Biomedical Informatics Commons^™

Network Analysis: An Application Of Graph Theory In Biology, Kiana Dunbar

Honors Theses

Graphs are simple, visual representations of entities as nodes connected by edges. They are used to convey relationships within a system. Networks are comprised of interrelated entities that are not easily separable, producing complex, structured data. These can be seen in social groups, highway systems, and even in biological systems. This paper surveys concepts in graph theory for application to the analysis of network data to understand disease. The features of graphs provide a useful framework for thinking about relationships between different genes or proteins. The structure of graphs is also compatible with a variety of machine learning tools. Especially …

Deep Learning-Based Automated Pneumonia Detection From Chest X-Rays: A Comparative Study Of Custom Cnn And Transfer Learning Architectures, Ahmed Sajim

Honors Theses

Pneumonia is a leading global cause of mortality, claiming approximately 2.5 million lives an-nually and placing exceptional diagnostic pressure on radiologists in resource-limited settings. Manual interpretation of chest X-ray (CXR) images is time-consuming, subject to inter-observer variability, and limited by radiologist availability. This thesis presents a systematic investiga-tion into deep learning-based automated pneumonia detection comparing five convolutional neural network (CNN) architectures: a custom-designed 2D CNN and four pretrained transfer learning models—ResNet, DenseNet, MobileNet, and VGG19.

A targeted data augmentation pipeline addresses the severe class imbalance in the Kag-gle Chest X-Ray Pneumonia dataset, expanding the Normal class from 1,583 to 9,495 …

How Does Cocaine Exposure Affect Early Gene Expression Changes In The Prefrontal Cortex (Pfc) And Striatum?, Saathvika Diviti

Honors Theses

Cocaine use disorder (CUD) remains a significant public health concern, yet the molecular mechanisms underlying individual susceptibility are poorly understood. This study investigates early transcriptional responses to acute cocaine exposure in two key brain regions implicated in addiction, the prefrontal cortex (PFC) and striatum, using genetically diverse Diversity Outbred (DO) mice. Paired tissue samples were collected following a standardized sensitization protocol and analyzed via bulk RNA sequencing. Differential expression analysis revealed 37 significantly differentially expressed genes in the striatum. These genes overlapped with gene sets associated with substance use, neurodevelopmental disorders, and immune signaling, implicating shared pathways in central nervous …