Key Publications

Key Publications
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Ming Y. Lu, Bowen Chen, Drew F. K. Williamson, Richard J. Chen, Melissa Zhao, Aaron K. Chow, Kenji Ikemura, Ahrong Kim, Dimitra Pouli, Ankush Patel, Amr Soliman, Chengkuan Chen, Tong Ding, Judy J. Wang, Georg Gerber, Ivy Liang, Long Phi Le, Anil V. Parwani, Luca L. Weishaupt & Faisal Mahmood* and “A Multimodal Generative AI Copilot for Human Pathology”

Nature 2024

Publisher’s Link STAT News Nature Biotech News Nature News Nature Briefing
Andrew H. Song, Mane Williams, Drew F.K. Williamson, Sarah S.L. Chow, Guillaume Jaume, Gan Gao, Andrew Zhang, Bowen Chen, Alexander S. Baras, Robert Serafin, Richard Colling, Michelle R. Downes, Xavier Farré, Peter Humphrey, Clare Verrill, Lawrence D. True, Anil V. Parwani, Jonathan T.C. Liu* & Faisal Mahmood* and “Analysis of 3D pathology samples using weakly supervised AI”

Cell 2024

Publisher’s Link Code MGB News
Anurag Vaidya, Richard J. Chen, Drew F. K. Williamson, Andrew H. Song, Guillaume Jaume, Yuzhe Yang, Thomas Hartvigsen, Emma C. Dyer, Ming Y. Lu, Jana Lipkova, Muhammad Shaban, Tiffany Y. Chen & Faisal Mahmood* and “Demographic bias in misdiagnosis by computational pathology models”

Nature Medicine 2024

Publisher’s Link Code HMS News
Richard J. Chen, Tong Ding, Ming Y. Lu, Drew F. K. Williamson, Guillaume Jaume, Andrew H. Song, Bowen Chen, Andrew Zhang, Daniel Shao, Muhammad Shaban, Mane Williams, Lukas Oldenburg, Luca L. Weishaupt, Judy J. Wang, Anurag Vaidya, Long Phi Le, Georg Gerber, Sharifa Sahai, Walt Williams, & Faisal Mahmood* and “Towards a general-purpose foundation model for computational pathology”

Nature Medicine 2024

Publisher’s Link Code HMS News
Ming Y. Lu, Bowen Chen, Drew F. K. Williamson, Richard J. Chen, Ivy Liang, Tong Ding, Guillaume Jaume, Igor Odintsov, Long Phi Le, Georg Gerber, Anil V. Parwani, Andrew Zhang and Faisal Mahmood* “A visual-language foundation model for computational pathology”

Nature Medicine 2024

Publisher’s Link Code HMS News
Muhammad Shaban, Yunhao Bai, Huaying Qiu, Shulin Mao, Jason Yeung, Yao Yu Yeo, Vignesh Shanmugam, Han Chen, Bokai Zhu, Jason L. Weirather, Garry P. Nolan, Margaret A. Shipp, Scott J. Rodig, Sizun Jiang* and Faisal Mahmood* “MAPS: pathologist-level cell type annotation from tissue images through machine learning”

Nature Communications 2024

Publisher’s Link Code Data
Richard J. Chen, Judy J. Wang, Drew F. K. Williamson, Tiffany Y. Chen, Jana Lipkova, Ming Y. Lu, Sharifa Sahai and Faisal Mahmood* and “Algorithmic fairness in artificial intelligence for medicine and healthcare”

Nature Biomedical Engineering 2023

Publisher’s Link
Andrew H. Song, Guillaume Jaume, Drew F. K. Williamson, Ming Y. Lu, Anurag Vaidya, Tiffany R. Miller and Faisal Mahmood*, ” Artificial intelligence for digital and computational pathology “

Nature Reviews Bioengineering

Publisher’s Link
Ming Y. Lu, Bowen Chen, Andrew Zhang, Drew F. K. Williamson, Richard J. Chen, Tong Ding, Long Phi Le, Yung-Sung Chuang, and Faisal Mahmood*, ” Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images “

CVPR 2023

Publisher’s Link
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 “A deep-learning model for transforming the style of tissue images from cryosectioned to formalin-fixed and paraffin-embedded”

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

arXiv Code
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

arXiv
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