022},
	booktitle=CVPR,
	eprint={2206.01103},
	archivePrefix={arXiv},
	primaryClass={cs.CV},
	url_arXiv = {https://arxiv.org/abs/2206.01103},
	url_Website = {https://yorkucvil.github.io/Noise2NoiseFlow/},
}

@inproceedings{Kousha2022ModelingsRGB,
	title={{Modeling sRGB Camera Noise with Normalizing Flows}},
	author={Shayan Kousha and Ali Maleky and Michael S. Brown and Marcus A. Brubaker},
	year={2022},
	booktitle=CVPR,
	eprint={2206.00812},
	archivePrefix={arXiv},
	primaryClass={cs.CV},
	url_arXiv = {https://arxiv.org/abs/2206.00812},
	url_Website = {https://yorkucvil.github.io/sRGBNoise/},
}

@inproceedings{Nam2022Learning,
	title={{Learning sRGB-to-Raw De-rendering with Content-Aware Metadata}},
	author={Seonghyeon Nam and Abhijith Punnappurath and Marcus A. Brubaker and Michael S. Brown},
	year={2022},
	booktitle=CVPR,
	eprint={2206.01813},
	archivePrefix={arXiv},
	primaryClass={eess.IV},
	url_arXiv = {https://arxiv.org/abs/2206.01813},
	url_Code = {https://github.com/SamsungLabs/content-aware-metadata},
}

@inproceedings{Brofos2021Adaptation,
      title={Adaptation of the Independent Metropolis-Hastings Sampler with Normalizing Flow Proposals}, 
      author={James A. Brofos and Marylou Gabri\'{e} and Marcus A. Brubaker and Roy R. Lederman},
      year={2022},
      booktitle=AISTATS,
      eprint={2110.13216},
      archivePrefix={arXiv},
      primaryClass={stat.CO},
      url_arXiv={https://arxiv.org/abs/2110.13216}
}

@inproceedings{AfifiWACV2021Auto,
      title={Auto White-Balance Correction for Mixed-Illuminant Scenes}, 
      author={Mahmoud Afifi and Marcus A. Brubaker and Michael S. Brown},
      year={2022},
      booktitle=WACV,
      eprint={2109.08750},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url_arXiv = {https://arxiv.org/abs/2109.08750},
      url_Code = {https://github.com/mahmoudnafifi/mixedillWB}
}

@inproceedings{woollard2022physics,
  title={Physics aware inference for the cryo-EM inverse problem: anisotropic network model heterogeneity, global pose and microscope defocus},
  author={Woollard, Geoffrey and Shekarforoush, Shayan and Wood, Frank and Brubaker, Marcus A. and Duc, Khanh Dao},
  booktitle={{NeurIPS Workshop on Machine Learning for Structural Biology}},
  year={2022},
  url_Paper={https://openreview.net/pdf?id=g0UBB4QLiEQ}
}

@inproceedings{DengNeurIPS2021Continuous,
  title={Continuous Latent Process Flows},
  author={Ruizhi Deng and Marcus A. Brubaker and Greg Mori and Andreas Lehrmann},
  year={2021},
  booktitle = NeurIPS,
  eprint={2106.15580},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  url_arXiv = {https://arxiv.org/abs/2106.15580},
}

@inproceedings{Afifi2021HistoGAN,
  title={HistoGAN: Controlling Colors of GAN-Generated and Real Images via Color Histograms}, 
  author={Mahmoud Afifi and Marcus A. Brubaker and Michael S. Brown},
  booktitle=CVPR,
  year={2021},
  eprint={2011.11731},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  url_arXiv = {https://arxiv.org/abs/2010.13821},
}

@inproceedings{Brofos2021ICMLWINNFManifold,
  title={Manifold Density Estimation via Generalized Dequantization},
  author={James A. Brofos and Marcus A. Brubaker and Roy R. Lederman},
  year={2021},
  booktitle = {{ICML Workshop on Invertible Neural Networks, Normalizing Flows, and Explicit Likelihood Models}},
  eprint={2102.07143},
  archivePrefix={arXiv},
  primaryClass={stat.ML},
  url_arXiv = {https://arxiv.org/abs/2102.07143},
  url_Code = {https://github.com/JamesBrofos/Manifold-Dequantization}
}

@inproceedings{Radovic2021ICMLWINNFAgent,
  title={Agent Forecasting at Flexible Horizons using ODE Flows},
  author={Alexander Radovic and Jiawei He and Janahan Ramanan and Marcus A. Brubaker and Andreas Lehrmann},
  year={2021},
  booktitle = {{ICML Workshop on Invertible Neural Networks, Normalizing Flows, and Explicit Likelihood Models}},
  url_Paper = {https://openreview.net/forum?id=MvjsWTCfXpA},
}

@inproceedings{Deng2021ICMLWTSContinuous,
  title={Continuous Latent Process Flows},
  author={Ruizhi Deng and Marcus A. Brubaker and Greg Mori and Andreas Lehrmann},
  year={2021},
  booktitle = {{ICML Workshop on Time Series}},
  eprint={2106.15580},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  url_arXiv = {https://arxiv.org/abs/2106.15580},
}

@inproceedings{Kousha2021CVPRWFGVCZeroshot,
  title={Zero-shot Learning with Class Description Regularization},
  author={Shayan Kousha and Marcus A. Brubaker},
  year={2021},
  booktitle = {{CVPR Workshop on Fine-Grained Visual Categorization}},
  eprint={2106.16108},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  url_arXiv = {https://arxiv.org/abs/2106.16108},
}

@misc{Bose2021EquivariantFlows,
  author = {Bose, Avishek Joey and Brubaker, Marcus A. and Kobyzev, Ivan},
  title = {Equivariant Finite Normalizing Flows},
  eprint={2110.08649},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  year = {2021},
  url_arXiv = {https://arxiv.org/abs/2110.08649},
}

@misc{Afifi2021CAMS,
      title={CAMS: Color-Aware Multi-Style Transfer}, 
      author={Mahmoud Afifi and Abdullah Abuolaim and Mostafa Hussien and Marcus A. Brubaker and Michael S. Brown},
      year={2021},
      eprint={2106.13920},
      archivePrefix={arXiv},
      primaryClass={cs.CV},
      url_arXiv = {https://arxiv.org/abs/2106.13920},
      url_Code = {https://github.com/mahmoudnafifi/color-aware-style-transfer}
}

@misc{SharmaDPTutorialPartII2021,
    title={{Differential Privacy Tutorial II: Machine Learning and Data Generation}},
    author={Guarav Sharma and Nidhi Hegde and Simon J.D. Prince and Marcus A. Brubaker},
    month=Mar,
    year={2021},
    url_blog={https://www.borealisai.com/en/blog/tutorial-13-differential-privacy-ii-machine-learning-and-data-generation/},
}

@misc{BrubakerDPTutorialPartI2021,
    title={{Differential Privacy Tutorial I: Introduction}},
    author={Marcus A. Brubaker and Simon J.D. Prince},
    month=Feb,
    year={2021},
    url_blog={https://www.borealisai.com/en/blog/tutorial-12-differential-privacy-i-introduction/}
}

@article{KobyzevPAMI2020,
  title={Normalizing Flows: An Introduction and Review of Current Methods},
  author={Kobyzev, Ivan and Prince, Simon J.D. and Brubaker, Marcus A.},
  journal=PAMI,
  year={2020},
  eprint={1908.09257},
  archivePrefix={arXiv},
  primaryClass={stat.ML},
  url_arXiv={https://arxiv.org/abs/1908.09257}
}

@article{GhorbaniSCA2020,
  title={Probabilistic Character Motion Synthesis using a Hierarchical Deep Latent Variable Model},
  author={Ghorbani, Saeed and Wloka, Calden and Etemad, Ali and Brubaker, Marcus A. and Troje, Nikolaus F.},
  journal={{Proceedings of Symposium on Computer Animation (SCA) in Computer Graphics Forum}},
  year={2020},
  volume={39},
  number={8},
  url_Paper = {https://doi.org/10.1111/cgf.14116},
  url_Local = {GhorbaniSCA2020.pdf}
}

@inproceedings{YuNeurIPS2020WaveletFlow,
  title={{Wavelet Flow: Fast Training of High Resolution Normalizing Flows}},
  author={Yu, Jason J. and Derpanis, Konstantinos and Brubaker, Marcus A.},
  booktitle=NeurIPS,
  year={2020},
  eprint={2010.13821},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  url_arXiv = {https://arxiv.org/abs/2010.13821},
  url_Website = {https://yorkucvil.github.io/Wavelet-Flow/},
  url_Code = {https://github.com/YorkUCVIL/Wavelet-Flow/}
}

@inproceedings{DengNeurIPS2020CNFP,
  title={{Modeling Continuous Stochastic Processes with Dynamic Normalizing Flows}},
  author={Deng, Ruizhi and Chang, Bo and Brubaker, Marcus A. and Mori, Greg and Lehrmann, Andreas},
  booktitle=NeurIPS,
  year={2020},
  eprint={2002.10516},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  url_arXiv = {https://arxiv.org/abs/2002.10516},
  url_Code = {https://github.com/BorealisAI/continuous-time-flow-process}
}

@inproceedings{JainiICML2020Tails,
  title={Tails of Lipschitz Triangular Flows},
  author={Jaini, Priyank and Kobyzev, Ivan and Brubaker, Marcus A. and Yu, Yaoliang},
  booktitle=ICML,
  year={2020},
  eprint={1907.04481},
  archivePrefix={arXiv},
  primaryClass={math.ST},
  url_arXiv={https://arxiv.org/abs/1907.04481}
}

@inproceedings{GoelAAAI2020,
  title={{Diachronic Embedding for Temporal Knowledge Graph Completion}},
  author={Rishab Goel and Seyed Mehran Kazemi and Marcus A. Brubaker and Pascal Poupart},
  booktitle=AAAI,
  year={2020},
  eprint={1907.03143},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  url_arXiv = {https://arxiv.org/abs/1907.03143},
  url_Paper={GoelAAAI2020.pdf}
}

@inproceedings{Deng2020Modeling,
  title={Modeling Continuous Stochastic Processes with Dynamic Normalizing Flows},
  author={Ruizhi Deng and Bo Chang and Marcus A. Brubaker and Greg Mori and Andreas Lehrmann},
  year={2020},
  booktitle = {{ICML Workshop on Invertible Neural Networks, Normalizing Flows, and Explicit Likelihood Models}},
  eprint={2002.10516},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  url_arXiv = {https://arxiv.org/abs/2002.10516},
}

@misc{Deng2020Variational,
    title={Variational Hyper RNN for Sequence Modeling},
    author={Ruizhi Deng and Yanshuai Cao and Bo Chang and Leonid Sigal and Greg Mori and Marcus A. Brubaker},
    year={2020},
    eprint={2002.10501},
    archivePrefix={arXiv},
    primaryClass={cs.LG},
    url_arXiv = {https://arxiv.org/abs/2002.10501},
}

@inproceedings{AbdelhamedICCV2019,
  title={{Noise Flow: Noise Modeling with Conditional Normalizing Flows}},
  author={Abdelrahman Abdelhamed and Marcus A. Brubaker and Michael S. Brown},
  booktitle=ICCV,
  year={2019},
  eprint={1908.08453},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  url_arXiv = {https://arxiv.org/abs/1908.08453},
  url_Paper={AbdelhamedICCV2019.pdf},
  url_Supplemental={AbdelhamedICCV2019-Supplemental.pdf},
  url_Code = {https://github.com/BorealisAI/noise_flow}
}

@inproceedings{MasoumzadehBMVC2019,
  title={{HydraPicker: Fully Automated Particle Picking in Cryo-EM by Utilizing Dataset Bias in Single Shot Detection}},
  author={Abbas Masoumzadeh and Marcus A. Brubaker},
  booktitle=BMVC,
  year={2019},
  url_Paper={MasoumzadehBMVC2019.pdf},
  url_Supplemental={MasoumzadehBMVC2019-Supplemental.zip},
  url_Code={https://github.com/AbbasMZ/HydraPicker_Colab}
}

@inproceedings{UllrichUAI2019,
  title={{Differentiable probabilistic models of scientific imaging with the Fourier slice theorem}},
  author={Karen Ullrich and Rianne van den Berg and Marcus A. Brubaker and David J. Fleet and Max Welling},
  booktitle=UAI,
  year={2019},
  eprint={1906.07582},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  url_arXiv = {https://arxiv.org/abs/1906.07582},
  url_Paper={UllrichUAI2019.pdf},
  url_OpenReview={https://openreview.net/forum?id=rJG7g9xnL4}
}

@inproceedings{SharmaIJCAI2019,
  title={{On the Effectiveness of Low Frequency Perturbations}},
  author={Yash Sharma and Gavin Weiguang Ding and Marcus A. Brubaker},
  booktitle=IJCAI,
  year={2019},
  eprint={1903.00073},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  url_Paper={SharmaIJCAI2019.pdf},
  url_arXiv={https://arxiv.org/abs/1903.00073}
}

@inproceedings{GoelNIPSW2019,
  author = {Rishab Goel and Seyed Mehran Kazemi and Marcus A. Brubaker and Pascal Poupart},
  title = {{Diachronic Embedding for Temporal Knowledge Graph Completion}},
  booktitle = {{NeurIPS Workshop on Graph Representation Learning}},
  month = Dec,
  year = {2019},
  eprint={1907.03143},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  url_arXiv = {https://arxiv.org/abs/1907.03143},
}

@inproceedings{MehrasaNIPSW2019,
  author = {Nazanin Mehrasa and Ruizhi Deng and Jiawei He and Bo Chang and Thibaut Durand and Mohamed Osama Ahmed and Marcus A. Brubaker and Greg Mori},
  title = {{Point Process Flows}},
  booktitle = {{NeurIPS Workshop on Learning with Temporal Point Processes}},
  month = Dec,
  year = {2019},
  eprint={1910.08281},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  url_arXiv = {https://arxiv.org/abs/1910.08281},
}

@misc{Kazemi2019Time2Vec,
    title={Time2Vec: Learning a Vector Representation of Time},
    author={Seyed Mehran Kazemi and Rishab Goel and Sepehr Eghbali and Janahan Ramanan and Jaspreet Sahota and Sanjay Thakur and Stella Wu and Cathal Smyth and Pascal Poupart and Marcus Brubaker},
    year={2019},
    eprint={1907.05321},
    archivePrefix={arXiv},
    primaryClass={cs.LG},
    url_arXiv = {https://arxiv.org/abs/1907.05321}
}

@inproceedings{Tesfaldet2018,
  author = {Matthew Tesfaldet and Marcus A. Brubaker and Konstantinos G. Derpanis},
  title = {{Two-Stream Convolutional Networks for Dynamic Texture Synthesis}},
  booktitle = CVPR,
  year = {2018},
  eprint={1706.06982},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  url_Website = {https://ryersonvisionlab.github.io/two-stream-projpage/},
  url_Paper = {Tesfaldet2017.pdf},
  url_arXiv = {http://arxiv.org/abs/1706.06982},
}

@inproceedings{LivneCRV2018,
  author = {Micha Livne and Leonid Sigal and Marcus A. Brubaker and David J. Fleet},
  title = {{Walking on Thin Air: Environment-Free Physics-based Markerless Motion Capture}},
  booktitle = CRV,
  year = {2018},
  eprint={1812.01203},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  url_arXiv = {http://arxiv.org/abs/1812.01203},
  url_Paper = {LivneCRV2018.pdf},
  url_Supplemental = {LivenCRV2018-Supplemental.pdf},
  url_Website = {https://research.seraphlabs.ca/u-of-t/performance-capture/},
  url_Video = {LivneCRV2018-Video.mp4}
}

@inproceedings{TesfaldetECCVW2018,
  title={{Convolutional Photomosaic Generation via Multi-scale Perceptual Losses}},
  author={Matthew Tesfaldet and Nariman Saftarli and Marcus A. Brubaker and Konstantinos G. Derpanis},
  booktitle={{ECCV Workshop on Computer Vision for Fashion, Art and Design}},
  year={2018},
  url_Website = {https://ryersonvisionlab.github.io/perceptual-photomosaic-projpage/},
  url_Paper = {TesfaldetECCVW2018.pdf},
} 

@article{PunjaniMM2018,
  title={Algorithmic Advances in Single Particle Cryo-EM Data Processing},
  volume={24},
  DOI={10.1017/S143192761800483X},
  number={S1},
  journal={Microscopy and Microanalysis},
  publisher={Cambridge University Press},
  author={Ali Punjani and Haowei Zhang and John Rubinstein and Marcus A. Brubaker and David J. Fleet},
  year={2018},
  pages={868-869},
  url_Paper = {https://www.cambridge.org/core/journals/microscopy-and-microanalysis/article/algorithmic-advances-in-single-particle-cryoem-data-processing/61EF1BBF379A76834B4347E8712A2E9A},
}

@inproceedings{BlakeNIPSW2018,
  author = {Christopher Blake and Luyu Wang and Giuseppe Castiglione and Christopher Srinivasa and Marcus A. Brubaker},
  title = {On Learning Wire-Length Efficient Neural Networks},
  booktitle = {{NeurIPS 2018 Workshop on Compact Deep Neural Network Representation with Industrial Applications}},
  month = Dec,
  year = {2018},
}

@article{BrubakerTechVibes2018,
  author = {Marcus A. Brubaker},
  title = {{The Integral Cross-Discipline Approach to Pushing AI Research}},
  journal = {techvibes.com},
  month = Feb,
  year = {2018},
  url = {https://techvibes.com/2018/02/07/the-integral-cross-discipline-approach-to-pushing-ai-research}
}

@article{PunjaniNatureMethods2017,
  author = {Ali Punjani and John L. Rubinstein and David J. Fleet and Marcus A. Brubaker},
  title = {{cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination}},
  journal = {{Nature Methods}},
  year = {2017},
  volume = {14},
  number = {3},
  pages = {{290 -- 296}},
  url_Preprint = {PunjaniCryoSPARCNMeth2017.pdf},
  url_Paper = {http://rdcu.be/o3Ac},
  url_Software = {https://cryosparc.com},
}

@article{CarpenterJSS2017,
  author = {Bob Carpenter and Andrew Gelman and Matt Hoffman and Daniel Lee and Ben Goodrich and Michael Betancourt and Marcus A. Brubaker and Jiqiang Guo and Peter Li and Allen Riddell},
  title = {{Stan: A Probabilistic Programming Language}},
  journal = {{Journal of Statistical Software}},
  volume = {76},
  number = {1},
  year = {2017},
  url_Paper = {CarpenterJSS2017.pdf},
  url_Website = {https://www.jstatsoft.org/article/view/v076i01},
  url_Software = {http://mc-stan.org},
}

@article{DuezJFS2017,
  author = {Pierre Duez and Todd Weller and Marcus A. Brubaker and Richard E. Hockensmith and Ryan Lilien},
  title = {Development and validation of a virtual examination tool for firearm forensics},
  journal = {Journal of Forensic Sciences},
  year = {2017},
  url_Paper = {https://doi.org/10.1111/1556-4029.13668}
}

@article{BrubakerCryoEMPAMI2016,
  author = {Ali Punjani and Marcus A. Brubaker and David J. Fleet},
  title = {{Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy}},
  journal = PAMI,
  year = {2017},
  url_Paper = {PunjaniCryoEMPAMI2016.pdf}
}

@inproceedings{MaLost2ICRA2017,
  author = {Wei-Chiu Ma and Shenlong Wang and Marcus A. Brubaker and Sanja Fidler and Raquel Urtasun},
  title = {{Find your Way by Observing the Sun and Other Semantic Cues}},
  booktitle = ICRA,
  year = {2017},
  eprint={1606.07415},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  url_Paper = {MaLost2ICRA2017.pdf},
  url_arXiv = {http://arxiv.org/abs/1606.07415},
  url_YouTube = {https://youtu.be/tOVWptik0qI}
}

@inproceedings{LuoLIDCWACV2017,
  author = {Zhi Hao Luo and Marcus A. Brubaker and Michael Brudno},
  title = {{Size and Texture-based Classification of Lung Tumors with 3D CNNs}},
  booktitle = WACV,
  year = {2017},
  url_Paper = {LuoLIDCWACV2017.pdf}
}

@article{BrubakerLostPAMI2016,
  author = {Marcus A. Brubaker and Andreas Geiger and Raquel Urtasun},
  title = {{Map-based Probabilistic Visual Self-Localization}},
  journal = PAMI,
  year = {2016},
  url_Paper = {BrubakerLostPAMI2016.pdf}
}

@inproceedings{WangDeepGPAISTATS2016,
  author = {Yali Wang and Marcus A. Brubaker and Brahim Chaib-draa and Raquel Urtasun},
  title = {{Sequential Inference for Deep Gaussian Process}},
  booktitle = AISTATS,
  year = {2016},
  url_Paper = {WangDeepGPAISTATS2016.pdf},
}

@article{WellerAFTEJournal2015,
  author = {Todd Weller and Marcus A. Brubaker and Pierre Duez and Ryan Lilien},
  title = {{Introduction and Initial Evaluation of a Novel Three-Dimensional Imaging and Analysis System for Firearm Forensics}},
  journal = {{Association of Firearm and Tool Mark Examiners (AFTE) Journal}},
  volume = {47},
  number = {4},
  pages = {198 -- 208},
  year = {2015},
  url_Journal = {https://afte.org/afte-journal}
}

@article{RubinsteinCryoEMAlignment2015,
  author = {John L. Rubinstein and Marcus A. Brubaker},
  title = {{Alignment of cryo-EM movies of individual particles by optimization of image translations}},
  journal = {{Journal of Structural Biology}},
  volume = {192},
  number = {2},
  pages = {188 -- 195},
  year = {2015},
  eprint={1409.6789},
  archivePrefix={arXiv},
  primaryClass={q-bio.QM},
  url_arXiv = {http://arxiv.org/abs/1409.6789},
  url_Paper = {http://dx.doi.org/10.1016/j.jsb.2015.08.007},
}

@article{ZhaoJSBAnisotropy2015,
  title = {{Description and comparison of algorithms for correcting anisotropic magnification in cryo-EM images}},
  author = {Jianhua  Zhao and Marcus A. Brubaker and Samir Benlekbir and John L. Rubinstein},
  journal = {{Journal of Structural Biology}},
  volume = {192},
  number = {2},
  pages = {209 -- 215},
  year = {2015},
  eprint={1501.05928},
  archivePrefix={arXiv},
  primaryClass={physics.ins-det},
  url_arXiv = {http://arxiv.org/abs/1501.05928},
  url_Paper = {http://dx.doi.org/10.1016/j.jsb.2015.06.014},
}

@article{Cao2015,
  author = {Yanshuai Cao and Marcus A. Brubaker and David J. Fleet and Aaron Hertzmann},
  title = {{Efficient Optimization for Sparse Gaussian Process Regression}},
  journal = PAMI,
  volume = {37},
  number = {12},
  pages = {2415 -- 2427},
  year = {2015},
  url_Paper = {Cao2015.pdf},
}

@inproceedings{BrubakerCryoEMCVPR2015,
  author = {Marcus A. Brubaker and Ali Punjani and David J. Fleet},
  title = {{Building Proteins in a Day: Efficient 3D Molecular Reconstruction}},
  booktitle = CVPR,
  year = {2015},
  eprint={1504.03573},
  archivePrefix={arXiv},
  primaryClass={cs.CV},
  url_Paper = {BrubakerCryoEMCVPR2015.pdf},
  url_arXiv = {http://arxiv.org/abs/1504.03573},
  url_Extended_Abstract = {BrubakerCryoEMCVPR2015-ExtAbs.pdf},
  url_GitHub = {https://github.com/mbrubake/cryoem-cvpr2015},
  url_Presentation = {http://techtalks.tv/talks/building-proteins-in-a-day-efficient-3d-molecular-reconstruction/61603/}
}

@inproceedings{BrubakerCryoEMBIC2015,
  author = {Marcus A. Brubaker and Ali Punjani and David J. Fleet},
  title = {{Efficient 3D Macromolecular Reconstruction with Electron Cryomicroscopy}},
  booktitle = {{BioImage Computing Workshop at IEEE Conference on Computer Vision and Pattern Recognition}},
  month = Jun,
  year = {2015},
}

@misc{CarpenterStanAD2015,
  author = {Bob Carpenter and Matthew D. Hoffman and Marcus A. Brubaker and Daniel Lee and Peter Li and Michael Betancourt},
  title = {{The Stan Math Library: Reverse-Mode Automatic Differentiation in C++}},
  archivePrefix = "arXiv",
  eprint = {1509.07164},
  primaryClass = "cs.MS",
  year = {2015},
  url_arXiv = {http://arxiv.org/abs/1509.07164},
}

@inproceedings{Wang2014,
  author = {Yali Wang and Marcus A. Brubaker and Brahim Chaib-draa and Raquel Urtasun},
  title = {{Bayesian Filtering with Online Gaussian Process Latent Variable Models}},
  booktitle = UAI,
  year = {2014},
  url_Paper = {Wang2014.pdf},
}

@inproceedings{BrubakerCryoEMNIPS2014,
  author = {Ali Punjani and Marcus A. Brubaker},
  title = {{Microscopic Advances with Large-Scale Learning: Stochastic Optimization for Cryo-EM}},
  booktitle = {{Neural Information Processing Systems Workshop: Machine Learning in Computational Biology (MLCB)}},
  month = Dec,
  year = {2014},
  eprinttype={arxiv},
  eprint = {1501.04656},
  url_arXiv = {http://arxiv.org/abs/1501.04656},
}

@article{Zhao2013,
  author = {Jianhua Zhao and Marcus A. Brubaker and John L. Rubinstein},
  title = {{TMaCS: A hybrid template matching and classification system for partially-automated particle selection}},
  journal = {Journal of Structural Biology},
  volume = {181},
  number = {3},
  pages = {234 -- 242},
  year = {2013},
  url_Paper = {http://dx.doi.org/10.1016/j.jsb.2012.12.010},
  url_Code = {http://www.sickkids.ca/Research/Rubinstein/Software/index.html},
}

@inproceedings{Cao2013,
  author = {Yanshuai Cao and Marcus A. Brubaker and Aaron Hertzmann and David J. Fleet},
  title = {{Efficient Optimization for Sparse Gaussian Process Regression}},
  booktitle = NeurIPS,
  year = {2013},
  eprint={1310.6007},
  archivePrefix={arXiv},
  primaryClass={cs.LG},
  url_Paper = {Cao2013.pdf},
  url_arXiv = {http://arxiv.org/abs/1310.6007},
  url_Website = {http://www.cs.toronto.edu/~caoy/opt_sgpr},
  url_Proceedings = {http://papers.nips.cc/paper/5087-efficient-optimization-for-sparse-gaussian-process-regression}
}

@inproceedings{Brubaker2013,
  author = {Marcus A. Brubaker and Andreas Geiger and Raquel Urtasun},
  title = {{Lost! Leveraging the Crowd for Probabilistic Visual Self-Localization}},
  booktitle = CVPR,
  year = {2013},
  url_Paper = {Brubaker2013.pdf},
  url_Supplemental = {Brubaker2013-Supplemental.pdf},
  url_Poster = {Brubaker2013-Poster.pdf},
  url_Slides = {Brubaker2013-Slides.pdf},
  url_Presentation = {http://techtalks.tv/talks/lost-leveraging-the-crowd-for-probabilistic-visual-self-localization/58677/},
  url_Video = {Brubaker2013-Video.mp4},
  url_YouTube = {http://youtu.be/4Z3shNPOdQA},
  url_Website = {http://www.cs.toronto.edu/~mbrubake/projects/map},
}

@INPROCEEDINGS{Brubaker2013WS,
  author = {Marcus A. Brubaker  and Andreas Geiger and Raquel Urtasun},
  title = {{Probabilistic Map Localization Through Visual Odometry}},
  booktitle = {{Proceedings of SUNw: Scene Understanding Workshop at IEEE Conference on Computer Vision and Pattern Recognition (CVPRW)}},
  year = {2013},
  url_Paper = {Brubaker2013WS.pdf},
  url_Workshop = {http://sunw.csail.mit.edu/2013},
}

@inproceedings{BrubakerAISTATS2012,
  author = {Marcus A. Brubaker and Mathieu Salzmann and Raquel Urtasun},
  title = {{A Family of {MCMC} Methods on Implicitly Defined Manifolds}},
  booktitle = AISTATS,
  year = {2012},
  url_Paper = {BrubakerAISTATS2012.pdf},
  url_Poster = {BrubakerAISTATS2012-Poster.pdf},
  url_Website = {http://www.cs.toronto.edu/~mbrubake/projects/cmcmc}
}

@PHDTHESIS{BrubakerPhD2011,
  author = {Marcus A. Brubaker},
  title = {{Physical Models of Human Motion for Estimation and Scene Analysis}},
  school = {University of Toronto},
  year = {2011},
  url_Thesis = {PhDThesis.pdf}
}

@article{BrubakerIJCV2010,
  author = {Marcus A. Brubaker and David J. Fleet and Aaron Hertzmann},
  title = {{Physics-based Person Tracking using the Anthropomorphic Walker}},
  journal = IJCV,
  volume = {87},
  pages = {140--155},
  number = {1},
  year = {2010},
  url_Paper = {BrubakerIJCV2010.pdf},
  url_Website = {http://www.cs.toronto.edu/~mbrubake/permanent/awalker}
}

@article{Jaitly2010,
  author = {Navdeep Jaitly and Marcus A. Brubaker and John Rubinstein and Ryan H. Lilien},
  title = {{A Bayesian Method for 3-D Macromolecular Structure Inference using Class Average Images from Single Particle Electron Microscopy}},
  journal = {Bioinformatics},
  year = {2010},
  volume = {26},
  pages = {2406-2415},
  url_Paper = {http://bioinformatics.oxfordjournals.org/cgi/reprint/btq456?ijkey=TR5pnBrtbyXdqN6&keytype=ref},
  url_Website = {http://compbio.cs.toronto.edu/cryoem/}
}

@inproceedings{BrubakerICCV2009,
  author = {Marcus A. Brubaker and Leonid Sigal and David J. Fleet},
  title = {{Estimating Contact Dynamics}},
  booktitle = ICCV,
  year = {2009},
  url_Paper = {BrubakerICCV2009.pdf},
  url_MocapResults = {BrubakerICCV2009-MocapResults.avi},
  url_MocapYouTube = {http://youtu.be/RbL0zx53DQg},
  url_VideoResults = {BrubakerICCV2009-VideoResults.avi},
  url_VideoYouTube = {http://youtu.be/NZ4U8oO--6M},
}

@inproceedings{Jaitly2009,
  author = {Navdeep Jaitly and Marcus A. Brubaker and John Rubinstein and Ryan Lilien},
  title = {{A Bayesian method for 3D reconstruction of macromolecular structure using class averages from single particle electron microscopy}},
  booktitle = {Neural Information Processing Systems Workshop: Machine Learning in Computational Biology (MLCB)},
  month = Dec,
  year = {2009},
}

@incollection{BrubakerAISE2009,
  author = {Marcus A. Brubaker and Leonid Sigal and David J. Fleet},
  title = {{Video-based People Tracking}},
  booktitle = {Handbook on Ambient Intelligence and Smart Environments},
  publisher = {Springer Verlag},
  editor = {H. Nakashima and H. Aghajan and J.C. Augusto},
  year = {2009},
  url_Paper = {BrubakerAISE2009.pdf},
}

@misc{BrubakerICCVTut2009,
  author = {Marcus A. Brubaker and Leonid Sigal and David J. Fleet},
  title = {{Physics-based Human Motion Modelling for people tracking: A short tutorial}},
  howpublished = {Tutorial at IEEE International Conference of Computer Vision, Kyoto,
	Japan},
  year = {2009},
}

@inproceedings{BrubakerCVPR2008,
  author = {Marcus A. Brubaker and David J. Fleet},
  title = {{The Kneed Walker for Human Pose Tracking}},
  booktitle = CVPR,
  year = {2008},
  url_Paper = {BrubakerCVPR2008.pdf},
  url_Video = {BrubakerCVPR2008-Results.avi},
  url_YouTube = {http://youtu.be/-rUM4ZxCD0I},
}

@inproceedings{Brubaker2007,
  author = {Marcus A. Brubaker and David J. Fleet and Aaron Hertzmann},
  title = {Physics-based person tracking using simplified lower-body dynamics},
  booktitle = CVPR,
  year = {2007},
  url_Paper = {BrubakerCVPR2007.pdf},
  url_Video = {BrubakerCVPR2007-Results.avi},
  url_YouTube = {http://youtu.be/IZhl9Fo7eUI},
}

@inproceedings{Brubaker2006,
  author = {Marcus A. Brubaker and David J. Fleet and Aaron Hertzmann},
  title = {{Physics-based Human Pose Tracking}},
  booktitle = {Neural Information Processing Systems Workshop: Evaluation of Articulated Human Motion and Pose Estimation (EHuM)},
  month = Dec,
  year = {2006},
}

@MASTERSTHESIS{BrubakerMSc2006,
  author = {Marcus A. Brubaker},
  title = {Physics-Based Priors for Human Pose Tracking},
  school = {University of Toronto},
  year = {2006},
  url_Thesis = {MScThesis.pdf}
}