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UF Health University of Florida
Medical Imaging Research for Translational Healthcare with Artificial Intelligence Laboratory Department of Medicine in the College of Medicine

Publications

Journal Papers

  1. Ates, G. C., Xin, Y., Gong, K., and Shao, W. DCFormer: Efficient 3D Vision-Language Modeling with Decomposed Convolutions 2025. (Under review in Nature Biomedical Engineering)
  2. Xin, Y., Ates, G. C., Gong, K., and Shao, W. Med3DVLM: An Efficient Vision-Language Model for 3D Medical Image Analysis. 2025. (Under review in IEEE Journal of Biomedical and Health Informatics)
  3. Imran, M., Krebs, J. R., Sivaraman, V. B., Zhang, T., Kumar, A., Ueland, W. R., Fassler, M. J., Huang, J., Sun, X., Wang, L., Shi, P., Rokuss, M., Baumgartner, M., Kirchhof, Y., Maier-Hein, K. H., Isensee, F., Liu, S., Han, B., Nguyen, B. T., Shin, D., Park, J.-W., Choi, M., Uhm, K.-H., Ko, S.-J., Lee, C., Chun, J., Kim, J. S., Zhang, M., Zhang, H., You, X., Gu, Y., Pan, Z., Liu, X., Liang, X., Tiefenthaler, M., Almar-Munoz, E., Schwab, M., Kotyushev, M., Epifanov, R., Wodzinski, M., Muller, H., Qayyum, A., Mazher, M., Niederer, S. A., Wang, Z., Yang, K., Ren, J., Korreman, S. S., Gao, Y., Zeng, H., Zheng, H., Zheng, R., Yue, J., Zhou, F., Liu, B., Cosman, A., Liang, M., Zhao, C., Upchurch, G. R. Jr., Ma, J., Zhou, Y., Cooper, M. A., Shao, W. Multi-Class Segmentation of Aortic Branches and Zones in Computed Tomography Angiography: The AortaSeg24 Challenge. 2025. (Under review in Medical Image Analysis)
  4. Jiang, H., Imran, M., Zhang, T., Zhou, Y., Liang, M., Gong, K. and Shao, W. Fast Denoising Diffusion Probabilistic Model for Medical Image-to-Image Generation. IEEE Journal of Biomedical and Health Informatics (Impact Factor: 6.7), 2025.
  5. Yu, B., Ozdemir, S., Dong, Y., Shao, W., Pan, T., Shi, K., and Gong, K. Robust Whole-body PET Image Denoising Using 3D Diffusion Models: Evaluation Across Various Scanners, Tracers, and Dose Levels. European Journal of Nuclear Medicine and Molecular Imaging (Impact Factor: 8.6), 2025.
  6. Sivaraman, V.B., Imran, M., Wei, Q., Muralidharan, P., Tamplin, M.R., Grumbach, I.M., Kardon, R.H., Wang, J., Zhou, Y., and Shao, W. RetinaRegNet: A zero-shot approach for retinal image registration. Computers in Biology and Medicine (Impact Factor: 7.0, 91% in Computer Science Applications), 2025.
  7. Imran, M., Krebs, J.R., Gopu, V.R.R., Fazzone, B., Sivaraman, V.B., Kumar, A., Viscardi, C., Heithaus, R.E., Shickel, B., Zhou, Y., Cooper, M.A., and Shao, W. CIS-UNet: Multi-Class Segmentation of the Aorta in Computed Tomography Angiography via Context-Aware Shifted Window Self-Attention. Computerized Medical Imaging and Graphics (Impact Factor: 5.4, 93% in Radiology, Nuclear Medicine and Imaging), 2024.
  8. Carrizales, J.W., Flakus, M.J., Fairbourn, D.D., Shao, W., Gerard, S.E., Bayouth, J.E., and Christensen, G.E., Reinhardt, J.M. 4DCT Image Artifact Detection Using Deep Learning. Medical Physics (Impact Factor: 4.5), 2024.
  9. Kumar, A., Jiang, H., Imran, M., Valdes, C., Leon, G., Kang, D., Nataraj, P., Zhou, Y., Weiss, M. D., and Shao, W. A Flexible 2.5D Medical Image Segmentation Approach with In-Slice and Cross-Slice Attention. Computers in Biology and Medicine (Impact Factor: 7.0, 91% in Computer Science Applications), 2024.
  10. Imran, M., Haq, B., Elbasi, E., Topcu, A. E., Shao, W. Transformer Based Hierarchical Model for Non-Small Cell Lung Cancer Detection and Classification. IEEE Access (Impact Factor: 3.9), 2024.
  11. Bitton, R.*, Shao, W.*, Chodakiewitz, Y. G., Brunsing, R. L., Sonn, G., Rusu, M., and Ghanouni, P. Intra-procedural diffusion weighted imaging predicts ablation zone during MRI guided focused ultrasound of prostate cancer. Radiology: Imaging Cancer (Impact Factor: 5.6, 92% in Radiology, Nuclear Medicine and Medical Imaging ), 2024.
  12. Imran, M., Nguyen, B., Pensa, J., Falzarano, S.M., Sisk, A.E., Liang, M., DiBianco, J.M., Su, L.M., Zhou, Y., Brisbane, W.G., and Shao, W. Image Registration of In Vivo Micro-Ultrasound and Ex Vivo Pseudo-Whole Mount Histopathology Images of the Prostate: A Proof-of-Concept Study. Biomedical Signal Processing and Control (Impact Factor: 4.9, 85% in Health Informatics), 2024.
  13. Zhou, S. R., Choi, M. H., Vesal, S., Kinnaird, A., Brisbane, W. G., Lughezzani, G., Maffei, D., Fasulo, V., Albers, P., Zhang, L., Kornberg, Z., Fan, R. E., Shao, W., Rusu, M., and Sonn, G. A. Inter-reader agreement of prostate cancer detection using micro-ultrasound: a multi-institutional study. European Urology Open Science (Impact Factor: 3.2, 60% in Urology), 2024.
  14. Krebs, J. R., Imran, M., Fazzone, B., Viscardi, C., Berwick, B., Stinson, G., Heithaus, E., Upchurch Jr., G. R., Shao, W., and Cooper, M. A. Volumetric Analysis of Acute Uncomplicated Type B Aortic Dissection Using an Automated Deep Learning Aortic Zone Segmentation Model. Journal of Vascular Surgery (Impact Factor: 3.9, 96% in Surgery), 2024.
  15. Shao, W., Vesal, S., Soerensen, S. J. C., Bhattacharya, I., Golestani, N., Yamashita, R., Kunder, C. A., Fan, R. E., Ghanouni, P., Brooks, J. D., Sonn, G. A., and Rusu, M. RAPHIA: A deep learning pipeline for the registration of MRI and whole-mount histopathology images of the prostate. Computers in Biology and Medicine (Impact Factor: 7.0, 91% in Computer Science Applications), 2024.
  16. Jiang, H., Imran, M., Muralidharan, P., Patel, A., Pensa, J., Liang, M., Benidir, T., Grajo, J.R., Joseph, J.P., Terry, R., DiBianco, J.M., Su, L.M., Zhou, Y., Brisbane, W.G., and Shao, W. MicroSegNet: A Deep Learning Approach for Prostate Segmentation on Micro-Ultrasound Images. Computerized Medical Imaging and Graphics (Impact Factor: 5.4, 93% in Radiology, Nuclear Medicine and Imaging), 2024.
  17. Xu, J., He, X., Shao, W., Bian, J., and Terry, R. Classification of Benign and Malignant Renal Tumors Based on CT Scans and Clinical Data Using Machine Learning Methods. Informatics (Impact Factor: 3.4), 2023.
  18. Priester, A., Fan, R. E., Shubert, J., Rusu, M., Vesal, S., Shao, W., Khandwala, Y. S., Marks, L. S., Natarajan, S., and Sonn, G. A. Prediction and Mapping of Intraprostatic Tumor Extent with Artificial Intelligence. European Urology Open Science (Impact Factor: 3.2, 60% in Urology), 2023.
  19. Flakus, M. J., Wuschner, A. E., Wallat, E. M., Shao, W., Meudt, J., Shanmuganayagam, D., Christensen, G. E., Reinhardt, J. M., and Bayouth, J. E. Robust quantification of CT-ventilation biomarker techniques and repeatability in a porcine model. Medical Physics (Impact Factor: 4.5), 2023.
  20. Flakus, M. J., Wuschner, A. E., Wallat, E. M., Graham, M., Shao, W., Shanmuganayagam, D., Christensen, G. E., Reinhardt, J. M., and Bayouth, J. E. Validation of CT-based ventilation and perfusion biomarkers with histopathology confirms radiation-induced pulmonary changes in a porcine model. Scientific Reports (Impact Factor: 4.6), 2023.
  21. Flakus, M. J., Wuschner, A. E., Wallat, E. M., Shao, W., Shanmuganayagam, D., Christensen, G. E., Reinhardt, J. M., Li, K., and Bayouth, J. E. Quantifying robustness of CT-ventilation biomarkers to image noise. Frontiers in Physiology (Impact Factor: 4.0), 2023.
  22. Pan, Y., Wang, D., Chaudhary, M. F. A., Shao, W., Gerard, S. E., Durumeric, O. C., Bhatt, S. P., Barr, R. G., Hoffman, E. A., Reinhardt, J. M., and Christensen, G. E. Robust Measures of Image-Registration-Derived Lung Biomechanics in SPIROMICS. Journal of Imaging (Impact Factor: 3.2), 2023.
  23. Hering, A., Hansen, L., Mok, T. C. W., Chung, A. C. S., Siebert, H., Häger, S., Lange, A., Kuckertz, S., Heldmann, S., Shao, W., and Others. Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning. IEEE Transactions on Medical Imaging (Impact Factor: 10.6, 97% in Radiology, Nuclear Medicine and Imaging), 2022.
  24. Bhattacharya, I., Khandwala, Y. S., Vesal, S., Shao, W., Yang, Q., Soerensen, S. J. C., Fan, R. E., Ghanouni, P., Kunder, C. A., Brooks, J. D., Hu, Y., Rusu, M., and Sonn, G. A. A review of artificial intelligence in prostate cancer detection on imaging. Therapeutic Advances in Urology (Impact Factor: 2.0), 2022.
  25. Shen, X., Shao, W., Wang, C., Liang, L., Chen, S., Zhang, S., Rusu, M., and Snyder, M. P. Deep learning-based pseudo-mass spectrometry imaging analysis for precision medicine. Briefings in Bioinformatics (Impact Factor: 9.5, 96% in Biomedical Research Methods), 2022.
  26. Moroianu, Ş. L., Bhattacharya, I., Seetharaman, A., Shao, W., Kunder, C. A., Sharma, A., Ghanouni, P., Fan, R. E., Sonn, G. A., and Rusu, M. Computational detection of extraprostatic extension of prostate cancer on multiparametric MRI using deep learning. Cancers (Impact Factor: 5.2), 2022.
  27. Bhattacharya, I., Lim, D. S., Aung, H. L., Liu, X., Seetharaman, A., Kunder, C. A., Shao, W., Soerensen, S. J. C., Fan, R. E., Ghanouni, P., To’o, K. J., Brooks, J. D., Sonn, G. A., and Rusu, M. Bridging the gap between prostate radiology and pathology through machine learning. Medical Physics (Impact Factor: 3.8), 2022.
  28. Bhattacharya, I., Seetharaman, A., Kunder, C., Shao, W., Chen, L. C., Soerensen, S. J. C., Wang, J. B., Teslovich, N. C., Fan, R. E., Ghanouni, P., Brooks, J. D., Sonn, G. A., and Rusu, M. Selective identification and localization of indolent and aggressive prostate cancers via CorrSigNIA: an MRI-pathology correlation and deep learning framework. Medical Image Analysis (Impact Factor: 10.9, 99% in Radiology, Nuclear Medicine and Imaging), 2022.
  29. Shao, W., Pan, Y., Durumeric, O.C., Reinhardt, J.M., Bayouth, J.E., Rusu, M., and Christensen, G.E. Geodesic density regression for correcting 4DCT pulmonary respiratory motion artifacts. Medical Image Analysis (Impact Factor: 10.9, 99% in Radiology, Nuclear Medicine and Imaging), 2021.
  30. Sood, R.R., Shao, W., Kunder, C., Teslovich, N.C., Wang, J.B., Soerensen, S.J.C., Madhuripan, N., Jawahar, A., Brooks, J.D., Ghanouni, P., Fan, R.E., Sonn, G.A., and Rusu, M. 3D Registration of pre-surgical prostate MRI and histopathology images via super-resolution volume reconstruction. Medical Image Analysis (Impact Factor: 10.9, 99% in Radiology, Nuclear Medicine and Imaging), 2021.
  31. Shao, W., Banh, L., Kunder, C.A., Fan, R.E., Soerensen, S.J.C., Wang, J.B., Teslovich, N.C., Madhuripan, N., Jawahar, A., Ghanouni, P., Brooks, J.D., Sonn, G.A., and Rusu, M. ProsRegNet: A deep learning framework for registration of MRI and histopathology images of the prostate. Medical Image Analysis (Impact Factor: 10.9), 2021.
  32. Shao, W., Patton, T. J, Gerard, S. E, Pan, Y., Reinhardt, J. M, Durumeric, O.C., Bayouth, J. E, and Christensen, G.E. N-Phase Local Expansion Ratio for Characterizing Out-of-Phase Lung Ventilation. IEEE Transactions on Medical Imaging (Impact Factor: 10.6, 97% in Radiological and Ultrasound Technology), 2020.
  33. Jacob, H., Gerard, S. E., Shao, W., Xin, Y., Cereda, M., Reinhardt, J. M., Christensen, G. E., Hoffman, E. A. and Kaczka, D. W. Effects of Lung Injury on Regional Aeration and Expiratory Constants: Insights form 4DCT Image Registration. Frontiers in Physiology (Impact Factor: 4.0), 2021.
  34. Soerensen, S. J. C., Fan, R. E., Seetharaman, A., Chen, L., Shao, W., Bhattacharya, I., Kim, Y.-h., Sood, R., Borre, M., Chung, B. I., To’o, K. J., Rusu, M., and Sonn, G. A. Deep learning improves speed and accuracy of prostate gland segmentations on magnetic resonance imaging for targeted biopsy. Journal of Urology (Impact Factor: 7.6, 97% in Urology), 2021.
  35. Seetharaman, A., Bhattacharya, I., Chen, L. C., Kunder, C. A., Shao, W., Soerensen, S. J. C., Wang, J. B., Teslovich, N. C., Fan, R. E., Ghanouni, P., Brooks, J. D., Too, K. J., Sonn, G. A., and Rusu, M. Automated detection of aggressive and indolent prostate cancer on magnetic resonance imaging Medical Physics (Impact Factor: 3.8), 2021.
  36. Herrmann, J., Gerard, S. E., Shao, W., Xin, Y., Cereda, M., Reinhardt, J. M., Christensen, G. E., Hoffman, E. A., and Kaczka, D. W. Effects of lung injury on regional aeration and expiratory time constants: insights from four-dimensional computed tomography image registration. Frontiers in Physiology (Impact Factor: 4.0), 2021.
  37. Rusu, M., Shao, W., Kunder, C., Wang, J., Soerensen, S. J. C., Teslovich, N, Sood, R., Chen, L., Fan, R., Ghanouni, P., Brooks, J., and Sonn G. Registration of pre-surgical MRI and whole-mount histopathology images from radical prostatectomy via RAPSODI. Medical Physics (Impact Factor: 3.8), 2020.
  38. Wallat, E. M., Flakus, M. J., Wuschner, A. E., Shao, W., Christensen, G. E., Reinhardt, J. M., Baschnagel, A. M., and Bayouth, J. E. Modeling the impact of out‐of‐phase ventilation on normal lung tissue response to radiation dose. Medical Physics (Impact Factor: 3.8), 2020.
  39. Jacob, H., Gerard, S.E., Shao, W., Hawley, M.L., Reinhardt, J.M., Christensen, G.E., Hoffman, E. A. and Kaczka, D. W. Quantifying Regional Lung Deformation Using Four-dimensional Computed Tomography: A Comparison of Conventional and Oscillatory Ventilation. Frontiers in Physiology (Impact Factor: 4.0), 2020.
  40. Shao, X., Chen, X., Yu, X., Hu, Y., Liu, L., Shi, F., Shao, W., and Mo, J. Nondestructive measurement of conformal coating thickness on printed circuit board with ultra-high resolution optical coherence tomography. IEEE Access (Impact Factor: 3.9), 2019.
  41. Koylu, C., Zhao, C., and Shao, W. Deep Neural Networks and Kernel Density Estimation for Detecting Human Activity Patterns from Geo-Tagged Images: A Case Study of Birdwatching on Flickr. ISPRS Int J Geo-Information (Impact Factor: 3.4), 2019.
  42. Patton, T. J., Gerard, S. E., Shao, W., Christensen, G. E., Reinhardt, J. M., and Bayouth, J. E. Quantifying ventilation change due to radiation therapy using 4 DCT Jacobian calculations. Medical Physics (Impact Factor: 3.8), 2018.

Conference Papers

  1. Gong, Y., Wang, G., Wu, J., Xing, Y., Yu, B., Zhou, H., Huang, Z., Hashimoto, F., Shao, W., and Gong, K. HRLReg: A Hierarchical Reinforcement Learning Framework for Deformable Image Registration. 2025. (Under review in ICCV)
  2. Zhang, T., Jiang, H., Gong, K., and Shao, W. Geodesic Diffusion Models for Medical Image-to-Image Generation. 2025. (Under review by MICCAI)
  3. Wang, F., Yu, Y., Shao, W., Zhou, Y., Yuille, A., and Xie, C. Scaling Laws in Patchification: An Image Is Worth 50,176 Tokens And More. ICML (Impact Score: 32.4, Acceptance Rate: 26.9%), 2025.
  4. Wang, F., Yang, T., Yu, Y., Ren, S., Wei, G., Wang, A., Shao, W., Zhou, Y., Yuille, A. and Xie, C. Adventurer: Optimizing Vision Mamba Architecture Designs for Efficiency. CVPR (Impact Score: 51.98, Acceptance Rate: 22.1%), 2025.
  5. Wang, F., Wang, J., Ren, S., Mei, J., Wei, G., Zhou, Y., Shao, W., Yuille, A. and Xie, C. Mamba-Reg: Vision Mamba Also Needs Registers. CVPR (Impact Score: 51.98, Acceptance Rate: 22.1%), 2025.
  6. Yu, B., Ozdemir, S., Dong, Y., Shao, W., Shi, K., and Gong, K. PET Image Denoising based on 3D Denoising Diffusion Probabilistic Model: Evaluations on Total-body Datasets. MICCAI (Impact Score: 10.9, Early Acceptance Rate: 11%), 2024.
  7. Cheng, Z., Wei, Q., Zhu, H., Wang, Y., Qu, L., Shao, W., and Zhou, Y. Unleashing the Potential of SAM for Medical Adaptation via Hierarchical Decoding. CVPR (Impact Score: 60.7, Acceptance Rate: 23.6%, 100% in Computer Vision and Pattern Recognition), 2024.
  8. Bhattacharya, I., Shao, W., Li, X., Soerensen, S. J. C., Fan, R. E., Ghanouni, P., Brooks, J. D., Sonn, G. A., and Rusu, M. ArtHiFy: artificial histopathology-style features for improving MRI-based prostate cancer detection. SPIE Medical Imaging (Impact Score: 4.4), 2024.
  9. Wei, Q., Yu L., Li, X., Shao, W., Xie, C., Xing, L., Zhou Y. Consistency-guided Meta-Learning for Bootstrapping Semi-Supervised Medical Image Segmentation. MICCAI (Impact Score: 10.9, Acceptance Rate: 31%), 2023.
  10. Bhattacharya, I., Shao, W., Soerensen, S.J.C., Fan, R.E., Wang, J.B., Kunder, C.A., Ghanouni, P., Sonn, G. and Rusu, M. Integrating zonal priors and pathomic MRI biomarkers for improved aggressive prostate cancer detection on MRI. SPIE Medical Imaging (Impact Score: 4.4), 2022. (Oral presentation).
  11. Shao, W., Vesal, S., Lim D., Li, C., Golestani, N., Alsinan, A., Fan, R., Sonn, G., Rusu, M. The Learn2Reg 2021 MICCAI Grand Challenge (PIMed Team). MICCAI (Impact Score: 10.9, Acceptance Rate: 31%), 2021.
  12. Shao, W., Bhattacharya, I., Soerensen, S.J.C., Kunder, C.A., Wang, J.B., Fan, R.E., Ghanouni, P., Brooks, J.D., Sonn, G. and Rusu, M. Weakly Supervised Registration of Prostate MRI and Histopathology Images. MICCAI (Impact Score: 10.9, Acceptance Rate: 31%), 2021.  
  13. Soerensen, S.J.C., Fan, R., Seetharaman, A., Chen, L., Shao, W., Bhattacharya, I., Borre, M., Chung, B., To’o, K., Sonn, G. and Rusu, M., 2021, February. ProGNet: prostate gland segmentation on MRI with deep learning. SPIE Medical Imaging (Impact Score: 4.4), 2021.
  14. Bhattacharya, I., Seetharaman, A., Shao, W., Sood, R., Kunder, C.A., Fan, R.E., Soerensen, S.J.C., Wang, J.B., Ghanouni, P., Teslovich, N.C., Brooks, J.D., Sonn, G. and Rusu, M. CorrSigNet: Learning CORRelated Prostate Cancer SIGnatures from Radiology and Pathology Images for Improved Computer Aided Diagnosis. MICCAI (Impact Score: 10.9, Acceptance Rate: 31%), 2020.
  15. Shao, W., Patton, T.J., Gerard, S.E., Pan, Y., Reinhardt, J.M., Bayouth, J.E., Durumeric, O.C., and Christensen, G.E. Detecting Out-of-Phase Ventilation Using 4DCT to Improve Radiation Therapy for Lung Cancer. International Workshop on Reconstruction and Analysis of Moving Body Organs, 2018. (Oral presentation)
  16. Shao, W., Gerard, S. E., Pan, Y., Patton, T. J., Reinhardt, J. M., Durumeric, O. C., Bayouth, J. E., and Christensen, G. E. Sensitivity Analysis of Jacobian Determinant Used in Treatment Planning for Lung Cancer. SPIE Medical Imaging (Impact Score: 4.4), 2018. (Oral presentation)
  17. Shao, W., Christensen, G. E., Johnson, H. J., Hyun Song, J., Durumeric, O. C., Johnson, C. P., Shaffer, J. J., Magnotta, V. A., Fiedorowicz, J. G. and Wemmie, J. A. Population Shape Collapse in Large Deformation Registration of MR Brain Images. CVPR Workshop (Impact Score: 10.9), 2016. (Oral Presentation).