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DTSTART;TZID=America/Los_Angeles:20260825T110000
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DTSTAMP:20260812T161153Z
CREATED:20260812T161153Z
LAST-MODIFIED:20260812T161153Z
UID:10015333-1787655600-1787662800@live-events-ucsc.pantheonsite.io
SUMMARY:Gomez\, J. (CSE) - Toward Sustainable and Secure Open Source Software: Discovery\, Measurement\, and Defense
DESCRIPTION: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 SSH. \nThe success of this backdoor was enabled by two failures. The first was technical: weaknesses in the software supply chain allowed a malicious actor to inject code into a widely trusted release. The second was human: the project’s only maintainer\, overwhelmed and burned out after years of maintaining critical infrastructure alone\, was the target of a multi-year social engineering campaign\, in which a malicious actor built trust under a false identity and gradually obtained commit access to the project. This incident shows that software security failures and sustainability failures are not independent: an overburdened\, unsupported maintainer is itself an attack surface. \nAcademic and scientific open source software (OSS) faces both of these crises simultaneously. Projects that critical infrastructure depends on are maintained by researchers\, students\, and faculty who contribute in their spare time\, without dedicated security training or institutional support. Existing security frameworks including NIST’s SSDF\, OWASP’s SCVS\, and SLSA were not designed with these communities in mind\, and policy efforts such as the EU Cyber Resilience Act have shown that mandates developed without community input risk harming the ecosystems they are meant to protect. \nThis dissertation addresses the sustainability and security of academic open source software through two parallel empirical research tracks. The sustainability track combines GitHub’s REST API with LLM-based filtering to discover and characterize over 216\,000 institutionally affiliated repositories across 32 academic and research institutions\, finding that while 84\% include a README\, only 23.4% carry a detectable license and fewer than 2% include a Contributing Guide. Building on this dataset\, we develop a maturity-staged sustainability framework that classifies projects into four lifecycle stages and generates targeted recommendations for Open Source Program Offices (OSPOs). \nThe security track examines whether post-9/11 trade security programs offer a workable model for OSS supply-chain policy\, finding that effective frameworks require voluntary incentives and direct community engagement rather than top-down mandates. We further evaluate five large language models on the OWASP Benchmark for vulnerability triage\, finding that o1-mini reduces false positives by 20% over the Semgrep baseline\, demonstrating the potential for automation to reduce the security burden on individual maintainers. \nTogether\, these contributions treat sustainability and security as interconnected problems. A project that cannot sustain itself cannot secure its code\, and this dissertation takes steps toward closing both gaps. \n  \nEvent Host: Juanita Gomez\, Ph.D. Candidate\, Computer Science & Engineering \nAdvisor: Alvaro Cardenas  \nZoom: https://ucsc.zoom.us/j/91057980344?pwd=XMMjHZVgbbLXfwxKehrTEbat18066o.1 \nPasscode: 292091
URL:https://live-events-ucsc.pantheonsite.io/event/gomez-j-cse-toward-sustainable-and-secure-open-source-software-discovery-measurement-and-defense/
LOCATION:Engineering 2\, Engineering 2 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260828T090000
DTEND;TZID=America/Los_Angeles:20260828T120000
DTSTAMP:20260819T161142Z
CREATED:20260819T161142Z
LAST-MODIFIED:20260819T161142Z
UID:10015346-1787907600-1787918400@live-events-ucsc.pantheonsite.io
SUMMARY:Saleem\, O. (ECE) - Coupled Evacuation Readiness and Post-Disaster Restoration for Vehicle-to-Grid Enabled Resilient Power–Transportation Networks
DESCRIPTION: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 governed by the same underlying resource\, i.e.\, electric vehicle batteries. On the other hand\, same underlying constraint\, a damaged\, congested transportation network. This dissertation develops an integrated framework that spans the full disaster lifecycle\, coupling evacuation-phase EV readiness assessment with restoration-phase vehicle-to-grid (V2G) coordination. \nThe work begins by establishing a quantitative ZEV Evacuation Readiness Score (ZEV Score) that assess community preparedness across exposure of the region to various natural disasters based on historical data\, vulnerabilities of the available infrastructure and the adaptive capacity of the infrastructure under stress. This work was afterwards extended to 44-indicator resilience framework across 6 domains i.e. community engagement\, charging infrastructure\, mobile and backup power\, transportation routing\, exposure\, equity\, and community engagement. Building on this foundation\, the dissertation introduces a novel restoration architecture that couples vehicle-routing-problem-based crew dispatch with game-theoretic V2G aggregation through a physics-consistent islanding-duration variable — the first framework to close the loop between road/grid repair scheduling and battery energy management. Validated on the IEEE RTS-79 network with Tesla Model 3 battery dynamics\, this coupling eliminates the “battery dead-zone” failure mode entirely\, reducing cumulative unsupported outage time from 54.3 to 0 hours under worst-case coordination scenarios\, while cutting total load shed by up to 18% beyond standalone repair coordination. \nTogether\, these contributions reframe EV fleets not merely as evacuation liabilities to be planned around\, but as a coordinated\, timeline-aware energy resource spanning both the flight from disaster and the recovery that follows. The dissertation’s proposed aims extend this integration towards stochastic damage scenarios\, heterogeneous mobile energy resources\, and a unified pre- to post-disaster co-optimization pipeline. Which offer both a technical bridge between restoration engineering and evacuation planning\, and a policy-relevant tool for California communities navigating a fully electrified\, climate-exposed future. \nEvent Host: Osman Saleem\, Ph.D. Student\, Electrical & Computer Engineering \nAdvisor: Keith Corzine & Leila Parsa  \nZoom: https://ucsc.zoom.us/j/96031345847?pwd=bjLMYhuyPyIMt7deiEKWRh35I7vjUW.1 \nPasscode: 544944
URL:https://live-events-ucsc.pantheonsite.io/event/saleem-o-ece-coupled-evacuation-readiness-and-post-disaster-restoration-for-vehicle-to-grid-enabled-resilient-power-transportation-networks/
LOCATION:Engineering 2\, Engineering 2 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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BEGIN:VEVENT
DTSTART;TZID=America/Los_Angeles:20260828T100000
DTEND;TZID=America/Los_Angeles:20260828T120000
DTSTAMP:20260813T164521Z
CREATED:20260813T164521Z
LAST-MODIFIED:20260813T164521Z
UID:10015336-1787911200-1787918400@live-events-ucsc.pantheonsite.io
SUMMARY:Nag\, S. (BMEB) - Personalized Diploid Genome Graphs for Accurate Somatic Variant Discovery
DESCRIPTION: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 misclassified as somatic. I propose replacing the generic reference with a personalized diploid genome graph constructed from a donor-specific assembly (DSA)\, which represents both inherited haplotypes of the individual. I will develop this framework by (1) generating haplotype-resolved\, telomere-to-telomere DSAs for cancer reference cell lines\, (2) developing haplotype-aware graph alignment and adapting DeepSomatic to call variants against personalized diploid genomes\, and (3) applying this approach across tissues from SMaHT donors to improve somatic mosaicism detection and characterize shared and tissue-specific mutations. \nEvent Host: Sagorika Nag\, Ph.D. Student\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Benedict Paten \nZoom: https://ucsc.zoom.us/j/99844148597?pwd=amp5Nhmj2UeodTADUdaJwZsKtscRMG.1 \nPasscode: 685655
URL:https://live-events-ucsc.pantheonsite.io/event/nag-s-bmeb-personalized-diploid-genome-graphs-for-accurate-somatic-variant-discovery/
LOCATION:Engineering 2\, Engineering 2 1156 High Street\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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