Decompositions of large-scale networks are central to many applications in graph mining, network science, and algorithm design. Over several decades, a rich body of work has developed techniques to partition networks with various different objectives. However, a noticeable gap persists between methods with strong theoretical guarantees, and those that perform well in practice. Practical algorithms […]

Narrative sandbox games rely heavily on simulation to produce emergent narrative experiences. Instead of featuring pre-authored central narratives, these games provide a play space, a sandbox, of various systems and mechanics players use to produce interesting narrative moments. This dissertation focuses on social simulation games, a subset of narrative sandbox games that drive the narrative […]

Online communities tell stories with the games they play. As continual updates, recurring monetization, and platforms for community discussions have flourished, we have seen a rise in video games using ongoing development to tell stories, and have a community interact with those stories and build upon them. In this dissertation, I study this phenomenon, which […]

T cell receptors (TCRs) mediate antigen-specific immune responses through recognition of peptides presented by major histocompatibility complex (pMHC) molecules. Accurately predicting TCR–pMHC interactions remains a major barrier to TCR-based immunotherapy, due to limitations in current models that fail to generalize beyond common viral epitopes and well-characterized HLA alleles. In this PhD proposal, I outline a […]

The explosive growth of genomic data, driven by advances in sequencing and inference technologies, presents both an opportunity and a challenge for evolutionary biology and public health. Existing visualization and analysis tools often fall short in handling the scale, complexity, and uncertainty of modern genomic datasets—especially in the areas of pathogen surveillance and ancestral recombination […]

Neurodevelopmental and neuropsychiatric disorders (NPDs), such as autism spectrum disorder and schizophrenia, are among the most heritable yet mechanistically complex conditions. While large-scale genomic studies have identified hundreds of high-confidence risk genes, the lack of scalable and integrative platforms has limited our ability to functionally characterize these genes. To address this, I am developing a […]

Machine learning endows autonomous systems to uncover underlying structures and physical laws from measured data and to leverage these models for prediction and decision-making. As the costs of data acquisition, processing, and storage decline—and sensors become increasingly widespread alongside ever-improving algorithms—artificial intelligence has attracted significant attention in research and industry. Machine-learning methods are particularly attractive […]

Collaborative virtual reality environments have the potential to greatly impact scientific progress, especially those relating to existential human problems. Within these virtual environments, scientists could view and interact with spatial […]

Program verification has been applied in many contexts (including videogames), but the scale and complexity of the examples that have been analyzed fall short of the ability to analyze many […]