Matching Items (53)
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
This dissertation is focused on developing an algorithm to provide current state estimation and future state predictions for biomechanical human walking features. The goal is to develop a system which is capable of evaluating the current action a subject is taking while walking and then use this to predict the future states of biomechanical features.
This work focuses on the exploration and analysis of Interaction Primitives (Amor er al, 2014) and their relevance to biomechanical prediction for human walking. Built on the framework of Probabilistic Movement Primitives, Interaction Primitives utilize an EKF SLAM algorithm to localize and map a distribution over the weights of a set of basis functions. The prediction properties of Bayesian Interaction Primitives were utilized to predict real-time foot forces from a 9 degrees of freedom IMUs mounted to a subjects tibias. This method shows that real-time human biomechanical features can be predicted and have a promising link to real-time controls applications.
This work focuses on the exploration and analysis of Interaction Primitives (Amor er al, 2014) and their relevance to biomechanical prediction for human walking. Built on the framework of Probabilistic Movement Primitives, Interaction Primitives utilize an EKF SLAM algorithm to localize and map a distribution over the weights of a set of basis functions. The prediction properties of Bayesian Interaction Primitives were utilized to predict real-time foot forces from a 9 degrees of freedom IMUs mounted to a subjects tibias. This method shows that real-time human biomechanical features can be predicted and have a promising link to real-time controls applications.
ContributorsClark, Geoffrey Mitchell (Author) / Ben Amor, Heni (Thesis advisor) / Si, Jennie (Committee member) / Berisha, Visar (Committee member) / Arizona State University (Publisher)
Created2018
Description
Reinforcement learning (RL) is a powerful methodology for teaching autonomous agents complex behaviors and skills. A critical component in most RL algorithms is the reward function -- a mathematical function that provides numerical estimates for desirable and undesirable states. Typically, the reward function must be hand-designed by a human expert and, as a result, the scope of a robot's autonomy and ability to safely explore and learn in new and unforeseen environments is constrained by the specifics of the designed reward function. In this thesis, I design and implement a stateful collision anticipation model with powerful predictive capability based upon my research of sequential data modeling and modern recurrent neural networks. I also develop deep reinforcement learning methods whose rewards are generated by self-supervised training and intrinsic signals. The main objective is to work towards the development of resilient robots that can learn to anticipate and avoid damaging interactions by combining visual and proprioceptive cues from internal sensors. The introduced solutions are inspired by pain pathways in humans and animals, because such pathways are known to guide decision-making processes and promote self-preservation. A new "robot dodge ball' benchmark is introduced in order to test the validity of the developed algorithms in dynamic environments.
ContributorsRichardson, Trevor W (Author) / Ben Amor, Heni (Thesis advisor) / Yang, Yezhou (Committee member) / Srivastava, Siddharth (Committee member) / Arizona State University (Publisher)
Created2018
Description
This thesis presents a family of adaptive curvature methods for gradient-based stochastic optimization. In particular, a general algorithmic framework is introduced along with a practical implementation that yields an efficient, adaptive curvature gradient descent algorithm. To this end, a theoretical and practical link between curvature matrix estimation and shrinkage methods for covariance matrices is established. The use of shrinkage improves estimation accuracy of the curvature matrix when data samples are scarce. This thesis also introduce several insights that result in data- and computation-efficient update equations. Empirical results suggest that the proposed method compares favorably with existing second-order techniques based on the Fisher or Gauss-Newton and with adaptive stochastic gradient descent methods on both supervised and reinforcement learning tasks.
ContributorsBarron, Trevor (Author) / Ben Amor, Heni (Thesis advisor) / He, Jingrui (Committee member) / Levihn, Martin (Committee member) / Arizona State University (Publisher)
Created2019
Description
Automated driving systems are in an intensive research and development stage, and the companies developing these systems are targeting to deploy them on public roads in a very near future. Guaranteeing safe operation of these systems is crucial as they are planned to carry passengers and share the road with other vehicles and pedestrians. Yet, there is no agreed-upon approach on how and in what detail those systems should be tested. Different organizations have different testing approaches, and one common approach is to combine simulation-based testing with real-world driving.
One of the expectations from fully-automated vehicles is never to cause an accident. However, an automated vehicle may not be able to avoid all collisions, e.g., the collisions caused by other road occupants. Hence, it is important for the system designers to understand the boundary case scenarios where an autonomous vehicle can no longer avoid a collision. Besides safety, there are other expectations from automated vehicles such as comfortable driving and minimal fuel consumption. All safety and functional expectations from an automated driving system should be captured with a set of system requirements. It is challenging to create requirements that are unambiguous and usable for the design, testing, and evaluation of automated driving systems. Another challenge is to define useful metrics for assessing the testing quality because in general, it is impossible to test every possible scenario.
The goal of this dissertation is to formalize the theory for testing automated vehicles. Various methods for automatic test generation for automated-driving systems in simulation environments are presented and compared. The contributions presented in this dissertation include (i) new metrics that can be used to discover the boundary cases between safe and unsafe driving conditions, (ii) a new approach that combines combinatorial testing and optimization-guided test generation methods, (iii) approaches that utilize global optimization methods and random exploration to generate critical vehicle and pedestrian trajectories for testing purposes, (iv) a publicly-available simulation-based automated vehicle testing framework that enables application of the existing testing approaches in the literature, including the new approaches presented in this dissertation.
One of the expectations from fully-automated vehicles is never to cause an accident. However, an automated vehicle may not be able to avoid all collisions, e.g., the collisions caused by other road occupants. Hence, it is important for the system designers to understand the boundary case scenarios where an autonomous vehicle can no longer avoid a collision. Besides safety, there are other expectations from automated vehicles such as comfortable driving and minimal fuel consumption. All safety and functional expectations from an automated driving system should be captured with a set of system requirements. It is challenging to create requirements that are unambiguous and usable for the design, testing, and evaluation of automated driving systems. Another challenge is to define useful metrics for assessing the testing quality because in general, it is impossible to test every possible scenario.
The goal of this dissertation is to formalize the theory for testing automated vehicles. Various methods for automatic test generation for automated-driving systems in simulation environments are presented and compared. The contributions presented in this dissertation include (i) new metrics that can be used to discover the boundary cases between safe and unsafe driving conditions, (ii) a new approach that combines combinatorial testing and optimization-guided test generation methods, (iii) approaches that utilize global optimization methods and random exploration to generate critical vehicle and pedestrian trajectories for testing purposes, (iv) a publicly-available simulation-based automated vehicle testing framework that enables application of the existing testing approaches in the literature, including the new approaches presented in this dissertation.
ContributorsTuncali, Cumhur Erkan (Author) / Fainekos, Georgios (Thesis advisor) / Ben Amor, Heni (Committee member) / Kapinski, James (Committee member) / Shrivastava, Aviral (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
Description
The first step in process improvement is to scope the problem, next is measure the current process, but if data is not readily available and cannot be manually collected, then a measurement system must be implemented. General Dynamics Mission Systems (GDMS) is a lean company that is always seeking to improve. One of their current bottlenecks is the incoming inspection department. This department is responsible for finding defects on parts purchased and is critical to the high reliability product produced by GDMS. To stay competitive and hold their market share, a decision was made to optimize incoming inspection. This proved difficult because no data is being collected. Early steps in many process improvement methodologies, such as Define, Measure, Analyze, Improve and Control (DMAIC), include data collection; however, no measurement system was in place, resulting in no available data for improvement. The solution to this problem was to design and implement a Management Information System (MIS) that will track a variety of data. This will provide the company with data that will be used for analysis and improvement. The first stage of the MIS was developed in Microsoft Excel with Visual Basic for Applications because of the low cost and overall effectiveness of the software. Excel allows update to be made quickly, and allows GDMS to collect data immediately. Stage two would be moving the MIS to a more practicable software, such as Access or MySQL. This thesis is only focuses on stage one of the MIS, and GDMS will proceed with stage two.
ContributorsDiaz, Angel (Author) / McCarville, Daniel R. (Thesis director) / Pavlic, Theodore (Committee member) / Industrial, Systems (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05