publications.bib

% Encoding: US-ASCII


@Article{bizon2014variant,
  Title                    = {Variant calling in low-coverage whole genome sequencing of a Native American population sample},
  Author                   = {Bizon, Chris and Spiegel, Michael and Chasse, Scott A and Gizer, Ian R and Li, Yun and Malc, Ewa P and Mieczkowski, Piotr A and Sailsbery, Josh K and Wang, Xiaoshu and Ehlers, Cindy L and others},
  Journal                  = {BMC genomics},
  Year                     = {2014},
  Number                   = {1},
  Pages                    = {85},
  Volume                   = {15},
  Publisher                = {BioMed Central Ltd}
}

@Article{Boker2011,
  Title                    = {{OpenMx}: An Open Source Extended Structural Equation Modeling Framework},
  Author                   = {Steven Boker and Michael Neale and Hermine Maes and Michael Wilde and Michael Spiegel and Timothy Brick and Jeffrey Spies and Ryne Estabrook and Sarah Kenny and Timothy Bates and Paras Mehta and John Fox},
  Journal                  = {Psychometrika},
  Year                     = {2011},
  Note                     = {[561 citations]},
  Number                   = {2},
  Pages                    = {306-317},
  Volume                   = {76},
  Abstract                 = {OpenMx is free, full-featured, open source, structural equation modeling
	(SEM) software. OpenMx runs within the R statistical programming
	environment on Windows, Mac OS-X, and Linux computers. The rationale
	for developing OpenMx is discussed along with the philosophy behind
	the user interface. The OpenMx data structures are introduced --
	these novel structures define the user interface framework and provide
	new opportunities for model specification. Two short example scripts
	for the specification and fitting of a confirmatory factor model
	are next presented. We end with an abbreviated list of modeling applications
	available in OpenMx 1.0 and a discussion of directions for future
	development.},
  Owner                    = {Michael},
  Timestamp                = {2010.07.24},
  URL                      = {http://www.springerlink.com/content/dg37445107026711/}
}

@InProceedings{Newhall2003,
  Title                    = {Nswap: A network swap module for linux clusters.},
  Author                   = {Newhall, Tia and Finney, Sean and Ganchev, Kuzman and Spiegel, Michael},
  Booktitle                = {Proceedings of the 9th European Conference on Parallel Processing ({Euro-Par})},
  Year                     = {2003},
  Editor                   = {Kosch, H., and Boszormenyi, L., and Hellwagner, H.},
  Note                     = {[47 citations]},
  Pages                    = {1160-1169},
  Series                   = {Springer Lecture Notes in Computer Science},
  Abstract                 = {Cluster applications that process large amounts of data, such as parallel
	scientific or multimedia applications, are likely to cause swapping
	on individual cluster nodes. These applications will perform better
	on clusters with network swapping support. Network swapping allows
	any cluster node with over-committed memory to use idle memory of
	a remote node as its backing store and to "swap" its pages over the
	network. As the disparity between network speeds and disk speeds
	continues to grow, network swapping will be faster than traditional
	swapping to local disk. We present Nswap, a network swapping system
	for heterogeneous Linux clusters and networks of Linux machines.
	Nswap is implemented as a loadable kernel module for version 2.4
	of the Linux kernel. It is a space-efficient and time-efficient implementation
	that transparently performs network swapping. Nswap scales to larger
	clusters, supports migration of remotely swapped pages, and supports
	dynamic growing and shrinking of Nswap cache (the amount of RAM available
	to store remote pages) in response to a node's local memory needs.
	Results comparing Nswap running on an eight node Linux cluster with
	100BaseT Ethernet interconnect and faster disk show that Nswap is
	comparable to swapping to local, faster disk; depending on the workload,
	Nswap's performance is up to 1.7 times faster than disk to between
	1.3 and 4.6 times slower than disk for most workloads. We show that
	with faster networking technology, Nswap will outperform swapping
	to disk.},
  Owner                    = {mspiegel},
  Timestamp                = {2008.08.11}
}

@Article{Olivier2011,
  Title                    = {{OpenMP} Task Scheduling Strategies for Multicore {NUMA} Systems},
  Author                   = {Stephen L. Olivier and Allan K. Porterfield and Kyle B. Wheeler and Michael Spiegel and Jan F. Prins},
  Journal                  = {International Journal of High Performance Computing Applications},
  Year                     = {2012},
  Month                    = {May},
  Note                     = {[45 citations]},
  Number                   = {2},
  Pages                    = {110-124},
  Volume                   = {26},
  Owner                    = {Michael},
  Timestamp                = {2011.09.05},
  URL                      = {http://hpc.sagepub.com/content/26/2/110}
}

@InProceedings{Reynolds2006,
  Title                    = {Capturing scientists' insight for {DDDAS}},
  Author                   = {Reynolds, Jr., Paul F. and Brogan, David C. and Carnahan, Joe and Loitiere, Yannick and Spiegel, Michael},
  Booktitle                = {Proceedings of the 2006 International Conference on Computational Science ({ICCS})},
  Year                     = {2006},
  Address                  = {Reading, U.K.},
  Editor                   = {Alexandrov, V.N., and Van Albada, G.D., and Sloot, P.M.A., and Dongarra, J.},
  Pages                    = {570-577},
  Series                   = {Springer Lecture Notes in Computer Science},
  Abstract                 = {One of the intended consequences of utilizing simulations in dynamic,
	data-driven application systems is that the simulations will adjust
	to new data as it arrives. These adjustments will be difficult because
	of the unpredictable nature of the world and because simulations
	are so carefully tuned to model specific operating conditions. Accommodating
	new data may require adapting or replacing numerical methods, simulation
	parameters, or the analytical scientific models from which the simulation
	is derived. In this research, we emphasize the important role a scientist's
	insight can play in facilitating the runtime adaptation of a simulation
	to accurately utilize new data. We present the tools that serve to
	capture and apply a scientist's insight about opportunities for,
	and limitations of, simulation adaptation. Additionaly, we report
	on the two ongoing collaborations that serve to guide and evaluate
	our research.},
  Owner                    = {mspiegel},
  Timestamp                = {2008.08.11}
}

@InProceedings{Reynolds2007,
  Title                    = {Validating evolving simulations in {COERCE}},
  Author                   = {Reynolds, Jr., Paul F. and Spiegel, Michael and Liu, Xinyu and Gore, Ross},
  Booktitle                = {Proceedings of the 2007 International Conference on Computational Science ({ICCS})},
  Year                     = {2007},
  Month                    = {May},
  Pages                    = {1238-1245},
  Abstract                 = {We seek to increase user confidence in simulations as they are adapted
	to meet new requirements. Our approach includes formal representation
	of uncertainty, lightweight validation, and novel techniques for
	exploring emergent behavior. Uncertainty representation, using formalisms
	such as Dempster-Shafer theory, can capture designer insight about
	uncertainty, enabling formal analysis and improving communication
	with decision and policy makers. Lightweight validation employs targeted
	program analysis and automated regression testing to maintain user
	confidence as adaptations occur. Emergent behavior validation exploits
	the semi-automatic adaptation capability of COERCE to make exploration
	of such behavior efficient and productive. We describe our research
	on these three technologies and their impact on validating dynamically
	evolving simulations.},
  Owner                    = {mspiegel},
  Timestamp                = {2008.08.11}
}

@InProceedings{Spiegel2005,
  Title                    = {A case study of model context for simulation composability and reusability},
  Author                   = {Spiegel, Michael and Reynolds, Paul F. and Brogan, David C.},
  Booktitle                = {Proceedings of the 2005 Winter Simulation Conference ({WSC})},
  Year                     = {2005},
  Address                  = {Piscataway, New Jersey},
  Editor                   = {Kuhl, M.E., and Steiger, N.M., and Armstrong, F.B., and Joines, J.A.},
  Note                     = {[48 citations]},
  Organization             = {Institute of Electrical and Electronics Engineers},
  Pages                    = {437-444},
  Abstract                 = {How much effort will be required to compose or reuse simulations?
	What factors need to be considered? It is generally known that composability
	and reusability are daunting challenges for both simulations and
	more broadly software design as a whole. We have conducted a small
	case study in order to clarify the role that model context plays
	in simulation composability and reusability. For a simple problem:
	compute the position and velocity of a falling body, we found that
	a reasonable formulation of a solution included a surprising number
	of implicit constraints. Equally surprising, in a challenge posed
	to a small group of capable individuals, no one of them was able
	to identify more than three-quarters of the ultimate set of validation
	constraints. We document the challenge, interpret its results, and
	discuss the utility our study will have in future investigations
	into simulation composition and reuse.},
  Owner                    = {mspiegel},
  Timestamp                = {2008.08.11}
}

@InCollection{Spiegel2006,
  Title                    = {{Perfect} {Developer} tool suite},
  Author                   = {Michael Spiegel},
  Booktitle                = {A Survey of Tools for Model Checking and Model-Based Development},
  Publisher                = {Technical Report CS-2006-17},
  Year                     = {2006},
  Address                  = {Department of Computer Science, University of Virginia},
  Editor                   = {Strunk, E. and Aiello, A. and Knight, J.},
  Pages                    = {53-57},
  Owner                    = {mspiegel},
  Timestamp                = {2008.08.11}
}

@InProceedings{Spiegel2006a,
  Title                    = {Grand challenge case studies in a simulation curriculum},
  Author                   = {Spiegel, Michael and Reynolds, Paul F. and Brogan, David C.},
  Booktitle                = {Proceedings of the 2006 Winter Simulation Conference ({WSC})},
  Year                     = {2006},
  Address                  = {Piscataway, New Jersey},
  Editor                   = {Perrone, L.F., and Wieland, F.P., and Liu, J., and Lawson, B.G., and Nicol, D.M., and Fujimoto, R.M.},
  Organization             = {Institute of Electrical and Electronics Engineers},
  Pages                    = {2242-2249},
  Abstract                 = {Students wishing to become experts in modeling and simulation (M&S)
	need to appreciate limitations of the technology. Our goal is to
	expose students to the current boundaries of simulation technology.
	To achieve this, we propose the incorporation of grand challenge
	case studies into a modeling and simulation curriculum. Grand challenge
	problems are defined as problems for which there does not exist a
	universally accepted solution (at present). We argue that grand challenge
	case studies are an excellent vehicle for discovering and appreciating
	current boundaries of M&S technology. We present three candidate
	case studies, one in detail - the ongoing U.S. Department of Energy
	analysis of Yucca Mountain as a location for nuclear waste storage
	- with supporting discussion about how these cases can enhance exploration
	of the challenges inM&S technology. We discuss the proposed Yucca
	Mountain storage facility, along with two other case studies, and
	examine their integration into M&S curricula.},
  Owner                    = {mspiegel},
  Timestamp                = {2008.08.11}
}

@TechReport{Spiegel2007,
  Title                    = {A proposal for computing with imprecise probabilities: A framework for multiple representations of uncertainty in simulation software},
  Author                   = {Michael Spiegel},
  Institution              = {Department of Computer Science, University of Virginia},
  Year                     = {2007},
  Number                   = {CS-2007-16},
  Abstract                 = {We propose the design and construction of a programming language for
	the formal representation of uncertainty in modeling and simulation.
	Modeling under uncertainty has been of paramount importance in the
	past half century, as quantitative methods of analysis have been
	developed to take advantage of computational resources. Simulation
	is gaining prominence as the proper tool of scientific analysis under
	circumstances where it is infeasible or impractical to directly study
	the system in question. This programming language will be built as
	an extension to the Modelica programming language, which is an acausal
	object-oriented language for hybrid continuous and discrete-event
	simulations [22]. Our language extensions will serve as a platform
	for the research into representation and calibration of imprecise
	probabilities in quantitative risk analysis simulations. Imprecise
	probability is used a generic term for any mathematical model which
	measures chance or uncertainty without crisp numerical probabilities.
	The explicit representation of imprecise probability theories in
	a domain-specific programming language will facilitate the development
	of efficient algorithms for expressing, computing, and calibrating
	imprecise probability structures. Computation with imprecise probability
	structures will lead to quantitative risk analyses that are more
	informative than analyses using traditional probability theory. We
	have three primary research objectives: (i) the exploration of efficient
	representational structures and computational algorithms of Dempster-Shafer
	belief structures; (ii) the application of the imprecise probabilities
	to representing variable dependence; and (iii) the exploration of
	various Dempster-Shafer combination rules for model calibration.
	At the completion of this dissertation, we will have produced the
	end-to-end design, implementation, and analysis of a programming
	language that will facilitate the future exploration of algorithms,
	software, and theory for quantitative uncertainty analysis in computer
	science.},
  Owner                    = {mspiegel},
  Timestamp                = {2008.08.11}
}

@Conference{Spiegel2008,
  Title                    = {Quantifying and Analyzing Uncertainty in Simulations to Enable User Understanding},
  Author                   = {Spiegel, Michael and Gore, Ross and Reynolds, Paul F.},
  Booktitle                = {Proceedings of the Modeling, Simulation, \& Gaming Student Capstone Conference},
  Year                     = {2008},
  Address                  = {Suffolk, VA},
  Note                     = {Recipient of best paper award in "Discipline of Modeling \& Simulation" track.},
  Organization             = {The Virginia Modeling, Analysis, \& Simulation Center (VMASC)},
  Abstract                 = {Quantitative methods of analysis have progressed faster than quantitative
	methods of capturing, representing, propagating and analyzing uncertainty
	in the realm of computational thinking, adversely affecting the quality
	of both scientific computational analysis, and important policy decisions.
	Uncertainty arises from incomplete model input information (aleatory
	uncertainty), incomplete model structure information (epistemic uncertainty),
	and incomplete understanding of model dynamics. We describe a work
	in progress computational approach, framework, and language, RiskModelica,
	that will 1) support representation, propagation, and calibration
	of aleatory uncertainty using probability theory, probability boxes,
	and Dempster-Shafer theory of evidence; 2) develop reliable methodologies
	- algorithms, data acquisition and management procedures, software
	and theory - for quantifying uncertainty in computer predictions;
	3) support exploration of epistemic uncertainty utilizing causal
	analysis, and static and dynamic program slicing to characterize
	the dependencies, causal relationships, and interactions of design
	decisions; and 4) as a way of gaining insight into uncertainties,
	enable subject matter experts to observe model characteristics under
	novel conditions of interest. These capabilities represent a revolutionary
	approach to capturing, representing, propagating, and analyzing quantitatively,
	uncertainties that arise in the process of computational thinking.},
  Owner                    = {mspiegel},
  Timestamp                = {2008.08.11}
}

@TechReport{Spiegel2009,
  Title                    = {The Dense Skip Tree: A Cache-Conscious Randomized Data Structure},
  Author                   = {Michael Spiegel and Reynolds, Jr., Paul F.},
  Institution              = {Department of Computer Science, University of Virginia},
  Year                     = {2009},
  Number                   = {CS-2009-05},
  Abstract                 = {We introduce the dense skip tree, a novel cache-conscious randomized
	data structure. Algorithms for search, insertion, and deletion are
	presented, and they are shown to have expected cost O(log n). The
	dense skip tree obeys the same asymptotic properties as the skip
	list and the skip tree. A series of properties on the dense skip
	tree is proven, in order to show the probabilistic organization of
	data in a cache-conscious design. Performance benchmarks show the
	dense skip tree to outperform the skip list and the self-balancing
	binary search tree when the working set cannot be contained in cache.},
  Owner                    = {ms6ep},
  Timestamp                = {2009.04.27}
}

@InProceedings{Spiegel2010,
  Title                    = {Lock-Free Multiway Search Trees},
  Author                   = {Michael Spiegel and Reynolds, Jr., Paul F.},
  Booktitle                = {Proceedings of the 39th Annual International Conference on Parallel Processing ({ICPP})},
  Year                     = {2010},
  Address                  = {San Diego, CA},
  Month                    = {September 13-16},
  Publisher                = {IEEE Computer Society},
  Abstract                 = {We propose a lock-free multiway search tree algorithm for concurrent
	applications with large working set sizes. Our algorithm is a variation
	of the randomized skip tree. We relax the ordering constraints among
	the nodes in the original skip tree definition. Optimal paths through
	the tree are temporarily violated by mutation operations, and eventually
	restored using online node compaction. Experimental evidence shows
	that our lock-free skip tree outperforms a highly tuned concurrent
	skip list under workloads of various proportions of operations and
	working set sizes. The max throughput of our algorithm is on average
	41% higher than the throughput of the skip list, and 129% higher
	on the workload of the largest working set size and read-dominated
	operations.},
  Owner                    = {Michael},
  Timestamp                = {2010.07.06},
  URL                      = {http://dx.doi.org/10.1109/ICPP.2010.68}
}

@TechReport{Spiegel2011,
  Title                    = {Lock-Free Multiway Search Trees as Priority Queues in Parallel Branch and Bound Applications},
  Author                   = {Michael Spiegel and Reynolds, Jr., Paul F.},
  Institution              = {Department of Computer Science, University of Virginia},
  Year                     = {2011},
  Month                    = {February},
  Number                   = {CS-2011-01},
  Abstract                 = {The lock-free skip tree is a cache-conscious concurrent data structure
	for many-core systems that shows significant performance improvements
	over the state of the art in concurrent data structure designs for
	those applications that must contend with the deleterious effects
	of the memory wall. In a previous study using a series of synthetic
	benchmarks, the lock-free skip tree was found to improve peak throughput
	by x1.8 to x2.3 relative to a state of the art lock-free skip list
	implementation when the working set size exceeds cache size. In this
	work, we study a class of application benchmarks that can be used
	to characterize the relative merits of the lock-free skip tree as
	compared to the lock-free skip list. In a series of four parallel
	branch-and-bound applications, two of the applications are x2.3 and
	x3.1 faster when using the skip tree as a concurrent priority queue
	as compared to the lock-free skip list priority queue. On a shared-memory
	supercomputer architecture the two branch-and-bound applications
	are x1.6 and x2.1 faster with the skip tree versus the skip list
	running at 80 hardware threads. Based on the four application benchmarks
	and a synthetic branch-and-bound application, a set of guidelines
	is offered for selecting the lock-free skip tree to use as a centralized
	priority queue in parallel branch-and-bound applications.},
  Owner                    = {ms6ep},
  Timestamp                = {2009.04.27},
  URL                      = {http://www.unc.edu/~mspiegel/publications/CS-2011-01.pdf}
}

@PhdThesis{Spiegel2011a,
  Title                    = {Cache-conscious concurrent data structures},
  Author                   = {Michael Spiegel},
  School                   = {University of Virginia},
  Year                     = {2011},
  Owner                    = {Michael},
  Timestamp                = {2011.04.26},
  URL                      = {http://mspiegel.github.io/publications/michael-spiegel-dissertation.pdf}
}

@comment{jabref-meta: selector_author:}

@comment{jabref-meta: selector_journal:}

@comment{jabref-meta: selector_keywords:}

@comment{jabref-meta: selector_publisher:}