Publications

Journal Publication

  1. T. Lu, J. Jorns, D. Ye, M. Patton, R. Fisher, A. Emmrich, T. Gilat-Schmidt„ T. Yen, B. Yu. "Automated assessment of breast margins in deep ultraviolet fluorescence images using texture analysis." Biomedical Optics Express, 13(9):5015–5034, September 2022.

  2. H. Hu, D. Helminiak, M. Yang, D. Unsihuay, R. Hilger, D. Ye, J. Laskin. "High-Throughput Mass Spectrometry Imaging with Dynamic Sparse Sampling." ACS Measurement Science Au, August 2022.

  3. J. Lee, J. Kang, S. Oh, D. Ye. "Multi-Domain Neumann Network with Sensitivity Maps for Parallel MRI Reconstruction." Sensors, 22(10):3943, May 2022.

  4. P. Jordan, P. Adamson, V. Bhattbhatt, S. Beriwal, S. Shen, O. Radermecker, S. Bose, L. Strain, M. Offe, D. Fraley, S. Principi, D. Ye, A. Wang, J. Van Heteren, N. Vo, T. Gilat-Schmidt. "Pediatric Chest-Abdomen-Pelvis and Abdomen-Pelvis CT Images with Expert Organ Contours." Medical Physics, 49(5):3523–3528, May 2022.

  5. J. Li, D. Ye, M. Kolsch, J. Wachs, C. Bouman. "Fast and Robust UAV to UAV Detection and Tracking from Video." IEEE Transactions on Emerging Topics in Computing, August 2021.

  6. T. Lu, J. Jorns, M. Patton, R. Fisher, A. Emmrich, T. Doehring, T. Gilat-Schmidt, D. Ye, T. Yen, B. Yu. "Rapid Assessment of Breast Tumor Margins using Deep Ultraviolet Fluorescence Scanning Microscopy." Journal of Biomedical Optics, 25(12), 126501, November 2020.

  7. HuBMAP Consortium (Purdue TTD: J. Laskin, D. Ye, K. Burnum-Johnson, P. Piehowski, C. Ansong, Y. Zhu). "The Human Body at Cellular Resolution: the NIH Human Biomolecular Atlas Program." Nature, 574:187–192, October 2019.

  8. Z. Chang, D. Ye, S. Srivastava, J-B. Thibault, K. Sauer, C. Bouman, "Prior-Guided Metal Artifact Reduction for Iterative X-Ray Computed Tomography." IEEE Transactions on Medical Imaging, 38(6):1532-1542, June 2019.

  9. S. Zhang, Z. Song, D. Godaliyadda, D. Ye, A. Chowdhury, A. Sengupta, G. Buzzard, C. Bouman, G. Simpson. "Dynamic Sparse Sampling for Confocal Raman Microscopy." Analytical Chemistry, 90(7):4461–4469, March 2018.

  10. D. Godaliyadda, D. Ye, M. Uchic, M. Groeber, G. Buzzard, C. Bouman. "A Framework for Dynamic Image Sampling Based on Supervised Learning." IEEE Transactions on Computational Imaging, 4(1):1–16, March 2018.

  11. A. Chowdhury, D. Ye, Z. Song, S. Zhang, H. Hedderich, B. Mallick, S. Thirunahari, S. Ramakrishnan, A. Sengupta, E. Gualtieri, C. Bouman, G. Simpson. "Second Harmonic Generation Guided Raman Spectroscopy for Sensitive Detection of Polymorph Transitions." Analytical Chemistry, 89(11):5958–5965, May 2017.

  12. N. Scarborough, D. Godaliyadda, D. Ye, D. Kissick, S. Zhang, J. Newman, M. Sheedlo, A. Chowdhury, R. Fischetti, C. Das, G. Buzzard, C. Bouman, G. Simpson. "Dynamic X-ray Diffraction Sampling for Protein Crystal Positioning." Journal of Synchrotron Radiation, 24(1):188–195, January 2017.

  13. R. Zhang, D. Ye, D. Pal, J-B. Thibault, K. Sauer, C. Bouman. "A Gaussian Mixture MRF for Model-Based Iterative Reconstruction." IEEE Transactions on Computational Imaging, 2(3):359–374, September 2016.

  14. B. Menzey, A. Jakaby, S. Bauery, J. Kalpathy-Cramery, K. Farahaniy, J. Kirbyy, Y. Burreny, N. Porzy, J. Slotboomy, R. Wiesty, L. Lancziy, E. Gerstnery, T. Arbel, B. Avants, N. Ayache, P. Buendia, D. Collins, N. Cordier, J. Corso, A. Criminisi, T. Das, H. Delingette, C. Demiralp, C. Durst, J. Festa, E. Geremia, B. Glocker, P. Golland, X. Guo, A. Hamamci, K. Iftekharuddin, R. Jena, N. John, E. Konukoglu, D. Lashkari, J. Mariz, R. Meier, S. Pereira, D. Precup, S. Price, T. Riklin-Raviv, S. Reza, M. Ryan, L. Schwartz, H. Shin, J. Shotton, C. Silva, N. Sousa, N. Subbanna, G. Szekely, T. Taylor O. Thomas, N. Tustison, G. Unal, M. Weber, M. Wintermark, D. Ye, L. Zhao, B. Zhao D. Zikic, M.l Prastaway, M. Reyesyz, K. Leemputyz. "The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)." IEEE Transactions on Medical Imaging, 34(10):1993–2024, October 2015.

  15. D. Ye, B. Desjardins, J. Hamm, H. Litt, K. M. Pohl. "Regional Manifold Learning for Disease Classification." IEEE Transactions on Medical Imaging, 33(6):1236–1247, June 2014.

  16. E. Konukoglu, B. Glocker, D. Ye, A. Criminisi, K. M. Pohl. "Discriminative Segmentation-based Evaluation through Shape Dissimilarity." IEEE Transactions on Medical Imaging, 31(12):2278–2289, December, 2012.

  17. J. Hamm, D. Ye, R. Verma, C. Davatzikos. "GRAM: A framework for geodesic registration on anatomical manifolds." Medical Image Analysis, 14(5):633–642, October 2010. MedIA-MICCAI Best Paper Award

  18. D. Ye, C. Davatzikos, H. Litt, "Characterizing Right Ventricular Shape Variations via Subject-adapted Voxel-based Morphometry: Application to CMR of Tetralogy of Fallot", Journal of Cardiovascular Magnetic Resonance, 12(Suppl. 1):237, January, 2010.

Peer-Reviewed Conference/Workshop

  1. H. Yu, T. Florian, V. Calhoun, D. Ye. "Deep Learning from Imaging Genetics for Schizophrenia Classification." In: Proceedings of the 2022 IEEE International Conference on Image Processing (ICIP 2022), October 16–19, 2022.

  2. T. To, S. Heidari, D. Ye. "Deep Learning for Breast Cancer Classification of Deep Ultraviolet Fluorescence Images toward Intra-Operative Margin Assessment." In: Proceedings of the 2022 IEEE International Engineering in Medicine and Biology Conference (EMBC 2022), July 11–15, 2022. Oral Presentation

  3. S. Baek, O. Lee, D. Ye. "Iodine-enhanced Liver Vessel Segmentation in Photon Counting Detector-based Computed Tomography using Deep Learning." In: Proceedings of the 2022 International Conference on Image Formation in X-Ray Computed Tomography (CT Meeting 2022), June 12–16, 2022.

  4. J. Nam, D. Ye, O. Lee. "Deep Learning-based Prior toward Normalized Metal Artifact Reduction in Computed Tomography." In: Proceedings of the 2022 International Conference on Image Formation in X-Ray Computed Tomography (CT Meeting 2022), June 12–16, 2022.

  5. S. Heidari, C. Kan, D. Ye. "Breast Cancer Histopathological Image Classification with Adversarial Image Synthesis." In: Proceedings of the 2021 IEEE International Engineering in Medicine and Biology Conference (EMBC 2021), October 30–November 5, 2021.

  6. C. Kan, R. Povinelli, D. Ye. "Enhancing Multi-Channel EEG Classification with Gramian Temporal Generative Adversarial Networks." In: Proceedings of the 2021 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2021), June 6–11, 2021.

  7. T. Lu, J. Jorns, M. Patton, R. Fisher, A. Emmrich, T. Doehring, T. Gilat-Schmidt, D. Ye, T. Yen, B. Yu. "Texture Analysis of Deep Ultraviolet Fluorescence Images for Intraoperative Assessment of Breast Tumor Margins ." In: Proceedings of the 2021 OSA Biophotonics Congress: Optics in the Life Sciences , April 12–16, 2021

  8. C. Kan, T. Gilat-Schmidt, D. Ye. "Enhancing Reproductive Organ Segmentation in Pediatric CT via Adversarial Learning." In: Proceedings of the 2021 SPIE International Conference on Medical Imaging (SPIE MI 2021) , February 14–18, 2021. Oral Presentation

  9. N. Lang, D. Saxena, T. Yen, J. Jorns, B. Yu, D. Ye. "Breast Cancer Magnification-independent Multi-class Histopathology Classification using Dual-step Model." In: Proceedings of the 2021 SPIE International Conference on Medical Imaging (SPIE MI 2021), February 14–18, 2021. Honorable Mention Poster Award

  10. N. Aboobacker, G. Gonzalez, F. Zhang, J.Wanek, P. Xue, G. Rao, D. Ye. "Improving Presentation Consistency of Radiographic Images using Deep Learning." In: Proceedings of the 2021 SPIE International Conference on Medical Imaging (SPIE MI 2021), February 14–18, 2021.

  11. D. Helminiak, H. Hu, J. Laskin, D. Ye. "Deep Learning Approach for Dynamic Sparse Sampling in Mass Spectrometry Imaging." In: Proceedings of the 2021 IS&T International Symposium on Electronic Imaging (EI 2021), January 18–22, 2021. Oral Presentation

  12. D. Won, S. An, S. Park, D. Ye. "Low-Dose CT Denoising using Octave Convolution with High and Low Frequency Bands." In: Proceedings of the 2020 International Workshop on PRedictive Intelligence In MEdicine (PRIME-MICCAI 2020), October 8, 2020

  13. K. Venkiteshwaran, N. Lang, D. Ye, D. Zitomer. "Predicting digester methane production using microbial community information: Can your biomass DNA data really be used to improve operations?" In: Proceedings of the 2020 Water Environment Federation's Technical Exhibition and Conference (WEFTEC 2020) , October 3–7, 2020. Oral Presentation

  14. C. Kan, N. Aboobacker, D. Ye. "Age-Conditioned Synthesis of Pediatric Computed Tomography with Auxiliary Classifier Generative Adversarial Networks." In: Proceedings of the 2020 IEEE International Symposium on Biomedical Imaging (ISBI 2020), April 3–7, 2020. Oral Presentation

  15. T. Lu, J. Jorns, M. Patton, R. Fisher, A. Emmrich, T. Doehring, T. Gilat-Schmidt, D. Ye, T. Yen, B. Yu. "Deep UV Fluorescence Scanning Microscopy for Breast Tumor Margin Detection." In: Proceedings of the 2020 SPIE International Conference on Photonics West (SPIE Photonics West 2020) , February 4–6, 2020

  16. B. Foster, D. Ye, C. Bouman. "Multi-target Tracking with an Event-based Vision Sensor and a Partial-update GMPHD Filter." In: Proceedings of the 2019 IS&T International Symposium on Electronic Imaging (EI 2019), January 13–17, 2019. Oral Presentation, Invited

  17. D. Ye, G. Buzzard, M. Ruby, C. Bouman. "Deep Back Projection for Sparse-View CT Reconstruction." In: Proceedings of the 2018 IEEE Global Conference on Signal and Information Processing (GlobalSIP 2018), November 26–29, 2018.

  18. A. Ziabari, D. Ye, S. Srivastava, J-B. Thibault, K. Sauer, C. Bouman. "3D Deep Residual Learning for CT Image Denoising with Multi-GPU Implementation." In: Proceedings of the 2018 Asilomar Conference on Signals, Systems, and Computers (Asilomar 2018), October 28 – 31, 2018.

  19. A. Ziabari, D. Ye, S. Srivastava, K. Sauer, J-B. Thibault, L. Fu, C. Bouman. "Model Based Iterative Reconstruction With Spatially Adaptive Sinogram Weights for Widecone Cardiac CT." In: Proceedings of the 2018 International Conference on Image Formation in X-ray Computed Tomography (CT Meeting 2018), May 20 – 23, 2018. Oral Presentation

  20. D. Ye, S. Srivastava, J-B. Thibault, K. Sauer, C. Bouman. "Deep Residual Learning for Model-based Iterative CT Reconstruction using Plug-and-Play Framework." In: Proceedings of the 2018 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2018), April 15 – 20, 2018. Oral Presentation, Invited

  21. D. Ye, J. Li, Q. Chen, J. Wachs, C. Bouman. "Deep Learning for Moving Object Detection and Tracking from a Single Camera in Unmanned Aerial Vehicles (UAVs)." In: Proceedings of the 2018 IS&T International Symposium on Electronic Imaging (EI 2018), January 28 – February 2, 2018. Oral Presentation, Invited, Best Paper Award

  22. S. Zhang, Z. Song, D. Godaliyadda, D. Ye, A. Chowdhury, A. Sengupta, G. Buzzard, C. Bouman, G. Simpson. "A Supervised Learning Approach for Dynamic Sampling in Raman Hyperspectral Imaging." In: Proceedings of the 2018 IS&T International Symposium on Electronic Imaging (EI 2018), January 28 – February 2, 2018. Oral Presentation

  23. S. Zhang, Z. Song, D. Godaliyadda, D. Ye, A. Sengupta, G. Buzzard, C. Bouman, G. Simpson. "Dynamic Sampling for Raman Imaging." In: Proceedings of the 2018 SPIE Photonics West (SPIE Photonics West 2018), January 27 – February 1, 2018. Oral Presentation

  24. D. Ye, S. Srivastava, J-B. Thibault, K. Sauer, C. Bouman. "ROI reconstruction for model based iterative reconstruction (MBIR) via a coupled dictionary learning." In: Proceedings of the 2017 SPIE Medical Imaging (SPIE MI 2017), February 11 – 16, 2017.

  25. S. Majee, D. Ye, G. Buzzard, C. Bouman. "A model based neuron detection approach using sparse location priors." In: Proceedings of the 2017 IS&T International Symposium on Electronic Imaging (EI 2017), January 29 – February 2, 2017. Oral Presentation.

  26. N. Scarborough, D. Godaliyadda, D. Ye, D. Kissick, S. Zhang, J. Newman, M. Sheedlo, A. Chowdhury, R. Fischetti, C. Das, G. Buzzard, C. Bouman, G. Simpson. "Synchrotron X-ray Diffraction Dynamic Sampling for Protein Crystal Positioning." In: Proceedings of the 2017 IS&T International Symposium on Electronic Imaging (EI 2017), January 29 – February 2, 2017. Oral Presentation.

  27. J. Li, D. Ye, T. Chung, M. Kolsch, J. Wachs, C. Bouman. "Multi-Target Detection and Tracking from a Single Camera in Unmanned Aerial Vehicles (UAVs)." In: Proceedings of the 2016 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2016), October 9 – 14, 2016. Oral Presentation

  28. D. Godaliyadda, D. Ye, M. Uchic, M. Groeber, M. Jackson, G. Buzzard, C. Bouman. "A Supervised Learning Approach for Dynamic Image Sampling." In: Proceedings of the 2016 IS&T International Symposium on Electronic Imaging (EI 2016), February 14 – 18, 2016. Oral Presentation

  29. P. Jin, D. Ye, C. Bouman. "Joint Metal Artifact Reduction and Segmentation of CT Images Using Dictionary-Based Image Prior and Continuous-Relaxed Potts Model." In: Proceedings of the 2015 IEEE International Conference on Image Processing (ICIP 2015), September 27 – 30, 2015. Oral Presentation, Best Paper Award Runner-Up

  30. D. Ye, S. Srivastava, D. Pal, J-B. Thibault, K. Sauer, C. Bouman. "Initial Condition for Fast Model-Based Iterative Reconstruction of Truncated Projection Data." In: Proceedings of the 2015 Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine (Fully3D 2015), May 31 – June 4, 2015.

  31. D. Ye, B. Desjardins, V. Ferrari, D. Metaxas, K. Pohl. "Auto-Encoding of Discriminating Morphometry From Cardiac MRI." In: Proceedings of the 2014 IEEE International Symposium on Biomedical Imaging (ISBI 2014), April 29 –May 2, 2014. Oral Presentation

  32. D. Ye, D. Zikic, B. Glocker, A. Criminisi, E. Konukoglu. "Modality Propagation: Coherent Synthesis of Patient-specific Scans with Data-driven Regularization." In: Proceedings of the 2013 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2013), September 22 –26, 2013.

  33. D. Ye, J. Hamm, B. Desjardins, K. Pohl. "FLOOR: Fusing Locally Optimal Registrations." In: Proceedings of the 2013 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2013), September 22 –26, 2013.

  34. D. Zikic, B. Glocker, E. Konukoglu, J. Shotton, A. Criminisi, D. Ye, C. Demiralp, O. Thomas, T. Das, R. Jena, S. J. Price. "Context-sensitive Classification Forests for Segmentation of Brain Tumor Tissues." In: Proceedings of the 2012 Multimodal Brain Tumor Segmentation Challenge (BRATS 2012), October 1, 2012. Oral Presentation, BRATS 2012 Challenge Winner

  35. D. Ye, J. Hamm, D. Kwon, C. Davatzikos, K. Pohl. "Regional Manifold Learning for Deformable Registration of Brain MR Images." In: Proceedings of the 2012 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2012), October 1 –5, 2013.

  36. Y. Ou, D. Ye, K. Pohl, C. Davatzikos. "Validation of DRAMMS among 12 popular methods in cross-subject cardiac MRI registration." In: Proceedings of the 2012 International Workshop on Biomedical Image Registration (WBIR 2012), July 7 –8, 2012. Oral Presentation

  37. D. Ye, J. Hamm, K. Pohl. "Combining Regional Metrics for Disease-Related Brain Population Analysis." In: Proceedings of the 2012 IEEE International Symposium on Biomedical Imaging (ISBI 2012), May 2 –5, 2012. Student Travel Award

  38. D. Ye, H. Litt, C. Davatzikos, K. Pohl. "Morphological Classification: Application to cardiac MRI of Tetralogy of Fallot." In: Proceedings of the 2011 International Conference on Functional Imaging and Modeling of the Heart (FIMH 2011), May 25 –27, 2011. Oral Presentation

  39. D. Ye, K. Pohl, C. Davatzikos. "Semi-Supervised Pattern Classification: Application to Structural MRI of Alzheimer’s Disease." In: Proceedings of the 2011 International Workshop on Pattern Recognition in NeuroImaging (PRNI 2011), May 16 –18, 2011. Oral Presentation, Student Travel Award

  40. N. Batmanghelich, D. Ye, K. Pohl, B. Taskar, C. Davatzikos. "Disease Classification and Prediction via Semi-supervised Dimensionality Reduction." In: Proceedings of the 2011 IEEE International Symposium on Biomedical Imaging (ISBI 2011), March 30 – April 2, 2011. Oral Presentation, Top 10 Student Paper

  41. D. Ye, K. Pohl, H. Litt, C. Davatzikos. "Groupwise Morphometric Analysis Based on High Dimensional Clustering." In: Proceedings of the 2010 IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA 2010), June 14, 2010.

  42. D. Ye, D. Kwon, I. Yun, S. Lee. "Fast Multi-scale Vessel Enhancement Filtering." In: Proceedings of the 2008 SPIE Medical Imaging (SPIE MI 2008), February 16 – 21, 2008.