VictorJuiz/thesis huggingface dataset:
Efficient Policy Learning for Robust Robot Grasping

While humans can grasp and manipulate novel objects with ease, rapid and reliable robot grasping of a wide variety of objects is highly challenging due to sensor noise, partial observability, imprecise control, and hardware limitations./nAnalytic approaches to robot grasping use models from physics to predict grasp success but require precise knowledge of the robot and objects in the environment, making them well-suited for controlled industrial applications but difficult to scale to many objects./nOn the other hand, deep neural networks trained on large datasets of grasps labeled with empirical successes and failures can rapidly plan grasps across a diverse set of objects, but data collection is tedious, robot-specific, and prone to mislabeling./nTo improve the efficiency of learning deep grasping policies, we propose a hybrid method to automate dataset collection by generating millions of synthetic 3D point clouds, robot grasps, and success metrics using analytic models of contact, collision geometry, and image formation./nWe present the Dexterity-Network (Dex-Net), a framework for generating training datasets by analyzing mechanical models of contact forces and torques under stochastic perturbations across thousands of 3D object CAD models./nWe describe dataset generation models for training policies to lift and transport novel objects from a tabletop or cluttered bin using a 3D depth sensor and a parallel-jaw (two-finger) or suction cup gripper./nTo study the effects of learning from massive amounts of training data, we generate datasets containing millions of training examples using distributed Cloud computing, simulations, and parallel GPU processing./nWe use these datasets to train robust grasping policies based on Grasp Quality Convolutional Neural Networks (GQ-CNNs) that take as input a depth image and a candidate grasp with up to five degrees of freedom and predict the probability of grasp success on an object in the image./nTo transfer from simulation to reality, we develop novel analytic grasp success metrics based on resisting disturbing forces and torques under stochastic perturbations and bounding an object's mobility under an energy field such as gravity./nIn addition, we study techniques in algorithmic supervision to guide dataset collection using full knowledge of the object geometry and pose in simulation./nWe explore extensions to learning policies that sequentially pick novel objects from dense clutter in a bin and that can rapidly decide which gripper hardware is best in a particular scenario./nTo substantiate the method, we describe thousands of experimental trials on a physical robot which suggest that deep learning on synthetic Dex-Net datasets can be used to rapidly and reliably plan grasps across a diverse set of novel objects for a variety of depth sensors, robot grippers, and robot arms./nResults suggest that policies trained on Dex-Net datasets can achieve up to 95% success in picking novel objects from densely cluttered bins at a rate of over 310 mean picks per hour with no additional training or tuning on the physical system.

Advisor: Goldberg, Ken
The Post-American Novel: 9/11, the Iraq War, and the Crisis of American Hegemony

This dissertation proposes a new analytical category for thinking about a subset of post-9/11 Anglophone novels that are engaged with the political aftermath of 9/11. I designate this category the post-American novel, distinguishing it from the category of 9/11 fiction. While the 9/11 novel is a sub-genre of national literature, focusing on the terrorist attacks as a national trauma, the post-American novel is a transnational literary form that decenters 9/11, either by contextualizing the terrorist attacks in relation to other historical traumas or by shifting focus to the “War on Terror.” I theorize the post-American novel as the literary expression of international opposition to the 2003 U.S. invasion of Iraq. International opposition to the Iraq War exposed the fractures in American global hegemony, and so I define the post-American novel as the historically-engaged novel of the crisis of American hegemony. I develop this argument through a detailed analysis of the political aesthetics of some representative post-American novels by four international writers. In various ways, these novels all diagnose post-9/11 American society from an international perspective and subvert the myth of American exceptionalism, though their forms of cultural and political critique are more far-ranging than this. The category of the post-American novel is not meant to herald the end of American literature. And though I peg its emergence to the second Iraq War, the category is flexible enough to encompass a range of contemporary novels by international writers who explore the role of the United States in a changing world.

Advisor: Jones, Donna V.
Precision Analytics: Learning and Optimization in the Personalized Setting

The recent increase in data and computing resource availability has made the use of data analytics more practical in practice than ever before. In particular, the ubiquity of technologies such as smartphones, wearable devices, and smart sensors has allowed for the collection of a large amount of individual level data. In contrast to traditional data analytics, which relies on wide sampling from a population to draw conclusions (i.e. cross-sectional sampling), this so called deep sampled data can be used through precision analytics to create customized experiences that better serve individuals and organizations. In this thesis, we explore this precision analytics framework that builds upon the fields of reinforcement learning and data driven decision making by extending their results to applications with individual level deep sampled data. One of the main applications of this framework is to systems where a decision maker is interested in applying an intervention (or policy) to affect the behavior of an individual agent or group of agents. Two key challenges that arise when analyzing such systems are that the decision maker may have scarce resources or high risk decisions that constrain how they apply their intervention, and that the decision maker may only have partial knowledge of how an agent will react to the intervention. The main focus of this thesis is to begin to analyze these challenges by providing predictive models that can accurately capture individual agent behavior, new estimation and machine learning techniques to efficiently estimate model parameters, and effective online and batch optimization methods to calculate these interventions. We will also discuss how these approaches can be implemented in practice, particularly in the precision healthcare setting.

Advisor: Aswani, Anil
The KSHV protein ORF68 is a proteasome-manipulating protein required for DNA packaging

Herpesviruses are large, double-stranded DNA viruses that have evolved over millions of years to become master manipulators of cellular machinery. Herpesviral research has taught us a great deal not only about strategies of viral replication and pathogenesis, but also about how cellular pathways work in the absence of infection. The end goal of viral infection is the production of progeny virions, which involves the packaging viral genomes into nascent capsids. This process is mechanistically conserved across the three herpesvirus subfamilies, with at least seven viral proteins being required for successful packaging to occur. Of these proteins, six have well characterized functions during the packaging process, while the function of the seventh remains largely unknown. In Kaposi’s sarcoma-associated herpesvirus (KSHV), this protein is encoded by ORF68 and here we aimed to elucidate its role in DNA packaging./nWe first generated an ORF68 mutant of KSHV that contained a premature termination codon (ORF68PTC) and confirmed that ORF68 was not required for viral gene expression or DNA replication but was essential for infectious virion production. Additionally, the KSHV ORF68PTC virus did not cleave or package viral DNA and exclusively accumulated immature B-capsids. Further biochemical characterization of ORF68 revealed several novel activities for this protein that significantly expand our understanding of its function. Unexpectedly, we found that ORF68 robustly binds DNA and exhibits metal-dependent nuclease activity towards dsDNA in vitro. These observations suggest a role in binding and catalytically processing the viral genome during packaging./nAdditionally, protein-protein interaction profiling of ORF68 revealed an association with multiple subunits of the proteasome, the main protein degradation apparatus of the cell. This led us to hypothesize that KSHV might control protein abundance, in part, through the ORF68-proteasome interaction. In support of this hypothesis, we revealed that ORF68 contains a canonical gate-opening motif observed in proteasome-interacting proteins. Deletion or blocking of this motif in ORF68 inhibited the degradation of a model substrate in transfected cells, suggesting that ORF68 may assemble on proteasomes to control substrate access. Notably, deletion of this motif from ORF68 in the context of KSHV infection prevented progeny virion production, indicating that this function is central to its role in the viral replication cycle. Finally, we observed proteasomes concentrated within replication compartments together with ORF68. Collectively, these data lead to a model in which ORF68 interactions with the proteasome may control protein turnover to facilitate viral DNA packaging.

Advisor: Glaunsinger, Britt A
A Most Dangerous Science: Discipline and German Political Philosophy, 1600-1648

This dissertation tracks the development of German political philosophy over the course of the first half of the seventeenth century, with an emphasis on the disciplinary, methodological, and pedagogical concerns of Politica writers. These figures produced large-scale technical textbooks on politics, which attempted to make sense of the chaotic civil sphere through the application of disciplinary structures. The main influences on their thought came from the sixteenth century: Aristotelianism, reason of state, natural law, and neostoicism were the competing traditions that they attempted to fit into comprehensive treatments of their subject./nGenerally, these thinkers have been organized by historians into schools divided by their political and confessional commitments. I argue that, while these factors were important, their disciplinary and methodological choices also decisively shaped their vision of politics, and indeed their positions on the critical questions of their day. I do this by focusing on four specific writers, one from each of the four faculties of the early modern university: Bartholomäus Keckermann from the arts faculty, Henning Arnisaeus from Medicine, Christoph Besold from Law, and Adam Contzen from Theology. I show how each Politica author’s disciplinary background inflected their construction of politics as an academic discipline, and how this in turn shaped their opinions on the confessional and constitutional debates which were then fracturing the Holy Roman Empire./nWhile the dissertation does focus on the differences among these figures, it also tracks a trajectory which they all participated in. I argue that their attempts to discipline politics as a subject resulted in the centering of the state as a disciplinary and administrative institution. Their motivation was to prevent political upheaval through the application of technical expertise, which meant that they were able to find ever more aspects of human life which required treatment under the rubric of political philosophy, because almost anything could be conceived of as either a threat or a source of strength for the political order. This in turn suggested a vastly expanded conception of the regulatory and disciplinary powers of the state. I thus contend that, although the Politica writers are mostly forgotten today, they represent a critical phase in the intellectual development of the idea of the state.

Advisor: Sheehan, Jonathan
Extracellular matrix and the origin of animal multicellularity

The evolution of animals from their unicellular ancestors was a major transition in evolutionary history that enabled the diversity and complexity of extant animals. Due to the lack of a clear fossil record of the progenitors of animals, we know relatively little about the first animals and the developmental events that predicated their evolution. My doctoral research utilized Salpingoeca rosetta, a model choanoflagellate and one of the closest living relatives of animals, to investigate the molecular changes that might have led to the origin of multicellularity in animals./nS. rosetta facultatively forms multicellular “rosettes” through serial cell division in a process reminiscent of early animal embryogenesis. To determine the genetic underpinnings of rosette development in S. rosetta, I performed a forward genetic screen for rosette defect mutants (Chapter 2). I identified a new class of mutants that aggregate promiscuously into amorphous clumps of cells, but that do not develop into orderly rosettes. Two clumpy mutants, named Jumble and Couscous, mapped to lesions in genes encoding predicted glycosyltransferases./nThe mutations in the jumble and couscous genes were shown to disrupt glycosylation patterns at the basal pole of the extracellular matrix (ECM). The only previously identified gene required for rosette formation, rosetteless, was found to encode a protein that localizes at the basal pole of cells in the ECM-filled center of rosettes. Thus, all three genes known to be required for rosette development in S. rosetta play a role in establishing the ECM of rosettes and implicate the ECM in the regulation of multicellular development./nBeyond the specific genes required for cell adhesion and cell signaling, animal multicellular development relies on transcriptional regulation of specific genes for cell differentiation. To examine the role of transcriptional regulation, I generated an improved S. rosetta genome assembly that allows for better annotation of regulatory regions and analyzed chromatin accessibility using an assay for transposase-accessible chromatin (ATAC-seq) in distinct S. rosetta cell types, including unicellular slow swimmers and rosettes (Appendix). Slow swimmers and rosettes were found to have nearly identical chromatin accessibility profiles—consistent with previous transcriptome sequencing that showed remarkably similar expression profiles between slow swimmers and rosettes./nTaken together, S. rosetta may rely on translational and/or post-translational regulation, including modification of the ECM, to build multicellular rosettes. Continuation of the forward genetic screen for rosette defects to saturation and utilization of recently developed methods for reverse genetics will allow future scientists to more fully elucidate the genetic basis of rosette development in S. rosetta and its possible homology to animal development.

Advisor: King, Nicole
Modified scattering for small data solutions to the cubic Schrödinger equation on product space

In this paper we consider the long time behavior of solutions to the cubic nonlinear Schr\"{o}dinger equation posed on the spatial domain $\mathbb{R}\times\mathbb{T}^{d}$, $1\leq d\leq4$. We first prove the local well-posedness in $C(I;L_x^2H_y^s)\cap C(I;L_{x,y}^4)$ for solutions with initial data $u_0\in H^{0,1}_xL_y^2\cap L_x^2H_y^s$. Then, for sufficiently small, smooth, decaying data, we prove global existence and derive modified asymptotic dynamics by using the wave packet method and normal form corrections. The modified scattering behavior on $\mathbb{R}\times\mathbb{T}^d$ combines the modified scattering of the cubic NLS on real line $\mathbb{R}$ with cubic NLS dynamics on torus. We also consider the corresponding asymptotic completeness problem.

Advisor: Tataru, Daniel Ioan
Talking Story: A community-developed digital storytelling intervention to promote colorectal cancer screening intention among church-attending Latinos

Introduction: Although colorectal cancer screening (CRCS) rates have improved for all racial and ethnic groups due to wider availability of screening, Latinos continue to have lower screening rates compared to non-Latino whites. Additionally, Latinos are more likely to be diagnosed with later stages of colorectal cancer (CRC), which can lead to higher rates of morbidity and mortality. More culturally-sensitive interventions are needed to reach this population. The majority of existing CRCS interventions are based in primary health care settings, only targeting a fraction of the Latino population. This pilot study explores the feasibility of developing and introducing a digital storytelling (DST) intervention in a community church setting and its potential to influence CRCS intention among Latinos./nMethods: For the first part of the study, the research team collaborated with ten influential church members to create digital stories about their previous CRC and CRCS experience. They were then interviewed to understand how developing a digital story influences their future screening practices and the promotion of CRCS to others. For the second part of the study, 20 participants were recruited between the ages of 50 to 75 who were not up-to-date with CRCS per United States Preventive Services Task Force (USPSTF) recommendations. They completed surveys assessing their intention to complete CRCS before and after viewing digital stories developed by fellow church members. Participants were then asked to participate in focus groups to understand, qualitatively, how the digital stories influenced their intention to complete CRCS./nResults: The digital story developers were inspired by the digital storytelling process and interested in sharing their digital stories with others in an effort to improve screening beyond the church setting. For those who viewed the digital stories, men and women with previous screening experience were motivated to consider different screening methods for future screening. Furthermore, those who had never completed CRCS reported increased willingness to complete CRCS after viewing the intervention. The DST intervention has potential to influence participants’ intention to complete first-time screening as well as the type of screening for those with previous screening experience due to the personal nature of the stories and humanizing of the CRCS process./nDiscussion: The introduction of a community-based DST intervention within a church setting is a feasible and novel strategy with the potential to influence more Latinos to complete CRCS and save lives. Future studies should consider this approach to test a DST intervention in multiple settings, topics and diverse populations.

Advisor: Bloom, Joan
Negatively Stereotyping Historically Black Colleges and Universities as an Intergroup Process

Educating enslaved Africans was illegal in antebellum America. However, in the mid-1800s philanthropists and the U.S. Congress established higher education institutions for newly freed people. From then until present, inequitable economic policy and the lower status of Historically Black Colleges and Universities (HBCUs), vs. Historically White Institutions (HWIs), have reified a hierarchical ordering of Black and White schools — consistent with Social Dominance Theory (Sidanius & Pratto, 1999). In four studies (n=1059), endorsement of negative HBCU stereotypes via the HBCU Stereotype Scale (HBCU-SS) captured individuals' mental representations of this hierarchical ordering in ways that illuminate connections between racialized educational spaces and intergroup attitudes more broadly. Studies 1 & 2 demonstrate a unifactor structure across all four samples and establish construct validity for both Black and White participants. For all participants, the HBCU-SS was predicted by preference for group inequality — via the Social Dominance Orientation scale. For Blacks, the HBCU-SS was uniquely related to measures of racial identity. For White individuals the HBCU-SS was related to political attitudes, measures of generalized prejudice, as well as motivations to control prejudice. Study three shows that when White participants read about governmental in HBCUs (vs. HWIs), they were more likely to negatively stereotype HBCUs, suggesting hierarchy-maintaining motivations may drive these perceptions. Lastly, study four shows that when White participants are primed with threat to their majority status in society, they increase their stereotyping of HBCUs and increase their endorsement of inequitable resource allocations toward HBCUs.

Advisor: Mendoza-Denton, Rodolfo
Development of Chemical Probes for Studying K+ in biology

Potassium (K+) occupies 4% of human body mass and is the most abundant intracellular cation. Potassium plays a vital role in regulating intracellular fluid volume, fluid transportation, and neuron signaling. Abnormal K+ fluctuations may lead to diseases such as anorexia, bulimia, heart disease, diabetes, and epilepsy. Recent study also has shown elevated level of K+ channel mutation in cancer cells. However, the physiology of K+ is insufficiently understood, due to the absence of ways to measure the change of K+ in cellular fluids with high spatial and temporal fidelity. This dissertation chronicles the design and applications of novel imaging probes and strategies for probing K+ both intracellularly and extracellularly. This work describes the first ratiometric probe and a new fluorescent turn-on probe for imaging intracellular K+; both probes utilize novel lariat-ether modified crown ether structure as K+ binding ionophore. Additionally, this work describes development of a new imaging tool for detecting H2O2 utilizing bioluminescence resonance energy transfer.

Advisor: Chang, Christopher
The role of oligodendrocytes and myelin in differential susceptibility to stress-induced anxiety

Human reactions to stress can range from nonchalance to crippling changes to mood and emotionality. Understanding the neural underpinnings of this individual variation is of critical importance to public health; however, the basis for differential susceptibility to stress remains poorly understood. Recently, the oligodendrocyte (the myelin-producing cell of the central nervous system) has been increasingly implicated in stress, plasticity, and mood and anxiety disorders. Furthermore, previous work from our lab has found that stress increases the production of oligodendrocytes in the hippocampus of rats. Whether changes to these glial cells are merely a secondary consequence of neural changes or whether they are a contributing factor to the outcomes of stress remains largely unknown. In the present studies, we investigated the role of these glial cells as both predictive and causative factors to stress-induced behavior. In Chapter 2, we describe how oligodendrocytes and myelin in the hippocampus correspond to long-term changes in anxiety-like behavior in an animal model of severe stress. While Chapter 2 focuses on males, Chapter 3 expands this work to females, and we discuss the differences between males and females in their responses to acute, severe stress. Together, these studies contribute to the understanding of differential susceptibility to stress and may provide new avenues for biomarkers and therapies.

Advisor: Kaufer, Daniela