Engineering Commons^™

An Empirical Study On The Classification Of Python Language Features Using Eye-Tracking, Jigyasa Chauhan

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

Python, currently one of the most popular programming languages, is an object-
oriented language that also provides language feature support for other programming
paradigms, such as functional and procedural. It is not currently understood how
support for multiple paradigms affects the ability of developers to comprehend that
code. Understanding the predominant paradigm in code, and how developers classify
the predominant paradigm, can benefit future research in program comprehension as
the paradigm may factor into how people comprehend that code. Other researchers
may want to look at how the paradigms in the code interact with various code smells.
To investigate how …

Attention In The Faithful Self-Explanatory Nlp Models, Mostafa Rafaiejokandan

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

Deep neural networks (DNNs) can perform impressively in many natural language processing (NLP) tasks, but their black-box nature makes them inherently challenging to explain or interpret. Self-Explanatory models are a new approach to overcoming this challenge, generating explanations in human-readable languages besides task objectives like answering questions. The main focus of this thesis is the explainability of NLP tasks, as well as how attention methods can help enhance performance. Three different attention modules are proposed, SimpleAttention, CrossSelfAttention, and CrossModality. It also includes a new dataset transformation method called Two-Documents that converts every dataset into two separate documents required by the …

Learnfca: A Fuzzy Fca And Probability Based Approach For Learning And Classification, Suraj Ketan Samal

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

Formal concept analysis(FCA) is a mathematical theory based on lattice and order theory used for data analysis and knowledge representation. Over the past several years, many of its extensions have been proposed and applied in several domains including data mining, machine learning, knowledge management, semantic web, software development, chemistry ,biology, medicine, data analytics, biology and ontology engineering.

This thesis reviews the state-of-the-art of theory of Formal Concept Analysis(FCA) and its various extensions that have been developed and well-studied in the past several years. We discuss their historical roots, reproduce the original definitions and derivations with illustrative examples. Further, we provide …

Bevers: A General, Simple, And Performant Framework For Automatic Fact Verification, Mitchell Dehaven

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

Fact verification has become an important process, primarily done manually by humans, to verify the authenticity of claims and statements made online. Increasingly, social media companies have utilized human effort to debunk false claims on their platforms, opting to either tag the content as misleading or false, or removing it entirely to combat misinformation on their sites. In tandem, the field of automatic fact verification has become a subject of focus among the natural language processing (NLP) community, spawning new datasets and research. The most popular dataset is the Fact Extraction and VERification (FEVER) dataset. In this thesis an end-to-end …

Sequence-Based Bioinformatics Approaches To Predict Virus-Host Relationships In Archaea And Eukaryotes, Yingshan Li

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

Viral metagenomics is independent of lab culturing and capable of investigating viromes of virtually any given environmental niches. While numerous sequences of viral genomes have been assembled from metagenomic studies over the past years, the natural hosts for the majority of these viral contigs have not been determined. Different computational approaches have been developed to predict hosts of bacteria phages. Nevertheless, little progress has been made in the virus-host prediction, especially for viruses that infect eukaryotes and archaea. In this study, by analyzing all documented viruses with known eukaryotic and archaeal hosts, we assessed the predictive power of four computational …

A Pipeline To Generate Deep Learning Surrogates Of Genome-Scale Metabolic Models, Achilles Rasquinha

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

Genome-Scale Metabolic Models (GEMMs) are powerful reconstructions of biological systems that help metabolic engineers understand and predict growth conditions subjected to various environmental factors around the cellular metabolism of an organism in observation, purely in silico. Applications of metabolic engineering range from perturbation analysis and drug-target discovery to predicting growth rates of biotechnologically important metabolites and reaction objectives within dierent single-cell and multi-cellular organism types. GEMMs use mathematical frameworks for quantitative estimations of flux distributions within metabolic networks. The reasons behind why an organism activates, stuns, or fluctuates between alternative pathways for growth and survival, however, remain relatively unknown. GEMMs …

Feed Forward Neural Networks With Asymmetric Training, Archit Srivastava

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

Our work presents a new perspective on training feed-forward neural networks(FFNN). We introduce and formally define the notion of symmetry and asymmetry in the context of training of FFNN. We provide a mathematical definition to generalize the idea of sparsification and demonstrate how sparsification can induce asymmetric training in FFNN.

In FFNN, training consists of two phases, forward pass and backward pass. We define symmetric training in FFNN as follows-- If a neural network uses the same parameters for both forward pass and backward pass, then the training is said to be symmetric.

The definition of asymmetric training in artificial …

Simulating Sub-Threshold Communication Channels Through Neurons, Richard Maina

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

Molecular Communication is an emerging paradigm with the potential to revolutionize the technology behind wearable and implantable devices and the broad range of functions they support, from tracking physical activity to medical diagnostics. This can be achieved through intra-body communication networks that take advantage of natural biological processes as a means of transmitting, propagating and receiving information. In this thesis we focus particularly on using the neuron as a means to facilitate information transfer for interconnected wearable or implantable devices through a technique known as sub-threshold electrical stimulation. We develop upon a prior work by introducing a linear model of …

Consemblex: A Consensus-Based Transcriptome Assembly Approach That Extends Consemble And Improves Transcriptome Assembly, Richard Mwaba

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

An accurate transcriptome is essential to understanding biological systems enabling omics analyses such as gene expression, gene discovery, and gene-regulatory network construction. However, assembling an accurate transcriptome is challenging, especially for organisms without adequate reference genomes or transcriptomes. While several methods for transcriptome assembly with different approaches exist, it is still difficult to establish the most accurate methods. This thesis explores the different transcriptome assembly methods and compares their performances using simulated benchmark transcriptomes with varying complexity. We also introduce ConSemblEX to improve a consensus-based ensemble transcriptome assembler, ConSemble, in three main areas: we provide the ability to use any …

Symbolic Ns-3 For Efficient Exhaustive Testing, Jianfei Shao

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

Exhaustive testing is an important type of simulation, where a user exhaustively simulates a protocol for all possible cases with respect to some uncertain factors, such as all possible packet delays or packet headers. It is useful for completely evaluating the protocol performance, finding the worst-case performance, and detecting possible design or implementation bugs of a protocol. It is, however, time consuming to use the brute force method with current NS-3, a widely used network simulator, for exhaustive testing. In this paper, we present our work on Sym-NS-3 for more efficient exhaustive testing, which leverages a powerful program analysis technique …

Machine Learning-Based Device Type Classification For Iot Device Re- And Continuous Authentication, Kaustubh Gupta

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

Today, the use of Internet of Things (IoT) devices is higher than ever and it is growing rapidly. Many IoT devices are usually manufactured by home appliance manufacturers where security and privacy are not the foremost concern. When an IoT device is connected to a network, currently there does not exist a strict authentication method that verifies the identity of the device, allowing any rogue IoT device to authenticate to an access point. This thesis addresses the issue by introducing methods for continuous and re-authentication of static and dynamic IoT devices, respectively. We introduce mechanisms and protocols for authenticating a …

Characterizing And Predicting Human Visual Perception Of Unmanned Aerial Vehicle Gestures, Paul Fletcher

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

Unmanned Aerial Vehicles (UAVs) are being used in public domains and hazardous environments where effective communication strategies are critical. UAV gesture techniques have been shown to communicate meaning to human observers and may be ideal in contexts that require lightweight systems such as unmanned aerial flight, however, this work may be limited to an idealized range of viewer perspectives. As gesture is a visual communication technique it is necessary to consider how the perception of a robot gesture may suffer from obfuscation or self-occlusion from some viewpoints. This thesis presents the results of three online user-studies that examine participants’ ability …