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
Muhammad Momin Rahman
Development of a Signal Flow Graph-Based De-Embedding Framework for Broadband Passive Linear Multiport RF & Microwave Networks with Applications to Power SplittersWhen & Where:
Nichols Hall, Room 317 (Richard K. Moore Conference Room)
Committee Members:
Carl Leuschen, ChairKenneth Demarest
Fernando Rodriguez-Morales
Abstract
Discrete passive components, including resistors, capacitors, inductors, and transformers, are fundamental to broadband 75-Ω radio-frequency (RF) systems, particularly in cable television (CATV) and hybrid fiber-coaxial (HFC) networks. These components are incorporated into power splitters, couplers, power inserters, and amplifiers to achieve desired frequency responses, impedance matching, and signal transmission characteristics. However, their electrical behavior becomes increasingly complex at higher frequencies due to parasitic resistance, inductance, capacitance, electromagnetic coupling, and distributed transmission-line effects. Consequently, accurate broadband characterization is essential for predicting component behavior and developing representative RF circuit models for simulation purposes.
A significant challenge arises when characterizing passive components with limited or unavailable manufacturer specifications, particularly when existing component inventories must be evaluated for broadband applications. Conventional measurement instruments, including digital multimeters, LCR meters, oscilloscopes, and function generators, generally lack the frequency range required for comprehensive RF characterization from 5 MHz to 3 GHz. Vector network analyzers (VNAs) enable complex scattering-parameter measurements across this frequency range; however, the measured response includes contributions from test fixtures, interconnections, and parasitic discontinuities that must be distinguished from the intrinsic response of the device under test (DUT).
This project investigates the development of a signal flow graph (SFG)-based de-embedding framework for broadband passive linear multiport RF networks. The methodology incorporates series-through and shunt-through DUT (CPWG) fixture configurations, conventional Open-Short and Short-Open de-embedding techniques, followed by lumped-element and distributed transmission-line representations of fixture parasitics. Scattering-parameter and ABCD-parameter analysis are employed to characterize fixture responses, while signal flow graph derivations provide a mathematical basis for analyzing interconnected multiport networks. Particular attention is given to fixture asymmetry, impedance discontinuities, and multiple signal propagation paths that complicate the extension of conventional two-port characterization methods to higher-order networks.
Experimental validation is conducted through the characterization of passive components with published impedance and quality-factor characteristics, enabling comparisons between extracted measurements, equivalent-circuit models, and manufacturer reference data. The methodology is subsequently applied to broadband power splitter networks used in CATV/HFC systems to investigate the accuracy and applicability of the proposed multiport de-embedding framework. The project aims to establish a systematic approach to broadband passive component characterization that integrates fixture modeling, network theory, and experimental measurement while reducing dependence on proprietary characterization data.
Fairuz Shadmani Shishir
Efficient and Privacy-Preserving Biomedical AI: From Precision Therapeutics Design to Private Clinical PredictionWhen & Where:
Eaton Hall, Room 2001B
Committee Members:
Sumaiya Shomaji, ChairTamzidul Hoque
Cuncong Zhong
Bishnu Sarker
Michael Hageman
Abstract
Accurate protein characterization, precision therapeutics design, and privacy-preserving clinical modeling are important challenges in biomedical artificial intelligence (AI). Addressing these challenges requires computational frameworks that are not only accurate and scalable but also capable of supporting reliable decision-making. This dissertation develops efficient, scalable, and reliable computational frameworks across three areas: Computational characterization of proteins, precision therapeutics design, and privacy-aware clinical representation learning. The first part of this dissertation focuses on efficient protein characterization at both the sequence and residue levels. GPCR-SLM, a knowledge-distilled small protein language model, classifies G-protein-coupled receptors (GPCRs), a family targeted by approximately 35% of FDA-approved drugs. Across 86 families, GPCR-SLM achieves 99% accuracy, outperforming BLAST (86.4%) and HMMER (91%), with a 33.5-fold speedup over large protein language models. Extending characterization to the residue level, a protein-metal-ion binding site prediction framework evaluates five protein language models and incorporates positional encoding to capture long-range dependencies. Under 10-fold cross-validation, it achieves a Matthews correlation coefficient of 0.89, with precision, recall, and F1 scores exceeding 95% across six metal ions.
Building on these protein characterization methods, the second part advances precision therapeutics design through uncertainty quantification and generative learning for therapeutic antibodies. NbBayesLM combines protein language model embeddings and physicochemical descriptors in a Bayesian neural network to predict nanobody thermostability. Evaluated on 10,630 VHH sequences, it achieves a mean absolute error of 1.89C and an R2 of 0.67 while estimating epistemic and aleatoric uncertainty to support candidate prioritization. CIgFlow employs classifier-free guidance to generate de novo, antigen-conditioned antibody sequences without fixed scaffolds or paired structural data. Generated sequences achieve a median OASis humanness score of 0.90 and mean predicted local distance difference test (pLDDT) score of 85.0, demonstrating promising novelty and diversity. The third part addresses privacy-aware clinical modeling using electrocardiograms (ECGs), which encode diagnostic information and sensitive demographic attributes. A variational autoencoder with dual discriminators suppresses demographic information while preserving clinically relevant representations.
Collectively, this dissertation advances efficient protein representation learning, computational antibody design, and privacy-preserving clinical AI, contributing methodological foundations for trustworthy biomedical applications.
Arturo Solorio
Performance Analysis of Mismatched Filtering for Stochastic WaveformsWhen & Where:
Nichols Hall, Room 246 (Executive Conference Room)
Committee Members:
Patrick McCormick, ChairShannon Blunt
Charles Mohr
Abstract
Mismatched filtering (MMF) is a widely used pulse compression technique that reduces cross-correlation sidelobe levels at the cost of some loss in signal-to-noise ratio (SNR). Applying MMF to stochastically generated radar waveforms makes the filter's performance inherently random, which can be problematic if the variability is excessive. As well as the computational cost being relatively high, as per pulse, a new MMF optimization is required. In this thesis, the feasibility of a fixed MMF strategy for stochastic radar waveforms to reduce computational cost is investigated. Two MMF formulations were evaluated, the optimal MMF (Diagonal Loaded Filter) and a projection-based MMF. Both filters were designed to minimize sidelobe energy within specified regions of the Cross-Ambiguity Function (CAF) for Stochastic Waveform Generation (StoWGe) waveforms, and their performance was assessed across multiple time-bandwidth products and sidelobe-regions for two center frequencies, Fc = 30 Ghz and Fc = 3.5 Ghz. The MMF performance was characterized using SNR loss and sidelobe depth over hundreds of trails. It is observed that the variability in SNR and sidelobe depth decreases as the waveform time-bandwdith product and the sidelobe region targeted for minimization increase, although the Fc = 3.5 GHz cases exhibited a plateau in achievable sidelobe depth. Additional validation using 1000-trail histograms and loop-back testing confirmed the robustness for the fixed MMF approach for higher time-bandwidth product stochastic waveforms. Where, overall, the results demonstrate that a fixed MMF strategy is feasible for stochastic waveforms when the time-bandwdith product and sidelobe region are sufficiently large. Furthermore, the Projection-based MMF provides a suboptimal alternative to the optimal MMF as it achieves comparable MMF performance when constrained to similar SNR-loss and may be desirable when the size of the domination eigenvalues is small relative to the filter length and can be efficiency obtained.
Past Defense Notices
Bhuneshwari Sharma Joshi
Applying ML Models for the Analysis of Bankruptcy PredictionWhen & Where:
Zoom Meeting, please email jgrisafe@ku.edu for defense link.
Committee Members:
Prasad Kulkarni, ChairDrew Davidson
David Johnson
Abstract
Bankruptcy prediction helps to evaluate the financial condition of a company and it helps not only the policymakers but the investors and all concerned people so they can take all required steps to avoid or to reduce the after-effects of bankruptcy. Bankruptcy prediction will not only help in making the best decision but also provides insight to reduce losses. The major reasons for the business organization’s failure are due to economic conditions such as proper allocation of resources, Input to policymakers, appropriate steps for business managers, identification of sector-wide problems, too much debt, insufficient capital, signal to Investors, etc. These factors can lead to making business unsustainable. The failure rate of businesses has tended to fluctuate with the state of the economy. The area of corporate bankruptcy prediction attains high economic importance, as it affects many stakeholders. The prediction of corporate bankruptcy has been extensively studied in economics, accounting, banking, and decision sciences over the past two decades. Many traditional approaches were suggested based on hypothesis testing and statistical analysis. Therefore, our focus and research are to come up with an approach that can estimate the probability of corporate bankruptcy and by evaluating its occurrence of failure using different machine learning models such as random forest, Random forest, XGboost, logistic method and choosing the one which gives highest accuracy. The dataset used was not well prepared and contained missing values, various data mining and data pre-processing techniques were utilized for data preparation. We use models such asRandom forest, Logistic method, random forest, XGBoost to predict corporate bankruptcy earlier to the occurrence. The accuracy results for accurate predictions of whether an organization will go bankrupt within the next 30, 90, or 180 days, using financial ratios as input features. The XGBoost-based model performs exceptionally well, with 98-99% accuracy.
Laurynas Lialys
Engineering laser beams for particle trapping, lattice formation and microscopyWhen & Where:
Nichols Hall, Room 246 (Executive Conference Room)
Committee Members:
Shima Fardad, ChairMorteza Hashemi
Rongqing Hui
Alessandro Salandrino
Xinmai Yang
Abstract
Having control over nano- and micro-sized objects' position inside a suspension is crucial in many applications such as: sorting and delivery of particles, studying cells and microorganisms, spectroscopy imaging techniques, and building microscopic size lattices and artificial structures. This control can be achieved by judiciously engineering optical forces and light-matter interactions inside colloidal suspensions that result in optical trapping. However, in the current techniques, to confine and transport particles in 3D, the use of high-NA (Numerical Aperture) optics is a must. This in turn leads to several disadvantages such as alignment complications, lower trap stability, and undesirable thermal effects. Hence, here we study novel optical trapping methods such as asymmetric counter-propagating beams where we have engineered the optical forces to overcome the aforementioned limitations. This system is significantly easier to align as it uses much lower NA optics which creates a very flexible manipulating system. This new approach allows the trapping and transportation of different shape objects, sizing from hundreds of nanometers to hundreds of micrometers by exploiting asymmetrical optical fields with higher stability. In addition, this technique also allows for significantly longer particle trapping lengths of up to a few millimeters. As a result, we can apply this method to trapping much larger particles and microorganisms that have never been trapped optically before. Another application that the larger trapping lengths of the proposed system allow for is the creation of 3D lattices of microscopic size particles and other artificial structures, which is one important application of optical trapping.
This system can be used to create a fully reconfigurable medium by optically controlling the position of selected nano- and micro-sized dielectric and metallic particles to mimic a certain medium. This “table-top” emulation can significantly simplify our studies of wave-propagation phenomena on transmitted signals in the real world.
Furthermore, an important application of an optical tweezer system is that it can be combined with a variety of spectroscopy and microscopy techniques to extract valuable, time-sensitive information from trapped entities. In this research, I plan to integrate several spectroscopy techniques into the proposed trapping method in order to achieve higher-resolution images, especially for biomaterials such as microorganisms.
Michael Cooley
Machine Learning for Navel Discharge ReviewWhen & Where:
Eaton Hall, Room 1
Committee Members:
Prasad Kulkarni, ChairDavid Johnson (Co-Chair)
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.
Vasudha Yenuganti
RNA Structure Annotation Based on Base Pairs Using ML Based ClassifiersWhen & Where:
Eaton Hall, Room 2001B
Committee Members:
Cuncong Zhong, ChairDavid Johnson
Prasad Kulkarni
Abstract
RNA molecules play a crucial role in the regulation of gene expression and other cellular processes. Understanding the three-dimensional structure of RNA is essential for predicting its function and interactions with other molecules. One key feature of RNA structure is the presence of base pairs, where nucleotides i.e., adenine(A), guanine(G), cytosine(C), and uracil(U), form hydrogen bonds with each other. The limited availability of high-quality RNA structural data combined with associated atomic coordinate errors in low resolution structures, presents significant challenges for extracting important geometrical characteristics from RNA's complex three-dimensional structure, particularly in terms of base interactions.
In this study, we propose an approach for annotating base-pairing interactions in low-resolution RNA structures using machine learning (ML) based classifiers and leveraging the more precise structural information available in high-resolution homologs to annotate base-pairing interactions in low-resolution structures. We first use DSSR tool to extract annotations of high-resolution RNA structures and extract distances of atoms of interacting base pairs. The distances serve as features, and 12 standard annotations are used as labels for our ML model. We then apply different ML classifiers, including support vector machines, neural networks, and random forests, to predict RNA annotations. We evaluate the performance of these classifiers using a benchmark dataset and report their precision, recall, and F1-score. Low-resolution RNA structures are then annotated based on the sequence-similarity with high-resolution structures and the corresponding predicted annotations.
For future aspects, the presented approach can also help to explore the plausible base pair interactions to identify conserved motifs in low-resolution structures. The detected interactions along with annotations can aid in the study of RNA tertiary structures, which can lead to a better understanding of their functions in the cell.
Venkata Nadha Reddy Karasani
Implementing Web Presence For The History Of Black WritingWhen & Where:
LEEP2, Room 1415
Committee Members:
Drew Davidson, ChairPerry Alexander
Hossein Saiedian
Abstract
The Black Literature Network Project is a comprehensive initiative to disseminate literature knowledge to students, academics, and the general public. It encompasses four distinct portals, each featuring content created and curated by scholars in the field. These portals include the Novel Generator Machine, Literary Data Gallery, Multithreaded Literary Briefs, and Remarkable Receptions Podcast Series. My significant contribution to this project was creating a standalone website for the Current Archives and Collections Index that offers an easily searchable index of black-themed collections. Additionally, I was exclusively responsible for the complete development of the novel generator tool. This application provides customized book recommendations based on user preferences. As a part of the History of Black Writing (HBW) Program, I had the opportunity to customize an open-source annotation tool called Hypothesis. This customization allowed for its use on all websites related to the Black Literature Network Project by the end users. The Black Book Interactive Project (BBIP) collaborates with institutions and groups nationwide to promote access to Black-authored texts and digital publishing. Through BBIP, we plan to increase black literature’s visibility in digital humanities research.
Michael Bechtel
Shared Resource Denial-of-Service Attacks on Multicore PlatformsWhen & Where:
Eaton Hall, Room 2001B
Committee Members:
Heechul Yun, ChairMohammad Alian
Drew Davidson
Prasad Kulkarni
Shawn Keshmiri
Abstract
With the increased adoption of complex machine learning algorithms across many different fields, powerful computing platforms have become necessary to meet their computational needs. Multicore platforms are a popular choice as they provide greater computing capabilities and can still meet different size, weight, and power (SWaP) constraints. However, contention for shared hardware resources between multiple cores remains a significant challenge that can lead to interference and unpredictable timing behaviors. Furthermore, this contention can be intentionally induced by malicious actors with the specific goals of delaying safety-critical tasks and jeopardizing system safety. This is done by performing Denial-of-Service (DoS) attacks that target shared resources such that the other cores in a system are unable to access them. When done properly, these shared resource DoS attacks can significantly impact performance and threaten system stability. For example, DoS attacks can cause >300X slowdown on the popular Raspberry Pi 3 embedded platform.
Motivated by the inherent risks posed by these DoS attacks, this dissertation presents investigations and evaluations of shared resource contention on multicore platforms, and the impacts it can have on the performance of real-time tasks. We propose various DoS attacks that each target different shared resources in the memory hierarchy with the goal of causing as much slowdown as possible. We show that each attack can inflict significant temporal slowdowns to victim tasks on target platforms by exploiting different hardware and software mechanisms. We then develop and analyze techniques for providing shared resource isolation and temporal performance guarantees for safety-critical tasks running on multicore platforms. In particular, we find that bandwidth throttling mechanisms are effective solutions against most DoS attacks and can protect the performance of real-time victim tasks.
Sarah Johnson
Formal Analysis of TPM Key Certification ProtocolsWhen & Where:
Nichols Hall, Room 246 (Executive Conference Room)
Committee Members:
Perry Alexander, ChairMichael 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.
Andrew Cousino
Recording Remote Attestations on the BlockchainWhen & Where:
Nichols Hall, Gemini Room
Committee Members:
Perry Alexander, ChairAlex Bardas
Drew Davidson
Abstract
Remote attestation is a process of establishing trust between various systems on a network. Until now, attestations had to be done on the fly as caching attestations had not yet been solved. With the blockchain providing a monotonic record, this work attempts to enable attestations to be cached. This paves the way for more complex attestation protocols to fit the wide variety of needs of users. We also developed specifications for these records to be cached on the blockchain.
Ragib Shakil Rafi
Nonlinearity Assisted Mie Scattering from NanoparticlesWhen & Where:
Eaton Hall, Room 2001B
Committee Members:
Alessandro Salandrino, ChairShima Fardad
Morteza Hashemi
Rongqing Hui
Judy Wu
Abstract
Scattering by nanoparticles is an exciting branch of physics to control and manipulate light. More specifically, there have been fascinating developments regarding light scattering by sub-wavelength particles, including high-index dielectric and metal particles, for their applications in optical resonance phenomena, detecting the fluorescence of molecules, enhancing Raman scattering, transferring the energy to the higher order modes, sensing and photodetector technologies. It recently gained more attention due to its near-field effect at the nanoscale and achieving new insights and applications through space and time-varying parametric modulation and including nonlinear effects. When the particle size is comparable to or slightly bigger than the incident wavelength, Mie solutions to Maxwell's equations describe these electromagnetic scattering problems. The addition and excitation of nonlinear effects in these high-indexed sub-wavelength dielectric and plasmonic particles might improve the existing performance of the system or provide additional features directed toward unique applications. In this thesis, we study the Mie scattering from dielectric and plasmonic particles in the presence of nonlinear effects. For dielectrics, we present a numerical study of the linear and nonlinear diffraction and focusing properties of dielectric metasurfaces consisting of silicon microcylinder arrays resting on a silicon substrate. Upon diffraction, such structures lead to the formation of near-field intensity profiles reminiscent of photonic nanojets and propagate similarly. Our results indicate that the Kerr nonlinear effect enhances light concentration throughout the generated photonic jet with an increase in the intensity of about 20% compared to the linear regime for the power levels considered in this work. The transverse beamwidth remains subwavelength in all cases, and the nonlinear effect reduces the full width. In the future, we want to optimize the performance through parametric modification of the system and continue our study with plasmonic structures in time–varying scenarios. We hope that with appropriate parametric modulation, intermodal energy transfer is possible in such structures. We want to explore the nonlinear excitation to transfer energy in higher-order modes by exploiting different wave-mixing interactions in time-modulated scatterers.
Anna Fritz
Negotiating Remote Attestation ProtocolsWhen & Where:
Nichols Hall, Room 246 (Executive Conference Room)
Committee Members:
Perry Alexander, ChairAlex 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.