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Description
The modern web presents an opportunity for educators and researchers to create tools that are highly accessible. Because of the near-ubiquity of modern web browsers, developers who hope to create educational and analytical tools can reach a large au- dience by creating web applications. Using JavaScript, HTML, and other modern web development technologies, Genie was developed as a simulator to help educators in biology, genetics, and evolution classrooms teach their students about population genetics. Because Genie was designed for the modern web, it is highly accessible to both educators and students, who can access the web application using any modern web browser on virtually any device. Genie demonstrates the efficacy of web devel- opment technologies for demonstrating and simulating complex processes, and it will be a unique educational tool for educators who teach population genetics.
ContributorsRoos, Benjamin Hirsch (Author) / Cartwright, Reed (Thesis director) / Wilson Sayres, Melissa (Committee member) / Mayron, Liam (Committee member) / Barrett, The Honors College (Contributor) / Computer Science and Engineering Program (Contributor)
Created2015-05
Description
Machine learning (ML) and deep learning (DL) has become an intrinsic part of multiple fields. The ability to solve complex problems makes machine learning a panacea. In the last few years, there has been an explosion of data generation, which has greatly improvised machine learning models. But this comes with a cost of high computation, which invariably increases power usage and cost of the hardware. In this thesis we explore applications of ML techniques, applied to two completely different fields - arts, media and theater and urban climate research using low-cost and low-powered edge devices. The multi-modal chatbot uses different machine learning techniques: natural language processing (NLP) and computer vision (CV) to understand inputs of the user and accordingly perform in the play and interact with the audience. This system is also equipped with other interactive hardware setups like movable LED systems, together they provide an experiential theatrical play tailored to each user. I will discuss how I used edge devices to achieve this AI system which has created a new genre in theatrical play. I will then discuss MaRTiny, which is an AI-based bio-meteorological system that calculates mean radiant temperature (MRT), which is an important parameter for urban climate research. It is also equipped with a vision system that performs different machine learning tasks like pedestrian and shade detection. The entire system costs around $200 which can potentially replace the existing setup worth $20,000. I will further discuss how I overcame the inaccuracies in MRT value caused by the system, using machine learning methods. These projects although belonging to two very different fields, are implemented using edge devices and use similar ML techniques. In this thesis I will detail out different techniques that are shared between these two projects and how they can be used in several other applications using edge devices.
ContributorsKulkarni, Karthik Kashinath (Author) / Jayasuriya, Suren (Thesis advisor) / Middel, Ariane (Thesis advisor) / Yu, Hongbin (Committee member) / Arizona State University (Publisher)
Created2021
Description
Open Design is a crowd-driven global ecosystem which tries to challenge and alter contemporary modes of capitalistic hardware production. It strives to build on the collective skills, expertise and efforts of people regardless of their educational, social or political backgrounds to develop and disseminate physical products, machines and systems. In contrast to capitalistic hardware production, Open Design practitioners publicly share design files, blueprints and knowhow through various channels including internet platforms and in-person workshops. These designs are typically replicated, modified, improved and reshared by individuals and groups who are broadly referred to as ‘makers’.
This dissertation aims to expand the current scope of Open Design within human-computer interaction (HCI) research through a long-term exploration of Open Design’s socio-technical processes. I examine Open Design from three perspectives: the functional—materials, tools, and platforms that enable crowd-driven open hardware production, the critical—materially-oriented engagements within open design as a site for sociotechnical discourse, and the speculative—crowd-driven critical envisioning of future hardware.
More specifically, this dissertation first explores the growing global scene of Open Design through a long-term ethnographic study of the open science hardware (OScH) movement, a genre of Open Design. This long-term study of OScH provides a focal point for HCI to deeply understand Open Design's growing global landscape. Second, it examines the application of Critical Making within Open Design through an OScH workshop with designers, engineers, artists and makers from local communities. This work foregrounds the role of HCI researchers as facilitators of collaborative critical engagements within Open Design. Third, this dissertation introduces the concept of crowd-driven Design Fiction through the development of a publicly accessible online Design Fiction platform named Dream Drones. Through a six month long development and a study with drone related practitioners, it offers several pragmatic insights into the challenges and opportunities for crowd-driven Design Fiction. Through these explorations, I highlight the broader implications and novel research pathways for HCI to shape and be shaped by the global Open Design movement.
This dissertation aims to expand the current scope of Open Design within human-computer interaction (HCI) research through a long-term exploration of Open Design’s socio-technical processes. I examine Open Design from three perspectives: the functional—materials, tools, and platforms that enable crowd-driven open hardware production, the critical—materially-oriented engagements within open design as a site for sociotechnical discourse, and the speculative—crowd-driven critical envisioning of future hardware.
More specifically, this dissertation first explores the growing global scene of Open Design through a long-term ethnographic study of the open science hardware (OScH) movement, a genre of Open Design. This long-term study of OScH provides a focal point for HCI to deeply understand Open Design's growing global landscape. Second, it examines the application of Critical Making within Open Design through an OScH workshop with designers, engineers, artists and makers from local communities. This work foregrounds the role of HCI researchers as facilitators of collaborative critical engagements within Open Design. Third, this dissertation introduces the concept of crowd-driven Design Fiction through the development of a publicly accessible online Design Fiction platform named Dream Drones. Through a six month long development and a study with drone related practitioners, it offers several pragmatic insights into the challenges and opportunities for crowd-driven Design Fiction. Through these explorations, I highlight the broader implications and novel research pathways for HCI to shape and be shaped by the global Open Design movement.
ContributorsFernando, Kattak Kuttige Rex Piyum (Author) / Kuznetsov, Anastasia (Thesis advisor) / Turaga, Pavan (Committee member) / Middel, Ariane (Committee member) / Takamura, John (Committee member) / Arizona State University (Publisher)
Created2020
Description
Next-generation sequencing is a powerful tool for detecting genetic variation. How-ever, it is also error-prone, with error rates that are much larger than mutation rates.
This can make mutation detection difficult; and while increasing sequencing depth
can often help, sequence-specific errors and other non-random biases cannot be de-
tected by increased depth. The problem of accurate genotyping is exacerbated when
there is not a reference genome or other auxiliary information available.
I explore several methods for sensitively detecting mutations in non-model or-
ganisms using an example Eucalyptus melliodora individual. I use the structure of
the tree to find bounds on its somatic mutation rate and evaluate several algorithms
for variant calling. I find that conventional methods are suitable if the genome of a
close relative can be adapted to the study organism. However, with structured data,
a likelihood framework that is aware of this structure is more accurate. I use the
techniques developed here to evaluate a reference-free variant calling algorithm.
I also use this data to evaluate a k-mer based base quality score recalibrator
(KBBQ), a tool I developed to recalibrate base quality scores attached to sequencing
data. Base quality scores can help detect errors in sequencing reads, but are often
inaccurate. The most popular method for correcting this issue requires a known
set of variant sites, which is unavailable in most cases. I simulate data and show
that errors in this set of variant sites can cause calibration errors. I then show that
KBBQ accurately recalibrates base quality scores while requiring no reference or other
information and performs as well as other methods.
Finally, I use the Eucalyptus data to investigate the impact of quality score calibra-
tion on the quality of output variant calls and show that improved base quality score
calibration increases the sensitivity and reduces the false positive rate of a variant
calling algorithm.
This can make mutation detection difficult; and while increasing sequencing depth
can often help, sequence-specific errors and other non-random biases cannot be de-
tected by increased depth. The problem of accurate genotyping is exacerbated when
there is not a reference genome or other auxiliary information available.
I explore several methods for sensitively detecting mutations in non-model or-
ganisms using an example Eucalyptus melliodora individual. I use the structure of
the tree to find bounds on its somatic mutation rate and evaluate several algorithms
for variant calling. I find that conventional methods are suitable if the genome of a
close relative can be adapted to the study organism. However, with structured data,
a likelihood framework that is aware of this structure is more accurate. I use the
techniques developed here to evaluate a reference-free variant calling algorithm.
I also use this data to evaluate a k-mer based base quality score recalibrator
(KBBQ), a tool I developed to recalibrate base quality scores attached to sequencing
data. Base quality scores can help detect errors in sequencing reads, but are often
inaccurate. The most popular method for correcting this issue requires a known
set of variant sites, which is unavailable in most cases. I simulate data and show
that errors in this set of variant sites can cause calibration errors. I then show that
KBBQ accurately recalibrates base quality scores while requiring no reference or other
information and performs as well as other methods.
Finally, I use the Eucalyptus data to investigate the impact of quality score calibra-
tion on the quality of output variant calls and show that improved base quality score
calibration increases the sensitivity and reduces the false positive rate of a variant
calling algorithm.
ContributorsOrr, Adam James (Author) / Cartwright, Reed (Thesis advisor) / Wilson, Melissa (Committee member) / Kusumi, Kenro (Committee member) / Taylor, Jesse (Committee member) / Pfeifer, Susanne (Committee member) / Arizona State University (Publisher)
Created2020