Computer Engineering Commons^™

A Natural Language Processing Approach To Malware Classification, Ritik Mehta

Master's Projects

Many different machine learning and deep learning techniques have been successfully employed for malware detection and classification. Examples of popular learning techniques in the malware domain include Hidden Markov Models (HMM), Random Forests (RF), Convolutional Neural Networks (CNN), Support Vector Machines (SVM), and Recurrent Neural Networks (RNN) such as Long Short-Term Memory (LSTM) networks. In this research, we consider a hybrid architecture, where HMMs are trained on opcode sequences, and the resulting hidden states of these trained HMMs are used as feature vectors in various classifiers. In this context, extracting the HMM hidden state sequences can be viewed as a …

Image-Based Classification Of Malware Using T-Sne Images, Vincent Stowbunenko

Master's Projects

This Master’s project proposes a novel technique for classifying malware using image-based methods. The approach involves generating t-SNE images from the EMBER dataset, which contains one million samples of both malware and benign files, each represented by over 2,000 features. The t-SNE technique is well-suited for capturing intricate patterns in complex datasets because it effectively maintains the local structure. These t-SNE images are then used as inputs to train two lightweight image classification models, SqueezeNet and MobileNet. Additionally, to provide a benchmark for comparison, a non-image classification model using LightGBM is also explored.

As part of the investigation, the project …

Metagenomic Survey Of Marine 16s Bacterial Communities Off Palmer Station In Antarctica, Daniel Salter

Master's Projects

This project surveys the metagenomic bacterial community composition in marine surface waters off Palmer Station, Western Antarctic Peninsula and correlates findings with temperature and salinity data. Marine bacterial communities play a vital role in nutrient cycling, but data on surface waters in this region are limited. Analyzing fifteen samples of 16S sequencing data from three austral summers, consistent dominance was observed by the classes Alphaproteobacteria, Gammaproteobacteria, and Flavobacteria. Correlation analysis confirmed significant relationships between taxa and environmental conditions. The observed trends suggest varying abilities of phyla to resist and adapt to changing environmental conditions. Notably, Alphaproteobacteria demonstrated adaptability to favorable …

Malware Classification Using Opcode N-Grams And Word Embeddings, Siddhita Joshi

Master's Projects

Malware is a serious risk to any software application whether it is standalone or over the network. In order to protect computer systems, it is essential to detect and classify malware effectively. Modern malware classification research focuses on Machine Learning and Deep Learning techniques to identify advanced malicious software. This project explores malware classification by combining two robust methods: n-grams and word embedding. By extracting opcode n-grams, we make use of sequential nature of malware execution to identify any local patterns within the malware executable.

We use word embedding methods such as Word2Vec, Doc2Vec, and FastText to produce dense vector …

Evaluation Of The Effect Of Walnut Extract On Sp1-Related Pathways, Jihan Yehia

Master's Projects

Walnut extract (WE) has shown promising anti-cancer effects, such as inducing apoptosis and moderating cell cycle progression. A previous study by Dr. Brandon White’s Lab at San Jose State University hypothesizes that WE can downregulate the expression of the pro-tumoral specificity protein 1 (Sp1) in triple negative breast cancer (TNBC). This project builds an RNA-seq pipeline that runs differential gene expression (DGE) analysis to study the effect of WE on TNBC, thereby offering a wider perspective on genes that may be affected by this treatment. The data used in this project originated from Illumina and Nanopore sequencing methods, and DGE …

Efficient Video Qoe Prediction In Intelligent O-Rans, Aditya Kulkarni

Master's Projects

Open Radio Access Network (O-RAN) is a platform developed by a collaboration between wireless operators, infrastructure vendors, and service providers for deploying mobile fronthaul and midhaul networks, built entirely on cloud-native principles. The vision of O-RAN lies in the virtualization of traditional wireless infrastructure components, like Central Units (CU), Radio Units (RU), and Distributed Units (DU). O-RAN decouples the above-mentioned wireless infrastructure components into opensource elements, operating consistently with other elements of different vendors in the network. Quality of Experience (QoE) deals with a user’s subjective measure of satisfaction. RAN Intelligent Controller (RIC) in O-RAN provides flexibility to intelligently program …

Unlearning Hidden Bias Between Refugees : An Initial Empirical Investigation, Akshay Sunil Gurnaney

Master's Projects

The challenges that refugees in various regions encounter are common knowledge. One such challenge is a bias among refugees on ethnocentric grounds. In particular, there are various articles that have pointed out the struggles faced by Syrian refugees in countries like Europe as a result of implicit bias. In fact, the media coverage of Syrian crises and the government responses to the same shed negative light on the refugees themselves. On the contrary, the media coverage of Ukrainian crises is very different with lesser restrictions from the governments.

This research attempts to identify the extent of implicit bias between Ukrainian …

Poriferal Vision: Using Mobilenet To Classify Sponge Spicules Through Transfer Learning, Brian Tran

Master's Projects

Global warming is an ongoing issue where the Earth is rapidly warming up. It negatively affects the growth of coral through ocean warming and ocean acidification. Many coral communities, home to a large variety of marine life, are expected to be severely impacted by these effects. Past evidence suggests that sponges will take over as the primary reef builders since many species of sponges have skeletons made of silica or glass which is not affected by ocean acidification. More research is needed to determine which kinds of sponge will most likely be able to thrive in today’s climate.

This can …

Evalsql - Automated Assessment Of Database Queries, Damanpreet Kaur

Master's Projects

In computer science programs, database is a fundamental subject taught through several undergraduate courses. These courses develop theoretical and practical concepts of databases. Building queries is a key aspect of this learning process, and students are assessed through assignments and quizzes. However, grading these assignments can be time-consuming for professors, and students usually receive feedback only after the deadlines have passed. As a result, students may miss the opportunity to improve their work and achieve better grades. To address this issue, it would be beneficial to provide students with immediate feedback on their submissions. EvalSQL is an automated system that …

Solving The Capacitated Vehicle Routing Problem Using A New Genetic Algorithm, Cajetan Rodrigues

Master's Projects

The Capacitated Vehicle Routing Problem (CVRP) [1, 2, 3] is an extension to the Vehicle Routing Problem (VRP), a well-known NP-hard optimization problem. In our CVRP, we are given a depot, the number of vehicles and their capacity, as well as a set of customers and their demands, both the depot and the set of customers lie in the Euclidean space. The goal is to find for each vehicle an optimal route (tour) starting and finishing at the depot, such that all customers are served exactly once.

In this study, we investigate the effectiveness of using a Genetic Algorithm (GA) …

Advances In Robustness Of Image-Based Malware Detection, Rishika Pamanji

Master's Projects

In recent years, deep learning has emerged as a powerful tool for image classification tasks. However, the performance of individual deep learning models can be limited by their architecture and training data. In this project, various Convolutional Neural Network (CNN) architectures are proposed to train the malware data for feature extraction for various color coordinates such as L, CMYK, RGB, RGBA, and YCbCr. Different optimization techniques like Stochastic Gradient Descent, Root Mean Square Propagation, Ada Delta, Adam, and Adaptive Gradient are used to minimize errors in the trained data, leading to enhanced accuracy. The proposed ensemble deep learning model for …

Visual Scene Classification Using Ensemble Of Machine Learning Classifiers, Rahul Ranganath

Master's Projects

Visual scenes represent the comprehensive visual information observed in a particular environment. Whether natural landscapes, urban settings, or designed interiors, visual scenes encompass the arrangement of elements that individuals perceive through their visual senses. Visual search is perhaps one of the most typical jobs that we carry out several times a day. This is one of the main paradigms for researching visual attention. Many visual task models have been put forward in an effort to better understand visual attention. Fixations and the rapid movement of the eye - saccades, define visual exploration and visual search. When we subject viewers to …

Identification Of Copy Number Variations (Cnvs) Of Epigenetic Factors Related To The Progression Of Pancreatic Ductal Adenocarcinoma (Pdac), Pavithra Raju

Master's Projects

Pancreatic ductal adenocarcinoma (PDAC) is a formidable challenge in oncology due to its aggressive form and late-stage detection. PDAC is known to be influenced by various epigenetic factors like DNA methylation and histone modifications. This study focuses on copy number variations (CNVs) within epigenetic factors which for their role in early diagnosis. Thus, paving the way for identification of potential biomarkers. The epigenetic pipeline was extended based on CNVs and the CNV modified sequences extracted were compared with the wild type sequences of epigenetic PDAC genes. The epigenetic gene KCNJ11 with copy number gain of CNV id 46771406 was used …

Analyzing The Benthic Cover Of Crustose Coralline Algae Using Mask-R Cnn, Rachana Ravindra

Master's Projects

Coral reefs, supporting 25% of marine biodiversity, confront challenges from local and global impacts like overfishing, runoff, acidification, and warming. Crustose Coralline Algae (CCA), pivotal for reef structure and coral settlement, are underrepresented in research. Current methods like Coral Point Count with Excel Extensions (CPCe) have limitations, relying on image quality and being time-consuming. This paper proposes computer vision and Mask R-CNN, a supervised machine learning model, for CCA analysis in reef images, considering color, texture, and shape. Results indicate promise in clustering and classifying organisms. The innovative technology reduces manual labor, enhancing image analysis, simplifying the understanding of CCA’s …

Ensemble Transformer Architecture For Efficient And Real Time Sign Language Translation, Sumeet Ghegade

Master's Projects

Sign language is a form of visual language that uses face expression and hand gestures to communicate thoughts and concepts. The term refers to multiple visual languages that share some common visual cues but differ in their grammar and syntax. Sign language translation (SLT) is a crucial step in closing the communication gap between hearing and hearingimpaired people. The study of SLT using machine learning has gotten a lot of interest during the last three years but despite progress, SLT research is still in its early phases. Most of the previous approaches first convert the signs to glosses and then …

Gesture Recognition Of Sign Language Alphabet Using Machine Learning Techniques, Gursimran Singh

Master's Projects

With the rising incidence of hearing loss, effective sign language recognition has become crucial for enhancing communication for individuals with hearing impairments. Traditional sensor-based recognition systems have been challenged by the complexities of realworld settings, prompting a shift toward more adaptable vision-based recognition systems. Distinct from previous studies, this work pioneers the use of ensemble methods with advanced filtering techniques on the Sign Language MNIST dataset, offering a novel perspective on sign language recognition. This research delves into the intersection of machine learning and image processing to develop a robust framework for sign language recognition. A range of filters, including …

Improving Developers' Understanding Of Regex Denial Of Service Tools Through Anti-Patterns And Fix Strategies, Sk Adnan Hassan, Zainab Aamir, Dongyoon Lee, James C. Davis, Francisco Servant

Department of Electrical and Computer Engineering Faculty Publications

Regular expressions are used for diverse purposes, including input validation and firewalls. Unfortunately, they can also lead to a security vulnerability called ReDoS (Regular Expression Denial of Service), caused by a super-linear worst-case execution time during regex matching. Due to the severity and prevalence of ReDoS, past work proposed automatic tools to detect and fix regexes. Although these tools were evaluated in automatic experiments, their usability has not yet been studied; usability has not been a focus of prior work. Our insight is that the usability of existing tools to detect and fix regexes will improve if we complement them …

An Empirical Study Of Pre-Trained Model Reuse In The Hugging Face Deep Learning Model Registry, Wenxin Jiang, Nicholas Synovic, Matt Hyatt, Taylor R. Schorlemmer, Rohan Sethi, Yung-Hsiang Lu, George K. Thiruvathukal, James C. Davis

Department of Electrical and Computer Engineering Faculty Publications

Deep Neural Networks (DNNs) are being adopted as components in software systems. Creating and specializing DNNs from scratch has grown increasingly difficult as state-of-the-art architectures grow more complex. Following the path of traditional software engineering, machine learning engineers have begun to reuse large-scale pre-trained models (PTMs) and fine-tune these models for downstream tasks. Prior works have studied reuse practices for traditional software packages to guide software engineers towards better package maintenance and dependency management. We lack a similar foundation of knowledge to guide behaviors in pre-trained model ecosystems.

In this work, we present the first empirical investigation of PTM reuse. …

Interest-Based Recommendation System Using Gmail Topic Modelling, Pranav Ghaskadbi

Master's Projects

Emails are a fundamental part of modern communication. Much of communicative discourse in modern society occurs over email, resulting in personal collections for each mail user which are rich in latent user’s interests. Conventional recommendation systems require historical data of user activity and interactions to derive user interests. The absence of activity and interaction data poses an interesting challenge for generating relevant recommendations for users. We were motivated to investigate approaches to identify user interests in the absence of historical data to generate personalized content recommendations. There is opportunity to derive user interests from email data, which can be used …

Identifying Potential Alzheimer’S Disease Biomarkers Beyond Amyloid-Beta And Tau, Frank Cai

Master's Projects

Alzheimer's Disease (AD) and other forms of Mild Cognitive Impairment (MCI) affect millions of people around the world. The buildup of Amyloid-Beta (Aβ) and Tau proteins in the brain produced by amyloid precursor protein (APP) has been identified as an important cofactor in the onset and progression of AD. However, although patients diagnosed with AD exhibit Aβ and Tau buildup, about 40% of the subjects with Aβ and Tau buildup are not diagnosed with AD. In this project, we hypothesize the involvement of other epigenetic interactions between APP and related genes in addition to the buildup of Aβ and Tau …

Classifying Sidewalk Materials Using Multi-Modal Data, Jiawei Liu

Dissertations and Theses

Navigating safely and independently presents considerable challenges for people who are blind or have low vision (BLV), as it requires a comprehensive understanding of their neighborhood environment. Our user study reveals that materials and objects on sidewalks play a crucial role in navigation tasks. Unfortunately, current methods for assessing sidewalk materials are suboptimal, often relying on labor-intensive and expensive manual assessments that fail to capture the full range of sidewalk features critical to individuals with BLV.

In response to this problem, this master’s thesis investigates deep learning approaches specifically designed for the classification of multi-modal sidewalk materials. The proposed framework …

Face Image And Video Analysis In Biometrics And Health Applications, Na Zhang

Graduate Theses, Dissertations, and Problem Reports (ETD)

Computer Vision (CV) enables computers and systems to derive meaningful information from acquired visual inputs, such as images and videos, and make decisions based on the extracted information. Its goal is to acquire, process, analyze, and understand the information by developing a theoretical and algorithmic model. Biometrics are distinctive and measurable human characteristics used to label or describe individuals by combining computer vision with knowledge of human physiology (e.g., face, iris, fingerprint) and behavior (e.g., gait, gaze, voice). Face is one of the most informative biometric traits. Many studies have investigated the human face from the perspectives of various different …

Machine Learning And Deep Learning Approaches For Gene Regulatory Network Inference In Plant Species, Sai Teja Mummadi

Dissertations, Master's Theses and Master's Reports

The construction of gene regulatory networks (GRNs) is vital for understanding the regulation of metabolic pathways, biological processes, and complex traits during plant growth and responses to environmental cues and stresses. The increasing availability of public databases has facilitated the development of numerous methods for inferring gene regulatory relationships between transcription factors and their targets. However, there is limited research on supervised learning techniques that utilize available regulatory relationships of plant species in public databases.

This study investigates the potential of machine learning (ML), deep learning (DL), and hybrid approaches for constructing GRNs in plant species, specifically Arabidopsis thaliana, …

Machine Learning For Biosensors, Gayathri Anapanani

Graduate Theses, Dissertations, and Problem Reports (ETD)

Biosensors have become increasingly popular as diagnostic tools due to their ability to detect and quantify biological analytes in a wide range of applications. With the growing demand for faster and more reliable biosensing devices, machine learning has become a valuable tool in enhancing biosensor performance. In this report, we review recent progress in the application of machine learning to biosensors. We discuss the potential benefits of using machine learning in biosensors, including improved sensitivity, selectivity, and accuracy. We also discuss the various machine learning techniques that have been applied to biosensors, including data preprocessing, feature extraction, and classification and …

Post-Implementation Erp Value Realization: A Decision Intelligence Framework, Manikantha Varaprasad Inakollu

Computer Science and Engineering Faculty Publications

Enterprise Resource Planning systems represent substantial organizational investments, yet many organizations struggle to realize expected benefits after implementation. This research develops a decision intelligence framework specifically designed to maximize ERP value realization during the critical post-implementation phase. While extensive literature addresses ERP implementation challenges, significantly less attention focuses on extracting value after systems go live. Our framework integrates data analytics, organizational learning, and strategic decision-making into a cohesive approach that transforms ERP systems from operational tools into strategic assets. Through analysis of post-implementation patterns across multiple organizations, we identify key decision points where intelligent interventions dramatically improve value capture. The …

Erp As A Digital Backbone: Redefining Enterprise Systems For Continuous Value Creation, Manikantha Varaprasad Inakollu

Computer Science and Engineering Faculty Publications

Enterprise Resource Planning systems have evolved from transactional processing tools into strategic digital backbones that orchestrate organizational value creation. This research examines how modern ERP implementations transcend traditional operational efficiency goals to enable continuous innovation, real-time decision-making, and ecosystem integration. Through analysis of contemporary ERP architectures and their impact on organizational capabilities, we demonstrate that successful digital transformation requires reconceptualizing ERP not as a software package but as an adaptive infrastructure supporting diverse business models. Our findings reveal that organizations treating ERP as a digital backbone achieve 35% higher agility scores and 42% faster time-to-market for new capabilities compared to …

Image-Based Malware Classification On Noise Extraction, Venkata Sai Sathwik Nadella

Master's Projects

Any malicious software designed to cause harm or damage to a computer system can be termed as malware. One common form of malware is as executable files. Such files are often used as a delivery mechanism for malware since they can be easily disguised as legitimate software and can be executed without raising suspicion. They are often used to exploit vulnerabilities in software, allowing malware to bypass security measures and gain access to sensitive information.

There are several methods used to detect malware in executable files, including Signaturebased detection, Behavioral-based detection, Heuristic-based detection, Sandboxing, Machine Learning and Artificial Intelligence (AI). …

Image-Based Malware Detection Using Convolutional Neural Network Techniques, Brandon Palomino

Master's Projects

In this study, we delve into the realm of malware detection and classification, leveraging the capabilities of different Convolutional Neural Networks (CNNs). Our approach involves transforming executable files into image formats and subsequently applying advanced CNN techniques for image recognition. The study emphasizes the use of two distinct CNN architectures: a traditional CNN model and a modified CNN variant known as a convolutional recurrent neural network (CRNN), each with unique structural and functional attributes. To effectively train these models, we adopt a transfer learning strategy, utilizing pre-existing CNN models that have been extensively trained on large-scale image datasets. This methodology …

Estimating Air Pollution Levels Using Machine Learning, Srujay Rao Devaraneni

Master's Projects

Air pollution has emerged as a substantial concern, especially in developing countries worldwide. An important aspect of this issue is the presence of PM2.5. Air pollutants with a diameter of 2.5 or less micrometers are known as PM2.5. Due to their size, these particles are a serious health risk and can quickly infiltrate the lungs, leading to a variety of health problems. Due to growing concerns about air pollution, technology like automatic air quality measurement can offer beneficial assistance for both personal and business decisions. This research suggests an ensemble machine learning model that can efficiently replace the standard air …

Efficient Gpu Implementation Of Automatic Differentiation For Computational Fluid Dynamics, Mohammad Zubair, Desh Ranjan, Aaron Walden, Gabriel Nastac, Eric Nielsen, Boris Diskin, Marc Paterno, Samuel Jung, Joshua Hoke Davis

Computer Science Faculty Publications

Many scientific and engineering applications require repeated calculations of derivatives of output functions with respect to input parameters. Automatic Differentiation (AD) is a method that automates derivative calculations and can significantly speed up code development. In Computational Fluid Dynamics (CFD), derivatives of flux functions with respect to state variables (Jacobian) are needed for efficient solutions of the nonlinear governing equations. AD of flux functions on graphics processing units (GPUs) is challenging as flux computations involve many intermediate variables that create high register pressure and require significant memory traffic because of the need to store the derivatives. This paper presents a …