Engineering Commons^™

Computational Solutions To Exosomal Microrna Biomarker Detection In Pancreatic Cancer, Thuy T. An

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Pancreatic cancer is the fourth leading cause of cancer death in the United States and the 5-year survival rate is only 5% to 10%. There are only a few non-specific symptoms associated with the early-stage cancer, therefore most patients are diagnosed in a late stage. Due to the lack of effective treatments and the fact that the early stage has a 39% 5-year survival rate, the biggest hope to control this disease is early detection. Therefore, discovery of effective and reliable non-invasive biomarkers for early detection of pancreatic cancer has been a major topic. Very recently, exosomal microRNAs have become …

Semantically Meaningful Sentence Embeddings, Rojina Deuja

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Text embedding is an approach used in Natural Language Processing (NLP) to represent words, phrases, sentences, and documents. It is the process of obtaining numeric representations of text to feed into machine learning models as vectors (arrays of numbers). One of the biggest challenges in text embedding is representing longer text segments like sentences. These representations should capture the meaning of the segment and the semantic relationship between its constituents. Such representations are known as semantically meaningful embeddings. In this thesis, we seek to improve upon the quality of sentence embeddings that capture semantic information.

The current state-of-the-art models are …

Comparative Analysis Of Kmer Counting And Estimation Tools, Ankitha Vejandla

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

The rapid development of next-generation sequencing (NGS) technologies for determining the sequence of DNA has revolutionized genome research in recent years. De novo assemblers are the most commonly used tools to perform genome assembly. Most of the assemblers use de Bruijn graphs that break the sequenced reads into smaller sequences (sub-strings), called kmers, where k denotes the length of the sub-strings. The kmer counting and analysis of kmer frequency distribution are important in genome assembly. The main goal of this research is to provide a detailed analysis of the performance of different kmer counting and estimation tools that are currently …

Power-Over-Tether Unmanned Aerial System Leveraged For Trajectory Influenced Atmospheric Sensing, Daniel Rico

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

The use of unmanned aerial systems (UASs) in agriculture has risen in the past decade and is helping to modernize agriculture. UASs collect and elucidate data previously difficult to obtain and are used to help increase agricultural efficiency and production. Typical commercial off-the-shelf (COTS) UASs are limited by small payloads and short flight times. Such limits inhibit their ability to provide abundant data at multiple spatiotemporal scales. In this thesis, we describe the design and construction of the tethered aircraft unmanned system (TAUS), which is a novel power-over-tether UAS configured for long-term, high throughput atmospheric monitoring with an array of …

A Real-World, Hybrid Event Sequence Generation Framework For Android Apps, Jun Sun

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Generating meaningful inputs for Android apps is still a challenging issue that needs more research. Past research efforts have shown that random test generation is still an effective means to exercise User-Interface (UI) events to achieve high code coverage. At the same time, heuristic search approaches can effectively reach specified code targets. Our investigation shows that these approaches alone are insufficient to generate inputs that can exercise specific code locations in complex Android applications.

This thesis introduces a hybrid approach that combines two different input generation techniques--heuristic search based on genetic algorithm and random instigation of UI events, to reach …

Aerial Flight Paths For Communication, Alisha Bevins

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

This body of work presents an iterative process of refinement to understand naive perception of communication using the motion of an unmanned aerial vehicle (UAV). This includes what people believe the UAV is trying to communicate, and how they expect to respond through physical action or emotional response. Previous work in this area sought to communicate without clear definitions of the states attempting to be conveyed. In an attempt to present more concrete states and better understand specific motion perception, this work goes through multiple iterations of state elicitation and label assignment. The lessons learned in this work will be …

Using Contextual Bandits To Improve Traffic Performance In Edge Network, Aziza Al Zadjali

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Edge computing network is a great candidate to reduce latency and enhance performance of the Internet. The flexibility afforded by Edge computing to handle data creates exciting range of possibilities. However, Edge servers have some limitations since Edge computing process and analyze partial sets of information. It is challenging to allocate computing and network resources rationally to satisfy the requirement of mobile devices under uncertain wireless network, and meet the constraints of datacenter servers too. To combat these issues, this dissertation proposes smart multi armed bandit algorithms that decide the appropriate connection setup for multiple network access technologies on the …

Using An Integrative Machine Learning Approach To Study Microrna Regulation Networks In Pancreatic Cancer Progression, Roland Madadjim

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

With advances in genomic discovery tools, recent biomedical research has produced a massive amount of genomic data on post-transcriptional regulations related to various transcript factors, microRNAs, lncRNAs, epigenetic modifications, and genetic variations. In this direction, the field of gene regulation network inference is created and aims to understand the interactome regulations between these molecules (e.g., gene-gene, miRNA-gene) that take place to build models able to capture behavioral changes in biological systems. A question of interest arises in integrating such molecules to build a network while treating each specie in its uniqueness. Given the dynamic changes of interactome in chaotic systems …

Teachability And Interpretability In Reinforcement Learning, Jeevan Rajagopal

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

There have been many recent advancements in the field of reinforcement learning, starting from the Deep Q Network playing various Atari 2600 games all the way to Google Deempind's Alphastar playing competitively in the game StarCraft. However, as the field challenges more complex environments, the current methods of training models and understanding their decision making become less effective. Currently, the problem is partially dealt with by simply adding more resources, but the need for a better solution remains.

This thesis proposes a reinforcement learning framework where a teacher or entity with domain knowledge of the task to complete can assist …

“The Revolution Will Not Be Supervised": An Investigation Of The Efficacy And Reasoning Process Of Self-Supervised Representations, Atharva Tendle

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Transfer learning technique enables training Deep Learning (DL) models in a data-efficient way for solving computer vision tasks. It involves pretraining a DL model to learn representations from a large and general-purpose source dataset, then fine-tuning the model using the task-specific target dataset. The dominant supervised learning (SL) approach for pretraining representations suffers from some limitations that include expensive labeling and poor generalizability. Recent advancements in the self-supervised learning (SSL) approach made it possible to learn effective representations from unlabeled data. The performance of the fine-tuned DL models based on pretrained SSL representations is on par with the state-of-the-art pretrained …