P
PAPER
chemical informatics
21–27
future work
33
vs . OpenEye ROCS
30 , 32
Parallel computing techniques
brain connectivity reconstruction
793
DBT
648
fast circuit optimization
basic problem
365–367
core method
367–369
future work
376
gate-level task scheduling
369–372
GPU-based
368–369
parallel gate implementation evaluation
372–373
performance evaluation
373–375
genome-matching
algorithms, implementations, evaluations
176–183
basic problem
173–174
benefits and limitations
183
core methods
174–176
CUDA-CPU execution
181
CUDA kernel parameter settings
180–181
data layout
179–180
future work
183
gaps and mismatches
181–182
genome encoding
177–178
hashing
182
performance scaling
182–183
smaller threads
181
target headers
178–179
target processing
180
LDPC
623
medical image processing
746 , 748
programmable graphics pipeline
427
Parallel distribution, BigDFT code
147
Parallel imaging (PI)
SPIRiT MRI
735
Parallelism
ant colony optimization
325
ASR
603 , 615
atlas construction
779
Barnes Hut n -body algorithm
75 , 86 , 89
B-spline registration
752
chemical informatics
19–20 , 22–23 , 25 , 27–28 , 32
CT image reconstruction
673
DFT
38 , 140
fast circuit optimization
365–366 , 368–370 , 376
Fast Graph Cuts
440 , 447
gate-level simulation
343–344 , 349 , 361–363
image de-mosaicing
585
machine learning
282 , 290
medical image processing
737–738
molecular electrostatics
43 , 49
MRI reconstruction
717
n -body simulation
113 , 116 , 122
object detection
536–537
pattern matching
185 , 190–192 , 196
photon transport
249
programmable graphics pipeline
434
radiographic image simulation
824
real-time speed-limit-sign recognition
498 , 514
SPIRiT MRI
729 , 732 , 735
SVM
296 , 304 , 310
SW algorithm
157
template-driven agent-based modeling
313
Parallelization techniques
ASR
615
black hole simulations
106
brain connectivity reconstruction
795
B-spline registration
762
CT image reconstruction
algorithms, implementations, evaluations
661–672
backprojection
669–672
backward mapping
669
basic problem
659
convolution
666 , 668–669
core methods
659–660
differentiation
663–666
forward mapping
666–668
future work
676
performance evaluation
672–675
projection's filtering
663–669
related work
675–676
DFT
145 , 149
facial animation
423
fast circuit optimization
366–368 , 376
FFT
637
Graph Cuts for computer vision
440 , 442–443 , 446
push operation
441–443
relabel operation
443–444
GSO calculations, overview
22–23
image/video processing
561
iterated function systems
264–265
LB model
383
LDPC
623
L’Ecuyer's multiple recursive generator MRG32k3a
233–234
machine learning
281 , 288
Mersenne Twister MT19937
238
molecular electrostatics
47
n -body simulation
129
radiographic image simulation
821 , 825
random number generators
L’Ecuyer's multiple recursive generator MRG32k3a
232–235
Mersenne Twister MT19937
237–242
overview
231–232
performance evaluation
242–245
Sobol generator
235–236
RNA folding problem
194 , 203–205
Sobol quasi-random generator
235–236
SPIRiT MRI
727 , 729 , 732 , 734–735
SVM
310
temporal data mining
214–215 , 217 , 219 , 221–222
Parallel local tracking, temporal data mining
216–217
Parallel programming
ASR
617
DBT
648
fast circuit optimization
374
image de-mosaicing
584
MRI reconstruction
709–710 , 712–713 , 715 , 720
Parallel scan, pattern matching
188–192 , 195–198
Pareto optimal set, CT reconstruction performance
707
Park-Miller pseudorandom number generator
334
Partial differential equations (PDEs)
atlas construction
778
brain connectivity reconstruction
794–795
ITK-based medical imaging
740
LB methods
383
Particle to multipole treecode (P2M), fast n -body simulations
115–116 , 120
Particle to particle treecode (P2P), fast n -body simulations
115–117 , 120 , 122–125
Path regeneration, random walks
implementation
406–408
overview
401–406 , 410
path regeneration
404–406
processing unit utilization
403
research results
408–410
sparse warps
404
Patterned-Pixel Group method (PPG), de-mosaicing
586 , 595–597
Pattern matching acceleration, with supercomputer clusters
algorithms, implementations, evaluations
187–192
antidiagonal approach
188–189
basic problem
185–186
core method
186–187
data packing
192
future work
196
hash tables
192
overlapping search
191–192
overview
193–196
reduced dependency
187–188
row/column parallel approach
188–191
Peak-to-sidelobe ratio (PSR), speed-limit-sign recognition
502
Pearson's correlation coefficient (PMCC), image/video processing
547–551 , 561–563
PENELOPE, radiographic image simulation
814–815 , 818 , 820 , 824 , 827–828
Perceptual linear prediction (PLP), speech models
613
Performance analysis
ABM with CUDA
321–323
AntMinerGPU
337–339
atlas construction
786–789
atlas construction tuning
785–786
BigDFT code
140 , 145–147 , 150
brain connectivity reconstruction
809–811
B-spline registration
767–769
CCL in CUDA
577–581
Chaos game algorithm
270–272
CT reconstruction
672–675 , 700–703
de-mosaicing
597–598
facial animation
424–425
fast circuit optimization
373–375
gate-level simulation
355–362
genome-matching acceleration
182–183
Graph Cuts for computer vision
447–448
GRASSY platform
100
image/video processing
551–552 , 554–560 , 565–566
large-scale FFT
639–641
LB methods
393–395
MRI reconstruction
719–720
object-detection with CUDA
541–543
programmable graphics pipeline in CUDA
433–434
radiographic image simulation
822–827
random number generators
242–245
speed-limit-sign recognition
507–513
SPIRiT MRI
733–734
stereo matching
486–493
temporal data mining
222–226
Pheromone
and ACO
326
AntMinerGPU
330 , 332–333 , 335 , 337
Photon buffer, photon transport
256
Photon density, LB methods
384–386
Photon transport
absorption sampling
254
basic physics
247–249
complete system
256–258
free path sampling
250–254
future work
259 , 261
implementation results
258–259
LB lighting model
394
overview
249–250
parallel random number generation
256
path divergence
249
radiation dose visualization
260–261
scattering direction
254–256
scattering in media
248
Pipeline model, VSM
465–466
Pixels
brain connectivity reconstruction
793–795 , 798–803 , 812
character recognition application
289
CT image reconstruction
666 , 670–672 , 695–696 , 703
Graph Cuts for computer vision
439 , 442 , 446–449
image de-mosaicing
583–597
image/video processing
548–550 , 552 , 554 , 556 , 560–563
iterated function systems
269
medical image processing
738–740 , 742–746
MRI reconstruction
711
order-independent transparency
428–434
radiographic image simulation
814–817 , 821–826
random walk path regeneration
401–403 , 406
speed-limit-sign recognition
499 , 505–507
SPIRiT MRI
728–730
volumentric
see Voxels
PKU McClus cluster
architecture
630–631
large-scale FFT
639–641
Planck constant, photon transport
248
Plant rendering
390–392
Plastics rendering
392–393
Playable Universal Capture
414
Pointer-chasing memory operations, Barnes Hut n -body algorithm via CUDA
75–76
Point-generation kernel, Chaos Game algorithm
267
Poisson-Boltzmann Equation (PBE), electrostatics algorithms
44
Poisson equation, and BigDFT code
134 , 137
Poisson problems, gravitation/electrostatics
113
Poisson process, temporal data mining
222
Poisson statistics, tomographic image reconstruction
689
Polymethyl methacrylate (PMMA), rendering
392–393
Population size, and AntMinerGPU performance
338–339
Positron emission tomography (PET)
basic principle
680
deformable registration algorithm
751–752
image reconstruction from randomly ordered lines
algorithms, implementations, evaluations
684–686
backprojection
686
challenges
681–682
core methods
682–684
forward-projection
685–687
future work
690–691
line-projection accuracy
688–690
list-mode image reconstruction
679–681
overview
684–685
processing time
686 , 688
vs . x-ray CT
682
Post-Newtonian (PN) approximation, overview
104–105
Precision issues
see also Double-precision (DP); ; Single-precision (SP)
astrophysics
101
black hole simulations
106
B-spline registration
751
CT image reconstruction
660
dynamical quadrature grids
35 , 39–40
GRASSY platform
97–99
image de-mosaicing
586
molecular electrostatics
55–56
object detection
521 , 532 , 540
radiographic image simulation
824
real-time stereo
475
PreElim algorithm, temporal data mining
220–222 , 224–226
Prefix sums
CCL
581
iterated function systems
270
object detection
527–528 , 534
template-driven agent-based modeling
314–315 , 320
temporal data mining
218–219
Processed gate, definition
370–371
Programmable graphics pipeline, for order-independent transparency
algorithms, implementations, evaluations
428–433
basic problem
427–428
core method
428
fixed-size A-buffer scheme
433
future work
435
multidepth test scheme
432–433
performance evaluation
433–434
pseudocode
431
system overview
428–431
Progressive multiresolution adaptive windows, real-time stereo on GP-GPU
algorithms, implementations, evaluations
475–485
basic problem
473–474
core method
475
cross-checking
484–485
foreground vs . full image
490–493
Middlebury evaluation
486–487
multiresolution background modeling
475–478
multiresolution vs . single resolution
487–490
multiresolution stereo matching
478–479
performance evaluation
486–493
single CUDA kernel
479–485
Projection kernel
definition
679
image reconstruction
685
tomographic image reconstruction
682 , 684–686
Projections-Over-Convex-Sets (POCS) method
OS-SIRT
695
SPIRiT MRI
726–727 , 733
Propagation
ASR graph traversal
608–610
belief propagation
487 , 620 , 627
electronic structure
59–72
fast circuit optimization
365–367
gate-level simulation
345 , 363
information in computer vision
447
random walk path regeneration
401–402
Prospective gate, fast circuit optimization
370–371 , 377
Pseudoknots, RNA folding
200
Push operation, Graph Cuts for computer vision
overview
440–441
parallel push implementation
441–443
parallel relabel implementation
443–444
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