Machine Learning Computer Science

Lopamudra Mukherjee

*** ****** ****, ********** ** Wisconsin-Whitewater, Whitewater WI 53190.

Æ cell: 716-***-**** Ó office: 262-***-**** Q ad5rdj@r.postjobfree.com Looking for consulting positions in the area of Machine Learning, Artificial Intelligence and Deep Learning. 10+ years of experience in these areas in research and software development. Academic Background

Ph.D. in Computer Science and Engineering, The State University of New York at Buffalo, September 2008; Dissertation Title: “An Algorithmic Perspective on Problems in Biological Imaging” Master of Science in Computer Science and Engineering, The State University of New York at Buffalo, May 2004.

Bachelor of Technology in Computer Science and Engineering, Institute of Engineering and Management, Calcutta, India, July 2002.

Employment

Machine Learning Consultant, Informatica October 2022- March 2023 Associate Professor (tenured), Computer Sciences, University of Wisconsin Whitewater Aug 2015 –present

Associate Scientist (summer), Department of Biostatistics and Medical Informatics, Univer- sity of Wisconsin Madison 2018 –present

Assistant Professor, Math and Computer Sciences, University of Wisconsin Whitewater Aug 2008

– Jul 2015

Teaching

Artificial Intelligence related courses:

1. CS 796 Deep Learning every spring staring 2024. Designed and developed the course. 2. CS 732 Machine Learning every fall staring 2017. Designed and developed the course. 3. CS 736 Image Processing and Computer Vision every Spring starting 2018. Designed and developed the course.

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4. CS 332 Artificial Intellidence every Fall starting 2018. Publications

Journals

1. Lopamudra Mukherjee,Md Abdul Kader Sagar, Jonathan N. Ouellette, Jyoti J. Watters, and Kevin W. Eliceiri “Joint regression-classification deep learning framework for analyzing fluorescence lifetime images using NADH and FAD”, Biomedical Optics Express 12(5), pp. 2703-2719 (2021)

[impact factor 3.562].

2. Lopamudra Mukherjee, Huu Dat Bui, Adib Keikhosravi, Agnes Loeffler, Kevin W. Eliceiri,

“Super-resolution recurrent convolutional neural networks for learning with multi-resolution whole slide images,” Journal of Biomedical Optics 24(12), 126003 (2019), doi: 10.1117/1.JBO.24.12.126003

[impact factor 2.78] .

3. Lopamudra Mukherjee, Bui Dat Huu, Adib Keikhosravi and Kevin W. Eliceiri, “Convolutional Neural Networks for Microscopic Image Superresolution”, Biomedical Optics Express 9, 5368-5386

(2018) [impact factor 4.23].

4. Artem Pliss, Andrew J. Fritz, Branislav Stojkovic, Hu Ding, Lopamudra Mukherjee, Sambit Bhattacharya, Jinhui Xu, and Ronald Berezney “Non-random Patterns in the Distribution of NOR-bearing Chromosome Territories in Human Fibroblasts: A Network Model of Interactions”, Journal of Cellular Physiology, 2014. [impact factor 3.874]. 5. Jiming Peng, Lopamudra Mukherjee, Vikas Singh, Dale Schuurmans, Linli Xu, “An efficient algorithm for maximal margin clustering”, Journal of Global Optimization, 2012. 6. Vikas Singh, Lopamudra Mukherjee, Jiming Peng, Jinhui Xu, “Ensemble Clustering using Semidefinite Programming with applications”, Machine Learning Journal, Volume 79(1), May, 2010. [impact factor 2.326].

7. Chris Hinrichs, Vikas Singh, Lopamudra Mukherjee, Guofan Xu, Moo K. Chung, Sterling C. Johnson, “Spatially augmented LP Boosting for AD classification with evaluations on the ADNI dataset”, NeuroImage, Volume 48(1), October, 2009. [impact factor 5.74]. 8. Narasimharao V. Marella, Sambit Bhattacharya, Lopamudra Mukherjee, Jinhui Xu, and Ronald Berezney, “Cell Type Specific Chromosome Territory Organization in the Interphase Nucleus of Normal and Cancer Cells”, Journal of Physiology, 2009. [impact factor 4.845]. 9. Michael J. Zeitz, Lopamudra Mukherjee, Sambit Bhattacharya, Ronald Berezney and Jinhui Xu “A Probabilistic Model for the Arrangement of a Subset of Human Chromosome Territories in WI38 Human Fibroblasts”, Journal of Physiology, 2009. [impact factor 4.845]. 10. Lopamudra Mukherjee, Vikas Singh, Jiming Peng, Jinhui Xu, Michael J. Zeitz, Ronald Berezney, “Generalized Median Graphs and applications”, Journal of Combinatorial Optimization, Volume 17(1), January, 2009.

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11. Vikas Singh, Lopamudra Mukherjee, Petru M. Dinu, Jinhui Xu, Kenneth R. Hoffmann,

“Limited view CT reconstruction and segmentation via constrained metric labeling”, Computer Vision and Image Understanding (Special Issue on Discrete Optimization in Computer Vision), Volume 112(1), October, 2008.

12. Kishore Malyavantham, Sambit Bhattacharya, Marcos Barbeitos, Lopamudra Mukherjee, Jinhui Xu, Frank Fackelmayer, Ronald Berezney “Identifying Functional Neighborhoods within the Cell Nucleus: Proximity Analysis of Early S-Phase Replicating Chromatin Domains to Sites of Transcription, RNA Polymerase II, HP1, Matrin 3 and SAF-A”, Journal of Celluluar Biochemsitry, 105(2), 2008. [impact factor 2.530].

13. Vikas Singh, Lopamudra Mukherjee, Jinhui Xu, Kenneth R. Hoffmann, Petru M. Dinu, Matthew Podgorsak, “Brachytherapy Seed Localization using Geometric and Linear Programming Techniques”, IEEE Transactions on Medical Imaging, Special Issue on Mathematical Methods in Biomedical Image Analysis, Volume 26(9), September, 2007. [impact factor 3.939] Conference papers (peer-reviewed)

14. Daniel Szegolowski, Lopamudra Mukherjee and Benjamin Whitcomb, “A Novel Dataset and Deep Learning Benchmark for Classical Music Form Recognition and Analysis”,23rd International Society of Music Information Retrieval Conference (ISMIR), 2022. 15. Zihang Meng, Lopamudra Mukherjee, Yichao Wu, Vikas Singh and Sathya N. Ravi, “Differ- entiable Optimization of Generalized Nondecomposable Functions using Linear Programs”, Neural Information Processing Systems (NeurIPS), 2021.

16. Lopamudra Mukherjee, Adib Keikhosravi and Kevin W. Eliceiri, “Neigborhood Regularized Image Superresolution for Applications to Microscopic Imaging”, Proceedings of International Symposium of Biomedical Imaging (ISBI), April, 2018. 17. Lopamudra Mukherjee, Sathya N. Ravi, Jiming Peng, Vikas Singh, “A Biresolution Spectral framework for Product Quantization”, Proceedings of Conference on Computer Vision and Pattern Recognition (CVPR), June, 2018.

18. Sathya N. Ravi, Yunyang Xiong, Lopamudra Mukherjee, Vikas Singh, “Filter Flow made Practical: Massively Parallel and Lock-Free”, Proceedings of Conference on Computer Vision and Pattern Recognition (CVPR), July, 2017.

19. Lopamudra Mukherjee, Jiming Peng, Trevor Sigmund,Vikas Singh,“Network Flow Formula- tions for Learning Binary Hashing.”, Proceedings of European Conference on Computer Vision

(ECCV), Oct, 2016.

20. Lopamudra Mukherjee, Sathya N. Ravi, Vamsi K. Ithapu, Tyler Holmes, Vikas Singh, “An NMF Perspective on Binary Hashing”, Proceedings of IEEE International Conference on Computer Vision (ICCV), Oct, 2015.

21. Jia Xu, Lopamudra Mukherjee, Yin Li, Jamieson Warner, James M. Rehg, Vikas Singh,

“Gaze-enabled Egocentric Video Summarization via Constrained Submodular Maximization”, Proceedings of Conference on Computer Vision and Pattern Recognition (CVPR), June, 2015. 3/6

22. Lopamudra Mukherjee, Fredick A Hall, ”Non-negative Sparse Coding with Regularizer for Image Classification”, Winter Conference on Computer Vision (WACV), January, 2015. 23. Maxwell D. Collins, Ji Liu, Jia Xu, Lopamudra Mukherjee, Vikas Singh, ”Spectral Clustering with a Convex Regularizer on Millions of Images”, Proceedings of European Conference on Computer Vision (ECCV), September, 2014. [acceptance (26.7%)]. 24. Jia Xu, Vamsi Ithapu,Lopamudra Mukherjee, James M. Rehg, Vikas Singh, “GOSUS: Grass- mannian Online Subspace Updates with Structured-sparsity”, Proceedings of IEEE International Conference on Computer Vision (ICCV), December, 2013. [acceptance (27.8%)]. 25. Lopamudra Mukherjee, Vikas Singh, Jia Xu, Maxwell D. Collins, ”Analyzing the Subspace Structure of Related Images: Concurrent Segmentation of Image Sets”, Proceedings of European Conference on Computer Vision (ECCV), October, 2012. 26. Lopamudra Mukherjee, Vikas Singh, Jiming Peng, “Scale Invariant cosegmentation for image groups”, Proceedings of Conference on Computer Vision and Pattern Recognition (CVPR), June, 2011. [also selected for Oral presentation, acceptance 3.5%]. 27. Lopamudra Mukherjee, Vikas Singh, Jiming Peng, Chris Hinrichs, “Learning Kernels for Normalized Cuts: Convex Relaxations and applications”, Proceedings of Conference on Computer Vision and Pattern Recognition (CVPR), June, 2010. [acceptance 27%]. 28. Lopamudra Mukherjee, Vikas Singh, Charles R. Dyer, “Half-integrality based algorithms for Cosegmentation of images”, Proceedings of Conference on Computer Vision and Pattern Recognition (CVPR), June, 2009. [also selected for Oral presentation: acceptance 4.1%]. 29. Vikas Singh, Lopamudra Mukherjee, Moo K. Chung, “Cortical surface thickness as a classifier: Boosting for autism classification”, Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI), September, 2008. [acceptance 35%]. 30. Vikas Singh, Lopamudra Mukherjee, Jiming Peng, Jinhui Xu, “Ensemble Clustering using Semidefinite Programming”, Advances in Neural Information Processing Systems (NIPS) 20, December, 2007. [also selected for Spotlight presentation: acceptance 10.3%]. 31. Vikas Singh, Petru M. Dinu, Lopamudra Mukherjee, Jinhui Xu, Kenneth R. Hoffmann,

“Limited view CT reconstruction via constrained metric labeling”, Proceedings of IEEE Computer Society Workshop on Mathematical Methods in Biomedical Image Analysis (IEEE MMBIA) in conjunction with ICCV, October, 2007. [acceptance 22/120 for oral (18.3%), also invited to International Journal of Computer Vision].

32. Lopamudra Mukherjee, Vikas Singh, Jiming Peng, Jinhui Xu, Michael J. Zeitz, Ronald Berezney, “Generalized Median Graphs: Theory and Applications”, Proceedings of IEEE In- ternational Conference on Computer Vision (ICCV), October, 2007. [acceptance 281/1190

(23.6%)].

33. Lopamudra Mukherjee, Vikas Singh, Jinhui Xu, Kishore Malyavantham, Ronald Berezney,

“On Mobility Analysis of Functional Sites from Time Lapse microscopic image sequences of living Cell Nucleus”, Proceedings of Medical Image Computing and Computer Assisted Intervention

(MICCAI), October, 2006. [acceptance 231/578 (39.9%)]. 4/6

34. Vikas Singh, Lopamudra Mukherjee, Jinhui Xu, Kenneth R. Hoffmann, “Solving the Brachyther- apy Seed Localization problem using Geometric and Linear Programming techniques”, Proceedings of ACM Symposium on Applied Computing (ACM SAC), April, 2006. [acceptance 300/927

(32%)].

35. Lopamudra Mukherjee, Vikas Singh, Jinhui Xu, Ronald Berezney, “Fitting Polygonal Regions for Matching 3D Polyhedra”, Proceedings of IS&T/SPIE International Symposium of Electronic Imaging: Vision Geometry XIV, Volume 6066, January, 2006. 36. Vikas Singh, Lopamudra Mukherjee, Jinhui Xu, Kenneth R. Hoffmann, Guang Xu, Zhenming Chen, “Efficient geometric techniques for reconstructing 3D vessel trees from biplane images” Proceedings of the ACM Annual Symposium on Computational Geometry (SoCG), June, 2005. 37. Vikas Singh, Lopamudra Mukherjee, Jinhui Xu, Kenneth R. Hoffmann, “Efficient Geometric Algorithms for Determining Motion and Shape Deformation of Coronary Vessels”, Proceedings of IEEE Engineering in Medicine and Biological Society (IEEE-EMBS), September, 2004. 38. Lopamudra Mukherjee, Jinhui Xu, Artem Pliss, Ronald Berezney “Efficient Algorithms for Motion and Deformation Recovery with Biological Applications”, Proceedings of IEEE System, Man, and Cybernetics (IEEE SMC), 2004.

Talks

1. IEEE Computer Vision and Pattern Recognition Conference, Colorado Springs, June 2011. 2. International Symposium of Mathematical Programming (ISMP), Chicago, August 2009. 3. IEEE Computer Vision and Pattern Recognition Conference, Miami, June 2009. 4. UWW - Department of Mathematics and Computer Science Colloquium, November 2008. Awards and Honors

2009 UWW Faculty Development Fellowship ($2500).

2007 Mark Diamond Research Fund Award.

2006-2007 Graduate Student Employees Union Professional Development Award. 2006 SPIE Travel Award for 2006.

2004 Student Award at IEEE-SMC.

2003-2007 Tuition scholarship (graduate), University at Buffalo, Buffalo. 1998-2002 J.R.D. Tata Merit scholarship for undergraduate studies. 1996 Rank 67th out of 400,000 students in West Bengal Madhyamik Pariksha (high school exam).

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Grant Support

1. PI on UWW Strategic Initiative Grant: “Invigorating Computer Science Education through Establishment of an Undergraduate Project Lab (CS HUB)”, 2013 - $49, 680. 2. PI on NSF Grant “CGV: Small: RUI: Analyzing subspace structure for group level image understanding”, 2012 — $231, 313.

3. Co-Investigator on NSF “Grant RI: Small: Endowing Graph-Based Image Segmentation with Global ’Advice’ ”, 2011 -– UWW share $28, 769.

4. Grant Writing fellowship (GWF) for Summer 2011, 2016 - $5000 5. Faculty Development Fellowship Summer 2010 - $2000 6. Faculty Development Award Spring 2010 - $2500

7. Faculty Development Fellowship Summer 2009, 2016, 2018 8. Fire Award Summer 2017, 2018 -$5000

Professional Activities

1. NSF Symposium on Cyber-Enabled Discovery and Innovation invited participant, September, 2007.

2. NIH Research Festival participant (about 20% applicants invited), October, 2006. 3. NSF Review Panelist for IIS October 2012.

4. Reviewer for Medical Physics, MeDIA, Knowledge and Information Systems, Transactions of Image Processing, Transactions on Biomedical Engineering, Signal Processing: Image Communication, Pattern Recognition Letters, PAMI, ICCV 2009-2017, CVPR 2011-2017, ECCV 2012-2017, MICCAI 2006-08, COCOON 2006, AAIM 2007, and COCOON 2007. Personal Information

Citizenship: USA

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