I2S Masters/ Doctoral Theses


All students and faculty are welcome to attend the final defense of I2S graduate students completing their M.S. or Ph.D. degrees. Defense notices for M.S./Ph.D. presentations for this year and several previous years are listed below in reverse chronological order.

Students who are nearing the completion of their M.S./Ph.D. research should schedule their final defenses through the EECS graduate office at least THREE WEEKS PRIOR to their presentation date so that there is time to complete the degree requirements check, and post the presentation announcement online.

Upcoming Defense Notices

Smriti Pranjal

NoBIAS: Non-coding RNA Base Interaction Annotation using Visual Snapshot

When & Where:


Slawson Hall, Rm 198

Degree Type:

PhD Comprehensive Defense

Committee Members:

Cuncong Zhong, Chair
Sumaiya Shomaji
Hongyang Sun
Zijun Yao
Xiaoqing Wu

Abstract

Non-coding RNAs fold into complex 3D structures that govern their biological functions, with RNA structural motifs (RSMs) serving as conserved building blocks of this architecture.
These motifs are defined by characteristic base-interaction patterns, making accurate identification and classification of RNA interactions essential for understanding RNA structure and function.

Despite their biological importance, accurately identifying and classifying these interactions remains challenging because the available data are highly variable in quality and scarce in quantity. This compromises annotation reliability, hinders the construction of trustworthy ground truth for systematic assessment, and restricts the supply of reliable training examples needed for supervised learning.

To address this, we introduce NoBIAS, the first resolution-aware, integrated machine learning-based suite for annotating base interactions from 3D RNA structures, inspired by human pattern recognition, augmented with structure prediction for data enrichment, and evaluated on a carefully curated, stratified benchmark.

NoBIAS is a hierarchical framework for RNA base-interaction annotation that integrates interaction-specific inductive biases with multimodal representation learning. By combining a convolution-augmented, rule-guided module for stacking interactions with complementary graph and image encoders for pairing interactions, NoBIAS captures both structural priors and local visual cues of RNA base doublets. A performance-calibrated logit fusion scheme then adaptively integrates modality-specific predictions based on local-structural resolution, enabling robust inference across heterogeneous 3D RNA structures.

Evaluation across multiple benchmark tiers: spanning consensus, homolog-supported, and manually verified cases, shows that NoBIAS consistently outperforms existing methods under increasingly challenging conditions. Together, the NoBIAS design and its evaluation framework provide a systematic foundation for robust RNA base-interaction annotation, enabling more reliable analysis of RNA structure under realistic uncertainty.


Md Mashfiq Rizvee

Hierarchical Probabilistic Architectures for Scalable Biometric and Electronic Authentication in Secure Surveillance Ecosystems

When & Where:


Eaton Hall, Room 2001B

Degree Type:

PhD Comprehensive Defense

Committee Members:

Sumaiya Shomaji, Chair
Tamzidul Hoque
David Johnson
Hongyang Sun
Alexandra Kondyli

Abstract

Secure and scalable authentication has become a primary requirement in modern digital ecosystems, where both human biometrics and electronic identities must be verified under noise, large population growth and resource constraints. Existing approaches often struggle to simultaneously provide storage efficiency, dynamic updates and strong authentication reliability. The proposed work advances a unified probabilistic framework based on Hierarchical Bloom Filter (HBF) architectures to address these limitations across biometric and hardware domains. The first contribution establishes the Dynamic Hierarchical Bloom Filter (DHBF) as a noise-tolerant and dynamically updatable authentication structure for large-scale biometrics. Unlike static Bloom-based systems that require reconstruction upon updates, DHBF supports enrollment, querying, insertion and deletion without structural rebuild. Experimental evaluation on 30,000 facial biometric templates demonstrates 100% enrollment and query accuracy, including robust acceptance of noisy biometric inputs while maintaining correct rejection of non-enrolled identities. These results validate that hierarchical probabilistic encoding can preserve both scalability and authentication reliability in practical deployments. Building on this foundation, Bio-BloomChain integrates DHBF into a blockchain-based smart contract framework to provide tamper-evident, privacy-preserving biometric lifecycle management. The system stores only hashed and non-invertible commitments on-chain while maintaining probabilistic verification logic within the contract layer. Large-scale evaluation again reports 100% enrollment, insertion, query and deletion accuracy across 30,000 templates, therefore, solving the existing problem of blockchains being able to authenticate noisy data. Moreover, the deployment analysis shows that execution on Polygon zkEVM reduces operational costs by several orders of magnitude compared to Ethereum, therefore, bringing enrollment and deletion costs below $0.001 per operation which demonstrate the feasibility of scalable blockchain biometric authentication in practice. Finally, the hierarchical probabilistic paradigm is extended to electronic hardware authentication through the Persistent Hierarchical Bloom Filter (PHBF). Applied to electronic fingerprints derived from physical unclonable functions (PUFs), PHBF demonstrates robust authentication under environmental variations such as temperature-induced noise. Experimental results show zero-error operation at the selected decision threshold and substantial system-level improvements as well as over 10^5 faster query processing and significantly reduced storage requirements compared to large scale tracking.


Fatima Al-Shaikhli

Optical Measurements Leveraging Coherent Fiber Optics Transceivers

When & Where:


Nichols Hall, Room 246 (Executive Conference Room)

Degree Type:

PhD Dissertation Defense

Committee Members:

Rongqing Hui, Chair
Shannon Blunt
Shima Fardad
Alessandro Saladrino
Judy Wu

Abstract

Recent advancements in optical technology are invaluable in a variety of fields, extending far beyond high-speed communications. These innovations enable optical sensing, which plays a critical role across diverse applications, from medical diagnostics to infrastructure monitoring and automotive systems. This research focuses on leveraging commercially available coherent optical transceivers to develop novel measurement techniques to extract detailed information about optical fiber characteristics, as well as target information. Through this approach, we aim to enable accurate and fast assessments of fiber performance and integrity, while exploring the potential for utilizing existing optical communication networks to enhance fiber characterization capabilities. This goal is investigated through three distinct projects: (1) fiber type characterization based on intensity-modulated electrostriction response, (2) coherent Light Detection and Ranging (LiDAR) system for target range and velocity detection through different waveform design, including experimental validation of frequency modulation continuous wave (FMCW) implementations and theoretical analysis of orthogonal frequency division multiplexing (OFDM) based approaches and (3) birefringence measurements using a coherent Polarization-sensitive Optical Frequency Domain Reflectometer (P-OFDR) system.

Electrostriction in an optical fiber is introduced by interaction between the forward propagated optical signal and the acoustic standing waves in the radial direction resonating between the center of the core and the cladding circumference of the fiber. The response of electrostriction is dependent on fiber parameters, especially the mode field radius. We demonstrated a novel technique of identifying fiber types through the measurement of intensity modulation induced electrostriction response. As the spectral envelope of electrostriction induced propagation loss is anti-symmetrical, the signal to noise ratio can be significantly increased by subtracting the measured spectrum from its complex conjugate. We show that if the field distribution of the fiber propagation mode is Gaussian, the envelope of the electrostriction-induced loss spectrum closely follows a Maxwellian distribution whose shape can be specified by a single parameter determined by the mode field radius.        

We also present a self-homodyne FMCW LiDAR system based on a coherent receiver. By using the same linearly chirped waveform for both the LiDAR signal and the local oscillator, the self-homodyne coherent receiver performs frequency de-chirping directly in the photodiodes, significantly simplifying signal processing. As a result, the required receiver bandwidth is much lower than the chirping bandwidth of the signal. Simultaneous multi-target of range and velocity detection is demonstrated experimentally. Furthermore, we explore the use of commercially available coherent transceivers for joint communication and sensing using OFDM waveforms.

In addition, we demonstrate a P-OFDR system utilizing a digital coherent optical transceiver to generate a linear frequency chirp via carrier-suppressed single-sideband modulation. This method ensures linearity in chirping and phase continuity of the optical carrier. The coherent homodyne receiver, incorporating both polarization and phase diversity, recovers the state of polarization (SOP) of the backscattered optical signal along the fiber, mixing with an identically chirped local oscillator. With a spatial resolution of approximately 5 mm, a 26 GHz chirping bandwidth, and a 200 us measurement time, this system enables precise birefringence measurements. By employing three mutually orthogonal SOPs of the launched optical signal, we measure relative birefringence vectors along the fiber.


Past Defense Notices

Dates

Prashanthi Mallojula

On the Security of Mobile and Auto Companion Apps

When & Where:


Nichols Hall 246 | Executive Conference Room

Degree Type:

PhD Comprehensive Defense

Committee Members:

Bo Luo, Chair
Alex Bardas
Fengjun Li
Hongyang Sun
Huazhen Fang

Abstract

Today’s smartphone platforms have millions of applications, which not only access users’ private data but also information from the connected external services and IoT/CPS devices. Mobile application security involves protecting sensitive information and securing communication between the application and external services or devices. We focus on these two key aspects of mobile application security.

In the first part of this dissertation, we aim to ensure the security of user information collected by mobile apps. Mobile apps seek consent from users to approve various permissions to access sensitive information such as location and personal information. However, users often blindly accept permission requests and apps start to abuse this mechanism. As long as a permission is requested, the state-of-the-art security mechanisms will treat it as legitimate. We ask the question whether the permission requests are valid? We attempt to validate permission requests using statistical analysis on permission sets extracted from groups of functionally similar apps. We detected mobile applications with abusive permission access and measure the risk of information leaks through each mobile application.

Second, we propose to investigate the security of auto companion apps. Auto companion apps are mobile apps designed to remotely connect with cars to provide features such as diagnostics, navigation, entertainment, and safety alerts. However, this can lead to several security threats, for instance, onboard information of vehicles can be tracked or altered through a malicious app. We design a comprehensive security analysis framework on automotive companion apps all stages of communication and collaboration between vehicles and companion apps such as connection establishment, authentication, encryption, information storage, and Vehicle diagnostic and control command access. By conducting static and network traffic analysis of Android OBD apps, we identify a series of vulnerability scenarios. We further evaluate these vulnerabilities with vehicle-based testing and identify potential security threats associated with auto companion apps.


Michael Nieses

Trustworthy Measurements of a Linux Kernel and Layered Attestation via a Verified Microkernel

When & Where:


Nichols Hall, Room 246

Degree Type:

PhD Comprehensive Defense

Committee Members:

Perry Alexander, Chair
Drew Davidson
Matthew Moore
Cuncong Zhong
Corey Maley

Abstract

Layered attestation is a process by which one can establish trust in a remote party. It is a special case of attestation in which different layers of the attesting system are handled distinctly. This type of trust is desirable because a vast and growing number of people depend on networked devices to go about their daily lives. Current architectures for remote attestation are lacking in process isolation, which is evidenced by the existence of virtual machine escape exploits. This implies a deficiency of trustworthy ways to determine whether a networked Linux system has been exploited. The seL4 microkernel, uniquely in the world, has machine-checked proofs concerning process confidentiality and integrity. The seL4 microkernel is leveraged here to provide a verified level of software-based process isolation. When complemented with a comprehensive collection of measurements, this architecture can be trusted to report its own corruption. The architecture is described, implemented, and tested against a variety of exploits, which are detected using introspective measurement techniques.


Blake Douglas Bryant

Building Better with Blocks – A Novel Secure Multi-Channel Internet Memory Information Control (S-MIMIC) Protocol for Complex Latency Sensitive Applications

When & Where:


Eaton Hall, Room 2001B

Degree Type:

PhD Dissertation Defense

Committee Members:

Hossein Saiedian, Chair
Arvin Agah
Perry Alexander
Bo Luo
Reza Barati

Abstract

Multimedia networking is the area of study associated with the delivery of heterogeneous data including, but not limited to, imagery, video, audio, and interactive content. Multimedia and communication network researchers have continually struggled to devise solutions for addressing the three core challenges in multimedia delivery: security, reliability, and performance. Solutions to these challenges typically exist in a spectrum of compromises achieving gains in one aspect at the cost of one or more of the others. Networked videogames represent the pinnacle of multimedia presented in a real-time interactive format. Continual improvements to multimedia delivery have led to tools such as buffering, redundant coupling of low-resolution alternative data streams, congestion avoidance, and forced in-order delivery of best-effort service; however, videogames cannot afford to pay the latency tax of these solutions in their current state.

I developed the Secure Multi-Channel Internet Memory Information Control (S-MIMIC) protocol as a novel solution to address these challenges. The S-MIMIC protocol leverages recent developments in blockchain and distributed ledger technology, coupled with creative enhancements to data representation and a novel data model. The S-MIMIC protocol also implements various novel algorithms for create, read, update, and delete (CRUD) interactions with distributed ledger and blockchain technologies. For validation, the S-MIMIC protocol was integrated with an open source open source First-Person Shooter (FPS) videogame to demonstrate its ability to transfer complex data structures under extreme network latency demands. The S-MIMIC protocol demonstrated improvements in confidentiality, integrity, availability and data read operations under all test conditions. Data write performance of S-MIMIC is slightly below traditional TCP-based networking in unconstrained networks, but matches performance in networks exhibiting 150 milliseconds of delay or more.

Though the S-MIMIC protocol was evaluated for use in networked videogames, its potential uses are far reaching with promising applicability to medical information, legal documents, financial transactions, information security threat feeds and many other use cases that require security, reliability and performance guarantees.


Archana Chalicheemala

A Machine Learning Study using Gene Expression Profiles to Distinguish Patients with Non-Small Cell Lung Cancer

When & Where:


Eaton Hall, Room 2001B

Degree Type:

MS Project Defense

Committee Members:

Zijun Yao, Chair
Prasad Kulkarni
Hongyang Sun


Abstract

Early diagnosis can effectively treat non-small cell lung cancer (NSCLC). Lung cancer cells usually have altered gene expression patterns compared to normal cells, which can be utilized to predict cancer through gene expression tests. This study analyzed gene expression values measured from 15227-probe microarray, and 290 patients consisting of cancer and control groups, to find relations between the gene expression features and lung cancer. The study explored k-means, statistical tests, and deep neural networks to obtain optimal feature representations and achieved the highest accuracy of 82%. Furthermore, a bipartite graph was built using the Bio Grid database and gene expression values, where the probe-to-probe relationship based on gene relevance was leveraged to enhance the prediction performance.


Yoganand Pitta

Insightful Visualization: An Interactive Dashboard Uncovering Disease Patterns in Patient Healthcare Data

When & Where:


Eaton Hall, Room 2001B

Degree Type:

MS Project Defense

Committee Members:

Zijun Yao, Chair
Prasad Kulkarni
Hongyang Sun


Abstract

As Electronic Health Records (EHRs) become more available, there is increasing interest in discovering hidden disease patterns by leveraging cutting-edge data visualization techniques, such as graph-based knowledge representation and interactive graphical user interfaces (GUIs). In this project, we have developed a web-based interactive EHR analytics and visualization tool to provide healthcare professionals with valuable insights that can ultimately improve the quality and cost-efficiency of patient care. Specifically, we have developed two visualization panels: one for the intelligence of individual patients and the other for the relevance among diseases. For individual patients, we capture the similarity between them by linking them based on their relatedness in diagnosis. By constructing a graph representation of patients based on this similarity, we can identify patterns and trends in patient data that may not be apparent through traditional methods. For disease relationships, we provide an ontology graph for the specific diagnosis (ICD10 code), which helps to identify ancestors and predecessors of a particular diagnosis. Through the demonstration of this dashboard, we show that this approach can provide valuable insights to better understand patient outcomes with an informative and user-friendly web interface.


Michael Cooley

Machine Learning for Navel Discharge Review

When & Where:


Eaton Hall, Room 1

Degree Type:

MS Project Defense

Committee Members:

Prasad Kulkarni, Chair
David Johnson
Jerzy Grzymala-Busse


Abstract

This research project aims to predict the outcome of the Naval Discharge Review Board decision for an applicant based on factors in the application, using Machine Learning techniques. The study explores three popular machine learning algorithms: MLP, Adaboost, and KNN, with KNN providing the best results. The training is verified through hyperparameter optimization and cross fold validation.

Additionally, the study investigates the ability of ChatGPT's API to classify the data that couldn't be classified manually. A total of over 8000 samples were classified by ChatGPT's API, and an MLP model was trained using the same hyperparameters that were found to be optimal for the 3000 size manual sample.The model was then tested on the manual sample. The results show that the model trained on data labeled by ChatGPT performed equivalently, suggesting that ChatGPT's API is a promising tool for labeling in this domain.


Sarah Johnson

Formal Analysis of TPM Key Certification Protocols

When & Where:


Nichols Hall, Room 246

Degree Type:

MS Thesis Defense

Committee Members:

Perry Alexander, Chair
Michael Branicky
Emily Witt


Abstract

Development and deployment of trusted systems often require definitive identification of devices. A remote entity should have confidence that a device is as it claims to be. An ideal method for fulfulling this need is through the use of secure device identitifiers. A secure device identifier (DevID) is defined as an identifier that is cryptographically bound to a device. A DevID must not be transferable from one device to another as that would allow distinct devices to be identified as the same. Since the Trusted Platform Module (TPM) is a secure Root of Trust for Storage, it provides the necessary protections for storing these identifiers. Consequently, the Trusted Computing Group (TCG) recommends the use of TPM keys for DevIDs. The TCG's specification TPM 2.0 Keys for Device Identity and Attestation describes several methods for remotely proving a key to be resident in a specific device's TPM. These methods are carefully constructed protocols which are intended to be performed by a trusted Certificate Authority (CA) in communication with a certificate-requesting device. DevID certificates produced by an OEM's CA at device manufacturing time may be used to provide definitive evidence to a remote entity that a key belongs to a specific device. Whereas DevID certificates produced by an Owner/Administrator's CA require a chain of certificates in order to verify a chain of trust to an OEM-provided root certificate. This distinction is due to the differences in the respective protocols prescribed by the TCG's specification. We aim to abstractly model these protocols and formally verify that their resulting assurances on TPM-residency do in fact hold. We choose this goal since the TCG themselves do not provide any proofs or clear justifications for how the protocols might provide these assurances. The resulting TPM-command library and execution relation modeled in Coq may easily be expanded upon to become useful in verifying a wide range of properties regarding DevIDs and TPMs.


Anna Fritz

Negotiating Remote Attestation Protocols

When & Where:


Nichols Hall, Room 246

Degree Type:

PhD Comprehensive Defense

Committee Members:

Perry Alexander, Chair
Alex Bardas
Drew Davidson
Fengjun Li
Emily Witt

Abstract

During remote attestation, a relying party prompts a target to perform some stateful measurement which can be appraised to determine trust in the target's system. In this current framework, requested measurement operations must be provisioned by a knowledgeable system user who may fail to consider situational demands which potentially impact the desired measurement. To solve this problem, we introduce negotiation: a framework that allows the target and relying party to mutually determine an attestation protocol that satisfies both the target's need to protect sensitive information and the relying party's desire for a comprehensive measurement. We designed and verified this negotiation procedure such that for all negotiations, we can provably produce an executable protocol that satisfies the targets privacy standards. With the remainder of this work, we aim to realize and instantiate protocol orderings ensuring negotiation produces a protocol sufficient for the relying party. All progress is towards our ultimate goal of producing a working, fully verified negotiation scheme which will be integrated into our current attestation framework for flexible, end-to-end attestations.