Matching Items (52)
Description
Modern, advanced statistical tools from data mining and machine learning have become commonplace in molecular biology in large part because of the “big data” demands of various kinds of “-omics” (e.g., genomics, transcriptomics, metabolomics, etc.). However, in other fields of biology where empirical data sets are conventionally smaller, more traditional statistical methods of inference are still very effective and widely used. Nevertheless, with the decrease in cost of high-performance computing, these fields are starting to employ simulation models to generate insights into questions that have been elusive in the laboratory and field. Although these computational models allow for exquisite control over large numbers of parameters, they also generate data at a qualitatively different scale than most experts in these fields are accustomed to. Thus, more sophisticated methods from big-data statistics have an opportunity to better facilitate the often-forgotten area of bioinformatics that might be called “in-silicomics”.
As a case study, this thesis develops methods for the analysis of large amounts of data generated from a simulated ecosystem designed to understand how mammalian biomechanics interact with environmental complexity to modulate the outcomes of predator–prey interactions. These simulations investigate how other biomechanical parameters relating to the agility of animals in predator–prey pairs are better predictors of pursuit outcomes. Traditional modelling techniques such as forward, backward, and stepwise variable selection are initially used to study these data, but the number of parameters and potentially relevant interaction effects render these methods impractical. Consequently, new modelling techniques such as LASSO regularization are used and compared to the traditional techniques in terms of accuracy and computational complexity. Finally, the splitting rules and instances in the leaves of classification trees provide the basis for future simulation with an economical number of additional runs. In general, this thesis shows the increased utility of these sophisticated statistical techniques with simulated ecological data compared to the approaches traditionally used in these fields. These techniques combined with methods from industrial Design of Experiments will help ecologists extract novel insights from simulations that combine habitat complexity, population structure, and biomechanics.
As a case study, this thesis develops methods for the analysis of large amounts of data generated from a simulated ecosystem designed to understand how mammalian biomechanics interact with environmental complexity to modulate the outcomes of predator–prey interactions. These simulations investigate how other biomechanical parameters relating to the agility of animals in predator–prey pairs are better predictors of pursuit outcomes. Traditional modelling techniques such as forward, backward, and stepwise variable selection are initially used to study these data, but the number of parameters and potentially relevant interaction effects render these methods impractical. Consequently, new modelling techniques such as LASSO regularization are used and compared to the traditional techniques in terms of accuracy and computational complexity. Finally, the splitting rules and instances in the leaves of classification trees provide the basis for future simulation with an economical number of additional runs. In general, this thesis shows the increased utility of these sophisticated statistical techniques with simulated ecological data compared to the approaches traditionally used in these fields. These techniques combined with methods from industrial Design of Experiments will help ecologists extract novel insights from simulations that combine habitat complexity, population structure, and biomechanics.
ContributorsSeto, Christian (Author) / Pavlic, Theodore (Thesis advisor) / Li, Jing (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2018
Description
Project portfolio selection (PPS) is a significant problem faced by most organizations. How to best select the many innovative ideas that a company has developed to deploy in a proper and sustained manner with a balanced allocation of its resources over multiple time periods is one of vital importance to a company's goals. This dissertation details the steps involved in deploying a more intuitive portfolio selection framework that facilitates bringing analysts and management to a consensus on ongoing company efforts and buy into final decisions. A binary integer programming selection model that constructs an efficient frontier allows the evaluation of portfolios on many different criteria and allows decision makers (DM) to bring their experience and insight to the table when making a decision is discussed. A binary fractional integer program provides additional choices by optimizing portfolios on cost-benefit ratios over multiple time periods is also presented. By combining this framework with an `elimination by aspects' model of decision making, DMs evaluate portfolios on various objectives and ensure the selection of a portfolio most in line with their goals. By presenting a modeling framework to easily model a large number of project inter-dependencies and an evolutionary algorithm that is intelligently guided in the search for attractive portfolios by a beam search heuristic, practitioners are given a ready recipe to solve big problem instances to generate attractive project portfolios for their organizations. Finally, this dissertation attempts to address the problem of risk and uncertainty in project portfolio selection. After exploring the selection of portfolios based on trade-offs between a primary benefit and a primary cost, the third important dimension of uncertainty of outcome and the risk a decision maker is willing to take on in their quest to select the best portfolio for their organization is examined.
ContributorsSampath, Siddhartha (Author) / Gel, Esma (Thesis advisor) / Fowler, Jown W (Thesis advisor) / Kempf, Karl G. (Committee member) / Pan, Rong (Committee member) / Sefair, Jorge (Committee member) / Arizona State University (Publisher)
Created2018
Description
This research develops heuristics to manage both mandatory and optional network capacity reductions to better serve the network flows. The main application discussed relates to transportation networks, and flow cost relates to travel cost of users of the network. Temporary mandatory capacity reductions are required by maintenance activities. The objective of managing maintenance activities and the attendant temporary network capacity reductions is to schedule the required segment closures so that all maintenance work can be completed on time, and the total flow cost over the maintenance period is minimized for different types of flows. The goal of optional network capacity reduction is to selectively reduce the capacity of some links to improve the overall efficiency of user-optimized flows, where each traveler takes the route that minimizes the traveler’s trip cost. In this dissertation, both managing mandatory and optional network capacity reductions are addressed with the consideration of network-wide flow diversions due to changed link capacities.
This research first investigates the maintenance scheduling in transportation networks with service vehicles (e.g., truck fleets and passenger transport fleets), where these vehicles are assumed to take the system-optimized routes that minimize the total travel cost of the fleet. This problem is solved with the randomized fixed-and-optimize heuristic developed. This research also investigates the maintenance scheduling in networks with multi-modal traffic that consists of (1) regular human-driven cars with user-optimized routing and (2) self-driving vehicles with system-optimized routing. An iterative mixed flow assignment algorithm is developed to obtain the multi-modal traffic assignment resulting from a maintenance schedule. The genetic algorithm with multi-point crossover is applied to obtain a good schedule.
Based on the Braess’ paradox that removing some links may alleviate the congestion of user-optimized flows, this research generalizes the Braess’ paradox to reduce the capacity of selected links to improve the efficiency of the resultant user-optimized flows. A heuristic is developed to identify links to reduce capacity, and the corresponding capacity reduction amounts, to get more efficient total flows. Experiments on real networks demonstrate the generalized Braess’ paradox exists in reality, and the heuristic developed solves real-world test cases even when commercial solvers fail.
This research first investigates the maintenance scheduling in transportation networks with service vehicles (e.g., truck fleets and passenger transport fleets), where these vehicles are assumed to take the system-optimized routes that minimize the total travel cost of the fleet. This problem is solved with the randomized fixed-and-optimize heuristic developed. This research also investigates the maintenance scheduling in networks with multi-modal traffic that consists of (1) regular human-driven cars with user-optimized routing and (2) self-driving vehicles with system-optimized routing. An iterative mixed flow assignment algorithm is developed to obtain the multi-modal traffic assignment resulting from a maintenance schedule. The genetic algorithm with multi-point crossover is applied to obtain a good schedule.
Based on the Braess’ paradox that removing some links may alleviate the congestion of user-optimized flows, this research generalizes the Braess’ paradox to reduce the capacity of selected links to improve the efficiency of the resultant user-optimized flows. A heuristic is developed to identify links to reduce capacity, and the corresponding capacity reduction amounts, to get more efficient total flows. Experiments on real networks demonstrate the generalized Braess’ paradox exists in reality, and the heuristic developed solves real-world test cases even when commercial solvers fail.
ContributorsPeng, Dening (Author) / Mirchandani, Pitu B. (Thesis advisor) / Sefair, Jorge (Committee member) / Wu, Teresa (Committee member) / Zhou, Xuesong (Committee member) / Arizona State University (Publisher)
Created2017
Description
Researchers and practitioners have widely studied road network traffic data in different areas such as urban planning, traffic prediction and spatial-temporal databases. For instance, researchers use such data to evaluate the impact of road network changes. Unfortunately, collecting large-scale high-quality urban traffic data requires tremendous efforts because participating vehicles must install Global Positioning System(GPS) receivers and administrators must continuously monitor these devices. There have been some urban traffic simulators trying to generate such data with different features. However, they suffer from two critical issues (1) Scalability: most of them only offer single-machine solution which is not adequate to produce large-scale data. Some simulators can generate traffic in parallel but do not well balance the load among machines in a cluster. (2) Granularity: many simulators do not consider microscopic traffic situations including traffic lights, lane changing, car following. This paper proposed GeoSparkSim, a scalable traffic simulator which extends Apache Spark to generate large-scale road network traffic datasets with microscopic traffic simulation. The proposed system seamlessly integrates with a Spark-based spatial data management system, GeoSpark, to deliver a holistic approach that allows data scientists to simulate, analyze and visualize large-scale urban traffic data. To implement microscopic traffic models, GeoSparkSim employs a simulation-aware vehicle partitioning method to partition vehicles among different machines such that each machine has a balanced workload. The experimental analysis shows that GeoSparkSim can simulate the movements of 200 thousand cars over an extensive road network (250 thousand road junctions and 300 thousand road segments).
ContributorsFu, Zishan (Author) / Sarwat, Mohamed (Thesis advisor) / Pedrielli, Giulia (Committee member) / Sefair, Jorge (Committee member) / Arizona State University (Publisher)
Created2019
Description
The shift in focus of manufacturing systems to high-mix and low-volume production poses a challenge to both efficient scheduling of manufacturing operations and effective assessment of production capacity. This thesis considers the problem of scheduling a set of jobs that require machine and worker resources to complete their manufacturing operations. Although planners in manufacturing contexts typically focus solely on machines, schedules that only consider machining requirements may be problematic during implementation because machines need skilled workers and cannot run unsupervised. The model used in this research will be beneficial to these environments as planners would be able to determine more realistic assignments and operation sequences to minimize the total time required to complete all jobs. This thesis presents a mathematical formulation for concurrent scheduling of machines and workers that can optimally schedule a set of jobs while accounting for changeover times between operations. The mathematical formulation is based on disjunctive constraints that capture the conflict between operations when trying to schedule them to be performed by the same machine or worker. An additional formulation extends the previous one to consider how cross-training may impact the production capacity and, for a given budget, provide training recommendations for specific workers and operations to reduce the makespan. If training a worker is advantageous to increase production capacity, the model recommends the best time window to complete it such that overlaps with work assignments are avoided. It is assumed that workers can perform tasks involving the recently acquired skills as soon as training is complete. As an alternative to the mixed-integer programming formulations, this thesis provides a math-heuristic approach that fixes the order of some operations based on Largest Processing Time (LPT) and Shortest Processing Time (SPT) procedures, while allowing the exact formulation to find the optimal schedule for the remaining operations. Computational experiments include the use of the solution for the no-training problem as a starting feasible solution to the training problem. Although the models provided are general, the manufacturing of Printed Circuit Boards are used as a case study.
ContributorsAdams, Katherine Bahia (Author) / Sefair, Jorge (Thesis advisor) / Askin, Ronald (Thesis advisor) / Webster, Scott (Committee member) / Arizona State University (Publisher)
Created2019
Description
I study the problem of locating Relay nodes (RN) to improve the connectivity of a set
of already deployed sensor nodes (SN) in a Wireless Sensor Network (WSN). This is
known as the Relay Node Placement Problem (RNPP). In this problem, one or more
nodes called Base Stations (BS) serve as the collection point of all the information
captured by SNs. SNs have limited transmission range and hence signals are transmitted
from the SNs to the BS through multi-hop routing. As a result, the WSN
is said to be connected if there exists a path for from each SN to the BS through
which signals can be hopped. The communication range of each node is modeled
with a disk of known radius such that two nodes are said to communicate if their
communication disks overlap. The goal is to locate a given number of RNs anywhere
in the continuous space of the WSN to maximize the number of SNs connected (i.e.,
maximize the network connectivity). To solve this problem, I propose an integer
programming based approach that iteratively approximates the Euclidean distance
needed to enforce sensor communication. This is achieved through a cutting-plane
approach with a polynomial-time separation algorithm that identies distance violations.
I illustrate the use of my algorithm on large-scale instances of up to 75 nodes
which can be solved in less than 60 minutes. The proposed method shows solutions
times many times faster than an alternative nonlinear formulation.
of already deployed sensor nodes (SN) in a Wireless Sensor Network (WSN). This is
known as the Relay Node Placement Problem (RNPP). In this problem, one or more
nodes called Base Stations (BS) serve as the collection point of all the information
captured by SNs. SNs have limited transmission range and hence signals are transmitted
from the SNs to the BS through multi-hop routing. As a result, the WSN
is said to be connected if there exists a path for from each SN to the BS through
which signals can be hopped. The communication range of each node is modeled
with a disk of known radius such that two nodes are said to communicate if their
communication disks overlap. The goal is to locate a given number of RNs anywhere
in the continuous space of the WSN to maximize the number of SNs connected (i.e.,
maximize the network connectivity). To solve this problem, I propose an integer
programming based approach that iteratively approximates the Euclidean distance
needed to enforce sensor communication. This is achieved through a cutting-plane
approach with a polynomial-time separation algorithm that identies distance violations.
I illustrate the use of my algorithm on large-scale instances of up to 75 nodes
which can be solved in less than 60 minutes. The proposed method shows solutions
times many times faster than an alternative nonlinear formulation.
ContributorsSurendran, Vishal Sairam Jaitra (Author) / Sefair, Jorge (Thesis advisor) / Mirchandani, Pitu (Committee member) / Grubesic, Anthony (Committee member) / Arizona State University (Publisher)
Created2019
Description
Ultimate Frisbee or "Ultimate," is a fast growing field sport that is being played competitively at universities across the country. Many mid-tier college teams have the goal of winning as many games as possible, however they also need to grow their program by training and retaining new players. The purpose of this project was to create a prototype statistical tool that maximizes a player line-up's probability of scoring the next point, while having as equal playing time across all experienced and novice players as possible. Game, player, and team data was collected for 25 different games played over the course of 4 tournaments during Fall 2017 and early Spring 2018 using the UltiAnalytics iPad application. "Amount of Top 1/3 Players" was the measure of equal playing time, and "Line Efficiency" and "Line Interaction" represented a line's probability of scoring. After running a logistic regression, Line Efficiency was found to be the more accurate predictor of scoring outcome than Line Interaction. An "Equal PT Measure vs. Line Efficiency" graph was then created and the plot showed what the optimal lines were depending on what the user's preferences were at that point in time. Possible next steps include testing the model and refining it as needed.
ContributorsSpence, Andrea Nicole (Author) / McCarville, Daniel R. (Thesis director) / Pavlic, Theodore (Committee member) / Industrial, Systems and Operations Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
This paper outlines the development of a software application that explores the plausibility and potential of interacting with three-dimensional sound sources within a virtual environment. The intention of the software application is to allow a user to become engaged with a collection of sound sources that can be perceived both graphically and audibly within a spatial, three-dimensional context. The three-dimensional sound perception is driven primarily by a binaural implementation of a higher order ambisonics framework while graphics and other data are processed by openFrameworks, an interactive media framework for C++. Within the application, sound sources have been given behavioral functions such as flocking or orbit patterns, animating their positions within the environment. The author will summarize the design process and rationale for creating such a system and the chosen approach to implement the software application. The paper will also provide background approaches to spatial audio, gesture and virtual reality embodiment, and future possibilities for the existing project.
ContributorsBurnett, Garrett (Author) / Paine, Garth (Thesis director) / Pavlic, Theodore (Committee member) / School of Humanities, Arts, and Cultural Studies (Contributor) / School of Arts, Media and Engineering (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Simulation games are widely used in engineering education, especially for industrial engineering and operations management. A well-made simulation game aids in achieving learning objectives for students and minimal additional teaching by an instructor. Many simulation games exist for engineering education, but newer technologies now exist that improve the overall experience of developing and using these games. Although current solutions teach concepts adequately, poorly-maintained platforms distract from the key learning objectives, detracting from the value of the activities. A backend framework was created to facilitate an educational, competitive, participatory simulation of a manufacturing system that is intended to be easy to maintain, deploy, and expand.
ContributorsChandler, Robert Keith (Author) / Clough, Michael (Thesis director) / Pavlic, Theodore (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
Temnothorax ants are a model species for studying collective decision-making. When presented with multiple nest sites, they are able to collectively select the best one and move the colony there. When a scout encounters a nest site, she will spend some time exploring it. In theory she should explore the site for long enough to determine both its quality and an estimate of the number of ants there. This ensures that she selects a good nest site and that there are enough scouts who know about the new nest site to aid her in relocating the colony. It also helps to ensure that the colony reaches a consensus rather than dividing between nest sites. When a nest site reaches a certain threshold of ants, a quorum has been reached and the colony is committed to that nest site. If a scout visits a good nest site where a quorum has not been reached, she will lead a tandem run to bring another scout there so that they can learn the way and later aid in recruitment. At a site where a quorum has been reached, scouts will instead perform transports to carry ants and brood there from the old nest. One piece that is missing in all of this is the mechanism. How is a quorum sensed? One hypothesis is that the encounter rate (average number of encounters with nest mates per second) that an ant experiences at a nest site allows her to estimate the population at that site and determine whether a quorum has been reached. In this study, encounter rate and entrance time were both shown to play a role in whether an ant decided to lead a tandem run or perform a transport. Encounter rate was shown to have a significant impact on how much time an ant spent at a nest site before making her decision, and encounter rates significantly increased as migrations progressed. It was also shown to individual ants did not differ from each other in their encounter rates, visit lengths, or entrance times preceding their first transports or tandem runs, studied across four different migrations. Ants were found to spend longer on certain types of encounters, but excluding certain types of encounters from the encounter rate was not found to change the correlations that were observed. It was also found that as the colony performed more migrations, it became significantly faster at moving to the new nest.
ContributorsJohnson, Christal Marie (Author) / Pratt, Stephen (Thesis director) / Pavlic, Theodore (Committee member) / Shaffer, Zachary (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-05