Defense Notices


All students and faculty are welcome to attend the final defense of EECS 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

Logan Schmalz

A Framework for Controlled Key Release

When & Where:


Nichols Hall, Room 246 (Executive Conference Room)

Committee Members:

Perry Alexander, Chair
Drew Davidson
Sankha Guria


Abstract

Modern security relies heavily on public key cryptography, and private keys and secrets in general must be protected from attackers. Against a highly-capable adversary it is ideal to store secrets outside of main memory, which is easy on general purpose systems with the now widely-available Trusted Platform Module (TPM) 2.0. However, the lack of integration between the TPM and the OS makes protecting secrets with automated availability needs difficult. We develop a strategy to authenticate OS entities and protect TPM-stored secrets without restricting access to the TPM, using standard features available on Linux---SELinux, Integrity Measurement Architecture (IMA), Extended Verification Module (EVM), and Linux Unified Key Setup (LUKS).


Pranav Sudhakar Raju

Information Theoretic Waveform Design and Receive Processing for Pulse Agile Radar

When & Where:


Nichols Hall, Room 246 (Executive Conference Room)

Committee Members:

James Stiles, Chair
Shannon Blunt
Patrick McCormick
Charles Mohr
Zsolt Talata

Abstract

Modern radar systems are increasingly required to operate in complex, dynamic environments where traditional waveform design and signal processing techniques reach fundamental limitations. To address this, waveform diversity has been utilized to increase design degrees of freedom and improve detection performance in challenging scattering scenarios. This dissertation leverages an information-theoretic framework to implement waveform design and receive processing techniques in pulse-agile radars.

First, a modification of Fishers Information known as Marginal Fishers Information is adapted specifically for application to pulse-agile radars, where the ensuing waveform sets are optimally designed to minimize the error covariance of the scene estimate, improving target detection. This methodology is applied to range-Doppler estimation, where some knowledge of the scattering scene is known a priori. By incorporating the a priori knowledge of the scene into the waveform design, the waveforms are able to inherently suppress the self-interference introduced by pulse-agility.

Second, the information theoretic framework is used to create pulse-agile receive processing techniques for range-only and range-Doppler estimation. The range-only implementation is an iterative minimum mean square error (MMSE) estimator similar to a Kalman filter, where the innovation-based update suited to pulse-agility, mirrors the Kalman filter’s correction step. The range-Doppler implementation leverages the same principles as the range-Doppler waveform design technique, where some knowledge of the scattering scenario a priori is used to suppress self-interference and improve the range-Doppler estimate in a desired region.

Both the waveform design and advanced receive processing techniques are first developed in the fast-time slow-time parameterization space, and then translated to a frequency-domain implementation to reduce computation complexity and improve tractability. Finally, future work is proposed to round out the content of the dissertation.


Sirisha Thippabhotla

From Fragments to Function: Computational Approaches for Reconstructing Biological Context in Metagenomic and Exosomal Discovery

When & Where:


Eaton Hall, Room 2001B

Committee Members:

Cuncong Zhong, Chair
Prasad Kulkarni
Fengjun Li
Zijun Yao
Liang Xu

Abstract

Advances in high-throughput Next Generation Sequencing (NGS) technologies have transformed our ability to study biological systems. However, a fundamental gap remains between generating data and interpreting it. Sequencing produces genomes, transcriptomes, and cell-derived signals as millions of short, fragmented sequences, resulting in the loss of biological context, specifically the long-range relationships that determine genes, structured RNAs, or regulatory signals. This work investigates computational and experimental approaches to improve functional discovery by reconstructing or preserving biological context. The concept is developed across three interconnected dimensions: sensitivity, scalability, and biological fidelity, demonstrating that context is lost and must be recovered at two distinct stages of the discovery process.

The first contribution handles the loss of context that occurs after sequencing. By representing metagenomic sequencing reads as connected paths in an assembly graph and guiding graph traversal with biological models, this work recovers both protein-coding and non-coding signals that conventional fragment-level analyses fail to detect, thereby revealing functional pathways that would otherwise be missed. The second contribution makes this recovery practical at scale by introducing a significantly faster framework that preserves the sensitivity of graph-based methods while reducing computational costs by over an order of magnitude, thus enabling the analysis of large present-day datasets.

The third contribution studies the loss of context prior to sequencing. Using extracellular vesicles as a model system, the findings show that cells cultured in conventional two-dimensional environments generate signals that differ from their physiological state. In contrast, cells cultured in three-dimensional models produce signals that closely resemble those observed in patients. This shows that an accurate biological model is essential for reliable discovery, since computational methods cannot recover signals that are fundamentally distorted at their origin.

Taken together, these contributions establish a set of methods and principles for extracting meaningful biological information from fragmented, high-throughput genomic data, thereby enabling more accurate functional discovery.


Harlan Williams

State-replicated key directories: Decoupling key distribution from the messaging service to prevent person-in-the-middle attacks

When & Where:


Zoom defense, please email jgrisafe@ku.edu for defense information.

Committee Members:

Hossein Saiedian, Chair
Arvin Agah
Perry Alexander


Abstract

End-to-end encrypted (E2EE) messaging services rely on the service operator to distribute authentic public keys. This arrangement protects users from external attackers, but fails catastrophically when the service itself acts maliciously. A service that distributes a spoofed key can silently decrypt, read, and re-encrypt its users' communications—undetectably, if users simply assume the service is trustworthy.

This thesis proposes and evaluates a state-replicated key directory, a model that decouples key distribution from the messaging service entirely. Instead of a single service controlling the directory, the directory is built and maintained across multiple decentralized nodes that follow a consensus and validation protocol. This design substantially raises the cost of key substitution attacks and, under well-defined assumptions, can prevent them outright.

We make three core contributions. First, we present End2, a fully functional browser-based E2EE messaging application that integrates a state-replicated key directory without modifying the underlying cryptographic session protocol. Second, we implement and compare three distinct key directory backends—centralized, permissionless blockchain (Ethereum), and permissioned blockchain (CometBFT)—and analyze their respective security and performance trade-offs. Third, we provide an empirical evaluation under realistic workloads, including upload and query latency, long-term performance degradation, validator failure resilience, and detection of malicious key insertions.

Our results show that a permissioned, Byzantine fault-tolerant key directory achieves query performance comparable to a centralized directory while providing substantially stronger security guarantees against service-side attacks. State-replicated key directories offer a practical and deployable path toward reducing the excessive trust placed in modern E2EE messaging providers.


Past Defense Notices

Dates

EHSAN HOSSEINI

Synchronization Techniques for Burst-Mode Continuous Phase Modulation

When & Where:


250 Nichols Hall

Committee Members:

Erik Perrins, Chair
Shannon Blunt
Lingjia Liu
Dave Petr
Tyrone Duncan

Abstract

Synchronization is a critical operation in digital communication systems, which establishes and maintains an operational link between transmitter and the receiver. As the advancement of digital modulation and coding schemes continues, the synchronization task becomes more and more challenging since the new standards require high-throughput functionality at low signal-to-noise ratios (SNRs). In this work, we address feedforward synchronization of continuous phase modulations (CPMs) using data-aided (DA) methods, which are best suited for burst-mode communications. In our transmission model, a known training sequence is appended to the beginning of each burst, which is then affected by additive white Gaussian noise (AWGN), and unknown frequency, phase, and timing offsets. 

Based on our transmission model, we derive the optimum training sequence for DA synchronization of CPM signals using the Cramer-Rao bound (CRB), which is a lower bound on the estimation error variance. It is shown that the proposed sequence minimizes the CRB for all three synchronization parameters, and can be applied to the entire CPM family. We take advantage of the structure of the optimized training sequence in order to derive a maximum likelihood joint timing and carrier recovery algorithm. Moreover, a frame synchronization algorithm is proposed, and hence, a complete synchronization scheme is presented in this work. 

The proposed training sequence and synchronization algorithm are extended to shaped-offset quadrature phase-shift keying (SOQPSK) modulation, which is considered for next generation aeronautical telemetry systems. Here, it is shown that the optimized training sequence outperforms the one that is defined in the draft telemetry standard as long as estimation error variances are considered. The overall bit error rate suggest that the optimized training sequence with a shorter length can be utilized such that the SNR loss is less than 0.5 dB of an ideal synchronization scenario.


MARTIN KUEHNHAUSEN

A Framework for Knowledge Derivation Incorporating Trust and Quality of Data

When & Where:


246 Nichols Hall

Committee Members:

Victor Frost, Chair
Luke Huan
Bo Luo
Gary Minden
Tyrone Duncan

Abstract

Today, across all major industries gaining insight from data is seen as an essential part of business. However, while data gathering is becoming inexpensive and relatively easy, analysis and ultimately deriving knowledge from it is increasingly difficult. In many cases, there is the problem of too much data such that important insights are hard to find. The problem is often not lack of data but whether knowledge derived from it is trustworthy. This means distinguishing “good” from “bad” insights based on factors such as context and reputation. Still, modeling trust and quality of data is complex because of the various conditions and relationships in heterogeneous environments. 

The new TrustKnowOne framework and architecture developed in this dissertation addresses these issues by describing an approach to fully incorporate trust and quality of data with all its aspects into the knowledge derivation process. This is based on Berlin, an abstract graph model we developed that can be used to model various approaches to trustworthiness and relationship assessment as well as decision making processes. In particular, processing, assessment, and evaluation approaches are implemented as graph expressions that are evaluated on graph components modeling the data. 

We have implemented and applied our framework to three complex scenarios using real data from public data repositories. As part of their evaluation we highlighted how our approach exhibits both the formalization and flexibility necessary to model each of the realistic scenarios. The implementation and evaluation of these scenarios confirms the advantages of the TrustKnowOne framework over current approaches.


YUANLIANG MENG

Building an Intelligent Knowledgebase of Brachiopod Paleontology

When & Where:


246 Nichols Hall

Committee Members:

Luke Huan, Chair
Brian Potetz
Bo Luo


Abstract

Science advances not only because of new discoveries, but also due to revolutionary ideas drawn from accumulated data. The quality of studies in paleontology, in particular, depends on accessibility of fossil data. This research builds an intelligent system based on brachiopod fossil images and their descriptions published in Treatise on Invertebrate Paleontology. The project is still developing and some significant achievements will be discussed here. 
This thesis has two major parts. The first part describes the digitization, organization and integration of information extracted from the Treatise. The Treatise is in PDF format and it is non-trivial to convert large volumes into a structured, easily accessible digital library. Three important topics will be discussed: (1) how to extract data entries from the text, and save them in a structured manner; (2) how to crop individual specimen images from figures automatically, and associate each image with text entries; (3) how to build a search engine to perform both keyword search and natural language search. The search engine already has a web interface and many useful tasks can be done with ease. 
Verbal descriptions are second-hand information of fossil images and thus have limitations. The second part of the thesis develops an algorithm to compare fossil images directly, without referring to textual information. After similarities between fossil images are calculated, we can use the results in image search, fossil classification, and so on. The algorithm is based on deformable templates, and utilizes expectation propagation to find the optimal deformation. Specifically, I superimpose a ``warp'' on each image. Each node of the warp encapsulates a vector of local texture features, and comparing two images involves two steps: (1) deform the warp to the optimal configuration, so the energy function is minimized; and (2) based on the optimal configuration, compute the distance of two images. Experiment results confirmed that the method is reasonable and robust.


WILLIAM DINKEL

Instrumentation and Evaluation of Distributed Computations

When & Where:


246 Nichols Hall

Committee Members:

Victor Frost, Chair
Arvin Agah
Prasad Kulkarni


Abstract

Distributed computations are a very important aspect of modern computing, especially given the rise of distributed systems used for applications such as web search, massively multiplayer online games, financial trading, and cloud computing. When running these computations across several physical machines it becomes much more difficult to determine exactly what is occurring on each system at a specific point in time. This is due to each server having an independent clock, thus making event timestamps inherently inaccurate across machine boundaries. Another difficulty with evaluating distributed experiments is the coordination required to launch daemons, executables, and logging across all machines, followed by the necessary gathering of all related output data. The goal of this research is to overcome these obstacles and construct a single, global timeline of events from all servers. 
We employ high-resolution clock synchronization to bring all servers within microseconds as measured by a modified version of the Network Time Protocol implementation. Kernel and user-level events with wall-clock timestamps are then logged during basic network socket experiments. These data are then collected from each server and merged into a single dataset, sorted by timestamp, and plotted on a timeline. The entire experiment, from setup to teardown to data collection, is coordinated from a single server. The timeline visualizations provide a narrative of not only how packets flow between servers, but also how kernel interrupt handlers and other events shape an experiment's execution.


DANIEL HEIN

Detecting Attack Prone Software Using Architecture and Repository Mined Change Metrics

When & Where:


2001B Eaton Hall

Committee Members:

Hossein Saiedian, Chair
Arvin Agah
Perry Alexander
Prasad Kulkarni
Reza Barati

Abstract

Billions of dollars are lost every year to successful cyber attacks that are fundamentally enabled by software vulnerabilities. Modern cyber attacks increasingly threaten individuals, organizations, and governments, causing service disruption, inconvenience,and costly incident response. Given that such attacks are primarily enabled by software vulnerabilities, this work examines whether or not existing change metrics, along with architectural modularity and maintainability metrics can be used to predict modules and files that might be analyzed or tested further to excise vulnerabilities prior to release. 
The problem addressed by this research is the residual vulnerability problem, or vulnerabilities that evade detection and persist in released software. Many modern software projects are over a million lines of code, composed of reused components of varying maturity. The sheer size of modern software, along with the reuse of existing open source modules, complicates the questions of where to look, and in what order to look, for residual vulnerabilities. Prediction models based on various code and change metrics (e.g.,churn) have shown promise as indicators of vulnerabilities at the file level. 
This work investigates whether change metrics, along with architectural metrics quantifying modularity and maintainability can be used to identify attack-prone modules. In addition to identifying or predicting attack prone files, this work also examines prioritization and ranking said predictions.


BEN PANZER

Estimating Geophysical Properties of Snow and Sea Ice from Data Collected by an Airborne, Ultra-Wideband Radar

When & Where:


317 Nichols Hall

Committee Members:

Carl Leuschen, Chair
Chris Allen
Prasad Gogineni
Fernando Rodriguez-Morales
Richard Hale

Abstract

Large-scale spatial observations of the global sea ice thickness and distribution rely on multiple satellite-based altimeters. Laser altimeters, such as the GLAS instrument aboard ICESat-1 and ATLAS instrument aboard ICESat-2, measure freeboard which is the snow and ice thickness above mean sea level. Deriving sea-ice thickness from these data requires estimating the snow depth on the sea ice. Current means of estimating the snow depth are climatological history, daily precipitation products, and/or data from passive microwave sensors, such as AMSR-E. Radar altimeters, such as SIRAL aboard CryoSat-2, do not have sufficient vertical range resolution to resolve both the air-snow and snow-ice interfaces over sea-ice. Additionally, there is significant ambiguity on the location of the peak return due to penetration into the snow cover. Regardless of the sensor, any error in snow-depth estimation amplifies sea-ice thickness errors due to the assumption of hydrostatic equilibrium used in deriving sea-ice thickness. There clearly is a need for an airborne sensor to provide spatially large-scale measurements of the snow cover in both polar regions to improve the accuracy of sea-ice thickness estimates and provide validation for the satellite-based sensors. 
The Snow Radar was developed at the Center for Remote Sensing of Ice Sheets and deployed as part of NASA Operation IceBridge since 2009 to directly measure snow thickness over sea ice. The radar is an ultra-wideband, frequency-modulated, continuous-wave radar now working over the frequency range of 2 GHz to 8 GHz, resulting in a vertical range resolution of approximately 4 cm after post-processing. The radar has been shown to be capable of detecting snow depth over sea ice from 10 cm to more than 2 meters and results from the radar compare well to multiple in-situ measurements and passive-microwave measurements. 
The focus of the proposed research is estimation of useful geophysical properties of snow-covered sea ice beyond snow depth and subsequent refinement and validation of the snow depth extraction. Geophysical properties of interest are: snow density and wetness, air-snow and snow-ice surface roughness, and sea ice temperature and salinity. Through forward modeling of the radar backscatter response and the corresponding inversion, large-scale estimation of these properties may be possible.


GOUTHAM SELVAKUMAR

Constructing an Environment and Providing a Performance Assesment of Android's Dalvik Virtual Machine on x86 and

When & Where:


250 Nichols Hall

Committee Members:

Prasad Kulkarni, Chair
Victor Frost
Xin Fu


Abstract

Android is one of the most popular operating systems (OS) for mobile touchscreen devices, including smart-phones and tablet computers. Dalvik is a process virtual machine (VM) that provides an abstraction layer over the Android OS, and runs the Java-based Android applications. The first goal of this project is to construct a development environment for conveniently investigating the properties of Android's Dalvik VM on contemporary x86 and ARM architectures. The normal development environment restricts the Dalvik VM to run on top of Android, and requires an updated Android image to be built and installed on the target device after any change to the Dalvik code. This update-build-install process unnecessarily slows down any Dalvik VM exploration. We have now discovered a (undisclosed) configuration that enables us to study the Dalvik VM as a stand-alone application on top of the Linux OS. 
The second goal of this project is to understand the translation/compilation sub-system in the Dalvik VM, experiment with various modifications to determine the best translation parameters, and compare the Dalvik VM's just-in-time (JIT) compilation characteristics (such as quality of code generated and compilation time) on the x86 and ARM systems with a state-of-the-art Java VM. As expected, we find that JIT compilation is able to significantly improve application performance over basic interpretation. Comparing Dalvik's generated code quality with the Java HotSpot VM, we observe that Dalvik's ARM target is a much more mature compared to Dalvik-x86. However, Dalvik's simple trace-based compilation generates code quality that is much worse as compared to HotSpot. Finally, our experiments also reveal the most effective JIT compilation parameters for the Dalvik VM, and its effect of benchmark performance and memory usage.


ADAM CRIFASI

Framework of Real-Time Optical Nyquist-WDM Receiver using Matlab and Simulink

When & Where:


2001B Eaton Hall

Committee Members:

Ron Hui, Chair
Shannon Blunt
Erik Perrins


Abstract

I investigate an optical Nyquist-WDM Bit Error Rate (BER) detection system. A transmitter and receiver system is simulated, using Matlab and Simulink, to form a working algorithm and to study the effects of the different processes of the data chain. The inherent lack of phase information in the N-WDM scheme presents unique challenges and requires a precise phase recovery system to accurately decode a message. Furthermore, resource constraints are applied by a cost-effective Field Programmable Gate Array (FPGA). To compensate for the speed, gate, and memory constraints of a budget FPGA, several techniques are employed to design the best possible receiver. I study the resource intensive operations and vary their resource utilization to discover the effect on the BER. To conclude, a full VHDL design is delineated, including peripheral initialization, input data sorting and storage, timing synchronization, state machine and control signal implementation, N-WDM demodulation, phase recovery, QAM decoding, and BER calculation.


TIANCHEN LI

Radar Cross-Section Enhancement of a 40 Percent Yak54 Unmanned Aerial Vehicle

When & Where:


2001B Eaton Hall

Committee Members:

Chris Allen, Chair
Ken Demarest
Ron Hui


Abstract

With increasing civilian use of unmanned aerial vehicles (UAVs), flight safety of these unmanned devices in populated area has become one of the most concerned issues among the operators and users. To reduce the rate of colliding, anti-collision systems based on airborne radar system and enhanced autopilot programs are developed. However, for most civilian UAVs being made of non-metal materials which has considerably low radar cross-section (RCS), those UAVs are really hard or even impossible to be detected by radars. This project aims to design a light-weight UAV mounted RCS enhancement device that can increase the visibility of the UAV for airborne radars which work in the frequency band near 
1.445 GHz. In this project, a 40% YAK54 radio controlled UAV is used as the subject UAV. The report also concentrates on the design of passive Van Atta Array reflector approach.


REID CROWE

Development and Implementation of a VHF High Power Amplifier for the Multi-Channel Coherent Radar Depth Sounder/Imager System

When & Where:


317 Nichols Hall

Committee Members:

Fernando Rodriguez-Morales, Chair
Chris Allen
Carl Leuschen


Abstract

This thesis presents the implementation and characterization of a VHF high power amplifier developed for the Multi-channel Coherent Radar Depth Sounder/Imager (MCoRDS/I) system. MCoRDS/I is used to collect data on the thickness and basal topography of polar ice sheets, ice sheet margins, and fast-flowing glaciers from airborne platforms. Previous surveys have indicated that higher transmit power is needed to improve the performance of the radar, particularly when flying over challenging areas. 
The VHF high power amplifier system presented here consists of a 50-W driver amplifier and a 1-kW output stage operating in Class C. Its performance was characterized and optimized to obtain the best tradeoff between linearity, output power, efficiency, and conducted and radiated noise. A waveform pre-distortion technique to correct for gain variations (dependent on input power and operating frequency) was demonstrated using digital techniques. 
The amplifier system is a modular unit that can be expanded to handle a larger number of transmit channels as needed for future applications. The system can support sequential transmit/receive operations on a single antenna by using a high-power circulator and a duplexer circuit composed of two 90° hybrid couplers and anti-parallel diodes. The duplexer is advantageous over switches based on PIN-diodes due to the moderately high power handling capability and fast switching time. The system presented here is also smaller and lighter than previous implementations with comparable output power levels.