SCI Publications

2008


C.T. Silva, J. Freire. “Software Infrastructure for Exploratory Visualization and Data Analysis: Past, Present and Future,” In Journal of Physics: Conference Series (SciDAC 2008 Conference), Vol. 125, 2008.


J. Spjut, D. Kopta, S. Kellis, S. Boulos, E. Brunvand. “TRaX: A Multi-Threaded Architecture for Real-Time Ray Tracing,” In Proceedings of the IEEE Symposium on Application Specific Processors, SASP 2008, Note: Awarded Best Paper, pp. (in press). 2008.


M. Steffen, S. Curtis, R.M. Kirby, J.K. Ryan. “Investigation of Smoothness-Increasing Accuracy-Conserving Filters for Improving Streamline Integration Through Discontinuous Fields,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 14, No. 3, pp. 680--692. 2008.


M. Steffen, R.M. Kirby, M. Berzins. “Analysis and Reduction of Quadrature Errors in the Material Point Method (MPM),” In International Journal for Numerical Methods in Engineering, Vol. 76, No. 6, pp. 922--948. 2008.
DOI: 10.1002/nme.2360


M. Steffen, P.C. Wallstedt, J.E. Guilkey, R.M. Kirby, M. Berzins. “Examination and Analysis of Implementation Choices within the Material Point Method (MPM),” In Computer Modeling in Engineering & Sciences, Vol. 31, No. 2, pp. 107--127. 2008.


J.G. Stinstra, M.A. Jolley, J.D. Tate, D.H. Brooks, J.K. Triedman, R.S. MacLeod. “The Role of Volume Conductivities in Simulation of Implantable Defibrillators,” In Computers in Cardiology, Bologna, Italy, 2008.


J.G. Stinstra, M. Jolley, M. Callahan, D.M. Weinstein, M. Cole, D.H. Brooks, J. Triedman, R.S. MacLeod. “Evaluation of Different Meshing Algorithms in the Computation of Defibrillation Thresholds in Children,” In Proceedings of the 29th Annual International Conference of the IEEE EMBS, pp. 1422-1425. 2008.
ISBN: 978-1-4244-0787-3


M. Styner, I. Oguz, T. Heimann, G. Gerig. “Minimum Description Length with Local Geometry,” In Proceedings of the 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2008), pp. 1283--1286. 2008.
DOI: 10.1109/ISBI.2008.4541238


D.R. Sutherland, Q. Ni, R.S. MacLeod, R.L. Lux, B.B. Punske. “Experimental Measures of Ventricular Activation and Synchrony,” In Pacing and Clinical Electrophysiology, Vol. 31, No. 12, pp. 1560--1570. December, 2008.


B. Taccardi, B.B. Punske, E. Macchi, R.S. MacLeod, P.R. Ershler. “Epicardial and Intramural Excitation During Ventricular Pacing: Effect of Myocardial Structure,” In The American Journal of Physiology - Heart and Circulatory Physiology, Vol. 294, No. 4, pp. H1753--1766. April, 2008.
DOI: 10.1152/ajpheart.01400.2007


T. Tasdizen. “Principal Components for Non-Local Means of Image Denoising,” In Proceedings of the International Conference on Image Processing (ICIP 2008), pp. 1728--1731. 2008.
PubMed ID: 19180227


T. Tasdizen , E. Jurrus, R. T. Whitaker. “Non-uniform Illumination Correction in Transmission Electron Microscopy,” In MICCAI Workshop on Microscopic Image Analysis with Applications in Biology, 2008.

ABSTRACT

Transmission electron microscopy (TEM) provides resolutions on the order of a nanometer. Hence, it is a critical imaging modality for biomedical analysis at the sub-cellular level. One of the problems associated with TEM images is variations in brightness due to electron imaging defects or non-uniform support films and specimen staining. These variations render image processing operations such as segmentation more difficult. The correction requires estimation of the global illumination field. In this paper, we propose an automatic method for estimating the illumination field using only image intensity gradients. The closed-form solution is very fast to compute.


L.T. Tran, J. Kim, M. Berzins. “An Introduction to the Material Point Method using a Case Study from Gas Dynamics,” In Numerical Analysis and Applied Mathematics: International Conference on Numerical Analysis and Applied Mathematics 2008. AIP Conference Proceedings, Vol. 1048, Edited by T.E. Simos and G. Psihoyios and Ch. Tsitouras, pp. 26--29. 2008.
ISBN: 978-0-7354-0576-9


X. Tricoche, R.S. MacLeod, C.R. Johnson. “Visual Analysis of Bioelectric Fields,” In Visualization in Medicine and Life Sciences, Mathematics and Visualization, Springer-Verlag, pp. 205--220. 2008.


J.K. Triedman, M. Jolley, J. Stinstra, D.H. Brooks, R.S. MacLeod. “Predictive Modeling of Defibrillation Using Hexahedral and Tetrahedral Finite Element Models: Recent Advances,” In Journal of Electrocardiology, Vol. 41, pp. 483--486. 2008.


S. Vakkalanka, M. DeLisi, G. Gopalakrishnan, R.M. Kirby, R. Thakur, W. Gropp. “Implementing Efficient Dynamic Formal Verification Methods for MPI Programs,” In Recent Advances in Parallel Virtual Machine and Message Passing Interface Lecture Notes in Computer Science, Dublin, Ireland, Vol. 5205, pp. 248--256. September, 2008.

ABSTRACT

We examine the problem of formally verifying MPI programs for safety properties through an efficient dynamic (runtime) method in which the processes of a given MPI program are executed under the control of an interleaving scheduler. To ensure full coverage for given input test data, the algorithm must take into consideration MPI’s out-of-order completion semantics. The algorithm must also ensure that nondeterministic constructs (e.g., MPI wildcard receive matches) are executed in all possible ways. Our new algorithm rewrites wildcard receives to specific receives, one for each sender that can potentially match with the receive. It then recursively explores each case of the specific receives. The list of potential senders matching a receive is determined through a runtime algorithm that exploits MPI’s operation ordering semantics. Our verification tool ISP that incorporates this algorithm efficiently verifies several programs and finds bugs missed by existing informal verification tools.


S. Vakkalanka, M. DeLisi, G. Gopalakrishnan, R.M. Kirby. “Scheduling Considerations for Building Dynamic Verification Tools for MPI,” In Proceedings of the 6th Workshop on Parallel and Distributed Systems: Testing, Analysis, and Debugging, Seattle, WA, PADTAD '08, Vol. 3, ACM, pp. 1--6. 2008.
ISBN: 978-1-60558-052-4
DOI: 10.1145/1390841.1390844


S. Vakkalanka, G. Gopalakrishnan, R.M. Kirby. “Dynamic Verification of MPI Programs with Reductions in Presence of Split Operations and Relaxed Orderings,” In Computer Aided Verification Lecture Notes in Computer Science , Vol. 5123, pp. 66--79. July, 2008.
DOI: 10.1007/978-3-540-70545-1_9

ABSTRACT

Dynamic verification methods are the natural choice for debugging real world programs when model extraction and maintenance are expensive. Message passing programs written using the MPI library fall under this category. Partial order reduction can be very effective for MPI programs because for each process, all its local computational steps, as well as many of its MPI calls, commute with the corresponding steps of all other processes. However, when dependencies arise among MPI calls, they are often a function of the runtime state. While this suggests the use of dynamic partial order reduction (DPOR), three aspects of MPI make previous DPOR algorithms inapplicable: (i) many MPI calls are allowed to complete out of program order; (ii) MPI has global synchronization operations (e.g., barrier) that have a special weak semantics; and (iii) the runtime of MPI cannot, without intrusive modifications, be forced to pursue a specific interleaving because of MPI’s liberal message matching rules, especially pertaining to ‘wildcard receives’. We describe our new dynamic verification algorithm ‘POE’ that exploits the out of order completion semantics of MPI by delaying the issuance of MPI calls, issuing them only according to the formation of match-sets, which are ample ‘big-step’ moves. POE guarantees to manifest any feasible interleaving by dynamically rewriting wildcard receives by specific-source receives. This is the first dynamic model-checking algorithm with reductions for (a large subset of) MPI that guarantees to catch all deadlocks and local assertion violations, and is found to work well in practice.


S.X. Vasquez, M.S. Hansen, A.N. Bahadur, M.F. Hockin, G.L. Kindlmann, L. Nevell, I.Q. Wu, D.J. Grunwald, D.M. Weinstein, G.M. Jones, C.R. Johnson, J.L. Vandeberg, M.R. Capecchi, C. Keller. “Optimization of Volumetric Computed Tomography for Skeletal Analysis of Model Genetic Organisms,” In The Anatomical Record: Advances in Integrative Anatomy and Evolutionary Biology, Vol. 291, pp. 475--487. 2008.
PubMed ID: 18286615


A.I. Veress, J.A. Weiss, R.H. Huesman, B.W. Reutter, S.E . Taylor, A. Sitek, B. Feng, Y. Yang, G.T. Gullberg. “Measuring Regional Changes in the Diastolic Deformation of the Left Ventricle of SHR Rats Using MicroPET Technology and Hyperelastic Warping,” In Annals of Biomedical Engingeering, Vol. 36, No. 7, pp. 1104--1017. 2008.