Georgia Institute of TechnologyMitchell Parry
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Robert Mitchell Parry, Ph.D.

Department of Biomedical Engineering
Georgia Institute of Technology and Emory University
313 Ferst Drive, Rm. 4238
Atlanta, GA 30332-0535


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Education

Ph.D. in Computer Science (December 2007)
Georgia Institute of Technology, Atlanta, GA
Advisor: Irfan Essa
Topic: Audio Source Separation
Title: Separation and Analysis of Multichannel Signals
Minor: Computational Music Analysis

M.S. in Computer Science (May 2006)
Georgia Institute of Technology, Atlanta, GA
Specialization: Graphics and Visualization

B.S. in Computer Science (May 2000)
University of Virginia, Charlottesville, VA
High Distinction
Minor: Electrical Engineering

Research and Work Experience

CCNE Postdoctoral Fellow in the Department of Biomedical Engineering with May D. Wang (2007-present)
Working in bioinformatics including imaging, visualization, biomarker selection, and quality control.

Graduate Research Assistant with Irfan Essa (2002-2007)
Conducting research on information retrieval, signal processing, pattern recognition, and their application to music and audio analysis.

Guided Research with Gil Weinberg (2004-2005)
Contributed computational rhythmic analysis such as stability and similarity for a robotic percussionist.

Guided Research with Mark Guzdial (2000-2002)
Explored music visualization, computer music and enhanced the music facilities in Squeak, an open-source implementation of Smalltalk-80.

Graduate Research Assistant with William Ribarsky (2000-2001)
Worked to incorporate real-time weather and high-resolution 3D city facades into a 3D interactive visualization of the earth (similar to Google Earth).

Student Programmer in the Network Systems Group at University of Virginia (Summer 2000)
Built a Linux driven console switch to provide remote administrative access to 24 network servers.

Publications

Journal Articles

Win Percentage: A Novel Measure for Assessing the Suitability of Machine Classifiers for Biological Problems
R. Mitchell Parry, John H. Phan, and May D. Wang
BMC Bioinformatics, 2012, 13(Suppl 3), p S7.

caCORRECT2: Improving Accuracy and Reliability of Microarray Data in the Presence of Artifacts
Richard A. Moffitt, Qiqin Yin-Goen, Todd H. Stokes, R. Mitchell Parry, James H. Torrance, John H. Phan, Andrew N. Young, and May D. Wang
BMC Bioinformatics, 2011, 12(1), p 383.
PubMed, DOI

k-Nearest Neighbor Models for Microarray Gene Expression Analysis and Clinical Outcome Prediction
R. Mitchell Parry*, Wendell Jones*, Todd H. Stokes*, John H. Phan, Richard A. Moffitt, Hong Fang, Leming Shi, Andre Oberthuer, Matthias Fischer, Weida Tong, and May D. Wang (* Equal contributing authors)
The Pharmacogenomics Journal, 2010, 10 (4), pp 292-309.
PubMed, DOI

The MAQC-II Project: A comprehensive study of common practices for the development and validation of microarray-based predictive models
The MicroArray Quality Control (MAQC) Consortium
Nature Biotechnology, 2010, 28 (8), pp 827-838.
PubMed, Google Scholar

Combining Two-Dimensional Diffusion-Ordered Nuclear Magnetic Resonance Spectroscopy, Imaging Desorption Electrospray Ionization Mass Spectrometry, and Direct Analysis in Real-Time Mass Spectrometry for the Integral Investigation of Counterfeit Pharmaceuticals
Leonard Nyadong, Glenn A. Harris, Stephane Balayssac, Asiri S. Galhena, Myriam Malet-Martino, Robert Martino, R. Mitchell Parry, May D. Wang, Facundo M. Fernandez, and Veronique Gilard
Analytical Chemistry, 2009, 81 (12), pp 48034812.
PubMed, Google Scholar

Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) Reveals Surface-mediated Antifungal Chemical Defense of a Tropical Seaweed
Amy L. Lane, Leonard Nyadong, Asiri Galhena, Elizabeth P. Stout, R. Mitchell Parry, May D. Wang, Mark E. Hay, Facundo M. Fernandez, and Julia Kubanek
Proc Natl Acad Sci USA, 2009, 106 (18), pp 7314-7319.
PubMed, Google Scholar

Full Conference Papers (Refereed)

Hypergeometric Similarity Measure for Spatial Analysis in Tissue Imaging Mass Spectrometry
Chanchala Kaddi, R. Mitchell Parry, and May D. Wang
In Proc. IEEE Int'l Conf. on Bioinformatics and Biomedicine (BIBM), 2011.

An Analysis of Scale and Rotation Invariance in the Bag-of-Features Method for Histopathological Image Classification
S. Hussain Raza, R. Mitchell Parry, Richard A. Moffitt, Andrew N. Young, and May D. Wang
In Proc. Int'l Conf. on Medical Image Computing and Computer Assisted Intervention (MICCAI), 2011.
DOI

Win Percentage: A Novel Measure for Assessing the Suitability of Machine Classifiers for Biological Problems
R. Mitchell Parry, John H. Phan, and May D. Wang
In Proc. ACM Conf. on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), 2011.

Automated Classification of Renal Cell Carcinoma Subtypes Using Bag-of-features
S. Hussain Raza, R. Mitchell Parry, Yachna Sharma, Qaiser Chaudry, Richard A. Moffitt, Andrew N. Young, and May D. Wang
In Proc. Int'l Conf. of the IEEE Engineering in Medicine and Biology Society, 2010.
PubMed, IEEE Xplore

Deblurring Molecular Images Using Desorption Electrospray Ionization Mass Spectrometry (Invited)
R. Mitchell Parry, Asiri S. Galhena, Facundo M. Fernandez, May D. Wang
Proc. of Int'l Conf. of the IEEE Engineering in Medicine and Biology Society, 2009
IEEE Xplore
paper, slides

Development of an Automatic Quantification Method for Cancer Tissue Microarray Study
Teresa H. Sanders, Todd H. Stokes, Richard A. Moffitt, Qaiser Chaudry, R. Mitchell Parry, and May D. Wang
In Proc. Int'l Conf. of the IEEE Engineering in Medicine and Biology Society, 2009.
PubMed, IEEE Xplore

Matrix Factorization Techniques for Analysis of Imaging Mass Spectrometry Data
Peter W. Siy, Richard A. Moffitt, R. Mitchell Parry, Yanfeng Chen, Ying Liu, M. Cameron Sullards, Alfred H. Merrill, Jr., May D. Wang
In Proc. IEEE Int'l Conf. on Bioinformatics and Bioengineering, 2008.
IEEE Xplore

Simple Quantification of Multiplexed Quantum Dot Staining in Clinical Tissue Samples
Matthew Caldwell, Richard A. Moffitt, Jian Liu, R. Mitchell Parry, Yachna Sharma, and May D. Wang
In Proc. Int'l Conf. of the IEEE Engineering in Medicine and Biology Society, 2008.
PubMed, IEEE Xplore, Google Scholar

Phase-aware Non-negative Spectrogram Factorization
R. Mitchell Parry and Irfan Essa
In Proc. Int'l Conf. on Independent Component Analysis and Source Separation, 2007.
Springer, Google Scholar
paper, bib, poster, code

Incorporating Phase Information for Source Separation via Spectrogram Factorization
R. Mitchell Parry and Irfan Essa
In Proc. Int'l Conf. on Acoustics, Speech, and Signal Processing, 2007.
IEEE Xplore, Google Scholar
paper, bib, poster

Source Detection Using Repetitive Structure
R. Mitchell Parry and Irfan Essa
In Proc. Int'l Conf. on Acoustics, Speech, and Signal Processing, 2006.
IEEE Xplore, Google Scholar
paper, bib, poster

Estimating the Spatial Position of Spectral Components in Audio
R. Mitchell Parry and Irfan Essa
In Proc. Int'l Conf. on Independent Component Analysis and Blind Source Separation, 2006.
Springer, Google Scholar
paper, bib, slides

Blind Source Separation Using Repetitive Structure
R. Mitchell Parry and Irfan Essa
In Proc. of Int'l Conf. on Digital Audio Effects, 2005.
Google Scholar
paper, bib, slides

Haile - A Perceptual Robotic Percussionist
Gil Weinberg, Scott Driscoll, and R. Mitchell Parry
In Proc. of Int'l Computer Music Conference, 2005.
Google Scholar
paper, bib

Musical Interactions with a Perceptual Robotic Percussionist
Gil Weinberg, Scott Driscoll, and R. Mitchell Parry
In Proc. of IEEE Int'l Workshop on Robot and Human Interactive Communication, 2005.
IEEE Xplore, Google Scholar
paper, bib

Feature Weighting for Segmentation
R. Mitchell Parry and Irfan Essa
In Proc. of Int'l Conf. on Music Information Retrieval, 2004.
Google Scholar
paper, bib, poster

Rhythmic Similarity through Elaboration
R. Mitchell Parry and Irfan Essa
In Proc. of Int'l Conf. on Music Information Retrieval, 2003.
Google Scholar
paper, bib, poster

Acquisition and Display of Real-time Atmospheric Data on Terrain
Tian-Yue Jiang, William Ribarsky, Tony Wasilewski, Nickolas Faust, Brendan Hannigan, and R. Mitchell Parry
In Eurographics-IEEE Visualization Symposium, pp. 15-24, 2001.
Google Scholar, Google Books
paper

Research Abstracts (Refereed)

Optimizing Alignment Algorithms to Quantify Cancer Signals in Next-Generation Sequencing Data
John H. Phan, Jenny Dale, Chang F. Quo, R. Mitchell Parry, Todd H. Stokes, and May D. Wang
In Annual Fall Meeting of the Biomedical Engineering Society, 2010.

Removing Population Structure in Genome-Wide Association Studies Using Supervised Methods
Andrew B. Dicks, R. Mitchell Parry, and May D. Wang
In Annual Fall Meeting of the Biomedical Engineering Society, 2010.

Computer Aided Diagnosis of Squamous Cell Carcinoma of Head and Neck
Yachna Sharma, R. Mitchell Parry, S. Hussain Raza, Qaiser Chaudry, Todd H. Stokes, X. Wang, Susan Muller, Zhuo Chen, and May D. Wang
In Annual Fall Meeting of the Biomedical Engineering Society, 2010.

Tissue Microarray Quality Control: A High Throughput IHC Classification and Scoring System
Teresa H. Sanders, Todd H. Stokes, Sovandy Hang, Adeel Yusuf, Richard A. Moffitt, R. Mitchell Parry, and May D. Wang.
In Annual Fall Meeting of the Biomedical Engineering Society, 2008.

Spectrogram Factorization Using Phase Information
R. Mitchell Parry and Irfan Essa
NIPS Workshop on Advances in Models for Acoustic Processing, 2006.
Google Scholar
paper, bib, poster (Note: See Longer version in ICASSP Paper above.)

Source Separation for Multichannel Music Audio
R. Mitchell Parry
Int'l Conf. on Music Information Retrieval Graduate School Proposal, 2004.
abstract, slides

Organization and Simplification of High-resolution 3D City Facades
R. Mitchell Parry, William Ribarsky, Christopher Shaw, Justin Jang, and Nickolas Faust
In Proc. of SPIE Vol. 4744, Radar Sensor Technology and Data Visualization, 2002.
SPIE, GVU Tech Report, Google Scholar
paper

Hierarchical Storage and Visualization of Real-Time 3D Data
R. Mitchell Parry, Brendan Hannigan, William Ribarsky, Chris D. Shaw, and Nickolas Faust
In Proceedings of SPIE Vol. 4368, Radar Sensor Technology and Data Visualization, 2001.
SPIE, Google Scholar
paper

Real-time Weather Data On Terrain
Christopher D. Shaw, T. Y. Jiang, R. Mitchell Parry, Beth Plale, Anthony A. Wasilewski, William Ribarsky, Nickolas L. Faust
In Proceedings of SPIE Vol. 4368, Radar Sensor Technology and Data Visualization, 2001.
SPIE, Google Scholar
paper

Invited Talks

Blind Source Separation in Music
R. Mitchell Parry
Invited talk at dorkbot Atlanta, Jan. 11, 2007.

Technical Reports and Theses (Unrefereed)

Separation and Analysis of Multichannel Signals
R. Mitchell Parry
Ph.D. Thesis at Georgia Institute of Technology (Advisor: Dr. Irfan Essa), Dec. 2007.
Google Scholar, Georgia Tech Theses and Dissertations]
paper

Musical Complexity and Top 40 Chart Performance
R. Mitchell Parry
Georgia Institute of Technology Technical Report GIT-GVU-04-04, February 2004.
Google Scholar, GVU Tech Report
paper , bib

Circuiting Helms Theater with Simulated Annealing
R. Mitchell Parry
Undergraduate Thesis at University of Virginia (Advisor: Dr. James Cohoon), May 2000.
paper

Poster Presentations

Adapting a Matlab-based Image Analysis Tool into a Grid-enabled Analytical Service
Chandrakant Jaybhaye, R. Mitchell Parry, Todd Stokes, Martin Ahrens, Qaiser Chaudry, and May D. Wang
caBIG® Annual Meeting, 2009.

Imaging Desorption Electrospray Ionization-Mass Spectrometry and Direct Analysis in Real Time Mass-Spectrometry for the Integral Investigation of Counterfeit Antimalarial Pharmaceuticals
Asiri Galhena, Leonard Nyadong, R. Mitchell Parry and May D. Wang, and Facundo Fernandez
57th ASMS Conf. on Mass Spectrometry, 2009.

omniBioMarker: A Bioinformatics Application For Enabling Personalized Oncology
John H. Phan, R. Mitchell Parry, Praveen Krishnaiah, and May D. Wang
caBIG® Annual Meeting, 2008.

caCorrect: a Suite of caBIG® Grid Services for Microarray Quality Control and Assessment
Richard Moffitt, Todd Stokes, John Phan, Qiqin Yin-Goen, Jian Liu, James Torrance, Matthew Caldwell, R. Mitchell Parry, Andrew Young, Shuming Nie, and May D. Wang
caBIG® Annual Meeting, 2008.


Teaching Experience

Instructing

Guest Instructor
Problems in Biomedical Engineering I (Fall 2010) taught by Wendy Newstetter
Developed and presented a lecture titled Design and Analysis of Experiments based on existing lecture slides. Added examples for testing if the Braves are a better than average baseball team and if the Phillies are better than the Braves.

Facilitator
Problems in Biomedical Engineering I (Spring 2009, Spring and Fall 2010) taught by May D. Wang
Facilitated a group of eight first-year undergraduates twice weekly while they worked on biomedical engineering problems using problem-based learning methodologies.

Guest Instructor (two semesters)
Introduction to Synthesized Computer Music (Spring and Fall 2004) taught by Gil Weinberg
Developed and presented two lectures titled Pitch and Rhythm Recognition and Spectrum Analysis. Led tutorials in Max/MSP graphical programming environment.

Assisting

Teaching Assistant (three semesters)
Computer Graphics (Fall 2002) taught by Jarek Rossignac
Computer Graphics (Summer 2002) taught by David Krum
Computer Graphics (Spring 2002) taught by Norberto Ezquerra
Coauthored and graded programming assignments. Developed grading criteria and evaluated open-ended assignments and group projects. Gave lectures on OpenGL programming. Provided individual student assistance during office hours for class sizes of approximately 40 students per semester.

Teaching Assistant at University of Virginia (three semesters)
Introduction to Computer Science (two semesters)
Software Development Methods (one semester)
Provided one-on-one C++ programming help to students in office hours and labs. Helped manage lab sessions and graded object-oriented programming assignments.

Mentoring

Chanchala Kaddi, PhD Student, Biomedical Engineering (Aug. 2009 - Present).
Guided Chanchala in quantitative methods for analyzing tissue imaging mass spectrometry.

Hussain Raza, PhD Student, Electrical and Computer Engineering (Aug. 2009 - Present).
Guided Hussain in image processing for cancer subtype classification and intra-operative imaging.

Nicholas Tzou, PhD Student, Electrical and Computer Engineering (Aug. 2010 - Dec. 2010).
Guided Hussain in image processing for cancer subtype classification and intra-operative imaging.

Andrew Dicks, Undergraduate Student, Biomedical Engineering (May 2009 - Aug. 2010).
Guided Andrew in analyzing the population structure in genome-wide association studies (GWAS).

Jeonggyu Lee, Masters Student, Computer Science (Aug. 2008 - Dec. 2008).
Guided Jeonggyu in the 3D modeling and visualization of a human stomach. This includes segmentation of 2D images slices, registration of adjacent slices, and interpolation into 3D mesh.

Andrea Barrett, Undergraduate Student, Biomedical Engineering (Aug. 2008 - May 2009).
Guided Andrea in developing a user interface for tissue imaging mass spectrometry data supporting region of interest selection, identification of ion co-localization, generation of publication quality images.

Peter Siy, Graduate Student, Electrical and Computer Engineering (Jan. 2008 - Dec. 2008).
Guided Peter in learning about source separation and applying it to tissue imaging mass spectrometry. This resulted in his first publications~{[}C10,A7{]}. Peter is now an analyst at McKinsey & Company.

Andrew Knight, Undergraduate Student, Computer Science (Jan. 2006 - May 2006).
Guided Andrew's first research experience on a music database visualization project. Andrew received his BS in 2006 and MS in 2007.

New Student Mentor, University of Virginia (Aug. 1999 - May 2000).
Point of contact for first-year undergraduate engineering students adjusting to college life.

Professional Activities


Honors

  • NIH CCNE Postdoctoral Fellowship (Nov. 2007 - Present)
  • Travel Award, Int'l Conf. on Independent Component Analysis and Blind Signal Separation (ICA 2006).

Other Press


Memberships

  • Association for Computing Machinery (ACM)
  • Institute of Electrical and Electronics Engineers (IEEE)
  • IEEE Engineering in Medicine and Biology Society (EMBS)
  • Biomedical Engineering Society (BMES)
  • FDA Microarray Quality Control (MAQC) Project

Technical Skills

  • Proficient in Matlab, C/C++, Java, Perl, PHP
  • Parallel computing using openMPI
  • Distributed computing using BOINC

Graduate Coursework


Undergrad


Other Projects

  • Audio Textures: Generating continuous music given a small set of examples. (Spring 2003)
  • Real-time visualization of musical tones. (Spring 2002)
  • Visualizing musical tones using a simple auditory model, self-organizing map, and spring system. (Fall 2001)
  • MusicMonitor: Control the background music while surfing the web or checking email in Squeak. (Spring 2001)


Last modified 17 August 2012 at 7:46 pm by Mitch Parry