Key Publications

Key Publications

ALL Publications

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Kutsev Bengisu Ozyoruk, Sermet Can, Berkan Darbaz, Kayhan Başak, Derya Demir, Guliz Irem Gokceler, Gurdeniz Serin, Uguray Payam Hacisalihoglu, Emirhan Kurtuluş, Ming Y. Lu, Tiffany Y. Chen, Drew F. K. Williamson, Funda Yılmaz, Faisal Mahmood, and Mehmet Turan and “Fast and scalable search of whole-slide images via self-supervised deep learning”

Nature Biomedical Engineering 2022

Publisher’s Link

Chengkuan Chen, Ming Y. Lu, Drew F. K. Williamson, Tiffany Y. Chen, Andrew J. Schaumberg, and Faisal Mahmood, “Fast and scalable search of whole-slide images via self-supervised deep learning”

Nature Biomedical Engineering 2022

Publisher’s Link Code HMS News

Richard J. Chen, Ming Y. Lu, Drew F.K. Williamson, Tiffany Y. Chen, Jana Lipkova, Zahra Noor, Muhammad Shaban, Maha Shady, Mane Williams, Bumjin Joo, and Faisal Mahmood, “Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning”

Cancer Cell 2022

Publisher’s Link Code Demo News Preview Animated Abstract

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 Preview Animated Abstract

Richard J. Chen, Chengkuan Chen, Yicong Li, Tiffany Y. Chen, Andrew D. Trister, Rahul G. Krishnan, and Faisal Mahmood, “Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning”

CVPR 2022 (Oral)

Publisher’s Link Code Oral Talk Video

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 Preview Animated Abstract

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

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

ICCV 2021

Publisher’s Link Article Supplement Code

Richard J. Chen, Ming Y. Lu, Jingwen Wang, Drew F. K. Williamson, Scott J. Rodig, Neal I. Lindeman, and Faisal Mahmood, “Pathomic Fusion: An Integrated Framework for Fusing Histopathology and Genomic Features for Cancer Diagnosis and Prognosis”

IEEE Transactions on Medical Imaging 2021

Publisher’s Link Nvidia News Video Code

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

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

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

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

Publisher’s Link

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

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

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

Taylor L. Bobrow, Faisal Mahmood, Miguel Inserni, Nicholas J. Durr, “DeepLSR: a deep learning approach for laser speckle reduction”

Biomedical Optics Express 2019

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

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

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

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

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

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

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

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

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

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

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