Barrett

Barrett, The Honors College at Arizona State University proudly showcases the work of undergraduate honors students by sharing this collection exclusively with the ASU community.

Barrett accepts high performing, academically engaged undergraduate students and works with them in collaboration with all of the other academic units at Arizona State University. All Barrett students complete a thesis or creative project which is an opportunity to explore an intellectual interest and produce an original piece of scholarly research. The thesis or creative project is supervised and defended in front of a faculty committee. Students are able to engage with professors who are nationally recognized in their fields and committed to working with honors students. Completing a Barrett thesis or creative project is an opportunity for undergraduate honors students to contribute to the ASU academic community in a meaningful way.

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An Empirical Study of View Construction for Multi-View Learning

Description
Multi-view learning, a subfield of machine learning that aims to improve model performance by training on multiple views of the data, has been studied extensively in the past decades. It is typically applied in contexts where the input features naturally form multiple groups or views. An example of a naturally…

Multi-view learning, a subfield of machine learning that aims to improve model performance by training on multiple views of the data, has been studied extensively in the past decades. It is typically applied in contexts where the input features naturally form multiple groups or views. An example of a naturally multi-view context is a data set of websites, where each website is described not only by the text on the page, but also by the text of hyperlinks pointing to the page. More recently, various studies have demonstrated the initial success of applying multi-view learning on single-view data with multiple artificially constructed views. However, there lacks a systematic study regarding the effectiveness of such artificially constructed views. To bridge this gap, this thesis begins by providing a high-level overview of multi-view learning with the co-training algorithm. Co-training is a classic semi-supervised learning algorithm that takes advantage of both labelled and unlabelled examples in the data set for training. Then, the thesis presents a web-based tool developed in Python allowing users to experiment with and compare the performance of multiple view construction approaches on various data sets. The supported view construction approaches in the web-based tool include subsampling, Optimal Feature Set Partitioning, and the genetic algorithm. Finally, the thesis presents an empirical comparison of the performance of these approaches, not only against one another, but also against traditional single-view models. The findings show that a simple subsampling approach combined with co-training often outperforms both the other view construction approaches, as well as traditional single-view methods.
ContributorsAksoy, Kaan (Author) / Maciejewski, Ross (Thesis director) / He, Jingrui (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2019-12

LEARNING FREE ENERGY PATHWAYS THROUGH DEEP LEARNING

Description

The focus of my honors thesis is to find ways to use deep learning in tandem with tools in statistical mechanics to derive new ways to solve problems in biophysics. More specifically, I’ve been interested in finding transition pathways between two known states of a biomolecule. This is because understanding…

The focus of my honors thesis is to find ways to use deep learning in tandem with tools in statistical mechanics to derive new ways to solve problems in biophysics. More specifically, I’ve been interested in finding transition pathways between two known states of a biomolecule. This is because understanding the mechanisms in which proteins fold and ligands bind is crucial to creating new medicines and understanding biological processes. In this thesis, I work with individuals in the Singharoy lab to develop a formulation to utilize reinforcement learning and sampling-based robotics planning to derive low free energy transition pathways between two known states. Our formulation uses Jarzynski’s equality and the stiff-spring approximation to obtain point estimates of energy, and construct an informed path search with atomistic resolution. At the core of this framework, is our first ever attempt we use a policy driven adaptive steered molecular dynamics (SMD) to control our molecular dynamics simulations. We show that both the reinforcement learning (RL) and robotics planning realization of the RL-guided framework can solve for pathways on toy analytical surfaces and alanine dipeptide.
ContributorsHo, Nicholas (Author) / Maciejewski, Ross (Thesis director) / Singharoy, Abhishek (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Computer Science and Engineering Program (Contributor)
Created2022-12