Ph.D. Presentations

Recently, a class of non-invasive hardware side-channel attacks has been discovered in field-programmable gate arrays (FPGAs). These attacks extract remnants of prior users’ activity that persist as transistor defect states within reconfigurable routing resources. These remnants are known as FPGA Pentimenti. Resistive random-access memory (ReRAM) is a compelling candidate for pentimenti-like attacks beyond FPGAs. However, […]

The electric grid is essential to modern society, and recent developments such as renewable energy sources (RESs), battery energy storage systems (ESSs), and microgrids (MGs) have necessitated novel computational methods for planning and operations. Machine learning offers a promising lever here, both as an accelerator for and proxy to traditional optimization-based problems. In this thesis, […]

Intracellular symbionts are microorganisms, such as bacteria, that live within host cells. These associations are widespread throughout the invertebrate tree of life, and can perform a diversity of key metabolic, immune-response, or other functions that the host is dependent on for survival or reproduction. Intracellular symbioses allow both the host and the symbiont to occupy […]

Centromeres ensure proper chromosome segregation during cell division, yet the organization and regulation of centromeric chromatin within satellite DNA arrays remain incompletely understood. Here, we leverage the complete diploid human genome benchmark (T2T-HG002) to provide a detailed study of centromeric sequence and chromatin architecture on individual haplotypes. Using adaptive-sampling-enriched, ultra-long-read DiMeLo-seq, we achieve single-molecule chromatin […]

As quantum computing transitions from theory to practice, understanding which algorithms suit near-term devices becomes critical. Current quantum computers are severely constrained by limited qubit counts, short coherence times, and high error rates that quickly degrade computation into noise. This thesis addresses two interconnected questions: what non-trivial computational tasks can near-term devices execute and how […]

Many genetics pipelines start by aligning sequencing reads to a reference genome. Aligners attempt to find the position in the reference sequence which best matches the read sequence, but this […]

Self-reflection holds significant potential for learning, behavior change, and emotional processing, yet designing technologies that effectively support it remains challenging, particularly when reflection involves difficult experiences such as failure. Most […]

The growing complexity of high-performance computing (HPC) systems poses a fundamental challenge for domain scientists, whose primary objective is to obtain scientifically valid results rather than to optimize resource utilization. […]

Modern software increasingly relies on distributed systems to provide accessible, scalable, and reliable services. Choreographic programming brings a global perspective to distributed system development: programmers write a single program that […]

Edge computing and distributed AI systems increasingly operate under heterogeneous resources, dynamic workloads, and frequent failures, requiring both adaptivity and fault tolerance for efficient execution. In heterogeneous edge clusters, nodes […]

Real-time monitoring of infectious disease outbreaks calls for statistical models that recover interpretable quantities such as the time-varying reproduction number from noisy count data, track posterior uncertainty, and run on […]

Due to their increasing complexity, autonomous decision-making agents rely on increasingly advanced algorithms, from classical control theory to reinforcement learning (RL) and, more recently, large vision-language models. While these algorithms […]

Graphics Processing Units (GPUs) have become essential platforms for parallel computing, supporting applications far beyond graphics. Central to GPU programming models is its memory consistency specification (MCS), which defines the […]