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 […]
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 […]
The 26th Annual UC Systemwide Bioengineering Symposium (BIC 2026) is taking place at UC Santa Cruz on August 22-23, 2026. The event will bring together faculty, researchers, students, industry representatives, […]
The 26th Annual UC Systemwide Bioengineering Symposium (BIC 2026) is taking place at UC Santa Cruz on August 22-23, 2026. The event will bring together faculty, researchers, students, industry representatives, non-profit organizations, and other stakeholders to explore bioengineering & AI in the heart of the redwood forest. BIC 2026 will foster new collaborations and showcase […]
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 […]
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 […]
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 […]
The accelerating adoption of zero-emission vehicles (ZEVs) in California is reshaping both the transportation and electrical grids at the moment as climate-driven disasters are intensifying in frequency and severity. This dual transition exposes a critical structural gap: existing resilience research treats pre-disaster evacuation readiness and post-disaster grid restoration as separate problems, even though both are […]
Many somatic variant-calling pipelines begin by aligning tumor and matched-normal sequencing reads to a single linear reference genome, such as GRCh38. Because every individual differs substantially from this reference, this approach can introduce reference bias, causing reads to map incorrectly or not at all and potentially leading to missed somatic variants or germline variants being […]
Verbal autopsy (VA) is a well developed tool to collect information describing deaths outside of hospitals by conducting surveys to the relatives and caregivers of the deceased person. It is routinely-implemented in low and middle income countries, where it often lacks sufficient resources to conduct the autopsy. The main task is to estimate both individual […]
This quarter, make time for you, for reflection, and for community!
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 […]
This quarter, make time for you, for reflection, and for community!
This quarter, make time for you, for reflection, and for community!
This quarter, make time for you, for reflection, and for community!
This quarter, make time for you, for reflection, and for community!
This quarter, make time for you, for reflection, and for community!
This quarter, make time for you, for reflection, and for community!