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  • To Encourage or to Restrict: the Label Dependency in Multi-Label Learning

    Yang, Zhuo (2022-06) [Dissertation]
    Advisor: Zhang, Xiangliang
    Committee members: Wang, Di; Moshkov, Mikhail; Feng, Zhuo
    Multi-label learning addresses the problem that one instance can be associated with multiple labels simultaneously. Understanding and exploiting the Label Dependency (LD) is well accepted as the key to build high-performance multi-label classifiers, i.e., classifiers having abilities including but not limited to generalizing well on clean data and being robust under evasion attack. From the perspective of generalization on clean data, previous works have proved the advantage of exploiting LD in multi-label classification. To further verify the positive role of LD in multi-label classification and address previous limitations, we originally propose an approach named Prototypical Networks for Multi- Label Learning (PNML). Specially, PNML addresses multi-label classification from the angle of estimating the positive and negative class distribution of each label in a shared nonlinear embedding space. PNML achieves the State-Of-The-Art (SOTA) classification performance on clean data. From the perspective of robustness under evasion attack, as a pioneer, we firstly define the attackability of an multi-label classifier as the expected maximum number of flipped decision outputs by injecting budgeted perturbations to the feature distribution of data. Denote the attackability of a multi-label classifier as C∗, and the empirical evaluation of C∗ is an NP-hard problem. We thus develop a method named Greedy Attack Space Exploration (GASE) to estimate C∗ efficiently. More interestingly, we derive an information-theoretic upper bound for the adversarial risk faced by multi-label classifiers. The bound unveils the key factors determining the attackability of multi-label classifiers and points out the negative role of LD in multi-label classifiers’ adversarial robustness, i.e. LD helps the transfer of attack across labels, which makes multi-label classifiers more attackable. One step forward, inspired by the derived bound, we propose a Soft Attackability Estimator (SAE) and further develop Adversarial Robust Multi-label learning with regularized SAE (ARM-SAE) to improve the adversarial robustness of multi-label classifiers. This work gives a more comprehensive understanding of LD in multi-label learning. The exploiting of LD should be encouraged since its positive role in models’ generalization on clean data, but be restricted because of its negative role in models’ adversarial robustness.
  • A comparison of solvents for their suitability as solvent-culture two phase systems for living extraction of microbial isoprenoids using the green microalga Chlamydomonas reinhardtii as a model organism

    AlKaff, Salma (2022-05-14) [Thesis]
    Advisor: Lauersen, Kyle J.
    Committee members: Saikaly, Pascal; Szekely, Gyorgy
    Biotechnology and metabolic engineering of microbes has become a mature technology in many host microorganisms. A key method for the capture and quantification of heterologous and natural microbially produced isoprenoid products is to incubate growing cultures with a bio-compatible solvent. This is a culture-solvent two phase system that allows the continuous extraction, or ‘milking’, of hydrophobic products produced from microbial hosts. Solvent milking systems are highly valuable because they allow capture and subsequent analytics to be performed in a relatively straightforward manner. However, the currently used solvents are petroleum-derived, or can be challenging to work with at scale. Therefore, this thesis sought to investigate the biocompatibility of alternative solvents, including some examples of “green solvents” derived from biomass sources, using a model microalga as a study organism that had been previously engineered to produce the heterologous sesquiterpenoid patchoulol. In total 22 solvents were investigated, their 50% lethal concentration (LC50) determined, and their abilities to accumulate patchoulol from the algal culture compared. Solvents that were not-immediately lethal to algal cells and accumulated patchoulol, were also tested for their capacities for further isolation of patchoulol out of the solvent, either in ethanol, methanol, or through solid phase extraction. This work provides a broad foundation of information which is important for future efforts at microbial product milking and solvent choices for bio-process designs, especially with engineered microalgae.
  • High-rate microbial electrosynthesis using a zero-gap flow cell and vapor-fed anode design

    Baek, Gahyun; Rossi, Ruggero; Saikaly, Pascal; Logan, Bruce (Water Research, Elsevier BV, 2022-05-13) [Article]
    Microbial electrosynthesis (MES) cells use renewable energy to convert carbon dioxide into valuable chemical products such as methane and acetate, but chemical production rates are low and pH changes can adversely impact biocathodes. To overcome these limitations, an MES reactor was designed with a zero-gap electrode configuration with a cation exchange membrane (CEM) to achieve a low internal resistance, and a vapor-fed electrode to minimize pH changes. Liquid catholyte was pumped through a carbon felt cathode inoculated with anaerobic digester sludge, with humidified N2 gas flowing over the abiotic anode (Ti or C with a Pt catalyst) to drive water splitting. The ohmic resistance was 2.4 ± 0.5 mΩ m2, substantially lower than previous bioelectrochemical systems (20–25 mΩ•m2), and the catholyte pH remained near-neutral (6.6–7.2). The MES produced a high methane production rate of 2.9 ± 1.2 L/L-d (748 mmol/m2-d, 17.4 A/m2; Ti/Pt anode) at a relatively low applied voltage of 3.1 V. In addition, acetate was produced at a rate of 940 ± 250 mmol/m2-d with 180 ± 30 mmol/m2-d for propionate. The biocathode microbial community was dominated by the methanogens of the genus Methanobrevibacter, and the acetogen of the genus Clostridium sensu stricto 1. These results demonstrate the utility of this zero-gap cell and vapor-fed anode design for increasing rates of methane and chemical productions in MES.
  • Nutritional control regulates symbiont proliferation and life history in coral-dinoflagellate symbiosis

    Cui, Guoxin; Liew, Yi Jin; Konciute, Migle K.; Zhan, Ye; Hung, Shiou-Han; Thistle, Jana; Gastoldi, Lucia; Schmidt-Roach, Sebastian; Dekker, Job; Aranda, Manuel (BMC Biology, Springer Science and Business Media LLC, 2022-05-13) [Article]
    Background The coral-Symbiodiniaceae symbiosis is fundamental for the coral reef ecosystem. Corals provide various inorganic nutrients to their algal symbionts in exchange for the photosynthates to meet their metabolic demands. When becoming symbionts, Symbiodiniaceae cells show a reduced proliferation rate and a different life history. While it is generally believed that the animal hosts play critical roles in regulating these processes, far less is known about the molecular underpinnings that allow the corals to induce the changes in their symbionts. Results We tested symbiont cell proliferation and life stage changes in vitro in response to different nutrient-limiting conditions to determine the key nutrients and to compare the respective symbiont transcriptomic profiles to cells in hospite. We then examined the effects of nutrient repletion on symbiont proliferation in coral hosts and quantified life stage transitions in vitro using time-lapse confocal imaging. Here, we show that symbionts in hospite share gene expression and pathway activation profiles with free-living cells under nitrogen-limited conditions, strongly suggesting that symbiont proliferation in symbiosis is limited by nitrogen availability. Conclusions We demonstrate that nitrogen limitation not only suppresses cell proliferation but also life stage transition to maintain symbionts in the immobile coccoid stage. Nutrient repletion experiments in corals further confirmed that nitrogen availability is the major factor limiting symbiont density in hospite. Our study emphasizes the importance of nitrogen in coral-algae interactions and, more importantly, sheds light on the crucial role of nitrogen in symbiont life history regulation.
  • Combinatorial Engineering Enables Photoautotrophic Growth in High Cell Density Phosphite-Buffered Media to Support Engineered Chlamydomonas reinhardtii Bio-Production Concepts

    Abdallah, Malak N.; Wellman, Gordon B.; Overmans, Sebastian; Lauersen, Kyle J. (Frontiers in Microbiology, Frontiers Media SA, 2022-05-13) [Article]
    Chlamydomonas reinhardtii has emerged as a powerful green cell factory for metabolic engineering of sustainable products created from the photosynthetic lifestyle of this microalga. Advances in nuclear genome modification and transgene expression are allowing robust engineering strategies to be demonstrated in this host. However, commonly used lab strains are not equipped with features to enable their broader implementation in non-sterile conditions and high-cell density concepts. Here, we used combinatorial chloroplast and nuclear genome engineering to augment the metabolism of the C. reinhardtii strain UVM4 with publicly available genetic tools to enable the use of inorganic phosphite and nitrate as sole sources of phosphorous and nitrogen, respectively. We present recipes to create phosphite-buffered media solutions that enable high cell density algal cultivation. We then combined previously reported engineering strategies to produce the heterologous sesquiterpenoid patchoulol to high titers from our engineered green cell factories and show these products are possible to produce in non-sterile conditions. Our work presents a straightforward means to generate C. reinhardtii strains for broader application in bio-processes for the sustainable generation of products from green microalgae.

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