VictorJuiz/thesis huggingface dataset:
Extracting and Using Preference Information from the State of the World

Typically when learning about what people want and don't want, we look to human action as evidence: what reward they specify, how they perform a task, or what preferences they express can all provide useful information about what an agent should do. This is essential in order to build AI systems that do what we intend them to do. However, existing methods require a lot of expensive human feedback in order to learn even simple tasks. This dissertation argues that there is an additional source of information that is rather helpful: the state of the world./nThe key insight of this dissertation is that when a robot is deployed in an environment that humans have been acting in, the state of the environment is already optimized for what humans want, and is thus informative about human preferences./nWe formalize this setting by assuming that a human H has been acting in an environment for some time, and a robot R observes the final state produced. From this final state, R must infer as much as possible about H's reward function. We analyze this problem formulation theoretically and show that it is particularly well suited to inferring aspects of the state that should not be changed -- exactly the aspects of the reward that H is likely to forget to specify. We develop an algorithm using dynamic programming for tabular environments, analogously to value iteration, and demonstrate its behavior on several simple environments. To scale to high-dimensional environments, we use function approximators judiciously to allow the various parts of our algorithm to be trained without needing to enumerate all possible states./nOf course, there is no point in learning about H's reward function unless we use it to guide R's decision-making. While we could have R simply optimize the inferred reward, this suffers from a "status quo bias": the inferred reward is likely to strongly prefer the observed state, since by assumption it is already optimized for H's preferences. To get R to make changes to the environment, we will usually need to integrate the inferred reward with other sources of preference information. In order to support such reward combination, we use a model in which R must maximize an unknown reward function known only to H. Learning from the state of the world arises as an instrumentally useful behavior in such a setting, and can serve to form a prior belief over the reward function that can then be updated after further interaction with H.

Advisor: Dragan, Anca
Russell, Stuart
Understanding and Designing Crystallographically Oriented Nanocrystal Assembly and Atomic Attachment

Colloidal semiconductor nanocrystals, often called quantum dots are small chunks of a bulk semiconducting material. Due to the small size of these materials, quantum mechanical effects modify their properties giving them atomic-like electronic energy levels. If these nanocrystals are brought close enough for the atomic-like states to couple, an artificial molecule or artificial solid may result from the coupling. Thus the assembly would display emergent properties distinct from the isolated nanocrystals. This may allow for the preparation of materials which have properties not displayed in natural materials./nOne difficulty is that in order for the coupling to be strong enough to see delocalized states, the nanocrystals must be atomically fused with an inorganic bridge. This attachment is irreversible and thus if the attachment is imperfect, it can trap atomic scale defects such as dislocations at the interface. These atomic scale defects will also interact with carriers potentially preventing the emergence of delocalized states. Currently there isn't a framework for understanding defects in imperfectly attached nanocrystals. As such it is difficult to rationally improve quality in these materials or identify new routes high quality attachment of semiconductor nanocrystals. To this end we aim to better understand the attachment of nanocrystals with a focus on the defects which may form and how to remove those defects./nIn this thesis, Chapter 1 outlines the important concepts related to the electronic properties of solids, confined semiconductor physics, nanocrystal synthesis and crystal defects needed to understand the work in this thesis. In Chapter 2, we study the oriented attachment of PbTe using in-situ transmission electron microscopy (TEM) to identify optimal attachment facets to minimize defect formation. In Chapter 3, we develop methods to attach CdSe nanocrystals on their prismatic facets, study the defect which form, and understand their removal mechanisms using in-situ TEM. The insights from these two studies are used in Chapter 4 to design a clean sheet approach to assemble and atomically attach CdSe/CdS nanocrystals into superlattices with long range translational and orientational order. Finally in Chapter 5, we discuss the outlook for preparing attached nanocrystal superlattices for realizing artificial band structures.

Advisor: Alivisatos, Paul
The Liliid and the Oddity: Macroevolution and development of underground storage organs in the order Liliales

Traditional botany focuses on the morphology, anatomy, and evolution of above-ground plant parts, but remarkable variation also exists underground. Underground storage organs (USOs), one example of understudied underground botany, include corms, bulbs, rhizomes, and stem- and root-derived tubers. These odd organs characterize geophytes, plants that produce perennating buds below ground and often store nutrients such as starch and water in USOs. Diverse underground morphology is particularly evident in the monocotyledenous order Liliales./nIn this dissertation, I examine the evolution and development of USOs across the order Liliales, or the ’liliids’. In Chapter 1, I take a macroevolutionary perspective to ask if plants with different USOs are evolving towards different climatic niche adaptive peaks across the order. I find that the presence of root tubers, especially rotund root tubers, is associated with lower temperature seasonality. Furthermore, I develop and describe a new analysis pipeline in statistical comparative phylogenetics for testing adaptive hypotheses. In Chapter 2, I zoom in on a particular liliid geophyte, Bomarea multiflora, to identify genes underlying root tuber formation by comparing the transcriptomes of root tubers vs. fibrous roots. I compare the genes identified in this study with patterns from USOs produced by other taxa to characterize to what extent processes are shared across non-homologous USOs and across deep evolutionary divergences. I find that many processes are shared despite these differences, indicating that parallel molecular mechanisms may underlie USO development. In Chapter 3, I describe a new R package, RevGadgets, that can process and visualize the output of complex phylogenetic analyses from the RevBayes phylogenetic graphical modelling software. RevGadgets is designed to provide user-friendly modular workflows and thus increase accessibility to more complex phylogenetic models. I illustrate core RevGadgets functionality through six use cases and provide examples of code and resulting figures./nTogether, these projects bring light to the outstanding diversity of below ground forms and begin the work of characterizing the evolution and development of this diversity. This work also illustrates the utility of establishing reproducible and user-friendly pipelines to increase the accessibility and versatility of complex statistical methods in comparative biology.

Advisor: Rothfels, Carl J.
An Integrated Approach to Three-Dimensional Bioprinting at Subfreezing Temperatures

There are over 100,000 patients on the US transplant list alone, and millions more needing transplants globally. Many of these transplant patients have little hope of getting a replacement organ in time to ensure survival. On-demand fabrication of organs and tissues using tissue engineering could provide a solution and save the lives of millions of transplant patients and patients with end-stage organ failure. A major component of fabricating these artificial tissues and organs is the construction of a scaffold, often with the cells incorporated, that simulates the appropriate tissue environment and guides the formation of complex tissue structures. Three-dimensional (3D) bioprinting has emerged as the most promising approach for developing these scaffold constructs, but despite significant advances, the technique faces various challenges. Some factors that have thus far limited the production of clinically relevant constructs include, insufficient mechanical properties for fabrication of full-scale organs, unsustainably long print times, and poor survival of the biological matter during and after printing due to lack of vascularization. Current techniques and emerging methods still fall short of addressing some of these limitations, so in order for continued advancement in this field, alternative approaches are needed./nThis work explores in detail a novel technique of doing 3D bioprinting at subfreezing temperatures, called 3D cryoprinting. 3D cryoprinting incorporates the benefits of ice formation at subfreezing temperatures and the flexibility afforded by super soft biomaterials to improve the fabrication of soft tissue scaffolds. This method utilizes controlled freezing to improve mechanical properties of the printed matrix while simultaneously cryopreserving the biological matter. In order to establish 3D cryoprinting as a viable alternative for 3D bioprinting, the challenges and unknown parameters associated with 3D cryoprinting such as the solidification in large objects, cell viability, structural stability during melting, and mass manufacturability are tackled. Several methods and models to control and understand freezing during cryoprinting are developed, including a thermal phase change model for controlling the freezing rate of biological matter during cryoprinting, which substantially improves the process outcome. A method that enables the preservation of the geometric shape after thawing, a crucial element to the viability of 3D cryoprinting, is also developed. And to speed up manufacture and enable mass manufacturing a modified process of cryoprinting is developed, called parallel multilayer cryolithography. The culmination of this work demonstrates that 3D cryoprinting could be a viable alternative for the fabrication of complex 3D tissue and organ scaffolds, especially in cases of super soft tissue scaffolds where other bioprinting methods have proven inadequate.

Advisor: Rubinsky, Boris
Structured Neural Models and Structured Decoding for Natural Language Processing

Neural sequence models have been applied with great success to a variety of tasks in natural language processing in recent years. However, because they generate their outputs one token at a time from left to right, they are not immediately suitable for domains where non-trivial output constraints must be satisfied for well-formedness, or where parallel decoding may be desirable for higher throughput. In this dissertation, we explore how we can overcome these limitations through the use of more highly structured models and more flexibly structured decoding algorithms./nOn the modeling side, we first introduce a span-based neural model for constituency parsing that permits efficient, globally optimal decoding over the space of parse trees using a chart-based dynamic program. We then present the Abstract Syntax Network, a tree-structured neural model for code generation whose scoring modules are composed together in a way that mirrors the syntactic structure of the program being produced. Next, turning to more flexible decoding algorithms for sequences, we demonstrate how the Transformer sequence model can be extended to accommodate blockwise parallel decoding for significant improvements in decoding speed without compromising accuracy. Finally, we present the Insertion Transformer, an insertion-based sequence model that enables out-of-order generation and logarithmic-time parallel decoding.

Advisor: Klein, Dan
Jordan, Michael
Molecular and shell biology – examining the biochemistry and physiology of prokaryotic nanocompartments

For many decades, it was thought that the phenomenon of cellular compartmentalization was exclusive to eukaryotes. Advances in cell imaging techniques have revealed that the presence of subcellular compartments is widespread throughout prokaryotes and that there exists a great diversity of organelles in bacteria and archaea. Recently, a new class of prokaryotic organelle has been discovered – the protein-bounded prokaryotic nanocompartments, also called encapsulins. Encapsulins are among the simplest of the prokaryotic organelles, often comprised of a two gene system; a shell-encoding gene and a cargo-encoding gene. Despite their simplicity, little is known about the biochemistry and physiological function of the encapsulins./nHere we investigate the structure and function of the encapsulin nanocompartments from various prokaryotes. First, we demonstrate that the existence of prokaryotic nanocompartments extends beyond the sequence homologs of the previously characterized encapsulins and that there exist additional, evolutionarily distinct families of encapsulins with unique cargo systems. We have characterized one of these new encapsulin families, which we name Family 2A, from the cyanobacteria Synechococcus elongatus PCC 7942. This encapsulin system hosts a cysteine desulfurase cargo enzyme that is directed to the interior of the nanocompartment via an N-terminal targeting sequence. We have determined the structure of the Family 2A encapsulin using cryo- electron microscopy to 2.2 Å resolution. This structure has yielded insights into the cargo- binding site within the organelle and the potential size and charge selectivity of the compartment. Additionally, we have characterized the cysteine desulfurase activity of the Family 2A encapsulin and show an increase in cargo enzyme activity upon encapsulation./nFinally, we examine the biochemistry and physiological role of a previously discovered encapsulin from Mycobacterium tuberculosis (Mtb). We demonstrate that the Mtb encapsulin is stable and active under the harsh conditions of the phagolysosome – the ecological niche we implicate the Mtb encapsulin is localized. Furthermore, we show Mtb encapsulin plays a functional role in Mtb’s resistance to oxidative stress./nTaken together, our work provides critical insight as to how the structure of the prokaryotic nanocompartments informs their function in vivo and show that this emerging class of protein-bounded organelle represents a new paradigm within the field of prokaryotic cell biology.

Advisor: Savage, David F
Replica Symmetry Breaking in the Random Regular k-NAE-SAT Problem

For several models of random constraint satisfaction problems, it was conjectured by physicists and later proved that a sharp satisfiability transition occurs. For random k-sat and related models it happens at constraint (clause) density α = αsat ≍ 2^k, where α is the number of constraints per variable. Just below the threshold, further results suggest that the solution space has a ”one- step replica symmetry breaking” (1rsb) structure of a large bounded number of near-orthogonal clusters inside {0, 1}^N ./nIn the unsatisfiable regime α > αsat, it is natural to consider the problem of max-satisfiability: violating the least number of constraints. This is a combinatorial optimization problem on the random energy landscape defined by the problem instance. For a simplified variant, the strong refutation problem, there is strong evidence that an algorithmic transition occurs around α = N^{k/2−1}. For α bounded in N, a very precise estimate of the max-sat value was obtained by Achlioptas, Naor, and Peres (2007), but it is not sharp enough to indicate the nature of the energy landscape. Later work (Sen, 2016; Panchenko, 2016) shows that for α very large (roughly, Ω(64k)) the max-sat value approaches the mean-field (complete graph) limit: this is conjectured to have a ”full replica symmetry breaking” (frsb) structure where near-optimal configurations form clusters within clusters, in an ultrametric hierarchy of infinite depth inside {0, 1}^N . A stronger form of frsb was shown in several recent works to have algorithmic implications (again, in complete graphs). Consequently we find it of interest to understand how the model transitions from 1rsb near αsat, to (conjecturally) frsb for large α. In this work we show that in the random regular k-nae-sat model, the 1rsb description breaks down already above α ≍ 4^k/k^3. This is proved by an explicit perturbation in the 2rsb parameter space. The choice of perturbation is inspired by the “bug proliferation” mechanism proposed by physicists (Montanari and Ricci-Tersenghi, 2003; Krzakala, Pagnani, and Weigt, 2004), corresponding roughly to a percolation-like threshold for a subgraph of dependent variables.

Advisor: Ganguly, Shirshendu
Hidden in Plain Sight: Cinematic Legacies of the Western, Greaser Cinema, and Chicanx Literature

When D.W. Griffith began filming The Greaser's Gauntlet in 1908, no one could have predicted that he would create an enduring character. This dissertation explores the history of the greaser character and its influence in American and Chicanx Literature. Beginning with The Greaser's Gauntlet, this study traces the greaser character and illuminates the history of greaser cinema in several films, including: Broncho Billy and the Greaser (1914) and Licking the Greaser's (1914/1918). The dissertation then argues that the images produced in these films are essential to establishing racialized representations of Mexican and Latinx characters in the U.S. film industry and in the social sphere. Next, the dissertation investigates artistic responses to the greaser character. In particular, the dissertation examines four novels—Nathanael West's Day of the Locust (1939), José Antonio Villareal's Pocho (1959), Oscar Zeta Acosta's Autobiography of a Brown Buffalo (1972), and The Revolt of the Cockroach People (1973)—to show how creative writers have reimagined and critiqued the character in their fictions.

Advisor: Padilla, Genaro
Treatments of a Surface Ion Trap: A Study of Electric-Field Noise near a Contaminated Metal Surface

All surfaces generate electric-field noise, yet the physical origins of this noise are not well understood. This has been an active area of research in the ion trapping community for the past two decades, as ions are highly sensitive to electric-field fluctuations. With our work, we aim to illuminate the microscopic processes that drive charge dynamics on metal surfaces, so as to enable the engineering of low noise quantum devices./nWe use single trapped calcium ions as detectors to study the 1/f noise generated by the surfaces of ion traps. We the study this noise by observing how it responds to changes in the properties of the trap surface. The surface properties are altered using treatments including prolonged heating, argon ion milling, and electron bombardment. In situ characterization tools are used to monitor the effects of these treatments. Our measurements are consistent with noise produced by an ensemble of thermally activated fluctuators, so our data is discussed in this context./nIn this dissertation, we present results from a lengthy series of surface treatment experiments, the majority of which took place on a single aluminum-copper substrate. The results of these experiments indicate that argon ion milling can lower noise both by removing contaminants and by altering the morphology of the trap surface. The effects of morphology are isolated from the effects of contaminant removal via heat treatments, which alter the structure of the surface without changing its chemical composition. Through electron bombardment experiments, we begin an exploration of the relationship between hydrocarbon adsorbate structure and electric-field noise. In addition, we compare the noise characteristics of a set of similarly fabricated traps, and determine that atmosphere exposure has a major impact on noise produced by aluminum-copper films./nThese experiments establish links between the electric-field noise characteristics and the microscopic properties of a contaminated metal trap surface. The insights we draw in this work can inform the next generation of ion trap engineering, storage, and treatment.

Advisor: Haeffner, Hartmut
Sensing the Electrical Activity of Cells Through Molecular Wires by Photoinduced-Electron Transfer

Fluorescent voltage sensitive dyes (VSDs) provide an attractive, complementary method to traditional electrophysiology techniques and are important tools for studying rapid changes of membrane potential in excitable cells. The VoltageFluor family of VSDs reports this rapid activity with high sensitivity using photoinduced-electron transfer (PeT) as the voltage sensitive trigger. This mechanism provides sub-millisecond response kinetics and our laboratory has shown it can be tuned by exchanging the identity of the electron donor and fluorophore. However, the identity and architecture of the molecular wire remained unexplored. The work presented herein addresses this gap in knowledge, exploring different strategies for tuning PeT through modifications to the molecular wire. Chapter 1 represents an initial attempt, replacing the link between the molecular wire and the fluorophore with an amide. This insulates the fluorophore to slow PeT and results in less sensitive, but brighter, indicators. However, membrane staining was poor with these new indicators and in vitro measurements did not predict brightness in cells. Chapter 2 builds upon the insight of Chapter 1, exchanging the phenylene-vinylene molecular wire for a fluorene monomer. This fluorene-based wire provided indicators with bright membrane stains, maintained voltage sensitivity, and was shown to be less phototoxic. Low voltage sensitivity limited the utility of the indicators. Chapter 3 addresses this limitation by adding conjugation to the scaffold with a vinyl spacer to make indicators with up to a 3.5-fold improvement in sensitivity over fluorene-based indicators. Finally, Chapter 4 describes a collaborative effort to assess the effect of aniline conformation on the voltage sensing properties of VoltageFluor indicators. We found the sensitivity and fluorescence lifetime of these conformationally restricted aniline could be tuned over an order of magnitude. These results show the importance of electronic interaction of the aniline with the molecular wire for a PeT-based voltage sensor.

Advisor: Miller, Evan W