skip to main content


Search for: All records

Creators/Authors contains: "Kim, S"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. We introduce randomized algorithms to Clifford's Geometric Algebra, generalizing randomized linear algebra to hypercomplex vector spaces. This novel approach has many implications in machine learning, including training neural networks to global optimality via convex optimization. Additionally, we consider fine-tuning large language model (LLM) embeddings as a key application area, exploring the intersection of geometric algebra and modern AI techniques. In particular, we conduct a comparative analysis of the robustness of transfer learning via embeddings, such as OpenAI GPT models and BERT, using traditional methods versus our novel approach based on convex optimization. We test our convex optimization transfer learning method across a variety of case studies, employing different embeddings (GPT-4 and BERT embeddings) and different text classification datasets (IMDb, Amazon Polarity Dataset, and GLUE) with a range of hyperparameter settings. Our results demonstrate that convex optimization and geometric algebra not only enhances the performance of LLMs but also offers a more stable and reliable method of transfer learning via embeddings. 
    more » « less
    Free, publicly-accessible full text available June 4, 2025
  2. Free, publicly-accessible full text available March 25, 2025
  3. USB Power Delivery (USBPD) is a state-of-the-art charging protocol for advanced power supply. Thanks to its high volume of power supply, it has been widely adopted by consumer devices, such as smartphones and laptops, and has become the de facto USB charging standard in both EU and North America. Due to the low-level nature of charging and the complexity of the protocol, USBPD is often implemented as proprietary firmware running on a dedicated microcontroller unit (MCU) with a USBPD physical layer. Bugs within these implementations can not only lead to safety issues, e.g., over-charging, but also cause security issues, such as allowing attackers to reflash USBPD firmware. This paper proposes FUZZPD, the first black-box fuzzing technique with dual-role state guidance targeting off-the-shelf USBPD devices with closed-source USBPD firmware. FUZZPD only requires a physical USB Type-C connection to operate in a plug-n-fuzz fashion. To facilitate the black-box fuzzing of USBPD firmware, FUZZPD manually creates a dual-role state machine from the USBPD specification, which enables both state coverage and transitions from fuzzing inputs. FUZZPD further provides a multi-level mutation strategy, allowing for fine-grained state-aware fuzzing with intra- and inter-state mutations. We implement FUZZPD using a Chromebook as the fuzzing host and evaluate it against 12 USBPD mobile devices from 7 different vendors, 7 USB hubs from 7 different vendors, and 5 chargers from 5 different vendors. FUZZPD has found 15 unique bugs, 9 of which have been confirmed by the corresponding vendors. We additionally conduct a comparison between FUZZPD and multiple state-of-the-art black-box fuzzing techniques, demonstrating that FUZZPD achieves code coverage that is 40% to 3x higher than other solutions. We then compare FUZZPD with the USBPD compliance test suite from USBIF and show that FUZZPD can find 7 more bugs with 2x higher code coverage. FUZZPD is the first step towards secure and trustworthy USB charging. 
    more » « less
  4. Studying unexpected, ephemeral, or transient events in ocean ecosystems, such as gelatinous zooplankton blooms, is important because it provides us with valuable data on how our oceans may be changing in response to climate change and other anthropogenic activities. However, planning for such events is nearly impossible and making use of opportunistically acquired data allows the marine science community to be adaptive and efficient given the logistical and financial constraints of time at sea and in the field. Because such sampling events are often responsive rather than planned, they are typically not accompanied by outreach and education efforts. This commentary considers if opportunistically acquired data sets can be applied to generate opportunistic outreach and education activities. A case study is provided with successes and caveats outlined.

     
    more » « less
  5. The bacterial strain JCVI-syn3.0 stands as the first example of a living organism with a minimized synthetic genome, derived from the Mycoplasma mycoides genome and chemically synthesized in vitro. Here, we report the experimental evolution of a syn3.0- derived strain. Ten independent replicates were evolved for several hundred generations, leading to growth rate improvements of > 15%. Endpoint strains possessed an average of 8 mutations composed of indels and SNPs, with a pronounced C/G- > A/T transversion bias. Multiple genes were repeated mutational targets across the independent lineages, including phase variable lipoprotein activation, 5 distinct; nonsynonymous substitutions in the same membrane transporter protein, and inactivation of an uncharacterized gene. Transcriptomic analysis revealed an overall tradeoff reflected in upregulated ribosomal proteins and downregulated DNA and RNA related proteins during adaptation. This work establishes the suitability of synthetic, minimal strains for laboratory evolution, providing a means to optimize strain growth characteristics and elucidate gene functionality. 
    more » « less
  6. Abstract

    The origin, evolution, and cycling of volatiles on the Moon are established by processes such as the giant moon forming impact, degassing of the lunar magma ocean, degassing during surface eruptions, and lunar surface gardening events. These processes typically induce mass‐dependent stable isotope fractionations. Mass‐independent fractionation of stable isotopes has yet to be demonstrated during events that release large volumes of gas on the moon and establish transient lunar atmospheres. We present quadruple sulfur isotope compositions of orange and black glass beads from drive tube 74002/1. The sulfur isotope and concentration data collected on the orange and black glasses confirm a role for magmatic sulfur loss during eruption. The Δ33S value of the orange glasses is homogenous (Δ33S = −0.029‰ ± 0.004‰, 2SE) and different from the isotopic composition of lunar basalts (Δ33S = 0.002‰ ± 0.004‰, 2SE). We link the negative Δ33S composition of the orange glasses to an anomalous sulfur source in the lunar mantle. The nature of this anomalous sulfur source remains unknown and is either linked to (a) an impactor that delivered anomalous sulfur after late accretion, (b) sulfur that was photochemically processed early during lunar evolution and was transported to the lunar mantle, or (c) a primitive sulfur component that survived mantle mixing. The examined black glass preserves a mass‐dependent Δ33S composition (−0.008‰ ± 0.006‰, 2SE). The orange and black glasses are considered genetically related, but the discrepancy in Δ33S composition among the two samples calls their relationship into question.

     
    more » « less
  7. Salpa thompsoniis an ephemerally abundant pelagic tunicate in the waters of the Southern Ocean that makes significant contributions to carbon flux and nutrient recycling in the region. WhileS. thompsoni, hereafter referred to as “salps”, was historically described as a polar-temperate species with a latitudinal range of 40 – 60°S, observations of salps in coastal waters of the Western Antarctic Peninsula have become more common in the last 50 years. There is a need to better understand the variability in salp densities and vertical distribution patterns in Antarctic waters to improve predictions of their contribution to the global carbon cycle. We used acoustic data obtained from an echosounder mounted to an autonomous underwater Slocum glider to investigate the anomalously high densities of salps observed in Palmer Deep Canyon, at the Western Antarctic Peninsula, in the austral summer of 2020. Acoustic measurements of salps were made synchronously with temperature and salinity recordings (all made on the glider downcasts), and asynchronously with chlorophyll-ameasurements (made on the glider upcasts and matched to salp measurements by profile) across the depth of the water column near Palmer Deep Canyon for 60 days. Using this approach, we collected high-resolution data on the vertical and temporal distributions of salps, their association with key water masses, their diel vertical migration patterns, and their correlation with chlorophyll-a. While salps were recorded throughout the water column, they were most prevalent in Antarctic Surface Water. A peak in vertical distribution was detected from 0 – 50 m regardless of time of day or point in the summer season. We found salps did not undergo diel vertical migration in the early season, but following the breakdown of the remnant Winter Water layer in late January, marginal diel vertical migration was initiated and sustained through to the end of our study. There was a significant, positive correlation between salp densities and chlorophyll-a. To our knowledge, this is the first high resolution assessment of salp spatial (on the vertical) and temporal distributions in the Southern Ocean as well as the first to use glider-borne acoustics to assess salpsin situ.

     
    more » « less
  8. The overwinter survival mechanisms of Antarctic krill, Euphausia superba , are poorly characterized, especially for juveniles. It has been suggested that juveniles adopt a mix of strategies characteristic of both larvae and adults. Like larvae, they may feed opportunistically throughout winter when food is available, and like adults they may be able to suppress their metabolism when food is scarce. In this study we look at the overwinter strategies of juvenile krill and how their reproductive development changes when energy input exceeds what is necessary for survival. We take a closer look at how the sexual maturation of juvenile krill progresses in response to different environmental conditions throughout the fall and winter. We exposed juvenile Antarctic krill to four different “food environment scenarios”, supplementing them with various diets from May to September 2019 that were representative of environmental conditions that they may encounter in different regions of the Western Antarctic Peninsula during autumn and winter. Each month, we measured the physiology and condition of the krill, and assessed the reproductive development of females. We found that when female juvenile krill have greater energy reserves than what is needed to survive the winter, they will begin to sexually mature. Further, when there are sufficient levels of the fatty acids eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and 16:4 ( n-1 ), krill are likely to be in a more reproductive advanced stage. However, when lipids, EPA, DHA and 16:4 ( n-1 ) are depleted throughout the winter, juvenile female krill lose their ability to develop reproductively. We also found that sexual development is an energy intensive process that requires high respiration rates in juvenile krill. Furthermore, when juvenile females expend energy maturing, their physiological condition declines. This trade-off between early reproductive development and condition in juvenile female krill has important implications for individual health and population fecundity. Gaining a better understanding of the mechanisms behind juvenile krill winter survival strategies and their consequences will allow us to predict how future change at the western Antarctic Peninsula may affect krill population dynamics, especially in light of a warming climate. 
    more » « less
  9. In recent years, substantial efforts have been made to understand the implications of climate change on Antarctic krill, Euphausia superba , because of their pivotal role in the Southern Ocean food web and in biogeochemical cycling. Winter is one of the least studied seasons in Antarctica and we have limited understanding about the strategies Antarctic krill use to survive the winter. In particular, data on the winter physiology and condition of juvenile Antarctic krill are severely lacking. From May to September (the austral autumn-winter) of 2019, we maintained juvenile Antarctic krill in large (1,330 L) aquarium tanks at Palmer Station, Antarctica and, at monthly time intervals, measured their physiology and condition. Each tank served as a “food environment scenario”, representing possible food environments the krill may encounter during winter along the Western Antarctic Peninsula. We found that, unlike adults, juvenile krill maintain relatively high respiration rates through the winter and respond positively to increased food concentrations by increasing their ingestion rates. Unlike larval krill, juveniles use lipid stores accumulated during the summer and autumn to sustain themselves through periods of starvation in the winter. We used our empirically derived measurements of physiology and condition to estimate the energy budget and growth potential of juvenile krill during the winter. We found that, given their comparatively high respiration rates, small juvenile krill (20 mg dry weight) would need to encounter food at concentrations of ~ 0.15 mg C L -1 daily to avoid loss of body carbon. Without sufficient lipid reserves, this value increases to ~ 0.54 mg C L -1 , daily. The health of juvenile krill in the wintertime is dependent on their ability to accumulate lipid stores in the summer and autumn and to find sufficient food during the winter. Changes in food availability to Antarctic krill throughout the year may become problematic to juvenile krill in the future. Understanding the variability in the winter energy budget of juvenile Antarctic krill will allow us to improve population models that make assumptions on seasonal growth patterns. 
    more » « less