Parallel simulated annealing using an adaptive resampling interval

Lou, Zhihao; Reinitz, John

doi:10.1016/j.parco.2016.02.001

Cited by 23 publications

(11 citation statements)

References 49 publications

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“…There are of course, other algorithms for performing function optimization on a cluster computer. MDAS is used here, however, because its worst-case speedup characteristics are known; it is scalable; and, because it only requires solution vectors to be sent out to workers but not sent back, it has reduced inter-compute node communication overhead relative to other parallel optimization algorithms such as the simulated annealing-based algorithms developed in [70] and [71]. Further, unlike algorithms such as simulated annealing, it always makes small steps from a feasible starting point and hence is less prone to becoming trapped in an infeasible region.…”

Section: Methodsmentioning

confidence: 99%

Developing political-ecological theory: The need for Many-Task Computing

Haas

2019

Preprint

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8Models of political-ecological systems can inform policies for managing ecosystems that 9 contain endangered species. One way to increase the credibility of these models is to 10 subject them to a rigorous suite of data-based statistical assessments. Doing so involves 11 statistically estimating the model's parameters, computing confidence intervals for these 12 parameters, determining the model's prediction error rate, and assessing its sensitivity to 13 parameter misspecification. 14 Here, these statistical algorithms along with a method for constructing politically fea-15 sible policies from a statistically fitted model, are coded as JavaSpaces TM programs that 16 run as compute jobs on either supercomputers or a collection of in-house workstations. 17 Several new algorithms for implementing such jobs in distributed computing environments 18 are described. 19 This downloadable code is used to compute each job's output for the management 20 challenge of conserving the East African cheetah (Acinonyx jubatus). This case study shows 21 that the proposed suite of statistical tools can be run on a supercomputer to establish the 22 credibility of a managerially-relevant model of a political-ecological system that contains 23 one or more endangered species. This demonstration means that the new standard of 24 credibility that any political-ecological model needs to meet before being used to inform 25 ecosystem management decisions, is the one given herein. 26 1 27 Keywords: social-ecological systems; ecosystem policymaking; agent-based modeling; 28 high performance computing; sensitivity analysis; statistical estimation of large models 29 1 Introduction 30There is a need to acknowledge the complexity of political-ecological systems and the signif-31 icant challenges to building theories of them [1]. Such systems lie at the interface between 32 social/political science and ecology. The complexity of each of these fields coupled with an 33 additional layer of complexity introduced by the interactions between sociological/political 34 systems and natural systems can result in highly complex system dynamics, i.e., ones that 35 are stiff, nonlinear, and possess feedback loops. For example, Schoon and Van der Leeuw [2] 36 note that systems composed of interacting sociological and ecological subsystems are quick 37 to change and rarely stay in equilibrium for long. Further, many state variables are needed 38 to describe both the decision making processes of the relevant social groups, and the func-39 tioning of the involved ecosystem. A political-ecological system is also referred to as a 40 socio-ecological system or social-ecological system (e.g., see [3]). The former term is em-41 phasized herein because those political actions and processes that drive social movements 42 are often initiated by groups seeking to gain increased political power [4]. Building such 43 models is more than an academic exercise. Indeed, the alarming decline in the planet's 44 biodiversity [5], creates a crucial need for credible politi...

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Section: Methodsmentioning

confidence: 99%

Developing political-ecological theory: The need for Many-Task Computing

Haas

2019

Preprint

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“…Several algorithms have been used to solve this challenge. Initial studies using gene circuits used a global optimization approach called parallel Lam Simulated Annealing (pLSA) [18,64]. pLSA is a robust optimization method, that is computationally costly.…”

Section: Reverse-engineering With Gene Circuitsmentioning

confidence: 99%

Life’s Attractors Continued: Progress in Understanding Developmental Systems Through Reverse Engineering and In Silico Evolution

Crombach¹,

Jaeger

2021

Evolutionary Systems Biology

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We present a progress report on our efforts to establish a new research program for evolutionary systems biology, based on reverse-engineering and in silico evolution. The aim is a mechanistic understanding of the genotype-phenotype map and its evolution. Our review focuses on the case study of the gap gene network in dipteran insects (flies and midges). This network is the top regulatory tier of the segmentation gene hierarchy, generating a pattern of overlapping expression domains that subdivide the embryo during early embryogenesis. It is one of the best-understood developmental regulatory networks today. We have studied this system in a comparative way, across three species: the vinegar fly, Drosophila melanogaster, the scuttle fly, Megaselia abdita, and the moth midge, Clogmia albipunctata. In this context, we discuss methodological challenges concerning data processing and model-fitting, consider different functional decompositions of the gap gene network, and highlight novel insights into network evolution by compensatory developmental system drift. Finally, we discuss the prospect of simulating the phylogenesis of the gap gene network using in silico evolution. We conclude by arguing that our case study is a first step towards a more systematic empirical investigation into the principles of network evolution.

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“…Lastly, we parallelize the sampling of the Markov chain over all available cores (ranging from 4 to 6 on current consumer hardware) following the adaptive resampling method of Lou and Reinitz [LR16].…”

Section: Further Implementation Detailsmentioning

confidence: 99%

Stackless Ray-Object Intersections Using Approximate Minimum Weight Triangulations: Results in 2D That Outperform Roped KD-Trees (And Massively Outperform BVHs)

Frederickx¹,

Dutré²

2021

Preprint

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Computing ray-object intersections is a key operation of ray tracers. Two wellknown data structures to accelerate this computation are the kd-tree (which partitions space) and the Bounding Volume Hierarchy (BVH, which partitions the primitives). A third type of structure is a Constrained Convex Space Partitioning (CCSP), whichlike the kd-tree -partitions space, but it does this in such a way that the geometric primitives exactly overlap with the boundaries of its cells. As a consequence, it is robust against ill-fitting cells that plague methods with axis-aligned cells (kd-tree, BVH) and it permits an efficient, stackless traversal.Within the computer graphics community, such CCSPs have received some attention in both 2D and 3D, but their construction methods were never directly aimed at minimizing their traversal cost -even having fundamentally opposing goals for Delaunay-type methods. Instead, for an isotropic and translation-invariant ray distribution the traversal cost is minimized when minimizing the weight: the total boundary size of all cells in the structure.We study the two-dimensional case using triangulations as CCSPs and explicitly minimize their total edge length using a simulated annealing process that allows for topological changes and varying vertex count. Standard Delaunay-based triangulation techniques have total edge lengths ranging from 10% higher to twice as high as our optimized triangulations for a variety of scenes, with a similar difference in traversal cost when using the triangulations for ray tracing. Compared to a idealised roped kdtree with stackless traversal, our triangulations require less traversal steps for all scenes that we tested and they are robust against the kd-tree's pathological behaviour when geometry becomes misaligned with the world axes. Moreover, the stackless traversal of our triangulations strongly outperforms a BVH, which always requires a top-down descent in the hierarchy. In fact, we show several scenes where the number of traversal operations for our triangulations decreases as the number of geometric primitives N increases, in contrast to the increasing log N behaviour of a BVH.

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Parallel simulated annealing using an adaptive resampling interval

Cited by 23 publications

References 49 publications

Developing political-ecological theory: The need for Many-Task Computing

Developing political-ecological theory: The need for Many-Task Computing

Life’s Attractors Continued: Progress in Understanding Developmental Systems Through Reverse Engineering and In Silico Evolution

Stackless Ray-Object Intersections Using Approximate Minimum Weight Triangulations: Results in 2D That Outperform Roped KD-Trees (And Massively Outperform BVHs)

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