Publications

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Preprints

Natalia Martinez, Guillermo Sapiro, Allen R Tannenbaum, Travis J Hollmann, Saad Nadeem. “ImPartial: Partial Annotations for Cell Instance Segmentation.” bioRxiv, 2021.

James Mathews, Cameron Crowe, Rami Vanguri, Margaret Callahan, Travis J Hollmann, and Saad Nadeem. “An exact test for significance of clusters in binary data.” arXiv, 2021.

Journal Papers

J27

Donghoon Lee, Ellen Yorke, Masoud Zarepisheh, Saad Nadeem*, Yu-Chi Hu*. “RMSim: Controlled Respiratory Motion Simulation on Static Patient Scans.” Physics in Medicine & Biology. (Accepted, 2022) * Equal Contribution

J26

Gourav Jhanwar*, Navdeep Dahiya*, Parmida Ghahremani, Masoud Zarepisheh, Saad Nadeem. “Domain knowledge driven 3D dose prediction using moment-based loss function.” Physics in Medicine & Biology. (Accepted, 2022)

J25

Parmida Ghahremani, Yanyun Li, Arie Kaufman, Rami Vanguri, Noah Greenwald, Michael Angelo, Travis J Hollmann, Saad Nadeem. “Deep Learning-Inferred Multiplex ImmunoFluorescence for Immunohistochemistry Image Quantification.” Nature Machine Intelligence, 4: 401-412, 2022.

J24

Rami S. Vanguri, Kathleen M. Fenn, Matthew R. Kearney, Qi Wang, Hua Guo, Douglas K. Marks, Christine Chin, Claire F. Alcus, Julia B. Thompson, Cheng-Shiun Leu, Hanina Hibshoosh, Kevin M. Kalinsky, James C. Mathews, Saad Nadeem, Travis J. Hollmann, Eileen P. Connolly. “Tumor immune microenvironment and response to neoadjuvant chemotherapy in hormone receptor/HER2+ early stage breast cancer.” Clinical Breast Cancer, 2022.

J23

Maryam Pourmaleki, Caitlin J Jones, Charlotte E Ariyan, Zheng Zeng, Mono Pirun, Daniel A Navarrete, Yanyun Li, Mianlei Zhang, Subhiksha Nandakumar, Carl Campos, Saad Nadeem, David S Klimstra, Claire F Temple-Oberle, Thomas Brenn, Evan J Lipson, Kara M Schenk, Julie E Stein, Janis M Taube, Michael G White, Raymond Traweek, Jennifer A Wargo, John M Kirkwood, Billel Gasmi, Stephanie L Goff, Alex D Corwin, Elizabeth McDonough, Fiona Ginty, Margaret K Callahan, Andrea Schietinger, Nicholas D Socci, Ingo K Mellinghoff, Travis J Hollmann. “Tumor MHC Class I Expression Associates with Intralesional Interleukin-2 Response in Melanoma.” Cancer immunology research, 2022.

J22

Shreeraj Jadhav, Mahsa Torkaman, Allen Tannenbaum, Saad Nadeem, and Arie Kaufman. “Volume Exploration Using Multidimensional Bhattacharyya Flow.” IEEE Transactions on Visualization and Computer Graphics. (Accepted, 2021)

J21

Donghoon Lee, Sadegh R Alam, Jue Jiang, Pengpeng Zhang, Yu-Chi Hu*, and Saad Nadeem*. “Deformation Driven Seq2Seq Longitudinal Tumor and Organs-at-Risk Prediction for Radiotherapy.” Medical Physics, 48 (9), 4784-4798, 2021. *Equal Contribution

J20

Navdeep Dahiya, Sadegh R Alam, Pengpeng Zhang, Si-Yuan Zhang, Anthony Yezzi, Saad Nadeem. “Multitask 3D CBCT-to-CT Translation and Organs-at-Risk Segmentation Using Physics-Based Data Augmentation.” Medical Physics, 48 (9), 5130-5141, 2021.

J19

Sadegh R Alam, Tianfang Li, Pengpeng Zhang, Si-Yuan Zhang, and Saad Nadeem. “Generalizable Cone Beam CT Esophagus Segmentation Using Physics-Based Data Augmentation.” Physics in Medicine & Biology, 66(6): 065008, 2021.

J18

Saad Nadeem*, Wookjin Choi*, Sadegh R Alam, Joseph O. Deasy, and Wei Lu. “Reproducible and Interpretable Spiculation Quantification for Lung Cancer Screening.” Computer Methods and Programs in Biomedicine, 200:105839, 2021. *Equal Contribution

J17

Donghoon Lee, Pengpeng Zhang, Saad Nadeem, Sadegh R Alam, Jue Jiang, Amanda Caringi, Natasha Allgood, Michalis Aristophanous, James G Mechalakos, Yuchi Hu. “Predictive dose accumulation for HN adaptive radiotherapy.” Physics in Medicine & Biology, 65(23): 235011, 2020.

J16

Chuang Wang, Sadegh R Alam, Siyuan Zhang, Yuchi Hu, Saad Nadeem, Neelam Tyagi, Andreas Rimner, Wei Lu, Maria Thor, Pengpeng Zhang. “Predicting spatial esophageal changes in a multimodal longitudinal imaging study via a convolutional recurrent neural network.” Physics in Medicine & Biology, 65(23): 235027, 2020.

J15

Saad Nadeem*, Anish K. Simhal*, Kimberly L.H. Carpenter, Joanne Kurtzberg, Allen Song, Allen Tannenbaum, Guillermo Sapiro, and Geraldine Dawson. “Measuring Robustness of Brain Networks in Autism Spectrum Disorder with Ricci Curvature.” Scientific Reports, 10:10819, 2020. *Equal Contribution

J14

James C. Mathews, Saad Nadeem, Maryam Pouryahya, Zehor Belkhatir, Joseph O. Deasy, Arnold J. Levine, and Allen Tannenbaum. “Functional Network Analysis Reveals an Immune Tolerance Mechanism in Cancer.” Proceedings of National Academy of Sciences (PNAS), 117(28):16339-16345, 2020.

J13

Sadegh R Alam, Maria Thor, Andreas Rimner, Neelam Tyagi, Si-Yuan Zhang, Li Cheng Kuo, Saad Nadeem, Wei Lu, Yu-Chi Hu, Ellen Yorke, and Pengpeng Zhang. “Quantification of accumulated dose and associated anatomical changes of esophagus using weekly Magnetic Resonance Imaging acquired during radiotherapy of locally advanced lung cancer.” Physics and Imaging in Radiation Oncology, 13:36-43, 2020.

J12

Saad Nadeem, Pengpeng Zhang, Andreas Rimner, Jan-Jakob Sonke, Joseph O. Deasy, and Allen Tannenbaum. “LDeform: Longitudinal Deformation Analysis for Adaptive Radiotherapy of Lung Cancer.” Medical Physics, 47(1):132-141, 2020.

J11

Sunil Koundal*, Rena Elkin*, Saad Nadeem, Yuechuan Xue, Stefan Constantinou, Simon Sanggaard, Xiaodan Liu, Brittany Monte, Feng Xu, William Van Nostrand, Maiken Nedergaard, Hedok Lee, Joanna Wardlaw, Helene Benveniste, and Allen Tannenbaum. “Glymphatic Optimal Mass Transport with Lagrangian Workflow Reveals Advective and Diffusion Driven Solute Transport.” Scientific Reports, 10(1):1-18, 2020. *Equal Contribution

J10

Saad Nadeem*, Rena Elkin*, Eve LoCastro, Ramesh Paudyal, Nancy Y. Lee, Amita Shukla-Dave, Joseph O. Deasy, and Allen Tannenbaum. “Optimal Mass Transport Kinetic Modeling for Head and Neck DCE-MRI: Initial Analysis.” Magnetic Resonance in Medicine, 82:2314-2325, 2019. *Equal Contribution

J9

Ji Hwan Park, Saad Nadeem, Saeed Boorboor, Joseph Marino, and Arie Kaufman. “CMed: Crowd Analytics for Medical Imaging Data.” IEEE Transactions on Visualization and Computer Graphics, 27(6): 2869 – 2880, 2019.

Supplementary Video

J8

James C. Mathews, Saad Nadeem, Arnold J. Levine, Maryam Pouryahya, Joseph O. Deasy, and Allen Tannenbaum. “Robust and Interpretable PAM50 Reclassification Exhibits Survival Advantage for Myoepithelial and Immune Phenotypes.” npj Breast Cancer, 5(30):1-9, 2019.

J7

Shreeraj Jadhav, Saad Nadeem, and Arie Kaufman. “FeatureLego: Volume Exploration Using Exhaustive Clustering of Super-Voxels.” IEEE Transactions on Visualization and Computer Graphics, 25(9): 2725-2737, 2019.

Supplementary Video

J6

Ming Ma, Joseph Marino, Saad Nadeem, and Xianfeng Gu. “Supine to Prone Colon Registration and Visualization Based on Optimal Mass Transport.” Graphical Models, 104(7):101031, 2019.

J5

Ji Hwan Park, Saad Nadeem, and Arie Kaufman. “GeoBrick: Exploration of Spatio-Temporal Data.” The Visual Computer, 35(2):191-204, 2019.

J4

Saad Nadeem, Xianfeng Gu, and Arie Kaufman. “LMap: Shape-Preserving Local Mappings for Biomedical Visualization.” IEEE Transactions on Visualization and Computer Graphics, 24(12): 3111-3122, 2018.

J3

Liang Shen, Dengming Zhu, Saad Nadeem, Zhaoqi Wang, and Arie Kaufman. “Radiative Transport Based Flame Volume Reconstruction from Videos.” IEEE Transactions on Visualization and Computer Graphics, 24(7): 2209-2222, 2018.

J2

Saad Nadeem, Zhengyu Su, Wei Zeng, Arie Kaufman, and Xianfeng Gu. “Spherical Parameterization Balancing Angle and Area Distortions.” IEEE Transactions on Visualization and Computer Graphics, 23(6):1663–1676, 2017.

J1

Saad Nadeem, Joseph Marino, Xianfeng Gu, and Arie Kaufman. “Corresponding Supine and Prone Colon Visualization Using Eigenfunction Analysis and Fold Modeling.” IEEE Transactions on Visualization and Computer Graphics, 23(1): 751-760, 2017.

Conference Proceedings

C21

Wookjin Choi, Navdeep Dahiya, Saad Nadeem. “CIRDataset: A large-scale Dataset for Clinically-Interpretable lung nodule Radiomics and malignancy prediction.” International Conference on Medical Imaging Computing and Computer Assisted Intervention (MICCAI), 2022.

C20

Shawn Mathew*, Saad Nadeem*, Arie Kaufman. “CLTS-GAN: Color-Lighting-Texture-Specular Reflection Augmentation for Colonoscopy.” International Conference on Medical Imaging Computing and Computer Assisted Intervention (MICCAI), 2022. *Equal Contribution

C19

Parmida Ghahremani*, Joseph Marino*, Ricardo Dodds*, Saad Nadeem. “DeepLIIF: An Online Platform for Quantification of Clinical Pathology Slides.” Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), pp. 21399-21405, 2022. *Equal Contribution

C18

Saad Nadeem*, Shawn Mathew*, and Arie Kaufman. “FoldIt: Haustral Folds Detection and Segmentation in Colonoscopy Videos.” International Conference on Medical Imaging Computing and Computer Assisted Intervention (MICCAI), 12903: 221-230, 2021 (Early Accept, Oral). *Equal Contribution

Supplementary Video

C17

Saad Nadeem*, Shawn Mathew*, and Arie Kaufman. “Visualizing Missing Surfaces In Colonoscopy Videos using Shared Latent Space Representations.” International Symposium on Biomedical Imaging (ISBI), 329-333, 2021. *Equal Contribution

Supplementary Video

C16

Saad Nadeem, Travis Hollmann, and Allen Tannenbaum. “Multimarginal Wasserstein Barycenter for Stain Normalization and Augmentation.” International Conference on Medical Imaging Computing and Computer Assisted Intervention (MICCAI), pp. 362-371, 2020.

C15

Rena Elkin, Saad Nadeem, Hedok Lee, Helene Benveniste, and Allen Tannenbaum. “Fisher-Rao Regularized Transport Analysis of the Glymphatic System and Waste Drainage.” International Conference on Medical Imaging Computing and Computer Assisted Intervention (MICCAI), pp. 573-582, 2020.

C14

Donghoon Lee, Sadegh R Alam, Saad Nadeem, Jue Jiang, Pengpeng Zhang, Yu-Chi Hu. “Longitudinal Prediction of Radiation-Induced Anatomical Changes of Parotid Glands During Radiotherapy Using Deep Learning.” MICCAI Workshop on PRedictive Intelligence In Medicine, pp. 123-132, 2020.

C13

Saad Nadeem*, Shawn Mathew*, Sruti Kumari, and Arie Kaufman. “Augmenting Colonoscopy using Extended and Directional CycleGAN for Lossy Image Translation.” IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pp. 4696-4705, 2020. *Equal Contribution

Supplementary Video

C12

Rena Elkin, Saad Nadeem, Eldad Haber, Klara Steklova, Hedok Lee, Helene Benveniste, and Allen Tannenbaum. “GlymphVIS: Visualizing Glymphatic Transport Pathways Using Regularized Optimal Transport.” International Conference on Medical Imaging Computing and Computer Assisted Intervention (MICCAI), 2018.

C11

Saad Nadeem*, Wookjin Choi*, Sadegh R Alam, Wei Lu, Joseph O. Deasy, and Allen Tannenbaum. “Interpretable Spiculation Quantification for Lung Cancer Screening.” MICCAI Workshop: Shape in Medical Imaging, 2018. *Equal Contribution (Oral Presentation)

C10

Sadegh R Alam, Wookjin Choi, Chia-Ju Liu, Saad Nadeem, Shan Tan, Hualiang Zhong, Wengen Chen, Abraham J. Wu, James G. Mechalakos, Joseph O. Deasy, and Wei Lu. “Quantification of Local Metabolic Tumor Volume Changes by Registering Blended PET-CT Images for Prediction of Pathologic Tumor Response.” MICCAI Workshop: Data-Driven Treatment Response Assessment, 2018. (Best Paper Award, Oral Presentation)

C9

Ji Hwan Park, Saad Nadeem, Joseph Marino, Kevin Baker, Matthew Barish, and Arie Kaufman. “Crowd-Assisted Polyp Annotation of Virtual Colonoscopy Videos.” SPIE Medical Imaging, 105790–105790-7, 2018 (Oral Presentation).

C8

Saeed Boorboor, Saad Nadeem, Ji Hwan Park, Kevin Baker, and Arie Kaufman. “Crowdsourcing Lung Nodules Detection and Annotation.” SPIE Medical Imaging, 105790–105790-7, 2018.

C7

Ji Hwan Park, Seyedkoosha Mirhosseini, Saad Nadeem, Joseph Marino, Arie Kaufman, Kevin Baker, and Matthew Barish. “Crowdsourcing for Identification of Polyp-Free Segments in Virtual Colonoscopy Videos.” SPIE Medical Imaging, 2017 (Oral Presentation).

C6

Ji Hwan Park, Saad Nadeem, Seyedkoosha Mirhosseini, and Arie Kaufman. “C2A: Crowd Consensus Analytics for Virtual Colonoscopy.” Proceedings of IEEE Visualization (VAST), 2016.

C5

Saad Nadeem and Arie Kaufman. “Multimodal Brain Visualization.” SPIE Medical Imaging, pp. 97881Y–97881Y, 2016.

C4

Saad Nadeem and Arie Kaufman. “Computer-Aided Detection of Polyps in Optical Colonoscopy Images.” SPIE Medical Imaging, pp. 978525–978525, 2016.

C3

Saad Nadeem and Arie Kaufman. “Visualization Framework for Colonoscopy Videos.” SPIE Medical Imaging, pp. 97861T–97861T, 2016.

C2

Saad Nadeem and Arie Kaufman. “Shape-based Multifeature Brain Parcellation.” SPIE Medical Imaging, pp. 978430–978430, 2016.

C1

Konstantin Dmitriev, Ievgeniia Gutenko, Saad Nadeem, and Arie Kaufman. “Pancreas and Cyst Segmentation.” SPIE Medical Imaging, pp. 97842C–97842C, 2016.

Patents

P7

Saad Nadeem, Yu-Chi Hu, Donghoon Lee, Pengpeng Zhang, and Sadegh R Alam. “Simulating realistic biomechanical motion for reduced-margins lung radiotherapy.”

[Provisional Patent Filed]

P6

Saad Nadeem and Travis J. Hollmann. “Virtual Multiplex Immunofluorescence Staining of Pathology Slides.”

[Provisional Patent Filed]

P5

Saad Nadeem. “Color Normalization and Augmentation for Robust and Generalizable Biomedical Image Analysis.”

[Provisional Patent Filed]

P4

Saad Nadeem, Sadegh R Alam, Tianfang Li, and Pengpeng Zhang. “Physics-Based CT and Cone Beam CT Quantification.”

[Provisional Patent Filed]

P3

Saad Nadeem, Maria Thor, Wookjin Choi, and Joseph O. Deasy. “An Image-Based Predictive Model for Recurrence in Early-Stage Non-Small Cell Lung Cancer.”

[Provisional Patent Filed]

P2

Saad Nadeem, Arie Kaufman, and Shawn Mathew. “Augmenting Colonoscopy Using Machine Learning.”

[Provisional Patent Filed]

P1

James Mathews, Saad Nadeem, Zehor Belkhatir, Maryam Pouryahya, Joseph O. Deasy, Arnold Levine, and Allen Tannenbaum. “De-cloaking cancer from the immune system via antibodies to cancer-produced pregnancy specific glycoprotein (PSK).”

[Provisional Patent Filed]