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  • Three silhouetted figures talking, overlaid with graphics of digital data, charts, and technology interfaces.

    Penunuri, G. (BMEB) – Genomic, Proteomic, and Computational Approaches to the Study of Host-Microbe Systems

    Biomedical Sciences Building 575 McLaughlin Drive
    Hybrid Event

    Host-microbe systems are core to some of biology’s most consequential interactions, from the pathogens that drive infectious disease to symbionts affecting agricultural pest control and vector-borne disease transmission. Yet unlike the model organisms that have driven most of modern molecular biology, the microbes at the center of these interactions are rarely genetically tractable: many cannot […]

  • Abstract digital illustration featuring gears and interconnected technology elements.

    Nava, A. (AM) – Machine-Learning Methods for Prediction of Biological Systems

    Engineering 2 Engineering 2 1156 High Street, Santa Cruz, CA
    Hybrid Event

    Advances in microscopy have enabled the collection of high-quality single-cell datasets, providing new opportunities to identify the mechanisms underlying complex biological processes. In this work, we develop machine-learning frameworks using single-cell temporal data with the goal of predicting and providing insights into these mechanisms. We produce frameworks for two biological systems, bacterial spore germination, the […]

  • Close-up abstract image of a circuit board with glowing lines and interconnected pathways.

    Huang, X. (CSE) – Scalable and Verifiable Reasoning for Medical Foundation Models

    Virtual Event

    This PhD research focuses on developing reliable medical foundation models capable of reasoning across textual, visual, and interactive clinical information. The work investigates three complementary directions: improving medical reasoning through test-time scaling, training multimodal medical models with verifiable rewards, and synthesizing high-quality visual question-answering data from biomedical literature using generator-verifier frameworks. Building on these efforts, […]

  • Close-up abstract image of a circuit board with glowing lines and interconnected pathways.

    Pawar, M. (CSE) – Understanding Representations, Reasoning, and Decision-Making in Autonomous Driving Models

    Virtual Event

    Modern autonomous-driving models increasingly rely on learned representations and generated reasoning to interpret complex scenes and produce predictions or actions. However, it remains unclear what information these models encode, how that information is exposed through common interpretation methods, and whether their stated reasoning meaningfully influences their behavior. This research investigates these questions across motion-forecasting and […]

  • Abstract digital illustration featuring gears and interconnected technology elements.

    Gomez, J. (CSE) – Toward Sustainable and Secure Open Source Software: Discovery, Measurement, and Defense

    Engineering 2 Engineering 2 1156 High Street, Santa Cruz, CA
    Hybrid Event

    In March 2024, a backdoor was discovered in xz Utils, a widely used open source data compression library present in nearly every major Linux distribution. The attack was discovered days before merging into major distributions, and if this had happened, it would have allowed attackers to execute arbitrary code on millions of systems worldwide via […]

  • Close-up abstract image of a circuit board with glowing lines and interconnected pathways.

    Kramer, A. (BMEB) – Scalable phylo-pangenomics

    Biomedical Sciences Building 575 McLaughlin Drive
    Hybrid Event

    The COVID-19 pandemic generated genomic data at unprecedented scale, with tens of millions of SARS-CoV-2 genomes deposited in public repositories and thousands of new sequences added each day. This dissertation develops methods for analyzing genomic datasets at this scale, unified by the idea that encoding genomes according to their evolutionary relationships can make otherwise intractable […]

  • Abstract digital illustration featuring gears and interconnected technology elements.

    Chen, Y. (STAT) – Flexible Bayesian Models for High-Dimensional and Longitudinal Discrete Data in Microbiome Studies

    Virtual Event

    Multivariate dependent discrete data routinely arise in microbiome studies. Analyzing these data presents interesting statistical challenges, such as high dimensionality, excess zeros, large heterogeneity across samples, and temporal dependence in longitudinal studies. Drawing inferences about objects of primary scientific interest—such as temporal trajectories of microbial abundance, microbial interactions, clusters of microbes similarly associated with environmental […]