Dissertations and Theses

Scientific Computing

• Dr. Schubert's Dissertation [ps] [pdf]
• ChuanChe "Jacob" Lee's Thesis on parallelizing the block min-max estimator [pdf]
  Jacob's thesis looks at parallelizing one of the estimators in my dissertation. He spent a lot of time looking at how to optimize in general the process, and the thesis would be a good start for others interested in estimation.
• Ehab (Williams) Aziz Rezk's Project on a Java Dynamic Systems Tool [pdf][zip]
  The pdf is a review version, but it is the only electronic copy I have, and I don't feel like scanning the book. The java code and applets are in the zip file. It is a really nice tool, that will be particularly helpful to those learning nonlinear systems.
• Natalie Wiser-Orozco's Thesis on Extensible Simulation Of Planets And Comets [pdf], and presentation [ppt]
  Natalie is an amazing gal, and she did a really neat thesis on how to create an extensible modeler for n-body systems. She started an open source project to continue the development. See her page on the thesis [html] and her open source project [html].

AI and Neural Nets

• Hanh Nguyen's Disertation on A Deep Convolutional Neural Network Approach for Biomedical Applications [pdf]
  Hanh worked on a deep CNN approach to detect and classify polyps in colonoscopy.

Magnetic Resonance Imaging (MRI)

• Tom S. Lee's Thesis on MRI distortion correction [pdf]
  Tom's thesis is an amazing 500 page tome on MRI and medical imaging in general. What can you say about something so impressive. It is a must read, if for nothing else than your humility. It is worthwhile to note that Tom won the thesis of the year for the entire CSU system. Read it and you won't be surprised.
• Zonqi "Ritchie" Cai's Thesis on MRI distortion correction [pdf]
  Ritchie finished his thesis on the next advance in MRI correction. It covers larger scanners and included a major redesign of both the phantom and the method to include parallelism and numerous other advances.

Proton Computed Tomography (pCT)

• Jihad Tafas's Thesis on Proton Computed Tomography (pCT) [pdf]
  Jihad is one of the nicest guys you will ever want to meet, and his thesis is the first on pCT, and it launched a major area of research for R2Labs. His thesis is more on the mathematical and physics side, though he does introduce several important algorithmic speedups, and was the basis of a journal publication (quite an accomplishment for a master's thesis).
• Scott McAllister's Thesis on using General Purpose Graphics Processing Units (GP-GPU) for Proton Computed Tomography (pCT) [pdf], and presentation [ppt]
  Scott continued the work done by Jihad Tafas on pCT, looking at using sparse matrices and various reconstruction algorithms to efficiently use GPGPU. Scott is one of the hardest working students I have known, and his thesis shows his dedication.
• Wenzhe Xue's Project on techniques for Proton Computed Tomography (pCT) [pdf]
  Wenzhe did a project comparing reconstruction techniques for pCT.
• Micah Witt's Thesis on Sparse GPU techniques for Proton Computed Tomography (pCT) [pdf]
  Micah did an exciting thesis on fast sparse techniques for pCT, and a simulation tool for generating realistic data sets. He already has several pubs from it.
• Blake Schultze's Thesis on Hardware/Software Hybrid for Parallel Computation in Proton Computed Tomography (pCT) [pdf], and presentation [pptx]
  Blake did some exciting things on improving detection of protons, space carving, and more.
• Sarah McCarty's Thesis on preprocessing and data storage for Proton Computed Tomography (pCT) [pdf]
  Sarah solved a problem we have had for almost a decade, and made reconstruction from raw data to final imaging possible, trackable, and accessible.
• John P. Stenson's Thesis on Chord Length Methods for Proton Computed Tomography (pCT) [pdf]
  John looked at the impact of chord length on image reconstruction in pCT.
• Paniz Karbasi's Dissertation on a fast parallel algorithm for Proton Computed Tomography (pCT) [pdf]
  Paniz was my first PhD student to finish. She did great work on fast pCT reconstruction getting the reconstruction time for a hundred million histories to around 40 seconds.
• Jordan Reeser's Thesis on use of straggling power in Proton Computed Tomography (pCT) [pdf]
  Jordan looked at how energy straggling can be used in pCT to improve the identification of edges.
• Blake Schultze's Dissertation on Proton Computed Tomography (pCT) [pdf]
  Blake did so much it is hard to write a short summary. His contributions range across GPU algorithm development, physics of pCT, new TVS algorithm, hull construction for reconstruction, etc.
• Zonqi "Ritchie" Cai's Dissertation on a parallel programming scheme for Proton Computed Tomography (pCT) [pdf]
  Ritchie did an amazing job on a way to parallelized ART (algebraic Reconstruction Technique) for pCT that uses guaranteed independent updates.

Intensity Modulated Proton Radiation Therapy (IMpRT)

• Aarohi Padhye's Thesis on Segmenation for IMpRT [pdf]
  Aarohi did the foundational work on generating high-resolution models from CT scans for use in IMpRT.

Functional Near-Infrared Spectroscopy Brain Monitoring

• Ha Hong Nguyen's Thesis on High-density Intraoperative Brain Monitoring During Cardiac Surgery [pdf]
  Ha did a lot of great work on brain monitoring during cardiac surgery, including taking data during actual surgeries.

Stereotactic Localization

• Mahesh Neupane's Thesis on patient alignment for functional proton neurosurgery [pdf]
  Mahesh was one of my first thesis students and he did an amazing job. In many ways my collaboration with LLUMC is because of the quality of his work. The only copy I have electronically is my last review copy, which had some errors he changed but I don't have that one. Still it has lots of good information.
• Fadi Shihadeh's Thesis on patient alignment for functional proton neurosurgery [pdf]
  Fadi's thesis is the culmination of three student's master's theses (Veysi Malkok, Mahesh Neupane, and Fadi Shihadeh). Fadi's precision, determination, and meticulous attention to detail shows in his fine scientific work.
• Yin "Grace" Chen's Thesis on localization and targeting
  Grace is finishing up her Thesis on localization and targeting with a proton beam is the next stage of the patient alignment problem.

Cellular Automata

• Brian Strader's Thesis on Cellular Automata (CA) for solving Partial Differential Equations (PDEs) [pdf], and presentation [ppt]
  Brian's thesis is blend of computer science and mathematics, which should be the starting point for several more theses. Brian has uncovered some relations, which provide important insight into the relations of poles and zeros, and how they in turn affect convergence and selection of step sizes. His presentation is an excellent example of how I like presentations done, particularly with complicated formulas.
• Jane Curnutt's Thesis on To Live and Die in CA [pdf], and presentation [ppt] and the presentation flyer [doc]
  A title that should make you want to read it. Jane has worked long and hard on this. She is great at what she does and at getting us to do things. It covers numerous results in CA theory and their application to life in extreme environments.
• Melissa Quintana's Thesis on Estimating the state of a Cellular Automata (CA) from pictures [pdf], and presentation [ppt]or the slightly smaller compatibility version[ppt] and the presentation flyer [doc]
  Melissa did an very important thesis in how to turn photograph(s) of patterned life into a CA model. This will no doubt be the launching point for at least one more thesis and will have a big impact on how we model biovermiculations, and thus also potentially how we look for life on Mars or other locations.

Bioinformatics (General)

• Elias Chibli's Thesis on a Multiprocessor Approach To Bit-Parallel Approximate String Matching [pdf]
  Elias's thesis looks at how to parallelize bit-parallel string matching. This is a very import area for bioinformatics, and bit-parallel algorithms were designed to exploit small scale parallelism on individual machines. Elias shows how to extend these algorithms to clusters, and is thus a very important result.
• Arokiya L. Monica Joseph's Project on a Smart Sequence Similarity Search (S4) System [pdf]
  Monica's project created a easy to use interface to BLAST and FASTA, including search saving, sharing, and intelligent system support. It was designed to help early users to bioinformatics, while still allowing all the power an experienced user expects. While not the final copy, it is the last I have electronically, but it is still quite useful.

Robotics and Machine Vision

• Anthony De La Loza's Thesis on a facial recognition and robotic control for paralyzed special needs students [pdf]
  Anthony was our outstanding graduate student in 2011, because he is both a great student and a caring person. His thesis is a nice piece of work that has a great application in helping paralyzed special needs students be able to feed themselves using robots and facial gestures.
• Tyler Hartwig's Thesis on super-resolution for hand-held cameras [pdf]
  Tyler tackled a problem I had that came from my cave-cameras, namely how can we use super-resolution with simple cameras potentially on a tripod to enhance resolution.
• Hanh Nguyen's Thesis on automated segmentation in medical imaging [pdf]
  Hanh did interesting work on automated segmention, which was used in our proton therapy work.

Logic and Embedded Systems

• Armani Batista's Thesis on GPS On The Lunar Sphere Utilizing Cubesats [pdf]
  Armani worked on using cubesats and embedded systems to implement a lunar version of GPS in an affordable way.
• Yu Yang's Thesis on Design and Automated Testing of PCI Express Interface of Proton Computed Tomography Detectors [pdf]
  Yu did foundational logic design of a transmit-receive engine at the PCI Express Transaction Layer for use on a Xilinx 7 series FPGA.
• George M. Onwubuya's Thesis on Developing Industrial Strength UVM for Academic Research and Teaching [pdf]
  George took his interest and industry experience in UVM and turned it into a comprehensive training method.

Parallel Processing

• Ryan Youngman's Thesis on Multi-Core Processors And The Future Of Parallelism In Software [pdf]
  Ryan's thesis is hardware perspective on how parallel software should be developed. It covers multi-cores and thread processing.
• Sammy D'Souza's Thesis on Parallelizing a Non-Deterministic Optimization Algorithm [pdf]
  Sammy's thesis on parallelization using shortcutting has some really amazing results!
• Faris Zuriekat's Thesis on a Parallel Remote Interactive Management Model [pdf]
  Faris's thesis introduces a parallel management model utilizing shortcutting to regain speed lost in management (a common problem). It is nicely done.