John Bardsley's Publications Page
Google Scholar Profile: here
Scientific Papers in Progress
Refereed Journal Articles
47. "Bayesian inverse problems with l1 priors: a Randomize-then-Optimize approach," with Zheng Wang, Antti Solonen, Tiangang Cui, Youssef M. Marzouk, , accepted in SIAM Journal on Scientific Computing, arXiv.
46. "A Metropolis-Hastings method for linear inverse problems with Poisson likelihood and Gaussian prior," with Aaron Luttman, International Journal of Uncertainty Quantification, Vol. 6, Iss. 1, pp. 35–55, 2016, PDF.
45. "Randomize-then-optimize for sampling and uncertainty quantification in electrical impedance tomography," with Aku Seppanen, Antti Solonen, Heikki Haario, and Jari Kaipio, SIAM Journal on Uncertainty Quantification, Vol. 3, pp. 1136–1158, 2015 PDF.
44. "Dealing with Boundary Artifacts in MCMC-Based Deconvolution," with Aaron Luttman, Linear Algebra and its Applications, vol. 473, pp. 339–358, 2015 PDF.
43. "Consequences of a refuge for the predator-prey dynamics of a wolf-elk system in Banff National Park, Alberta, Canada," with Joshua Goldberg and Mark Hebblewhite, PLoS ONE, 9(3), 2014: e91417. doi:10.1371/journal.pone.0091417. PDF
42. "Analysis of the Gibbs sampler for hierarchical inverse problems," with Sergios Agapiou, Omiros Papaspiliopoulos, and Andrew M. Stuart, SIAM Journal on Uncertainty Quantification, vol. 2, iss. 1, pp. 511-544, 2014 PDF.
41. "Randomize-then-Optimize: a method for sampling from posterior distributions in nonlinear inverse problems," with Antti Solonen, Heikki Haario, and Marko Laine, SIAM Journal on Scientific Computing, Volume 36, Issue 4, pp. A1359-C399, 2014 PDF.
40. "Optimization-based Sampling for the Ensemble Kalman filter," with Antti Solonen, Alexander Bibov, and Heikki Haario, International Journal of Uncertainty Quantification, vol. 4, iss. 4, pp. 349-364, 2014, PDF
39. "Efficient MCMC-Based Image Deblurring with Neumann Boundary Conditions," with Marylesa Howard and Jim Nagy, Electronic Transactions in Numerical Analysis, vol. 40, pp. 476 - 488, 2013 PDF
38. "Gaussian Markov Random Field Priors for Inverse Problems," Inverse Problems and Imaging, vol. 7, no. 2, 2013, pp. 397 - 416 PDF.
37. "An ensemble Kalman filter using the conjugate gradient sampler", with Antti Solonen, Albert Parker, Heikki Haario, and Marylesa Howard, International Journal
for Uncertainty Quantification, Vol. 3, No. 4, 2013, pp. 357–370 PDF.
36. "Krylov subspace approximate Kalman filtering," with Albert Parker, Antti Solonen, and Marylesa Howard, Numerical Linear Algebra with Applications, Vol. 20, 2013, pp. 171-184, PDF. Citation #20 is errorneous - it should be: W.Y. Yang, I.M. Navon and P. Courtier, A new Hessian preconditioning method applied to variational data assimilation experiments using NASA general circulation models, MONTHLY WEATHER REVIEW, 124(5), 1996, pp. 1000-1017.
35. "Laplace-distributed increments, the Laplace prior, and edge-preserving regularization," Journal of Inverse and Ill-Posed Problems, Volume 20, Issue 3, 2012, pp. 271–285, PDF.
34. "MCMC-Based Image Reconstruction with Uncertainty Quantification," SIAM Journal on Scientific Computing, Vol. 34, No. 3, 2012, pp. A1316–A1332, PDF.
33. "An MCMC Method for Uncertainty Quantification in Nonnegativity Constrained Inverse Problems," with Colin Fox, Inverse Problems in Science and Engineering, Vol. 20, No. 4, 2012, pp. 477-498 PDF.
32. "A Computational Framework for Total Variation-Regularized Positron Emission Tomography", with John Goldes, Numerical Algorithms, 57(2), 2011, p. 255 PDF.
31. "Applications of a Nonnegatively Constrained Iterative Method with Statistically Based Stopping Rules to CT, PET, and SPECT Imaging," Electronic Transactions in Numerical Analysis, 38, 2011, pp. 34-43. PDF
30. "Techniques for regularization parameter and hyper-parameter selection in PET and SPECT imaging", with John Goldes, Inverse Problems in Science and Engineering, 19(2), 2011, p. 267-280. PDF
29. "Structured Linear Algebra Problems in Adaptive Optics Imaging", with Sarah Knepper and Jim Nagy, Advances in Computational Mathematics, vol. 5, issue 2-4, 2011, pp. 103-117 PDF.
28. "Hierarchical Regularization for Edge-Preserving Reconstruction of PET Images", with Daniela Calvetti and Erkki Somersalo, Inverse Problems, 26(3), 2010, 035010 PDF.
27. "An Iterative Method for Edge-Preserving MAP Estimation when Data-Noise is Poisson," with John Goldes, SIAM Journal on Scientific Computing, Vol.32, No.1, published online Feb 5, 2010 PDF.
26. "The variational Kalman filter and an efficient implementation using limited memory BFGS", with H. Auvinen, H. Haario, and T. Kauranne, Int. J. for Numerical Methods in Fluids, 64, 3, pp. 314--335, 2010 PDF.
25. "A Theoretical Framework for the Regularization of Poisson Likelihood Estimation Problems," Inverse Problems and Imaging, Vol. 4, No. 1, February 2010 p. 11-17 PDF.
24. "An Analysis of Regularization by Diffusion for Ill-Posed Poisson Likelihood Estimation," with N'djekornom Laobeul, Inverse Problems in Science and Engineering, Volume 17, Issue 4, June 2009 , pages 537 - 550. PDF.
23. "Total Variation-Penalized Poisson Likelihood Estimation for Ill-Posed Problems," with Aaron Luttman, Advances in Computational Mathematics, Volume 31, Issue 1, (2009), Page 35-59. PDF.
22. "Regularization Parameter Selection Methods for Ill-Posed Poisson Maximum Likelihood Estimation", with John Goldes, Inverse Problems, 25 (2009) 095005 PDF.
21. "Large-Scale Kalman Filtering Using the Limited Memory BFGS Method", with H. Auvinen, H. Haario, and T. Kauranne, Electronic Transactions in Numerical Analysis, Vol. 35, 2009, pp. 217-233 PDF.
20. "A Fixed Point Formulation of the k-Means Algorithm and a Connection to Mumford-Shaw", with Aaron Luttman, Applied Math E-Notes, vol. 9, 2009, pp. 274-276. PDF.
19. "Tikhonov Regularized Poisson Likelihood Estimation: Theoretical Justification and a Computational Method," with N'djekornom Laobeul, Inverse Problems in Science and Engineering, Volume 16, Issue 2 January 2008 , pages 199 - 215 PDF.
18. "The Stabilizing Properties of Nonnegativity Constraints in Least-Squares Image Reconstruction," with Jorma Merikoski and Roberto Vio, Int. J. of Pure and Applied Mathematics, vol. 43, no. 1, 2008, pp. 95-109 PDF.
17. "An Efficient Phase and Object Estimation Scheme for Phase-Diversity Time Series Data," IEEE Transactions on Image Processing, volume 17, issue 1, 2008, p. 9-15 PDF.
16. "An Analysis of Methods for Wavefront Reconstruction From Gradient Measurements in Adaptive Optics," Int. J. of Pure and Applied Mathematics, Vol. 42, No. 1, 2008, pp. 71-81 PDF.
15. "Wavefront Reconstruction Methods for Adaptive Optics Systems on Ground-Based Telescopes," SIAM Journal on Matrix Analysis and Application, Volume 30 Issue 1, 2008, pp. 67-83 PDF.
14. "Stopping Rules for a Nonnegatively Constrained Iterative Method for Ill-Posed Poisson Imaging Problems," BIT Numerical Mathematics, Volume 48, Number 4, December, 2008, pp. 651-664 PDF.
13. "An Efficient Computational Method for Total Variation-Penalized Poisson Likelihood Estimation," Inverse Problems and Imaging, vol. 2, no. 2, 2008, pp. 167 - 185 PDF.
12. "Wellposedness for Systems Arising in Time Domain Electromagnetics in Dielectrics," with H. T. Banks, Int. J. of Pure and Applied Mathematics 46 (2008), no. 1, 1-18.PDF.
11. "Analysis of Pattern Formation on the Surface of Respiring Leaves," with Aaron Luttman and Emily Stone, Physica D, Vol 232, Issue 2, 2007, pp. 142-155. PDF.
10. "A Variational Approach to Image Segmentation for Botanical Data," with Aaron Luttman, SIAM Journal on Scientific Computing, Vol 29, Issue 4, 2007, pp. 1550-1566.PDF.
This paper was featured in Science Magazine's Editors' Choice column. PDF. Erratum in SISC Vol 30, Issue 1, p. 548 PDF.
09. "A Computational Method for the Restoration of Images With an Unknown, Spatially-Varying Blur," with Stuart Jeffries, Jim Nagy and Bob Plemmons, Optics Express, vol. 14, Iss. 5, 2006, pp. 1767-1782, PDF.
08. "Covariance-Preconditioned Iterative Methods for Nonnegatively Constrained Astronomical Imaging," with Jim Nagy, SIAM Journal on Matrix Analysis and Applications, Vol. 27, No. 4, 2006, pp. 1184-1198, PDF.
07. "Least-Squares methods with Poissonian noise: analysis and
a comparison with the Richardson-Lucy algorithm," with R. Vio and W. Wamsteker,
Astronomy and Astrophysics, 436, 2005, pp. 741-755 PDF.
06. "Dealing with edge effects in least-squares image deconvolution problems," with R. Vio, M. Donatelli, and W. Wamsteker, Astronomy and Astrophysics, vol. 442, pp. 397-403, 2005. PDF
05. "A Nonnegatively Constrained Trust Region Algorithm for the
Restoration of Images with an Unknown Blur," Electronic Transactions in
Numerical Analysis, vol. 20, 2005, pp. 139-153.
04. "Parameter Identification for a Dispersive Dielectric
in 2D Electromagnetics: Forward and Inverse Methodology with Statistical
Considerations," with H. T. Banks, Int. J. of Computational
and Numerical Analysis and Applications, vol. 5, No. 1, 2004, pp. 13-49.
03. "A Limited Memory, Quasi-Newton Preconditioner for Nonnegatively Constrained
Image Reconstruction," Journal of the Optical
Society of America A, vol. 21, no. 5, 2004, pp. 724-731.
02. "A Nonnnegatively Constrained Convex Programming Method for Image
Reconstruction," with C.R. Vogel, SIAM Journal on
Scientific Computing, vol. 25, no. 4, 2004, pp. 1326-1343.
01. "Computational Methods for a Large-Scale Inverse Problem Arising in
Atmospheric Optics," with Luc Gilles and C.R. Vogel, Inverse Problems,
18, 2002, pp. 237-252.
Non-refereed Conference Proceedings, Technical Reports, and Abandoned Papers.
6. "MATLAB Software for Supervised Classification in Remote Sensing and Image Processing", submitted with Marylesa Howard, Mark Lorang, Chris Gotschalk PDF, codes with GUI . This is my most
requested piece of software, though I've not been able to get the paper published ... yet.
5. "A Matrix Theoretic Derivation of the Kalman Filter," University of Montana Technical Report #32, 2008, PDF. The Kalman filter for the numerical linear algebra fan. I've submitted it a couple of times, but it doesn't fit well in typical journals and so has been rejected. I wrote it when learning the Kalman filter and wanted a derivation that fit my background in computational mathematics.
4. "Wavefront Estimation for Adaptive Optics Systems on Ground-Based Telescopes," PAMM Volume 7, Issue 1 , Pages 1021701 - 1021702, 2008, Proceedings of the 2007 International Conference of Industrial and Applied Mathematics, PDF.
3. "Blind Iterative Restoration of Images with Spatially-Varying Blur," with Stuart Jeffries, Jim Nagy and Bob Plemmons, 2005 AMOS Technical Conference Proceedings, PDF.
2. "An Inverse Problem in X-Ray Radiography," with V. Korostyshevskiy,
L.C. Parra, S. LaVoie, T.J. Leiterman, J. Reese, B. Song, Technical Report,
Center for Research in Scientific Computation, CRSC-TR01-27, NCSU, 2001.
1. "A Bound-Constrained Levenburg-Marquardt Algorithm for a Class of Parameter Identification
Problems Arising in Electromagnetics," PDF. See MATLAB code here.
Reflections on Research
2009: (i) some of the papers I'm writing reference my own work too heavily - it's time to move on from those topics; (ii) quantity increasingly means less to me and quality more; (iii) the relationships I've built are at least as important as the work that I've done; (iv) my impatience has been both a blessing and a curse; and (v) working with students has been the most challenging, rewarding, and (it seems to me) impactful part of the job.
2016: (i) my interests and energies have focused as the years have gone by, and I expect that they will continue to do so; (ii) seven years ago, I could not have predicted what I would be working on today, and in the next seven years, I hope that my interests will change as much or more; (iii) staying engaged and passionate about research has required increased attention and intention as the years have gone by, and going forward, I hope that I can maintain, or grow, my engagement and passion for research; (iv) my research relationships remain very important, and I want them to continue to grow; (v) mentoring students remains one of my favorite parts of the job, and I hope for many more opportunities to play the mentor role; and finally, (vi) I'm increasingly interested in doing service within my research community.