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Undergraduate Posters

Undergraduate Poster Session #8

Subevent of Undergraduate Poster Session

Phillips Lobby

Eastern Time (US & Canada)

Starts at: 2025-03-01 10:45AM

Ends at: 2025-03-01 12:00PM

Explorations of Machine Learning Methodologies to Enhance the Design of RNA-based Dopamine Biosensors

James Craven ⟨cravenj6@winthrop.edu⟩

Abstract:

In this project, we seek to understand how we can utilize machine learning (ML) to inform the design of biosensors to emit a strong fluorescence in the presence of dopamine. Dopamine is a neurotransmitter and plays a role in a variety of functions such as memory, learning, and reward systems. Detecting dopamine levels could help with diagnosing addiction, mental illness, and neurodegenerative disorders. We develop a framework for one-hot encoding nucleotide sequences for training ML models, create a data preprocessing pipeline to pad sequences and normalize output values, and construct neural net model architecture for training on both sequence and numerical data. Using a published toehold switch dataset along with a ribosensor dataset, we explore the accuracy of several different regression models in predicting biosensor effectiveness by training on both nucleotide sequence data and calculated thermodynamic parameter data. We find that a neural network model, specifically a multilayer perceptron, typically outperforms other regression models such as linear regression, random forests, and support vector machines in both datasets, and that training on sequence data appears to be more predictive than training on thermodynamic parameter data. We also suggest potential directions to pursue transfer learning between the two datasets.

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