• Parallel Computing
• Adaptive Sampling, Clinical Trials, and Statistics
• Scientific Computing and Computational Science, especially Space and Earth Modeling
• Theoretical Computer Science
• Serial Algorithms and Data Structures
• Discrete Mathematics: Graph Theory, Combinatorics, Geometry, Codings, Probability
• Operator Theory, Analysis
• Other Research (including Neural Networks)
• Teaching-Related Publications

Here is my standard academic vita. Several of the papers mentioned there are omitted here since an updated version was publshed later.

Here are some simple explanations of response adaptive sampling and parallel computing

Overview of Research Interests.

Home page.

Parallel Computing

Talks

• Space, Time, Power: Evolving Concerns for Parallel Algorithms, a talk about the evolution of goals/concerns of parallel models and algorithms, including cellular automata, mesh connected computers, reconfigurable meshes, and power-constrained algorithms for mesh connected computers. It mentions zebra networks and rat algorithms, along with more mundane computers such as the BlueGene and Earth Simulator, and abstract models such as PRAMs and quantum computers. Note that the time required by cellular automata can be viewed as the limits of classical physics, since it takes a constant amount of time to move a fixed distance. Further, the power-constained algorithms examine the question of how much energy is needed to solve a problem using classical physics, and the peak energy vs. time tradeoffs.

Books Authored

• R. Miller and Q.F. Stout, Parallel Algorithms for Regular Architectures: Meshes and Pyramids, MIT Press, 1996.
  Keywords: parallel computing, parallel algorithms, mesh computer, VLSI algorithms, pyramid, data movement operations, graph algorithms, image processing, computational geometry, lower bounds, optimal algorithms.

• Q.F Stout and C. Jablonowski, Parallel Computing 101. While not a standard book, the notes for this tutorial are essentially a book overviewing parallel computing and how to develop efficient parallel programs. The tutorial and notes are continually being updated.
  Keywords: parallel programming, performance, MPI, OpenMP, Amdahl's law, software engineering, scientific computing, supercomputing, load balancing, code tuning.

Books Edited

• H. Li and Q.F. Stout, eds., Reconfigurable Massively Parallel Computers, Prentice Hall, 1991.

• D.W. Walker and Q.F. Stout, eds., Proceedings 5th Distributed Memory Computing Conference, IEEE Computer Society, 2 vols., 1990.

• M. Wolfe and Q.F. Stout, Proceedings 6th Distributed Memory Computing Conference, IEEE Computer Society, 1991.

• Q.F. Stout, ed., Proceedings 1992 International Conference on Parallel Processing, Vol. III Algorithms and Applications, Computer Science Press.

Chapters in Books

• R. Miller and Q.F. Stout, Algorithmic techniques for networks of processors, in CRC Handbook of Algorithms and Theory of Computation, 2nd ed, M. Atallah, ed., CRC Press, 2009, pp. 46:1-46:18.
  Keywords: algorithmic paradigms, divide-and-conquer, pipelining, master-slave, mapping problem, weak embeddings, mesh computer, pyramid, hypercube, PRAM, distributed memory, shared memory.    abstract   paper.pdf 

• Q.F. Stout and J. Hardwick, Parallel programs for adaptive designs, Handbook of Parallel Computing and Statistics, E. Kontoghiorghes, ed., Marcel Dekker, 2006, pp. 347-373.
  Keywords: multi-arm bandit models, dynamic programming, clinical trial, delayed response, response adaptive sampling, parallelizing recursive equations, sequential analysis.    abstract   paper.pdf

• T. Gombosi et al., Adaptive mesh refinement MHD for global space weather simulations, Space Plasma Simulation, J. Buchner, C.T. Dum, M. Scholer, eds., Lecture Notes in Physics 615, Springer-Verlag, 2003, pp. 251-279.
  Keywords: solution adaptive mesh refinement, AMR, MHD, space environment modeling, adaptive grid.     abstract   paper.pdf

• J. Hardwick, R. Oehmke, and Q.F. Stout, Optimal adaptive designs for delayed response models: exponential case, MODA6: Model Oriented Data Analysis, A. Atkinson, P. Hackl, W. Mueller, eds., Physica Verlag, 2001, pp. 127-134.
  Keywords: delayed response, sequential analysis, dynamic programming, computational learning theory, active learning, bandit models, parallel computing, response adaptive sampling, clinical trial, design of experiments, clinical trial.    abstract   paper.pdf

• R. Miller and Q.F. Stout, Algorithmic techniques for networks of processors, in CRC Handbook of Algorithms and Theory of Computation, M. Atallah, ed., CRC Press, 1999, pp. 46:1-46:19.
  Keywords: algorithmic paradigms, divide-and-conquer, pipelining, master-slave, mapping problem, weak embeddings, mesh computer, pyramid, hypercube, PRAM, distributed memory, shared memory.    abstract   paper.pdf 

• S. Colley, J.P. Hayes, T.N. Mudge, J. Palmer, and Q.F. Stout, A microprocessor-based hypercube supercomputer, in Multi-Microprocessors, A. Gupta, ed., IEEE Press, 1987, pp. 250-260. Reprint of article first appearing in IEEE Micro 6 (1986), pp. 6-17. This article won the IEEE Micro ``Best Article Award'' for 1986.
  Keywords: hypercube computer, supercomputing, store-and-forward message passing, I/O systems, medium-grain parallel computer, software.

• Q.F. Stout, Pyramid algorithms optimal for the worst case, in Parallel Computer Vision, L. Uhr, ed., Academic Press, 1987, pp. 147-168.
  Keywords: mesh local, perimeter bound, strongly global, image processing, communication lower bounds, component labeling, data squares, data movement operations, data square pyramid computer, parallel computing.

• Q.F. Stout, Hypercubes and pyramids, in Pyramidal Systems for Computer Vision, V. Cantoni and S. Levialdi, eds., NATO ASI Series ARW Vol. F 25, Springer-Verlag, 1986, pp. 75-89.
  Keywords: hypercube computers, pyramid algorithms, graph embeddings, image processing, hyper-pyramid     abstract   paper.pdf

• Q.F. Stout, An algorithmic comparison of meshes and pyramids, in Evaluation of Multicomputers for Image Processing, L. Uhr, K. Preston, S. Levialdi, and M.J.B. Duff, eds., Academic Press, 1986, pp. 107-121.
  Keywords: parallel computer, mesh, pyramid, image algorithms, convexity, component labeling, divide-and-conquer.

Journals and Conference Proceedings

• Q.F. Stout, Low power mesh algorithms for image problems, arXiv 2212.02640
  Keywords: fine-grain mesh-connected computer, low power, image processing, connected components, closest point problems, maze     abstract   paper.pdf

• T. Lewis and Q.F. Stout, A framework for recursive algorithms on low-energy sensor networks, Int'l. J. Parallel, Emergent, and Distrib. Sys. 91, 2018.

• Y. An and Q.F. Stout, Optimal algorithms for a mesh-connected computer with limited additional global bandwidth, Proc. IPDPS 2017, 51-61.

• Y. An and Q.F.Stout, Optimal algorithms for graphs and images on a shared memory mesh, Proc. IPDPS 2016,

• P. Poon and Q.F. Stout, An optimal time-power tradefoff for sorting on a mesh-connected computer with on-chip optics, Int.'l. J. Networking and Computing 4, 2014, 70-77.

• P. Poon and Q.F. Stout, Time-power tradeoffs for sorting on a mesh-connected computer with optical connections, Proc. IPDPS 2013.
  Keywords: minimize peak power, low energy, optical network on chip NoC, pyramid interconnection, sorting, nearest neighbor, minimum spanning tree, dark silicon     abstract   paper.pdf

• J. Lipman and Q.F. Stout, Analysis of delays caused by local synchronization, SIAM J. Computing 39 (2010), pp. 3860-3884.
  Keywords: synchronization delay, overhead, performance analysis, barrier, geometric distribution, heavy-tailed distribution, stochastic task times, idle time    abstract   paper.pdf

• Q.F. Stout, Algorithms minimizing peak energy on mesh-connected systems, preliminary results in Symp. Parallelism in Algorithms and Architectures (SPAA) 2006.
  Keywords: peak power consumption, energy, rat algorithm, image processing, graph algorithm, mesh.    abstract   paper.pdf
  Only the abstract was presented at SPAA, and the full paper was not published. The talk Space, Time, Power: Evolving Concerns for Parallel Algorithms mentions some of these results, as does the paper Low power mesh algorithms for image problems

• C. Jablonowski et al., Block-structured adaptive grids on the sphere: advection experiments, Monthly Weather Review 134 (2006), 3691-3713.
  Keywords: adaptive mesh refinement, AMR, atmospheric modeling, spherical adaptive grid, adaptive block, weather, climate    abstract   paper.pdf

• J. Hardwick, R. Oehmke, Q.F. Stout, New adaptive designs for delayed responses, Journal of Statistical Planning and Inference 136 (2006), pp, 1940-1955.
  Keywords: hyperopic design, bandit models, randomized play-the-winner, response adaptive sampling.    abstract   paper.pdf

• J.E. Penner et al., Development of an atmospheric climate model with self-adapting grid and physics, J. Physics Conf. Series 16 (2005), pp. 353-357.
  Keywords: adaptive mesh refinement, AMR, atmospheric modeling, spherical adaptive grid, adaptive block, climate, weather.    abstract   paper.pdf

• G. Toth et al., Space Weather Modeling Framework: a new tool for the space science community (2005), J. Geophysical Research 110, A12226, doi:10.1029/2005JA011126.
  Keywords: scientific computing framework, high performance computing, space environment modeling, grid coupling, SWMF.     abstract   paper.pdf

• C. Jablonowski et al., ``Adaptive grids for weather and climate models'', ECMWF Proc. Recent Developments in Numerical Methods for Atmospheric and Climate Modeling (2004), pp. 233-250.
  Keywords: climate modeling, weather, solution adaptive mesh refinement, AMR, spherical adaptive grid, adaptive block.     abstract   paper.pdf

• G. Toth et al., A physics-based software framework for Sun-Earth connection modeling, Multiscale Coupling of Sun-Earth Processes, Proc. Conf. on the Sun-Earth Connection, Kona, Hawaii, 2004, A. T. Y. Lui, Y. Kamide, and G. Consolini, eds., Elsevier, pp. 383-397.
  Keywords: parallel computing, high-performance computing, software engineering, space environment modeling, coupling.    abstract   paper.pdf

• T.I. Gombosi et al., Solution adaptive MHD for space plasmas: Sun-to-Earth simulations, Computers in Science and Engineering 6 (2004), pp. 14-35.
  Keywords: adaptive mesh refinement, parallel computing, geoscience.    abstract   paper.pdf

• T. Gombosi et al., ``Adaptive mesh refinement MHD for global simulations'', Proc. ISSS-6 (2001), 8 p.
  Keywords: solution adaptive mesh refinement, AMR, space plasma simulations.     abstract   paper.pdf

• R. Oehmke and Q.F. Stout, ``Parallel adaptive blocks on the sphere'', Proc. 10th SIAM Conf. Parallel Processing for Scientific Computing (2001).
  Keywords: adaptive mesh refinement, AMR, data structure, parallel computing, geoscience, multi-scale modeling, spherical adaptive grid, geometric decomposition, high performance computing.    abstract   paper.pdf

• D.L. De Zeeuw et al., ``An adaptive MHD method for global space weather simulations'', IEEE Trans. Plasma Science 28 (2000), pp. 1956-1965.
  Keywords: space weather, adaptive mesh refinement, MHD, supercomputing, Sun-Earth, space physics, scientific computing.    abstract   paper.pdf

• C.R. Clauer et al., High performance computer methods applied to predictive space weather simulations, IEEE Trans. Plasma Science 28 (2000), pp. 1931-1937.
  Keywords: space weather, adaptive mesh refinement, MHD, supercomputing, Sun-Earth, space physics, scientific computing.    abstract   paper.pdf

• R. Oehmke, J. Hardwick, and Q.F. Stout, ``Scalable algorithms for adaptive statistical designs'', Proceedings SC 2000 (Supercomputing), 16 p. Finalist, Best Paper. Reprinted in Scientific Programming 8 (2001), pp. 183-193.
  Keywords: dynamic programming, computational learning theory, active learning, bandit models, dynamic domain decomposition, memory-intensive computing, response adaptive sampling, message-passing, load balancing, sequential analysis, performance analysis, experimental algorithms, recursive equations, design of experiments, MPI, IBM SP, OpenMP, SGI Origin.    abstract   paper.pdf

• J. Hardwick, R. Oehmke, and Q.F. Stout, ``A program for sequential allocation of three Bernoulli populations'', Computational Statistics and Data Analysis 31 (1999), pp. 397-416.
  Keywords: bandit models, dynamic programming, response adaptive sampling, sequential sampling, clinical trial, high-performance computing, load balancing, recursive equations.    abstract   paper.pdf

• A.A. Poe and Q.F. Stout, ``Load balancing 2-phased geometrically based problems'', Proc. 9th SIAM Conf. Parallel Processing for Scientific Computing (1999).
  Keywords: multi-weight load balancing, graph partitioning, ham sandwich theorem, geometric decomposition, impact analysis, crash simulation, domain decomposition, discrete computational geometry, multiple constraints.    abstract   paper.pdf

• T. Tabe and Q.F. Stout, ``The use of the MPI communication library in the NAS Parallel Benchmarks'', submitted.
  Keywords: message passing, trace analysis, performance evaluation, scientific computing, distributed memory, communication kernel.    abstract   paper.pdf

• Q.F. Stout et al., ``Adaptive parallel computation of a grand-challenge problem: Prediction of the path of a solar-corona mass ejection'', Proc. SC98.
  Keywords: magnetohydrodynamics (MHD), space weather prediction, adaptive mesh refinement, Cartesian, adaptive block, Riemann solver, upwind schemes, scientific computing.    abstract   paper.html   paper.pdf

• M. Livingston and Q.F. Stout, ``Shift-product networks'', Mathematical and Computational Modeling, 1998, to appear.
  Keywords: interconnection networks, scalable networks, shuffle-exchange networks, Cayley graphs, product graphs, de Bruijn network, commodity components.    abstract   paper.pdf

• P.D. MacKenzie and Q.F. Stout, ``Ultra-fast expected time parallel algorithms'', J. Algorithms 26 (1998), pp. 1-33.
  Keywords: ultrafast, padded sort, geometry algorithms, CRCW PRAM, Voronoi diagram, all nearest neighbors, closest pair, relative neighborhood graph, Delaunay triangulation, largest empty circle, lower bounds, randomized algorithm.    abstract   paper.pdf

• Q.F. Stout et al., ``Adaptive blocks: A high-performance data structure'', Proc. SC97.
  Keywords: adaptive data structure, Cartesian, cache, high performance computing, mesh, refinement, oct-tree, scientific computing.    abstract   paper.html   paper.pdf

• T. Gombossi et al., ``Multiscale modeling of heliospheric plasmas'', High Performance Computing 1997, pp. 46-51.
  Keywords: magnetohydrodynamics, MHD, adaptive mesh refinement (AMR), Riemann solver, Cray T3D, solar wind, high-performance computing, HPCC, NASA Grand Challenge Investigator Team, upwind scheme, space plasma, scientific computing.    abstract   paper.pdf

• D. Van Wieren and Q.F. Stout, ``Ultrafast graph algorithms on reconfigurable meshes'', Proc. 2nd Work. on Reconfigurable Architectures (1995), pp. 1-13.
  Keywords: ultrafast algorithms, reconfigurable mesh, rmesh, MasPar, edge cover, Hamiltonian cycle, spanning trees, randomized algorithm.    abstract  paper.pdf

• T. Tabe, J. Hardwick and Q.F. Stout, ``Statistical analysis of communication on the IBM SP2'', Computing Science and Statistics 27 (1995), pp. 347-351.
  Keywords: MPI, collective communication, MPI_ALLTOALL, MPI_SEND, resampling, performance evaluation, message passing, operating systems, interrupts, heavy tails, benchmarking.    abstract   paper.pdf

• R. Miller, V.K. Prasanna Kumar, D. Reisis and Q.F. Stout, ``Parallel computations on reconfigurable meshes'', IEEE Trans. on Computers 42 (1993), pp. 678-692.
  Keywords: reconfigurable mesh, image algorithms, graph algorithms, parallel algorithms, VLSI, mesh, PRAM, mesh-of-trees, pyramid computer, component labeling, global or, prefix calculation, parity, xor.    abstract   paper.pdf

• P.D. MacKenzie and Q.F. Stout, ``Optimal parallel construction of Hamiltonian cycles and spanning trees in random graphs'', Proc. 5th ACM Symp. Parallel Algorithms and Architectures (1993), pp. 224-229.
  Keywords: ultrafast algorithms, CRCW PRAM, edge cover, lower bounds, parallel target shooting, randomized algorithm.    abstract   paper.pdf

• E. Cohen, R. Miller, E.M. Sarraf and Q.F. Stout, ``Efficient convexity and domination algorithms for fine- and medium-grain hypercube computers'', Algorithmica 7 (1992), pp. 51-75.
  Keywords: convex hull, domination, sorting, hypercube algorithms, computational geometry, worst-case, expected case.    abstract   paper.pdf

• Q.F. Stout, ``Ultrafast parallel algorithms and reconfigurable meshes'', Proc. DARPA Software Technology Conference (1992), pp. 184-188.
  Keywords: pram, rmesh, randomization, lower bounds, padded sort, graph theory, image processing.    abstract   paper.pdf

• E. Hao, P.D. Mackenzie and Q.F. Stout, ``Selection on the reconfigurable mesh'', Proc. Frontiers 1992: 4th Symp. on Frontiers of Massively Parallel Computation (1992), pp. 38-45.
  Keywords: rmesh, lower bound, median, selection, 2-dimensional linear programming.     abstract   paper.pdf

• H. Li and Q.F. Stout, ``Reconfigurable SIMD parallel processors'', Proc. of the IEEE 79 (1991), pp. 429-443.
  Keywords: reconfigurable mesh, rmesh, connected components, image processing, fault tolerance, ultrafast algorithm.    abstract   paper.pdf

• M.L. Livingston and Q.F. Stout, ``Fault tolerance of the cyclic buddy subcube location scheme in hypercubes'', Proc. 6th Distributed Memory Computing Conf. (1991), IEEE, pp. 34-41.
  Keywords: fault tolerance, subcube location, subcube allocation, hypercube computer, buddy system, gray-coding, folded hypercube, projective hypercube.    abstract   paper.pdf

• R. Miller and Q.F. Stout, ``Computing convexity properties of images on a pyramid computer'', Algorithmica 6 (1991), pp. 658-684.
  Keywords: Pyramid computer, convexity, digitized pictures, digital geometry, image processing, parallel computing, parallel algorithms, data movement operations, bandwidth limitations, lower bounds.    abstract   paper.pdf

• P.D. MacKenzie and Q.F. Stout, ``Asymptotically efficient hypercube algorithms for computational geometry (preliminary version)'', Proc. 3rd Symp. Frontiers Massively Parallel Computation, (1990), pp. 8-11.
  Keywords: divide-and-conquer, hypercube sorting, domination, nearest neighbors, Voronoi diagram.    abstract   paper.pdf

• P.D. MacKenzie and Q.F. Stout, ``Practical hypercube algorithms for computational geometry (preliminary version)'', Proc. 3rd Symp. Frontiers Massively Parallel Computation, (1990), pp. 75-80.
  Keywords: divide-and-conquer, bitonic sort, domination, nearest neighbors, iso-oriented intersections, visibility, cross-stitching.    abstract   paper.pdf

• Q.F. Stout and B. Wagar, ``Intensive hypercube communication: Prearranged communication in link-bound machines'', J. of Parallel and Distributed Computing 10 (1990), pp. 167-181.
  Keywords: hypercube computer, n-cube, parallel communication, all-to-all communication, personalized communication, broadcasting, routing, permutations, matrix transpose, histogramming.    abstract   paper.pdf

• R. Miller and Q.F. Stout, ``Seymour: a portable parallel programming language'', Structured Programming 11 (1990), pp. 157-171.
  Keywords: parallel programming paradigms, global data movement operations, portable parallel programs, efficiency.    abstract

• R. Miller and Q.F. Stout, ``Mesh computer algorithms for computational geometry'', IEEE Trans. on Computers C-38 (1989), pp. 321-340.
  Keywords: parallel algorithms, mesh computer, computational geometry, planar point data, convexity, proximity, area, intersection.    abstract  paper.pdf

• M.L. Livingston and Q.F. Stout, ``Parallel allocation algorithms for hypercubes and meshes'', Proc. 4th Conf. on Hypercubes, Concurrent Computers, and Applications (1989), pp. 59-66.
  Keywords: subcube allocation, buddy system, cyclic buddy system, submesh allocation, torus.    abstract   paper.pdf

• R. Fenrich, R. Miller and Q.F. Stout, ``Hypercube algorithms for some NP-hard packing problems'', Proc. 4th Conf. on Hypercubes, Concurrent Computers, and Applications (1989), pp. 769-776.
  Keywords: 2-dimensional bin packing, best fit, NP-hard, parallel computing, hypercube computer, level algorithms.   abstract

• R. Miller and Q.F. Stout, ``Optimal hypercube algorithms for labeled images'', Algorithms and Data Structures: Proc. WADS '89, Springer-Verlag Lec. Notes in Comp. Sci. 382 (1989), pp. 517-528.
  Keywords: Parallel algorithms, hypercube computer, convexity, area, perimeter, diameter, smallest enclosing rectangle, image analysis, divide-and-conquer.   abstract   paper.pdf

• M.L. Livingston and Q.F. Stout, ``Distributing resources in hypercube computers'', Proc. 3rd Conf. on Hypercube Concurrent Computers and Applications (1988), ACM, pp. 222-231.
  Keywords: hypercube, subcube fault-tolerance, codes, buddy allocation, disk placement, parallel computing.   abstract   paper.pdf

• J. Gordon and Q.F. Stout, ``Hypercube message routing in the presence of faults'', Proc. 3rd Conf. on Hypercube Concurrent Computers and Applications (1988), ACM, pp. 318-327.
  Keywords: hypercube computer, fault tolerance, randomized routing, random graph, communication link, processor.   abstract   paper.pdf

• Q.F. Stout, ``Mapping vision algorithms to parallel architectures'', Proc. of the IEEE 76 (1988), pp. 982-995.
  Keywords; simulation, parallel algorithms, mesh, pyramid, hypercube, mesh-of-trees, PRAM, shared memory, lower bounds, data movement operations, computational geometry, image processing, graph algorithms.    abstract   paper.pdf

• Q.F. Stout, ``Constant-time geometry on PRAMs'', Proc. 1988 Int'l. Conf. on Parallel Processing, vol. III, IEEE, pp. 104-107.
  abstract   paper.pdf

• D.A. Buell et al., ``Parallel algorithms and architectures: Report of a workshop'', J. Supercomputing 1 (1988), pp. 301-325.

• R. Miller and Q.F. Stout, ``Efficient parallel convex hull algorithms'', IEEE Trans. Computers C-37 (1988), pp. 1605-1618.
  Keywords: AKS network, computational geometry, convex hull, EREW PRAM, hypercube, mesh, mesh-of-trees, reconfigurable mesh, pyramid, parallel algorithms, divide-and-conquer.   abstract  paper.pdf

• R. Miller and Q.F. Stout, ``Simulating essential pyramids'', IEEE Trans. Computers C-37 (1988), pp. 1642-1648.
  Keywords: pyramid computer, image processing, hypercube, rmesh, mesh computer, mesh-of-trees.    abstract   paper.pdf

• R. Miller and Q.F. Stout, ``Portable parallel algorithms for geometric problems'', Proc. 2nd Symp. Frontiers of Massively Parallel Computation (1988), pp. 195-198.
  Keywords: portable parallel algorithms, computational geometry, data movement operations, distributed memory parallel computers.   abstract  paper.pdf

• M.L. Livingston and Q.F. Stout, ``Fault tolerance of allocation schemes in massively parallel computers'', Proc. 2nd Symp. Frontiers of Massively Parallel Computation (1988), pp. 491-494.
  Keywords: fault tolerance, allocation, hypercube computer, mesh, torus, buddy system.   abstract  paper.pdf

• R. Miller and Q.F. Stout, ``Data movement techniques for the pyramid computer'', SIAM J. on Computing 16 (1987), pp. 38-60.
  Keywords: pyramid computer, graph algorithms, image processing, component labeling, mesh computer, data movement operations.     abstract  paper.pdf

• Q.F. Stout, ``Supporting divide-and-conquer algorithms for image processing'', J. of Parallel and Distributed Computing 4 (1987), pp. 95-115.
  Keywords: regular architectures, parallel algorithms, languages, bandwidth limitations, distributed memory, hypercube, mesh, pyramid, PRAM, shared memory, fine-grain, medium-grain, parallel programming paradigms.   abstract   paper.pdf

• Q.F. Stout, ``Meshes with multiple buses'', Proc. 27th IEEE Symp. on Foundations of Computer Science (1986), pp. 264-273.
  Keywords: row broadcasting, mesh computer, cooperative problem solving, cooperative speedup, optimal stepwise simulation, or, minimum, component labeling, spanning forest, tree, pyramid, mesh-of-trees, layouts.   abstract  paper.pdf

• R. Miller and Q.F. Stout, ``Geometric algorithms for digitized pictures on a mesh-connected computer'', IEEE Trans. on Pattern Analysis and Machine Intelligence 7 (1985), pp. 216-228.
  Keywords: mesh computer, computational geometry, convexity, digitized images, digital geometry, minimal paths, nearest neighbors, diameter, farthest points, divide-and-conquer.   abstract  paper.pdf

• Q.F. Stout, ``Mesh and pyramid computers inspired by geometric algorithms'', Proc. Work. on Algorithm-Guided Parallel Architectures for Automatic Target Recognition (1985), pp. 293-315.

• Q.F. Stout, ``Pyramid computer solutions of the closest pair problem'', J. of Algorithms 6 (1985), pp. 200-212.
  Keywords: pyramid cellular automata, self-organizing, pyramid computers, closest pair, computational geometry, nearest neighbors, parallel algorithms, finite automaton.   abstract   paper.pdf

• Q.F. Stout, ``Tree-based graph algorithms for some parallel computers'', Proc. 1985 Int'l. Conf. on Parallel Processing, IEEE, pp. 727-730.
  Keywords: parallel graph algorithms, component labeling, unordered edge input, spanning forest, descendant functions, ancestor functions, preorder, postorder.   abstract   paper.pdf

• R. Miller and Q.F. Stout, ``Varying diameter and problem size in mesh-connected computers'', Proc. 1985 Int'l. Conf. on Parallel Processing, IEEE, pp. 697-699.
  Keywords: mesh computer, semigroup operations, component labeling, image algorithms, convex hull, minimal spanning forest, communication bounds.    abstract   paper.pdf

• Q.F. Stout, ``Optimal component labeling algorithms for mesh-connected computers and VLSI'', arXiv 1502.01435.
  Keywords: minimal spanning forest, minimal spanning tree, component labeling, mesh-connected computer   abstract   paper.pdf

• Q.F. Stout, ``Topological matching'', Proc. 15th ACM Symp. on Theory of Computing (1983), pp. 24-31.
  Keywords: image processing, deformation, self-organizing cellular automata (array), clerks, mesh computer, tree isomorphism.   abstract   paper.pdf

• Q.F. Stout, ``Sorting, merging, selecting, and filtering on tree and pyramid machines'', Proc. 1983 Int'l. Conf. on Parallel Processing, IEEE, pp. 214-221.
  Keywords: pyramid computer, x-tree, tree computer, sorting, merging, selection, median filtering, image processing.   abstract   paper.pdf

• Q.F. Stout, ``Mesh-connected computers with broadcasting'', IEEE Trans. on Computers C-32 (1983), pp. 826-830.
  Keywords: bus, broadcasting, mesh computer, median, selection, semigroup computation, sorting, communication lower bounds.   abstract   paper.pdf

• Q.F. Stout, ``Drawing straight lines with a pyramid cellular automaton'', Information Processing Letters 15 (1982), pp. 233-237.
  Keywords: self-organizing finite state automata, pyramid computer, digital line, clerks, parallel algorithms.    abstract   paper.pdf

• Q.F. Stout, ``Broadcasting in mesh-connected computers'', Proc. 1982 Conf. Information Sciences and Systems, pp. 85-90.
  Keywords: image algorithms, geometry, 2-dimensional, semigroup operations.    abstract   paper.pdf

• Q.F. Stout, ``Using clerks in parallel processing'', Proc. 23rd IEEE Symp. on Foundations of Computer Science (1982), pp. 272-279.
  Keywords: self-organizing cellular array, pyramid cellular automata, finite automata, mesh computer, pyramid computer, connected components, image processing, digital circle, clerks, simulation    abstract   paper.pdf

Adaptive Sampling, Clinical Trials, Statistics

statistical computing, sequential allocation, response adaptive sampling, active learning, controlled clinical trial, biostatistics, adaptive design, design of experiments, ethical clinical trial, dynamic programming, backward induction, stochastic optimization, machine learning, computational learning theory, active learning, Bayesian design, dynamical systems, dynamic index, bandit models.

Book Chapters

• Q.F. Stout and J. Hardwick, Parallel programs for adaptive designs, Handbook of Parallel Computing and Statistics, E. Kontoghiorghes, ed., Marcel Dekker, 2006, pp. 347-373.
  Keywords: multi-arm bandit models, dynamic programming, speedup, clinical trial, delayed response, response adaptive sampling, parallelizing recursive equations, sequential analysis.    abstract   paper.pdf

• J. Hardwick, R. Oehmke, and Q.F. Stout, Optimal adaptive designs for delayed response models: exponential case, MODA6: Model Oriented Data Analysis, A. Atkinson, P. Hackl, W. Mueller, eds., Physica Verlag, 2001, pp. 127-134.
  Keywords: delayed response, sequential analysis, dynamic programming, computational learning theory, active learning, multi-arm bandit models, parallel computing, clinical trial, recursive equations, design of experiments, medical ethics, clinical trial, backward induction.    abstract   paper.pdf

• J. Hardwick and Q.F. Stout, Optimizing a unimodal response function for binary variables, in Optimum Design 2000, A. Atkinson, B. Bogacka, and A. Zhigljavsky, eds., Kluwer, 2001, pp. 195-208.
  Keywords: nonparametric, shape-constrained, competing failure modes, unimodal regression, phase I/II, bandit, approximate Gittins index, stochastic approximation, Polya urn, up and down, Markov chain, random walk.    abstract   paper.pdf  

• J. Hardwick and Q.F. Stout, Flexible algorithms for creating and analyzing adaptive sampling procedures, in New Developments and Applications in Experimental Design, N. Flournoy, W.F. Rosenberger, and W.K. Wong, eds., Institute of Math. Stat. Lecture Notes -- Monograph Series, vol. 34, 1998, pp. 91-105.
  Keywords: bandit problems, algorithms, high-performance computing, staged procedure, group sampling, clinical trial, switching, robustness, biostatistics, path induction, parallel computing.    abstract   paper.pdf

• J. Hardwick and Q.F. Stout, Exact computational analyses for adaptive designs, in Adaptive Designs, N. Flournoy and W.F. Rosenberger, eds., Institute of Math. Stat. Lecture Notes Monograph Series Vol. 25, 1995, pp. 223-237.
  Keywords: constrained dynamic programming, forward induction, path induction, backward induction, multiple criteria, ethical clinical trials, bandit problems, controlled clinical trial.    abstract   paper.pdf

Journals and Conferences

• J. Hardwick and Q.F. Stout, Optimal reduced isotonic regression, Proceedings Interface 2012: Future of Statistical Computing.
  Keywords: step function, histogram, piecewise constant approximation, reduced isotonic regression, monotonic, segmentation     abstract   paper.pdf

• J. Hardwick and Q.F. Stout, Response adaptive designs for balancing complex objectives, submitted.
  Keywords: controlled clinical trial, Gittins index, multiple objectives, dynamic programming, bandit problem, optimal tradeoff, multiple objectives, modified bandit design     abstract   paper.pdf

• J. Hardwick and Q.F. Stout, Response adaptive designs that incorporate switching costs and constraints, Journal of Statistical Planning and Inference 137 (2007), 2654-2665.
  Keywords: switching costs, constraints, hyperopic procedure, bandit problem, nonlinear Bayes risk, dynamic programming    abstract   paper.pdf

• J. Hardwick, R. Oehmke, Q.F. Stout, New adaptive designs for delayed response models, Journal of Statistical Planning and Inference 136 (2006), pp. 940-1955.
  Keywords: randomized play-the-winner, hyperopic design, bandit problem.    abstract   paper.pdf

• Q.F. Stout and J. Hardwick, Optimal screening designs with flexible cost and constraint structures, Journal of Statistical Planning and Inference 132 (2005), pp. 149-162.
  Keywords: drug testing, acceptance-rejection sampling, staged procedure, stopping rule, biostatistics, design of experiments.    abstract   paper.pdf

• J. Hardwick, M.C. Meyer, and Q.F. Stout, Directed walk designs for dose response problems with competing failure modes, Biometrics 59 (2003), pp. 229-236.
  Keywords: adaptive sampling, phase I/II clinical trial, biostatistics, sequential allocation, random walk, shape-constrained regression, parametric, nonparamentric, Bayesian, frequentists, smooothed, curve estimation, design of experiments, toxicity, medical ethics, controlled clinial trial    abstract   paper.pdf

• J. Hardwick and Q.F. Stout, Optimal few-stage designs, Journal Statistical Planning and Inference 104 (2002), pp. 121-145.
  Keywords: two-stage, three-stage, controlledd clinical trial, medical ethics, group allocation, staged procedure, design of experiments, selection, estimation, bandit problems, product of means.    abstract   paper.pdf  

• R. Oehmke, J. Hardwick, and Q.F. Stout, Scalable algorithms for adaptive statistical designs, Proc. SC 2000 (Supercomputing), 16 p. Reprinted in Scientific Programming 8 (2001), pp. 183-193.
  Keywords: dynamic programming, computational learning theory, active learning, multi-arm bandit, message-passing, dynamic domain decomposition, memory-intensive computing, load balancing, sequential analysis, performance analysis, experimental algorithms, parallel computing, clinical trial, recursive equations, design of experiments, medical ethics, clinical trial, delayed response, backward induction, MPI, OpenMP.    abstract   paper.pdf

• J. Hardwick and Q.F. Stout, Using path induction to evaluate sequential allocation procedures, SIAM J. Scientific Computing 21 (1999), pp. 67-87.
  Keywords: backward induction, forward induction, staged allocation, group sampling, sequential, path counting, Bayesian, bandit problems.    abstract   paper.pdf

• J. Hardwick, R. Oehmke, and Q.F. Stout, A program for sequential allocation of three Bernoulli populations, Computational Statistics and Data Analysis 31 (1999), pp. 397-416.
  Keywords: parallel computing, clinical trial, high-performance computing, load balancing, recursive equations, design of experiments, ethical clinical trial, multi-arm bandit, controlled clinical trial    abstract   paper.pdf

• J. Hardwick, C. Page and Q.F. Stout, Sequentially deciding between two experiments for estimating a common success probability, J. Amer. Statistical Assoc. 93 (1998), pp. 1502-1511.
  Keywords: batch testing, risk assessment, infection rate, grouped data, composite testing, pooled data, omniscient allocation biostatistics.    abstract   paper.pdf

• J. Hardwick, R. Oehmke, and Q.F. Stout, Adaptive allocation in the presence of missing outcomes, Computing Science and Statistics 30 (1998), pp. 219-223.
  Keywords: censored observations, bandit, clinical trial, dynamic programming.    abstract  paper.pdf

• J. Landrum, J. Hardwick, and Q.F. Stout, Predicting algorithm performance, Computing Science and Statistics 30 (1998), pp. 309-314.
  Keywords: computer performance prediction, adaptive sampling, change-point, experimental algorithms, regression, extrapolation, design of experiments, benchmarking.    abstract  paper.pdf

• J. Hardwick and Q.F. Stout, Optimal allocation for estimating the mean of a bivariate polynomial, Sequential Analysis 15 (1996), pp. 71-90.
  Keywords: nonlinear estimation, robustness, myopic, hyperopic, product, Bayesian, fault tolerance.    abstract   paper.pdf   Here is a web version of a hour-long Talk that overviews all of this material and more.

• J. Hardwick and Q.F. Stout, Optimal adaptive equal allocation rules, Computing Science and Statistics 24 (1992), pp. 597-601.
  Keywords: curtailment, probability of correct selection, equal allocation, vector at a time, clinical trial.    abstract   paper.pdf

• J. Hardwick and Q.F. Stout, Bandit strategies for ethical sequential allocation, Computing Science and Statistics 23 (1991), pp. 421-424.
  Keywords: ethical clinical trial, Gittins index, power, probability of correct selection, indifference region, adaptive clinical trial, medical ethics, biostatistics    abstract   paper.pdf

Scientific Computing and Computational Science, especially Space and Earth Modeling

Widget

• We didn't create this, and I don't know who did, but a widget that shows images of the heliosphere's magnetic field generated by our programs appears in www.apple.com/downloads/dashboard/information/ccmcspaceweatherwidget.html

Books Authored

• Q.F Stout and C. Jablonowski, Parallel Computing 101. While not a standard book, the notes for this tutorial are essentially a book overviewing parallel computing and how to develop efficient parallel programs. The tutorial and notes are continually being updated.
  Keywords: parallel programming, performance, MPI, OpenMP, Amdahl's law, software engineering, scientific computing, supercomputing, vendors, load balancing, code tuning.

Chapters in Books

• T. Gombosi et al., Adaptive mesh refinement MHD for global space weather simulations, Space Plasma Simulation, J. Buchner, C.T. Dum, M. Scholer, eds., Lecture Notes in Physics 615, Springer-Verlag, 2003, pp. 251-279.
  Keywords: solution adaptive mesh refinement, AMR, MHD, space environment modeling, Cartesian adaptive grid, adaptive block.     abstract   paper.pdf

Journals and Conference Proceedings

• G. Toth et al., Adaptive numerical algorithms in space weather modeling, J. Computational Phys. 231 (2012), 870-903.

• B. van der Holst et al., CRASH: a block-adaptive mesh code for radiative shock hydrodynamis - implementation and verification, Astrophysical J. Sup. 194:23 (2011), 20p.

• R.P. Drake et al., Radiative effects in radiative shocks in shock tubes, High Energy Density Physics 7 (2011), 130-140.

• N.G. Andronova et al., Application of 3-d spherical shell adative mesh refinement to an atmospheric model with a vertical Lagrangian coodinate, Proc. SCIDAC 2010, 124-127.

• C. Jablownowski, R.C. Oehmke and Q.F. Stout, Block-structured adaptive meshes and reducted grids for atmospheric general circulation models, Proc. Trans. Royal Soc. A 367 (2009), 4497-4522.

• J. Penner et al., Three-dimensional adaptive mesh refinement on a spherical shell for atmospheric models with Lagrangian coordinates, J. Physics Conf. Series 78, Proc. SciDAC 2007

• C. Jablonowski et al., Block-structured adaptive grids on the sphere: advection experiments, Monthly Weather Review 134 (2006), 3691-3713.
  Keywords: adaptive mesh refinement, AMR, atmospheric modeling, spherical adaptive grid, adaptive block.    abstract   paper.pdf

• J.E. Penner et al., Development of an atmospheric climate model with self-adapting grid and physics, J. Physics Conf. Series 16 (2005), pp. 353-357.
  Keywords: adaptive mesh refinement, AMR, atmospheric modeling, climate modeling, spherical adaptive grid, adaptive block.    abstract   paper.pdf

• G. Toth et al., Space Weather Modeling Framework: a new tool for the space science community (2005), J. Geophysical Research 110, A12226, doi:10.1029/2005JA011126.
  Keywords: scientific computing framework, high performance computing, space environment modeling, grid coupling, SWMF.     abstract   paper.pdf

• C. Jablonowski et al., ``Adaptive grids for weather and climate models'', ECMWF Proc. Recent Developments in Numerical Methods for Atmospheric and Climate Modeling (2004), pp. 233-250.
  Keywords: climate modeling, weather, solution adaptive mesh refinement, AMR, spherical adaptive grid, adaptive block.     abstract   paper.pdf

• G. Toth et al., ``A physics-based software framework for Sun-Earth connection modeling'', Multiscale Coupling of Sun-Earth Processes, Proc. Conf. on the Sun-Earth Connection, Kona, Hawaii, 2004, A. T. Y. Lui, Y. Kamide, and G. Consolini, eds., Elsevier, pp. 383-397.
  Keywords: parallel computing, high-performance computing, software engineering, space environment modeling, coupling.    abstract   paper.pdf

• T.I. Gombosi et al., ``Solution adaptive MHD for space plasmas: Sun-to-Earth simulations'', Computers in Science and Engineering 6 (2004), pp. 14-35.
  Keywords: adaptive mesh refinement, parallel computing, geoscience.    abstract   paper.pdf

• T. Gombosi et al., ``Adaptive mesh refinement MHD for global simulations'', Proc. ISSS-6 (2001), 8 p.
  Keywords: solution adaptive mesh refinement, AMR, space plasma simulations.     abstract   paper.pdf

• R. Oehmke and Q.F. Stout, ``Parallel adaptive blocks on the sphere'', Proc. 10th SIAM Conf. Parallel Processing for Scientific Computing (2001).
  Keywords: adaptive mesh refinement, data structure, parallel computing, geoscience, multi-scale modeling, adaptive spherical grid, geometric decomposition, high performance computing.    abstract   paper.pdf

• D.L. De Zeeuw et al., ``An adaptive MHD method for global space weather simulations'', IEEE Trans. Plasma Science 28 (2000), pp. 1956-1965.
  Keywords: space weather, adaptive mesh refinement, MHD, supercomputing, Sun-Earth, space physics, scientific computing.    abstract   paper.pdf

• C.R. Clauer et al., ``High performance computer methods applied to predictive space weather simulations'', IEEE Trans. Plasma Science 28 (2000), pp. 1931-1937.
  Keywords: space weather, adaptive mesh refinement, MHD, supercomputing, Sun-Earth, space physics, scientific computing.    abstract   paper.pdf

• T.I. Gombossi et al., ``Multiscale MHD simulation of a coronal mass ejection and its interaction with the magnetosphere-ionosphere system'', J. Atmospheric and Solar-Terrestrial Physics 62 (2000), pp. 1515-1525.
  Keywords: space weather, coronal mass ejection, magnetosphere, ionosphere     abstract   paper.pdf

• J. Hardwick and Q.F. Stout, Using path induction to evaluate sequential allocation procedures, SIAM J. Scientific Computing 21 (1999), pp. 67-87.
  Keywords: backward induction, forward induction, staged allocation, group sampling, sequential, path counting, Bayesian, bandit problems.    abstract   paper.pdf

• A.A. Poe and Q.F. Stout, Load balancing 2-phased geometrically based problems, Proc. 9th SIAM Conf. Parallel Processing for Scientific Computing (1999).
  Keywords: multi-weight load balancing, graph partitioning, ham sandwich theorem, geometric decomposition, impact analysis, crash simulation, domain decomposition, discrete computational geometry, multiple constraints.    abstract   paper.pdf

• C.P.T Groth et al., ``A parallel solution-adaptive scheme for ideal magnetohydrodynamics'', Proc. 14th AIAA Conf. Computational Fluid Dynamics (1999), 17p.
  Keywords: MHD, approximate Riemann solver, upwind finite-volume     abstract   paper.pdf

• J. Landrum, J. Hardwick, and Q.F. Stout, Predicting algorithm performance, Computing Science and Statistics 30 (1998), pp. 309-314.
  Keywords: computer performance prediction, adaptive sampling, change-point, experimental algorithms, regression, extrapolation, design of experiments, benchmarking.    abstract  paper.pdf

• Q.F. Stout et al., ``Adaptive parallel computation of a grand-challenge problem: Prediction of the path of a solar-corona mass ejection'', Proc. SC98.
  Keywords: magnetohydrodynamics (MHD), space weather prediction, adaptive mesh refinement, Cartesian, adaptive blocks, Riemann solver, upwind schemes, scientific computing.    abstract   paper.html   paper.pdf

• Q.F. Stout et al., ``Adaptive blocks: A high-performance data structure'', Proc. SC97.
  Keywords: adaptive data structure, Cartesian, cache, high performance computing, mesh, adaptive mesh refinement, AMR, oct-tree, scientific computing.    abstract   paper.html   paper.pdf

• T. Gombossi et al., ``Multiscale modeling of heliospheric plasmas'', High Performance Computing 1997, pp. 46-51.
  Keywords: magnetohydrodynamics, MHD, adaptive mesh refinement (AMR), Riemann solver, Cray T3D, solar wind, high-performance computing, HPCC, NASA Grand Challenge Investigator Team, upwind scheme, space plasma, scientific computing.    abstract   paper.pdf

Theoretical Computer Science

Talks

• Space, Time, Power: Evolving Concerns for Parallel Algorithms, a talk about the evolution of goals/concerns of parallel models and algorithms, including cellular automata, mesh connected computers, reconfigurable meshes, and power-constrained algorithms for mesh connected computers. It also mentions real parallel computers: zebra networks, BlueGene and Earth Simulator; and additional theory models: PRAMs and quantum computers.

Book

• R. Miller and Q.F. Stout, Parallel Algorithms for Regular Architectures: Meshes and Pyramids, MIT Press, 1996.
  Keywords: parallel computing, parallel algorithms, mesh computer, VLSI algorithms, pyramid, data movement operations, graph algorithms, image processing, computational geometry, lower bounds, optimal algorithms.

Journals and Conference Proceedings

• J. Lipman and Q.F. Stout, Analysis of delays caused by local synchronization, SIAM J. Computing 39 (2010), pp. 3860-3884.
  Keywords: synchronization delay, overhead, performance analysis, barrier, geometric distribution, heavy-tailed distribution, stochastic task times, idle time    abstract   paper.pdf

• Q.F. Stout, Algorithms minimizing peak energy on mesh-connected systems, preliminary results in Symp. Parallelism in Algorithms and Architectures (SPAA) 2006.
  Keywords: peak power consumption, energy, rat algorithm, image processing, graph algorithm, mesh.    abstract   paper.pdf

• A.A. Poe and Q.F. Stout, Load balancing 2-phased geometrically based problems, Proc. 9th SIAM Conf. Parallel Processing for Scientific Computing (1999).
  Keywords: multi-weight load balancing, graph partitioning, ham sandwich theorem, geometric decomposition, impact analysis, crash simulation, domain decomposition, discrete computational geometry, multiple constraints.    abstract   paper.pdf

• P.D. MacKenzie and Q.F. Stout, Ultra-fast expected time parallel algorithms, J. Algorithms 26 (1998), pp. 1-33.
  Keywords: ultrafast, padded sort, geometry algorithms, CRCW PRAM, Voronoi diagram, all nearest neighbors, closest pair, relative neighborhood graph, Delaunay triangulation, largest empty circle, lower bounds, randomized algorithm.    abstract   paper.pdf

• D. Van Wieren and Q.F. Stout, ``Ultrafast graph algorithms on reconfigurable meshes'', Proc. 2nd Work. on Reconfigurable Architectures (1995), pp. 1-13.
  Keywords: ultrafast algorithms, reconfigurable mesh, rmesh, MasPar, edge cover, Hamiltonian cycle, spanning trees, randomized algorithm.    abstract   paper.pdf

• R. Miller, V.K. Prasanna Kumar, D. Reisis and Q.F. Stout, Parallel computations on reconfigurable meshes, IEEE Trans. on Computers 42 (1993), pp. 678-692.
  Keywords: reconfigurable mesh, image algorithms, graph algorithms, parallel algorithms, VLSI, mesh, PRAM, mesh-of-trees, pyramid computer, component labeling, global or, prefix calculation, parity, xor.    abstract   paper.pdf

• P.D. MacKenzie and Q.F. Stout, Optimal parallel construction of Hamiltonian cycles and spanning trees in random graphs, Proc. 5th ACM Symp. Parallel Algorithms and Architectures (SPAA) (1993), pp. 224-229.
  Keywords: ultrafast algorithms, CRCW PRAM, edge cover, lower bounds, parallel target shooting, randomized algorithm.    abstract   paper.pdf

• R. Machlin and Q.F. Stout, The complex behavior of simple machines, in Emergent Computation, S. Forrest, ed., MIT Press, 1991, pp. 85-98. Reprint of paper first appearing in Physica D 42 (1990), pp. 85-98.
  Keywords: Turing machines, emergent systems, halting problem, Busy Beaver problem, halting probability, complexity.    abstract   paper.pdf

• R. Miller and Q.F. Stout, Efficient parallel convex hull algorithms, IEEE Trans. Computers C-37 (1988), pp. 1605-1618.
  Keywords: AKS network, computational geometry, convex hull, EREW PRAM, hypercube, mesh, mesh-of-trees, reconfigurable mesh, pyramid, parallel algorithms, divide-and-conquer.   abstract  paper.pdf

• Q.F. Stout, Meshes with multiple buses, Proc. 27th IEEE Symp. on Foundations of Computer Science (FOCS) (1986), pp. 264-273.
  Keywords: broadcasting, mesh computer, cooperative problem solving, cooperative speedup, optimal stepwise simulation, or, minimum, component labeling, spanning forest, tree, pyramid, mesh-of-trees, layouts.    abstract  paper.pdf

• Q.F. Stout, Pyramid computer solutions of the closest pair problem, J. of Algorithms 6 (1985), pp. 200-212.
  Keywords: pyramid cellular automata, pyramid computers, closest pair, computational geometry, nearest neighbors, parallel algorithms, finite automaton.   abstract   paper.pdf

• Q.F. Stout, ``Optimal component labeling algorithms for mesh-connected computers and VLSI'', arXiv 1502.01435.
  Keywords: minimal spanning forest, minimal spanning tree, component labeling, mesh-connected computer   abstract   paper.pdf

• Q.F. Stout, Topological matching, Proc. 15th ACM Symp. on Theory of Computing (STOC) (1983), pp. 24-31.
  Keywords: image processing, deformation, cellular automata (array), clerks, mesh computer, tree isomorphism.   abstract   paper.pdf

• Q.F. Stout, Mesh-connected computers with broadcasting, IEEE Trans. on Computers C-32 (1983), pp. 826-830.
  Keywords: bus, broadcasting, mesh computer, median, selection, semigroup computation, sorting, communication lower bounds.   abstract   paper.pdf

• Q.F. Stout, Drawing straight lines with a pyramid cellular automaton, Information Processing Letters 15 (1982), pp. 233-237.
  Keywords: self-organizing finite state automata, pyramid computer, digital line, clerks, parallel algorithms.    abstract   paper.pdf

• Q.F. Stout, Using clerks in parallel processing, Proc. 23rd IEEE Symp. on Foundations of Computer Science (FOCS) (1982), pp. 272-279.
  Keywords: self-organizing cellular array, pyramid cellular automata, finite automata, mesh computer, pyramid computer, connected components, image processing, digital circle, clerks, emulate, parallel algorithm.    abstract   paper.pdf

• Q.F. Stout, Broadcasting in mesh-connected computers, Proc. 1982 Conf. Information Sciences and Systems, pp. 85-90.
  Keywords: image algorithms, geometry, 2-dimensional, semigroup operations.    abstract   paper.pdf

Serial Algorithms and Data Structures

There are several papers involving regression, so I put together an overview of my work on shape constrained regression (isotonic, unimodal, step). I also keep a table of the fastest (in O-notation) isotonic regression algorithms known to date.

• Q.F. Stout, Best L_p isotonic regression, p ∈ {0, 1, ∞}, arXiv 2306:00269
  Keywords: Best L₀ isotonic regression, monotonic regression, L₁ regression, L_∞, strict regression, lex regression, best median     extended abstract     paper

• Q.F. Stout, L_p isotonic regression using an L₀ approach, arXiv 2107.00251
  Keywords: L₁ isotonic regression, L_p monotonic regression, maximum flow, violator graph, Hamming distance, multidimensional coordinate-wise orderings     extended abstract     paper

• Q.F. Stout, L₀ isotonic regression with secondary objectives, arXiv 2106.00279
  Keywords: strong L₀ isotonic regression, monotonic relabeling, L_p isotonic regression with Hamming distance penalty, ordinal response, distance to monotonicity    abstract   paper.pdf

• Q.F. Stout, L_∞ isotonic regression for linear, multidimensional, and tree orders, arXiv 1507.02226
  Keywords: minimax error, coordinate-wie ordering, rendezvous graph, bounded error envelope, nonconstructive feasibility test     abstract   paper.pdf

• J.P Hardwick and Q.F. Stout, Optimal reduced isotonic regression.
  Keywords: step function, v-optimal histogram, k-means, piecewise constant approximation    abstract   paper.pdf

• Q.F. Stout, An algorithm for L_∞ approximation by step functions.
  Keywords: step function, variable width histogram, piecewise constant approximation, reduced isotonic regression, k-center, mini-max error, bounded error envelopes     abstract   paper.pdf

• J. Hardwick and Q.F. Stout, Optimal reduced isotonic regression, Proceedings Interface 2012: Future of Statistical Computing.
  Keywords: step function, histogram, piecewise constant approximation, reduced isotonic regression, monotonic, segmentation     abstract   paper.pdf

• Q.F. Stout, Strict L_∞ isotonic regression, J. Optimization Theory and Appl. 152 (2012), pp. 121-135.
  Keywords: "best best" L_∞ approximation, isotonic regression, monotonic mapping, shape constrained    abstract   paper.pdf

• Q.F. Stout, Isotonic regression for multiple independent variables, Algorithmica 71 (2015), pp. 450-470.
  Keywords: nonparametric, weighted isotonic or monotonic regression, multidimensional, order-embedding, multidimensional divide-and-conquer, shape constrained, rendezvous graph    abstract   paper.pdf

• Q.F. Stout, Isotonic regression via partitioning, Algorithmica 66 (2013), pp. 93-112.
  Keywords: L_1, nonparametric, shape-constrained, median regression, weighted isotonic or monotonic regression, linear ordering, tree, bivariate, multidimensional, DAG    abstract   paper.pdf

• Q.F. Stout, Weighted L_∞ isotonic regression, J. Computer Sys. and Sci. 91 (2018), pp. 69-81.
  Keywords: nonparametric, shape-constrained, weighted isotonic or monotonic regression, partial order, linear ordering, domination, multidimensional divide-and-conquer    abstract   paper.pdf

• Q.F. Stout, Unimodal regression via prefix isotonic regression, Computational Statistics and Data Analysis 53 (2008) p. 289-297. doi:10.1016/j.csda.2008.08.005
  Keywords: nonparametric, shape-constrained, weighted isotonic or monotonic regression, scan, parallel prefix, umbrella ordering, least squares, pool adjacent violators (PAV), median regression, minimax, persistent data structure.    abstract   paper.pdf

• A.A. Poe and Q.F. Stout, Load balancing 2-phased geometrically based problems, Proc. 9th SIAM Conf. Parallel Processing for Scientific Computing (1999).
  Keywords: multi-weight load balancing, graph partitioning, ham sandwich theorem, geometric decomposition, impact analysis, crash simulation, domain decomposition, discrete computational geometry, multiple constraints.    abstract   paper.pdf

• J. Landrum, J. Hardwick, and Q.F. Stout, Predicting algorithm performance, Computing Science and Statistics 30 (1998), pp. 309-314.
  Keywords: computer performance prediction, adaptive sampling, change-point, experimental algorithms, regression, extrapolation, design of experiments, benchmarking.    abstract  paper.pdf

• D.M. Pennock and Q.F. Stout, Exploiting a theory of phase transitions in three-satisfiability problems, Proceedings American Association of Artificial Intelligence, 1996, pp. 253-258.
  Keywords: satisfiability, 3-SAT, phase transition, constraint satisfaction, pruning, heuristic search, NP-complete, NP-hard, classification.    abstract   paper.pdf

• M.L. Livingston and Q.F. Stout, Constant time computation of minimum dominating sets, Congresses Numerantium 105 (1994), pp. 116-128.
  Keywords: codes, covering, domination, packing, matching, perfect domination, grid graph, product graph, mesh, torus, dynamic programming, finite state space, resource allocation, regular architecture, algorithms.    abstract   paper.pdf    Here are some related open questions and conjectures.

• C.A. Shaffer and Q.F. Stout, Linear-time distance transforms for quadtrees, Computer Vision, Graphics, and Image Processing: Image Understanding 54 (1991), pp. 215-223.
  Keywords: quadtrees, hierarchical data structures, chessboard distance, medial axis, QMAT, top-down traversal, neighbored traversal.    abstract   paper.pdf

• Q.F. Stout and B.L. Warren, Tree rebalancing in optimal time and space, Commun. of the ACM 29 (1986), pp. 902-908.
  Keywords: binary search trees, vines, perfect balance, optimal search, sorting, data structures.    abstract  paper.pdf

• Q.F. Stout and B.L. Warren, Tree algorithms for unbiased coin tossing with a biased coin, Annals of Probability 12 (1984), pp. 212-222.
  Keywords: bias, finite distributions, coin, lattice algorithm, tree algorithm, random number generation, multinomial termination.    abstract   paper.pdf

Discrete Mathematics: Graph Theory, Geometry, Combinatorics, Codings, Probability

• J. Lipman and Q.F. Stout, Analysis of delays caused by local synchronization, SIAM J. Computing 39 (2010), pp. 3860-3884.
  Keywords: synchronization delay, overhead, performance analysis, barrier, geometric distribution, heavy-tailed distribution, stochastic task times, idle time    abstract   paper.pdf

• D.M. Pennock and Q.F. Stout, Exploiting a theory of phase transitions in three-satisfiability problems, Proceedings American Association of Artificial Intelligence, 1996, pp. 253-258.
  Keywords: satisfiability, 3-SAT, phase transition, constraint satisfaction, pruning, heuristic search, NP-complete, NP-hard, classification.    abstract   paper.pdf

• J.D. Masters, Q.F. Stout, and D.M. Van Wieren, Unique Domination in Cross-Product Graphs, Congresses Numerantium 118 (1996), pp. 49-71.
  Keywords: coverings, product graph, cross-product, dominating set, unique domination, grid graph, perfect dominating set, torus, cube-connected cycles.    abstract   paper.pdf

• M.L. Livingston and Q.F. Stout, Constant time computation of minimum dominating sets, Congresses Numerantium 105 (1994), pp. 116-128.
  Keywords: codes, covering, domination, packing, matching, perfect domination, grid graph, product graph, mesh, torus, dynamic programming, finite state space, resource allocation, regular architecture, algorithms.    abstract   paper.pdf
  Here are some related open questions and conjectures.

• N. Graham, F. Harary, M.L. Livingston and Q.F. Stout, Subcube fault-tolerance in hypercubes, Information and Computation 102 (1993), pp. 280-314.
  Keywords: hypercube computer, n-cube, fault-tolerance, k-independent sets, partitions, resource allocation.    abstract   paper.pdf

• D. Van Wieren, M.L. Livingston and Q.F. Stout, Perfect dominating sets on cube-connected cycles, Congresses Numerantium 97 (1993), pp. 51-70.
  Keywords: perfect dominating set, cube-connected cycles, parallel computer, perfect code, vertex-vertex domination, graph theory, interconnection network, resource allocation, regular architecture.    abstract   paper.pdf

• M.L. Livingston and Q.F. Stout, Perfect dominating sets, Congressus Numerantium 79 (1990), pp. 187-203.
  Keywords: perfect codes, domination, packings, mesh, torus, hypercube, cube-connected cycles, de Bruijn graph, tree, dag, dynamic programming.    abstract   paper.pdf

• M.L. Livingston and Q.F. Stout, Embeddings in hypercubes, Mathematical and Computer Modelling 11 (1988), pp. 222-227.
  Keywords: hypercube computer, n-cube, embedding, dilation, expansion, cubical, packing, random graphs, critical graphs, parallel computing.    abstract   paper.pdf

• M.L. Livingston and Q.F. Stout, Distributing resources in hypercube computers, Proc. 3rd Conf. on Hypercube Concurrent Computers and Applications (1988), ACM, pp. 222-231.
  Keywords: hypercube, subcube fault-tolerance, codes, buddy allocation, disk placement, parallel computing.    abstract   paper.pdf

• Q.F. Stout, Hypercubes and pyramids, in Pyramidal Systems for Computer Vision, V. Cantoni and S. Levialdi, eds., NATO ASI Series ARW Vol. F 25, Springer-Verlag, 1986, pp. 75-89.
  Keywords: hypercube computers, pyramid algorithms, graph embeddings, image processing, hyper-pyramid     abstract   paper.pdf

• Q.F. Stout and B.L. Warren, Tree algorithms for unbiased coin tossing with a biased coin, Annals of Probability 12 (1984), pp. 212-222.
  Keywords: bias, finite distributions, coin, lattice algorithm, tree algorithm, random number generation, multinomial termination.    abstract   paper.pdf

• Q.F. Stout, Searching and encoding for infinite ordered sets, Int'l. J. Computer and Information Sciences 11 (1982), pp. 55-72.
  Keywords: unbounded search, binary encodings, prefix codes, search codes, linear order, infinite sets.    abstract   paper.pdf

• Q.F. Stout, Improved prefix encodings of the natural numbers, IEEE Trans. on Information Theory IT-26 (1980), pp. 607-609.
  Keywords: unbounded search, binary encoding, prefix codes, septenary code, integers, natural numbers, long strings.    abstract   paper.pdf

• M. Livingston and Q.F. Stout, Shift-product networks, Mathematical and Computational Modeling, 1998, to appear.
  Keywords: interconnection networks, scalable networks, shuffle-exchange networks, Cayley graphs, product graphs, de Bruijn network, parallel computer, commodity components.    abstract   paper.pdf

• Q.F. Stout, Order types of words over a countable alphabet, in preparation.
  Keywords: lexical (lexicographic) ordering, dictionaries, finite words, countable alphabet, order types, total orders, search.

• Q.F. Stout, Packings in hypercubes, in preparation.
  Keywords: hypercube, graph embedding, packing, cubical, tree, cycle, biconnected components.

• Q.F. Stout, Embedding criterion for e-cube routing, in preparation.
  Keywords: hypercube computer, graph embedding, e-cube routing, dimension order, link contention.

Operator Theory, Analysis

• Q.F. Stout, On Levi's duality between permutations and convergent series, J. London Mathematical Society 34 (1986), pp. 67-80.
  Keywords: convergent series, alternating series, absolutely convergent series, permutations, duality, semigroup    abstract   paper.pdf

• Q.F. Stout, The numerical range of a weighted shift, Proc. American Mathematical Society 88 (1983), pp. 495-502.
  Keywords: weighted unilateral or bilateral shift, Hilbert space, numerical radius, numerical range, tri-diagonal matrix, circular shift, circularly symmetric functions.    abstract   paper.pdf

• Q.F. Stout, Schur products of operators and the essential numerical range, Trans. American Mathematical Society 264 (1981), pp. 39-47.
  Keywords: Schur multiplication, Hadamard multiplication, essential numerical range, matrix representations, Schatten classes, Hilbert space.    abstract   paper.pdf

• Q.F. Stout, Schur multiplication on B(l_p,l_q), J. Operator Theory 5 (1981), pp. 231-243.
  Keywords: Schur multiplication, Banach algebra, maximal ideal space, Stone-Cech compactification, operator theory, l_p spaces.   abstract   paper.pdf

Other Research

• A. Nesky and Q.F. Stout, Generating artificial core users for interpretable condensed data, arXiv:2102.03674. paper.pdf

• A. Nesky and Q.F. Stout, Neural networks with block diagonal inner product layers: a look at neural network architecture through the lens of random matricies, Neural Computing and Applications 32, 2020, 6755-6767. paper.pdf

• A. Nesky and Q.F. Stout, Training neural networks using predictor-corrector gradient descent, Proc. ICANN 2018, part III, 51-61. paper.pdf

• A. Nesky and Q.F. Stout, Neural networks with block diagonal inner product layers, Proc. ICANN 2018, part III, 62-72. paper.pdf

• Q.F. Stout, Behind the scenes of HPCC, in Suggesting Computer Science Agendas for High Performance Computing, U. Vishkin, ed., Assoc. Computing Machinery, 1994, pp. 156-158.
  Keywords: HPCC, funding, planning, instrumentation, parallel computing, supercomputing, graphics, professional training and degrees.

• Q.F. Stout and P. Woodworth, Relational databases, American Mathematical Monthly 90 (1983), pp. 101-118.
  Keywords: relational databases, normal forms, selection, projection, lossless decomposition.

Teaching-Related Publications

• Q.F. Stout and C. Jablonowski, ``Parallel Computing 101'', tutorial notes that are continuously being updated. Here is more information about the tutorial.

• G. Bachelis, D.A. James, B.R. Maxim and Q.F. Stout, Bringing algorithms to life: cooperative computing activities using students as processors, School Science and Mathematics 94 (1994), pp. 176-186.
  Keywords: parallel algorithms, cooperation, sorting, addition, multiplication, sieving for primes, sorting, efficiency, systolic, pipelining.

Copyright © 1995-2024 Quentin F. Stout