Geometric Approaches to Big Data Modeling and Performance Prediction

Big Data frameworks (e.g., Spark) have many configuration parameters, such as memory size, CPU allocation, and the number of nodes (parallelism). Regular users and even expert administrators struggle to understand the relationship between different parameter configurations and the overall performance of the system. In this work, we address this challenge by proposing a performance prediction framework to build performance models with varied configurable parameters on Spark. We take inspiration from the field of Computational Geometry to construct a d-dimensional mesh using Delaunay Triangulation over a selected set of features. From this mesh, we predict execution time for unknown feature configurations. To minimize the time and resources spent in building a model, we propose an adaptive sampling technique to allow us to collect as few training points as required. Our evaluation on a cluster of computers using several workloads shows that our prediction error is lower than the state-of-art methods while having fewer samples to train

The extracellular matrix regulates myoblast migration during wound healing.

Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.Mammalian skeletal muscle can regenerate after injury and this response is primarily mediated by the satellite cell, a muscle stem cell. Following injury, satellite cells are activated to myoblasts, undergo rapid proliferation, migrate towards the injury site, and subsequently differentiate into myotubes in order to facilitate functional muscle repair. Fibrosis, caused by the secretion of structural extracellular matrix (ECM) proteins such as collagen I and fibronectin, by fibroblasts, impairs complete functional repair of the muscle. In this study, the role of the microenvironment during wound conditions was assessed by analysing the effect of specific extracellular matrix and growth factors on myoblast migration. The role of the Rho/ROCK pathway as a possible mechanism in mediating the effects seen was investigated. In order to analyse wound repair in an in vitro setting, we optimised and improved a wound healing model specifically designed for skeletal muscle repair. To this end we also developed a co-culture assay using primary myoblasts and fibroblasts isolated from the same animal. The studies showed that collagen I and fibronectin both increased myoblast migration in a dose-dependent manner. Decorin displayed opposing effects on cellular movement, significantly increasing collagen I-stimulated, but not fibronectin-stimulated, migration of myoblasts. ROCK inhibitor studies revealed a significant increase in migration on uncoated plates following inhibition with Y-27632 compared to untreated control. When cells were cultured on ECM components (Matrigel, collagen I, or fibronectin), the inhibitory effect of Y-27632 on migration was reduced. Analysis of ROCK and vinculin expression, and localization at the leading front, showed that ROCK inhibition resulted in loosely packed focal adhesion complexes (matrix dependent). A reduced adhesion to the ECM could explain the increased migration rates observed upon inhibition with Y-27632. We also investigated the role of TGF-β and decorin during wound repair, as TGF-β is a known pro-fibrotic agent. TGF-β treatment decreased wound closure rates; however, the addition of decorin with TGF-β significantly increased wound closure. The addition of ECM components, Matrigel and collagen I enhanced the effect seen in response to TGF-β and decorin; however, fibronectin negated this effect, with no increase in migration seen compared to the controls. In conclusion, the importance of extracellular matrix components in regulating myoblast migration and therefore skeletal muscle wound repair was demonstrated. We emphasize that, in order to gain a better understanding of skeletal muscle wound repair, the combination of ECM and growth factors released during wounding need to be utilised in assays which mimic the in vivo environment more closely

d-Simplexed : Adaptive Delaunay Triangulation or Performance Modeling and Prediction on Big Data Analytics

Big Data processing systems (e.g., Spark) have a number of resource configuration parameters, such as memory size, CPU allocation, and the number of running nodes. Regular users and even expert administrators struggle to understand the mutual relation between different parameter configurations and the overall performance of the system. In this paper, we address this challenge by proposing a performance prediction framework, called $d$-Simplexed, to build performance models with varied configurable parameters on Spark. We take inspiration from the field of Computational Geometry to construct a d-dimensional mesh using Delaunay Triangulation over a selected set of features. From this mesh, we predict execution time for various feature configurations. To minimize the time and resources in building a bootstrap model with a large number of configuration values, we propose an adaptive sampling technique to allow us to collect as few training points as required. Our evaluation on a cluster of computers using WordCount, PageRank, Kmeans, and Join workloads in HiBench benchmarking suites shows that we can achieve less than 5% error rate for estimation accuracy by sampling less than 1% of data.Peer reviewe

Cat States and Single Runs for the Damped Harmonic Oscillator

We discuss the fate of initial states of the cat type for the damped harmonic oscillator, mostly employing a linear version of the stochastic Schr\"odinger equation. We also comment on how such cat states might be prepared and on the relation of single realizations of the noise to single runs of experiments.Comment: 18, Revte

Linear stochastic wave-equations for continuously measured quantum systems

While the linearity of the Schr\"odinger equation and the superposition principle are fundamental to quantum mechanics, so are the backaction of measurements and the resulting nonlinearity. It is remarkable, therefore, that the wave-equation of systems in continuous interaction with some reservoir, which may be a measuring device, can be cast into a linear form, even after the degrees of freedom of the reservoir have been eliminated. The superposition principle still holds for the stochastic wave-function of the observed system, and exact analytical solutions are possible in sufficiently simple cases. We discuss here the coupling to Markovian reservoirs appropriate for homodyne, heterodyne, and photon counting measurements. For these we present a derivation of the linear stochastic wave-equation from first principles and analyze its physical content.Comment: 34 pages, Revte

Warming accelerates belowground litter turnover in salt marshes – insights from a Tea Bag Index study

Salt marshes play an important role in the global carbon cycle due to the large amount of organic carbon stored in their soils. Soil organic carbon formation in these coastal wetland ecosystems is strongly controlled by the plant primary production and initial decomposition rates of plant belowground biomass and litter. This study used a field warming experiment to investigate the response of belowground litter breakdown to rising temperature (+1.5 and +3.0◦C) across whole-soil profiles (0–60 cm soil depth) and the entire intertidal flooding gradient ranging from the pioneer zone via the low marsh to high marsh. We used standardized plant materials, following the Tea Bag Index approach, to assess the initial decomposition rate (k) and the stabilization factor (S) of labile organic matter inputs to the soil system. While k describes the initial pace at which labile (= hydrolyzable) organic matter decomposes, S describes the part of the labile fraction that does not decompose during deployment in the soil system and stabilizes due to biochemical transformation. We show that warming strongly increased k consistently throughout the entire soil profile and across the entire flooding gradient, suggesting that warming effects on the initial decomposition rate of labile plant materials are independent of the soil aeration (i.e., redox) status. By contrast, negative effects on litter stabilization were less consistent. Specifically, warming effects on S were restricted to the aerated topsoil in the frequently flooded pioneer zone, while the soil depth to which stabilization responded increased across the marsh elevation gradient via the low to high marsh. These findings suggest that reducing soil conditions can suppress the response of belowground litter stabilization to rising temperature. In conclusion, our study demonstrates marked differences in the response of initial decomposition rate vs. stabilization of labile plant litter to rising temperature in salt marshes. We argue that these differences are strongly mediated by the soil redox status along flooding and soil-depth gradients

Investigation of the potential ingestion rates of different sourveld grasses by cattle and sheep

Quantification of the potential ingestion rates of different grasses is important for modelling purposes but is difficult to achieve under field conditions. The ingestion rates of the sourveld species Alloteropsis semialata, Andropogon appendiculatus, Cynodon dactylon, Eragrostis plana, Heteropogon contortus, Hyparrhenia hirta, Themeda triandra and Tristachya leucothrix were determined by presenting plants growing in pots to confined sheep and a single steer. Sheep intake rates were highest for H. contortus (6.82 g DM min−1) and lowest for A. appendiculatus (4.01 g DM min−1) but most between‐species differences were non‐significant. Steer intake rates were highest for E. plana and A. semialata (32 g DM min−1) and lowest for H. hirta (24.3 g DM min−1) but again, most between‐species differences were nonsignificant. The results obtained suggest that there is little difference in the potential ingestion rate of most sourveld species and indicate that the methodology employed has potential as research tool