Publications

  • Publications

Selected Journal Publications

Jana Lipkova, Tiffany Y. Chen, Ming Y. Lu, Richard J. Chen, Maha Shady, Mane Williams, Jingwen Wang, Zahra Noor, Richard N. Mitchell, Mehmet Turan, Gulfize Coskun, Funda Yilmaz, Derya Demir, Deniz Nart, Kayhan Basa, Nesrin Turhan, Selvinaz Ozkara, Yara Banz, Katja E. Odening, and Faisal Mahmood, "Deep learning-enabled assessment of cardiac allograft rejection from endomyocardial biopsies"

Nature Medicine 2022

Publisher's Link Code Demo News
nat_medicine
Ming Y. Lu, Tiffany Y. Chen, Drew F. K. Williamson, Melissa Zhao, Maha Shady, Jana Lipkova and Faisal Mahmood, "AI-based Pathology Predicts Origins for Cancers of Unknown Primary"

Nature 2021

Publisher's Link Code Demo News
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Ming Y. Lu, Drew F. K. Williamson, Tiffany Y. Chen, Richard J. Chen, Matteo Barrberi and Faisal Mahmood, "Data Efficient and Weakly Supervised Computational Patholog on Whole Slide Images"

Nature Biomedical Engineering 2021

arXiv Publisher's Link Code Demo
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Richard J. Chen, Ming Y. Lu, Jingwen Wang, Drew F. K. Williamson, Scott J. Rodig, Neal I. Lindeman, Faisal Mahmood, "Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis"

IEEE Transactions on Medical Imaging 2021

arXiv Publisher's Link Code Video Media Coverage
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Ming Y. Lu, Dehan Kong, Jana Lipkova, Richard J. Chen, Rajendra Singh, Drew F. K. Williamson, Tiffany Y. Chen, & Faisal Mahmood, "Federated Learning for Computational Pathology on Gigapixel Whole Slide Images"

Medical Image Analysis 2021

arXiv Publisher's Link Code
MedIA
Richard J. Chen, Ming Y. Lu, Tiffany Y. Chen, Drew F. K. Williamson & Faisal Mahmood, "Synthetic data in machine learning for medicine and healthcare"

Nature Biomedical Engineering 2021

Publisher's Link
UBVtI35V_400x400
Kutsev Bengisu Ozyoruk, Guliz Irem Gokceler, Taylor L.Bobrow, Gulfize Coskuna, Kagan Incetana, Yasin Almalioglu, Faisal Mahmood, Eva Curto, Luis Perdigoto, Marina Oliveira, Hasan Sahin, Helder Araujo, Henrique Alexandrino, Nicholas J.Durr, Hunter B.Gilbert, Mehmet Turan, "EndoSLAM dataset and an unsupervised monocular visual odometry and depth estimation approach for endoscopic videos"

Medical Image Analysis 2020

Publisher's Link
MedIA
Yasin Almalioglu, Kutsev Bengisu Ozyoruk, Abdulkadir Gokce, Kagan Incetan, Guliz Irem Gokceler, Muhammed Ali Simsek, Kivanc Ararat, Richard J. Chen, Nicholas J. Durr, Faisal Mahmood, Mehmet Turan, "EndoL2H: Deep Super-Resolution for Capsule Endoscopy"

IEEE Transactions on Medical Imaging 2020

arXiv Publisher's Link
TMI_Cover
Mason T. Chen, Faisal Mahmood, Faisal Mahmood, Jordan A. Sweer, Nicholas J. Durr "GANPOP: Generative Adversarial Network Prediction of Optical Properties from Single Snapshot Wide-field Images"

IEEE Transactions on Medical Imaging 2019

arXiv Publisher's Link Code
TMI_Cover
Mehmet Turan, Yasin Almalioglu, Hunter B. Gilbert, Faisal Mahmood, Nicholas J. Durr, Helder Araujo, Alp Eren Sarı, Anurag Ajay, and Metin Sitti, "Learning to Navigate Endoscopic Capsule Robots"

IEEE Robotics and Automation Letters 2019.

Publisher's Link Code
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Faisal Mahmood, Daniel Borders, Richard Chen, Gregory N. McKay, Kevan J. Salimian, Alexander Baras, and Nicholas J. Durr. "Deep Adversarial Training for Multi-Organ Nuclei Segmentation in Histopathology Images."

IEEE Transactions on Medical Imaging 2019

Publisher's Link arXiv Code
TMI_Cover
Taylor L. Bobrow, Faisal Mahmood, Miguel Inserni, Nicholas J. Durr, "DeepLSR: a deep learning approach for laser speckle reduction"

Biomedical Optics Express 2019

Publisher's Link arXiv Code
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Gregory N. McKay, Faisal Mahmood, Nicholas J. Durr, ”Large dynamic range autorefraction with a low-cost diffuser wavefront sensor"

Biomedical Optics Express 2019

Publisher's Link arXiv Reviews Media Coverage
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Faisal Mahmood, Richard Chen, Nicholas J. Durr, ”Unsupervised Reverse Domain Adaption for Synthetic Medical Images via Adversarial Training"

IEEE Transactions on Medical Imaging 2018

Publisher's Link arXiv Reviews Media Coverage
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Faisal Mahmood, N.Durr, ”Deep Learning and Conditional Random Fields-based Depth Estimation and Topographical Reconstruction from Conventional Endoscopy”

Medical Image Analysis 2018

Publisher's Link arXiv Reviews
MedIA
Faisal Mahmood, R. Chen , S. Sudarsky, D. Yu, N. Durr, Deep Learning with Cinematic Rendering:Fine-Tuning Deep Neural Networks Using Photorealistic Medical Images

Physics in Medicine and Biology 2018

Publisher's Link arXiv Reviews Media Coverage
PMB_Cover
Faisal Mahmood, N. Shahid, U. Skoglund et al., ”Adaptive Graph-based Total Variation for Tomographic Reconstructions”

IEEE Signal Processing Letters 2017

Publisher's Link arXiv Reviews Code
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Faisal Mahmood, L.G. ¨Ofverstedt, U. Skoglund et al., ”An Extended Field-based Method for Noise Removal from Electron Tomographic Reconstructions”

IEEE Access 2017

Publisher's Link Reviews
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Faisal Mahmood, M. Toots, L.G. ¨Ofverstedt, U. Skoglund et al., ”Algorithm and Architecture Optimization for 2D Discrete Fourier Transforms with Simultaneous Edge Artifact Removal”

International Journal of Reconfigurable Computing 2017

Publisher's Link Reviews
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D. Mohan, P. Kumar, Faisal Mahmood, J. Dauwels et al., ”Effect of Subliminal Priming on Subjective Perception of Images: A Machine Learning Approach”

PLoS One 2016

Publisher's Link Reviews Data
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Peer Reviewed Conference Publications

Richard J. Chen, Ming Y. Lu, Wei-Hung Weng, Tiffany Y. Chen, Drew F.K. Williamson, Trevor Manz, Maha Shady, Faisal Mahmood, ”Multimodal Co-Attention Transformer for Survival Prediction in Gigapixel Whole Slide Images”

ICCV 2021

arXiv Publisher's Link Code
iccv2021
Jingwen Wang, Ming Y. Lu, Richard J. Chen,Faisal Mahmood, ”Weakly Supervised Prostate TMA Classification via Graph Convolutional Networks”

IEEE International Symposium on Biomedical Imaging 2020

arXiv
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Ming Y. Lu, Richard J. Chen, Jingwen Wang, Debora Dillon, Faisal Mahmood, ”Semi-Supervised Histology Classification using Deep Multiple Instance Learning and Contrastive Predictive Coding”

NeurIPS Machine Learning for Healthcare (ML4H) Workshop 2019

Publisher's Link arXiv
ML4H
Richard J. Chen, Taylor L. Bobrow, Thomas Athey, Faisal Mahmood, N.J. Durr, ”SLAM Endoscopy enhanced by adversarial depth prediction ”

2019 KDD Workshop on Applied Data Science for Healthcare

Publisher's Link arXiv
KDD19
Faisal Mahmood, Wenhao Xu, Nicholas J. Durr, Jeremiah W. Johnson, Alan Yuille, ”Structured Prediction using cGANs with Fusion Discriminator”

2019 ICLR Workshop on Deep Generative Models for Highly Structured Data

Publisher's Link arXiv Reviews
ICLR
Faisal Mahmood, N.Durr, ”Topographical Reconstructions from Monocular Optical Colonoscopy Images via Deep Learning”

IEEE International Conference on Biomedical Imaging (ISBI), 2018

Publisher's Link arXiv Reviews Code
IEEE-ISBI
Faisal Mahmood, N.Durr, ”Deep Learning-based Depth Estimation from a Synthetic Endoscopy Image Training Set”

Proceedings of SPIE Medical Imaging 2018

Publisher's Link arXiv Reviews Code
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D. Bailey, Faisal Mahmood, U. Skoglund, ”Reducing the Cost of Removing Border Artifacts in Fourier Transforms”

CInternational Symposium on Highly Efficient Accelerators and Reconfigurable Technologies (HEART 2017), Bochum, Germany

Publisher's Link arXiv Reviews Code
Faisal Mahmood, N. Shahid, P. Vandergheynst U. Skoglund, ”Graph-based Sinogram denoising for Tomographic Reconstructions”

38th IEEE Engineering in Medical & Biology Conference (EMBC) 2016, Orlando, FL

Publisher's Link arXiv Reviews Code
Faisal Mahmood, M. Toots, U. Skoglund et al., ”2D Fast Fourier Transforms with Edge Artifact Removal using Optimized Periodic Plus Smooth Decomposition for Real-Time Applications”

IEEE Field Programmable Technology (FPT) 2015 Queenstown, New Zealand

Publisher's Link arXiv Reviews Code
P. Kumar, Faisal Mahmood, J. Dauwels et al., ”On the Effect of Subliminal Priming on Subjective Perception of Images: A Machine Learning Approach”

IEEE Engineering in Medicine and Biology (EMBC) 2014, Chicago, IL

Publisher's Link arXiv Reviews Code
Faisal Mahmood, A. Zia et al., ”An Intelligent Approach for Generation of Muscular Electrotherapy Stimulation Waveforms”

IEEE EMB BHI 2012, Shenzen, China & Hong Kong, SAR

Publisher's Link arXiv Reviews Code
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Patents

Faisal Mahmood, L.G. ¨Ofverstedt & U. Skoglund, ”Extended Field Iterative Reconstruction Technique (EFIRT) for Correlated Noise Removal from 3D Reconstructions” US Grant: US 14/770,245 PCT: PCT/JP2014/001214
Google Patents USPTO Link
OE3004
Faisal Mahmood, M. Toots, L.G. Ofverstedt & U. Skoglund, ”2D Discrete Fourier Transform With Simultaneous Edge Artifact Removal For Real-Time Applications” PCT Application Number: PCT/JP2016/003401
Google Patents USPTO Link
OE3004
Nicholas J. Durr, Taylor L. Bobrow, Faisal Mahmood “Deep Learning based Laser Speckle Reduction for Imaging" [Provisional Patent Filed]
OE3004
Nicholas J. Durr, Faisal Mahmood and G. McKay “Computational Lightfield Ophthalmoscope - Lensless Simulta- neous Aberration Correction and Retinal Imaging” [Provisional Patent Filed]
OE3004

Dissertation

Algorithmic and Architectural Developments for Cryo-Electron Tomography.

PhD Thesis

OIST Repository Link
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