Browsing by Subject "Simulation"
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Item An approach for determining relative input parameter importance and significance in artificial neural networks(Elsevier, 2007) Kemp, Stanley J.; Zaradic, Patricia A.; Hansen, FrankArtificial neural network (ANN) models are powerful statistical tools which are increasingly used in modeling complex ecological systems. For interpretation of ANN models, a means of evaluating how systemic parameters contribute to model output is essential. Developing a robust, systematic method for interpreting ANN models is the subject of much current research. We propose a method using sequential randomization of input parameters to determine the relative proportion to which each input variable contributes to the predictive ability of the ANN model (termed the holdback input randomization method or HIPR method). Validity of the method was assessed using a simulated data set in which the relationship between input parameters and output parameters were completely known. Simulated data sets were generated with known linear, nonlinear, and collinear relationships. The HIPR method was performed repetitively on ANN models trained on these data sets. The method was successful in predicting rank order of importance on all data sets, performing as well as or better than the recently proposed connectivity weight method. One main advantage of using this method relative to others is that results can be obtained without making assumptions regarding the architecture of the ANN model used. These results also serve to illustrate the consistency and information content of ANN models in general, and highlight their potential use in exploring ecological relationships. The HIPR method is a robust, simple, general procedure for interpreting complex ecological systems as captured by ANN models.Item Efficient Simulation of a Reaction-Diffusion System with a Fast Reaction in the Asymptotic Limit(2012-09-25) Wang, Guan; Churchill, Aaron; Seidman, Thomas I.We study a reaction-diffusion system of three chemical species, where two chemicals react with a much faster reaction rate than the other reaction in the model. We are interested in the asymptotic limit as the fast reaction rate becomes infinite. This forces the reaction interface to have an asymptotically small width with asymptotically large height. This interface is moving in time and causes interior layers that are progressively more challenging and costly for numerical simulations of the three species model, as the singularity becomes sharper with larger reaction rates. But in the asymptotic limit, an equivalent two component model can be defined that is significantly cheaper computationally and allows for effective studies for the model. The equivalence is demonstrated by the analytical definition of the two component model and by comparing numerical results to ones for the three species model with progressively larger reaction rates, which also demonstrate the computational efficiency. The state-of-the-art finite element package COMSOL Multiphysics is used for the simulations, thus also showing a practical way how to handle and visualize moving interior layers in reaction-diffusion systems. COMSOL is popular in many areas of engineering and the sciences and thus the mathematical example here can provide guidance to a wide range of users with models consisting of partial differential equations.Item Factors Affecting OptiX Performance in Ray Tracing for Metrology(2022-01-01) Stein, Peter; Engel, Don; Computer Science and Electrical Engineering; Computer ScienceWith the increasing prevalence of ray tracing cores in modern graphics cards, ray tracing based applications can see huge running time improvements. Simulations for x-rays and other electromagnetic radiation have long used ray tracing to predict results to allow for more narrow testing regimens to reduce the number of expensive experiments to run. OptiX is an API developed by NVIDIA to make hardware accelerated ray tracing applications easier and it has been shown to speed up many different ray tracing electromagnetic radiation simulations. Because there are many different approaches to scene and data representation, knowing how different simulation factors affect the running time of an OptiX simulation can help suggest which approaches and applications are the most applicable. This work explores the trends of running time against a variety of factors seen in a basic x-ray particle simulation, from scene representation, to simulation accuracy, to the amount and type of recorded data. We found that OptiX scales logarithmically in rendering time as a function of the number of scene objects, whereas loading the scene into the main data structures and increasing the number of rays scale linearly. Many strategies that reduce the number of triangles and other primitives that need to be loaded have the potential to greatly improve running time, such as adding spheres as primitives, or eliminating unneeded voxels in a voxel grid. Knowing these trends and comparisons between methods can lead to smarter design choices in production code, like choosing to recast from a new location in the same scene versus regenerating it. It can also lead to interesting future research, such as whether work to reduce voxel grids into sparse grids or independent meshes is faster than simpler approaches.Item Psychosis Simulation and Mental Health Video Effects on Young Adult Attitudes Toward People with Schizophrenia(2016-01-01) Denenny, Danielle; Schiffman, Jason; Psychology; PsychologyPublic stigma towards people with schizophrenia is prevalent in the United States and interferes with seeking professional help, recovery, and quality of life. Brief interventions have been disseminated yet their active ingredients and impact on specific aspects of stigma are poorly understood. The present study evaluated the effects of two contact videos (one standard and one enhanced with factors theorized to facilitate greater effects), a psychosis simulation, and their combination on perceived dangerousness, social distance, belief in forced treatment, and negative emotions toward people with schizophrenia within a college-age population. Participants (N = 170) were each randomly assigned to one video (control, standard, or enhanced) and one audio recording (control or simulation). Two sets of analyses were conducted for each outcome: immediate effects (primary analyses) and three-week effects (secondary analyses), yielding eight 2 (Time) x 2 (Audio) x 3 (Video) mixed design ANOVAs. Results indicated that the contact videos significantly reduced several negative attitudes and emotions when compared to the control video, although in many cases, this difference was not significant if the simulation followed the video. The enhanced video did not have greater effects than the standard video. Thus, contact videos have the potential for small immediate and longer-term effects on stigma in a college-age population. Recommendations are made for optimizing interventions and future research directions.Item Simulation of the Evolution of Information Content in Transcription Factor Binding Sites Using a Parallelized Genetic Algorithm(2011-07-30) Cornish, Joseph; Forder, Robert; Erill, Ivan; Gobbert, Matthias K.The analysis of transcription factor binding motifs may aid in understanding the process by which transcription factors recognize their binding sites. We wish to investigate the likelihood that transcription factors use correlation between positions instead of conservation of single positions as a mechanism for binding site recognition. We implement a genetic algorithm in parallel using a server-client organization to simulate the evolution of these binding sites. A performance analysis of the parallel algorithm showed significantly improved performance over the serial counterpart. The results of the simulation indicate that overall correlation is unlikely to be used in transcription factor binding site recognition.Item Water Quality Monitoring of Maryland’s Tidal Waterways(2012) Le, Rosemary K.; Rackauckas, Christopher V.; Ross, Anne S.; Ulloa, NehemiasThe Chesapeake Bay and its surrounding tributaries are home to over 3,600 species of plants and animals. In order to assess the health of the region, the Maryland Department of Natural Resources (DNR) monitors various parameters, such as dissolved oxygen, with monitoring stations located throughout the tidal waterways. Utilizing data provided by DNR, we assessed the waterways for areas of water quality concern. We analyzed the percentage of the readings taken for each parameter that failed to meet the threshold values and used the Wilcoxon Signed-Rank Test to determine the statuses of the stations. In order to assess the applicability of the Wilcoxon Test given the positive skew in the data, a simulation was performed. This simulation demonstrated that log-transforming the data prior to performing the Wilcoxon Test helped reduce the Type I Error. Furthermore, we ranked the stations using a set of multiple comparison methods: a version of the Tukey Test on variance-transformed proportions, the Bonferroni adjustment method, a Bayesian method, and the Benjamini-Hochberg rejection method. Also, we conducted a trend analysis for the five stations in the Corsica River. To aid in the presentation of our analyses, we constructed an interactive GUI (Graphical User Interface) for use by researchers and the general public.