VictorJuiz/thesis huggingface dataset:
Uncovering Human Visual Priors

Visual perception can be understood as an inferential process that combines noisy sensory information with internalized knowledge drawn from previous experience. In statistical Bayesian terms, internal representations of the visual environment can be understood as posterior estimates obtained by weighting imperfect sensory information (a likelihood) by internalized biases (a prior). Given limited perceptual resources, it is advantageous for the visual system to capitalize on predictable regularities of the visual world, and internalize them in the form of priors. This dissertation presents novel findings in the domain of spatial vision and visual memory, as well as some new work on memory for the 3D orientation of objects. In all cases, an unprecedented signal-to-noise ratio, achieved by employing serial reproduction chains (a ``telephone game'' procedure) combined with non-parametric kernel density estimation techniques, reveals a number of stunning intricacies in the prior for the first time. Methodological implications, as well as implications for amending prior empirical findings and revisiting past theoretical explanations are discussed.

Advisor: Griffiths, Thomas
Skill Learning for Industrial Robot Manipulators

Industrial robots have been kept upgraded for decades to achieve extraordinary accuracy, speed, and repeatability. However, even the most advanced manipulator today is functioning as a programmable machine, instead of an intelligent agent. This deficiency of intelligence restricts robots from broader applications. To meet the increasing demand for automation, it is essential to make industrial robots more skillful and intelligent. Under this background, the objective of this dissertation is to develop generic and efficient methodologies to teach robots novel skills. Three major approaches including model-based learning, model-free learning and analogy-based learning are discussed and explored. A series of skills such as assembly, grasping, tracking and motion planning, have been successfully taught to industrial manipulators and evaluated by experiments./nAs the name implies, model-based learning tries to formulate skills analytically based on physical models. In Chapter 2, an auto-alignment skill is developed for robotic assembly by constructing a novel contact model. Robots are enabled to predict tilt angles between assembly parts from force/torque measurement and perform fine assembly from large misalignment conditions. With this skill model, traditional procedures such as the installation of positioning fixtures and manual alignment can be skipped, which saves tremendous preparation efforts for robotic assembly./nHowever, not always system models can be constructed, especially for those complicated scenarios. The model-free approach is then developed to learn control policies by regressing general parametric functions. In Chapter 3, a compliant robotic force controller is learned from human demonstration. A human operator holds a specially-designed handle and demonstrates to robots the compliant insertions. The Gaussian mixture regression is introduced to fit motion patterns from measured data. This approach enables to transfer the compliant assembly skill from humans to robots efficiently and intuitively./nBesides model-based and model-free learning, an analogy-based leaning approach is proposed in Chapter 4. The distinct idea is that instead of pursuing a control policy either constructed by models or regressed from data, we discover the correlation between scenarios, i.e., analogy. The past scenario that bears a strong similarity with the current one will be identified, and a mapping function between these two scenes will be constructed. Applying the mapping function, the past problem-solving action can be transferred to a new one that is feasible for the current scenario. This analogy-based approach has been implemented in multiple industrial tasks, and taught robots various skills such as grasping versatile objects (Chapter 5), tracking and manipulating deformable objects (Chapter 6) and efficient motion re-planning for similar scenarios (Chapter 7).

Advisor: Tomizuka, Masayoshi
Electronic Interfaces for Bacteria-Based Biosensing

Bacterial sensing systems have evolved to detect complex biomolecules, operating near fundamental physical limits for biosensing. No modern engineered biosensor has managed to match the efficiency of bacterial systems, which optimize for each sensing application under constraints on response time and sensitivity. An emerging approach to address this shortfall is to build biosensors that electronically couple microbes and devices to combine the sensing capabilities of bacteria with the communication and data processing capabilities of electronics. This dissertation presents three techniques that advance engineering at the interface between bacteria and electronics, all working towards the integration of living material into hybrid biosensing platforms. In the first technique, we embed current-producing Shewanella oneidensis inside a conductive PEDOT:PSS matrix to electronically interface and structure the bacteria into 3D conductive biocomposite films to our specifications. In the second technique, we observe large numbers of chemotactic bacterial flagellar motor (BFM) behavior to infer environmental conditions, using machine learning to co-opt Escherichia coli's motor response for the front end of a biosensor. In the final technique, we demonstrate progress towards a method to electronically monitor BFM rotation over time for electrochemical biosensing. Together, this body of work contributes to more functional interfaces between silicon- and carbon-based materials for advanced biosensing applications including persistent in situ environmental sensing and microbiorobotics.

Advisor: Maharbiz, Michel M.
A Smoothed Particle Hydrodynamics Model for the Simulation of Laser Fusion Additive Manufacturing Processes

Additive Manufacturing (AM), aka 3D-Printing, is a broad class of rapidly emerging manufacturing technologies that build-up parts layer-by-layer through the addition of raw materials, under the guidance of a digital model. They are set to revolutionize the manufacturing world by allowing for rapid production of net-shape, customizable, ready-to-use parts in a variety of novel materials and designs. The development of numerical methods suited to the simulation of AM processes is of prime importance to industry and academia./nIn this work, the Smoothed Particle Hydrodynamics (SPH) method, a Lagrangian mesh-free numerical scheme, is adapted for the first time to resolve thermal-mechanical-material fields in a range of Laser Fusion Additive Manufacturing processes. The method is capable of simulating large-deformation, free-surface melting, flow, and re-solidification of metallic materials with complex physics and material geometries. A novel SPH formulation for modeling isothermally-incompressible fluids, which allows for the accurate simulation of thermally driven liquid metal expansion/contraction, is presented and verified. Fundamental validation of the methodology is performed via comparison with real world, spot laser welding experiments. The methodology is then used to investigate the the specific Additive Manufacturing Process of the Selective Laser Melting of Metallic, micro-scale Particle Beds. The physics of a track deposition process is explored through numerical experiments and the influence of processing parameters on the finished laser weld track quality is investigated. The SPH method is found to be a viable and promising numerical tool for simulating laser fusion driven Additive Manufacturing processes.

Advisor: Zohdi, Tarek
Can we explain the human mind and experience? Perceptions of the limits of science

Can science ever fully explain what it is like to fall in love, to undergo a religious transformation, or to have a child? For some types of experiences, people seem to give special status to their own introspective knowledge over other types of information, especially scientific information, an inherently third-personal source./nAcross these three sets of studies, I demonstrate that people privilege their own first-person knowledge over science when it comes to highly personal aspects of the human mind and experience. In Chapter 2, I show that people judge science as being unable to ever explain aspects of the mind to which they feel that they have privileged introspective access – the types of mental phenomena that only the experiencer herself can truly know. In Chapter 3, I extend this finding to show that these commitments hold important consequences for people’s moral judgments. Finally, in Chapter 4 I demonstrate that people privilege their own first-person knowledge over scientific information when making decisions about personally transformative decisions./nThese findings advance the literature on folk epistemology, but also illustrate that epistemic commitments have important consequences for moral judgments and how people approach decision-making in their everyday lives.

Advisor: Lombrozo, Tania
Storage and Packaging for an Empire: Agricultural Economics of West-Central Italy, c. 200 BCE-200 CE

The emergence of Rome’s far-flung territorial empire resulted in a sophisticated regime for the storage and distribution of foodstuffs. This dissertation focuses on a ceramic container used for the storage of wine and oil, the dolium, to investigate how Rome’s long-distance, large-scale food supply system impacted craftsmen and agricultural workers in west-central Italy during the period of c. 200 BCE-200 CE. It studies the processes, materials, and skills invested in over three hundred dolia and dolium fragments from Cosa, Pompeii, and Ostia to bring to light the workforces that produced, repaired, used, and maintained these costly investments that were important not only for agriculture, but also food storage in urban settlements. With a lucrative wine market developing overseas, viticultural areas expanded and the demand for wine and large-scale wine fermentation and storage containers exploded. Dolium producers used the same technique (coil-building), but the scale of production differed between the settlements. Potters designed and expanded the dolium, but it was risky and expensive to produce these vessels; dolium production became increasingly subsumed under large opus doliare workshops, owned by wealthy aristocrats, senators, and members of the imperial family. By the second century CE, artisans of urban opus doliare workshops that produced dolia, bricks, and tile had developed their methods and vessel design in close alignment; the success of these major workshops was so great that the Tiber River Valley had been transformed into antiquity’s Ceramic Valley, a hub of ceramic and terracotta production. Building such large vessels, however, was a task fraught with risk, and craftspeople had to develop new methods in their routines, some of which were derived from traditional pottery mending techniques while others were entirely new creations inspired by the architectural industries. The types of damage for dolia, and the methods and materials for their repairs, not only shed light on developments in dolium repair technology, but also on the different workforces. Craftspeople aligned and experimented with their methods, interacting also with the architectural industry to develop new techniques to build these vessels. As the storage regime for Rome became more sophisticated, the utility and importance of dolia extended from production sites to urban settlements, supporting and perhaps even driving raising levels of urbanism. Over time, the very practices and technologies of storage themselves cast a wider net that drew in many potters, architectural workers, farmers, porters, and unskilled workers to propel an ancient global food supply.

Advisor: Peña, J. Theodore
Development of Inter- and Intra-cellular Components of Direction Selectivity in The Mammalian Retina

The mouse brain contains over 70 million neurons that form around a trillion connections, or synapses, with one another. Different synaptically connected networks of neurons are organized with varying circuit motifs to receive information and transform that information into a relevant output for the animal. The visual system, and in particular the retina, has served as a classic model for elucidating how neuronal circuits perform these computations. The focus of this dissertation was to understand how the inter-neuronal and sub-neuronal aspects of the direction selective circuit in the retina develop and operate to extract the directions of object motion from the milieu of information in the visual scene. The key neuron in this circuit is the starburst amacrine cell. The dendrites of starburst cells exhibit specific responses to motion in the visual scene that depend upon the dendrite’s orientation within the retina. These signals are then propagated through a stereotyped asymmetric arrangement of synaptic connections from multiple starburst cells onto direction selective ganglion cells, which transmit this directional information to the brain. I begin by summarizing the current understanding of how the direction selective circuit develops and operates in Chapter I. Then, experimental evidence is provided that seeks to answer outstanding questions regarding the development of direction selective circuit components and their roles within the mature circuit. First, in Chapter II, I investigate how the asymmetric synaptic connections between starburst cells and direction selective ganglion cells develop. I find that the mature direction selective circuit wiring diagram results from a subcellularly specified synaptogenesis program, rather than synaptic pruning or strengthening. Next, in Chapter III I investigate how the direction selective responses within the starburst cell dendrites are generated. I find that a skewed distribution of excitatory inputs onto the dendrite is sufficient to produce these responses. In Chapter IV, I explore how starburst cell dendritic morphology influences direction selective circuit computations. I find that starburst cell morphology aligns the subcellular starburst cell computation with the appropriate post-synaptic ganglion cell and that the dense plexus of starburst dendrites is required to produce directionally discriminate responses in the ganglion cell. In addition, I find that the subcellular directional computation in starburst cells is performed at the end of the bipolar cell input distribution along the dendrite identified in Chapter III. In Chapter V I seek to identify the molecular determinants of the asymmetric wiring program identified in Chapter II. These preliminary results will provide a basis for further exploration of direction selective circuit development. Together, these results reveal how the morphology, connectivity, and biophysical properties of neurons are arranged during development to generate the amazing computational abilities of neuronal circuits.

Advisor: Feller, Marla B
Race, Containment, and the Settler-Imperial Politics of the Green Revolution

From roughly the early 1940s to the early 1970s, the United States led a set of international capital-intensive agricultural research, technology, and education transfer initiatives. These initiatives were designed to facilitate a more expansive market agrarianism, increase agricultural yields, and combat hunger amidst concerns of a rapidly growing population. Yet, named the “Green Revolution,” these initiatives, in their push for the development of industrial agriculture oriented to the global market, ultimately preempted peasant unrest and undermined larger revolutionary action as they reconstituted states as guarantors of agricultural markets in service of U.S. state power and transnational capitalism./nThis dissertation, Race, Containment, and the Settler-Imperial Politics of the Green Revolution, recognizes the Green Revolution as an exercise in the risk management of racial capitalism during a period of great social upheaval: when overlapping, internationalized anticolonial and civil rights movements named the limits of racial democracy and risked undercutting postwar U.S. state power and transnational capitalism. Race, Containment, and the Settler-Imperial Politics of the Green Revolution argues that the mid-twentieth century technical, scientific, and education cooperation efforts, and paired innovations in governance and administration, elaborated upon U.S. state-led and capital-intensive efforts to cultivate forms of Native and Black market agrarianisms developed in the early-twentieth century./nOperating in service of the accumulation of wealth and the exercise of geopolitical power, the Green Revolution remade peoples and places in accordance with the anti-Black and settler colonial logics of the plantation and reservation. Additionally, the transit of the plantation and the reservation toward such ends was based upon domestic innovations in U.S. slave and settler capitalisms. The framework of agricultural technical and scientific cooperation and paired innovations in governance and administration during the mid-twentieth crystallized the emergent trope of “development.” Yet, problematizations of the plantation and reservation in the early twentieth century prefigured such developments globally.

Advisor: Iles, Alastair
Feldman, Keith P.
Articulatory uniformity through articulatory reuse: insights from an ultrasound study of Sūzhōu Chinese

This thesis explores the role of uniformity of speech articulation in shaping phonological systems of contrast and their phonetic implementations. The observable effect of uniformity for an individual speaker is that a given phonological primitive (such as a distinctive feature value or gesture, depending on one's theoretical framework) tends to be implemented with maximum articulatory similarity across the speech sounds sharing that primitive. Although less discussed than other organizing principles in substance-based phonology such as phonetic dispersion (Liljencrants and Lindblom, 1972), focalization due to quantal effects (Stevens and Keyser, 1989; Schwartz et al., 1997b), or articulatory ease (Martinet, 1955; Lindblom, 1990), uniformity has been observed in a range of the world's languages, mainly in the timing of laryngeal articulations in stop inventories (Keating, 2003; Chodroff and Wilson, 2017) but also in place-of-articulation primitives (Maddieson, 1996; Chodroff, 2017)./nHowever, uniformity has typically been formulated as a purely linguistic constraint. A primary aim of this dissertation is to motivate uniformity as emerging from domain-general biases that shape complex systems of goal-oriented action more broadly, thereby shedding light on the substantive basis and structure of phonological systems. To this end, I describe a model in which articulatory uniformity emerges from articulatory reuse during learning. During the language acquisition process, a learner's internal model (mapping the effects of motor controls applied to the speech articulators to their outcomes) is not yet fully developed. Under these conditions, a "model-free" learning strategy based on bootstrapping off of the learner's already-mastered skills (exploitation, rather than exploration) may predominate, such that phonological categories whose outputs are perceptually similar may come to be produced with the same articulatory primitives./nThis thesis tests aspects of the model of uniformity-through-reuse with an experiment on Sūzhōu Chinese, whose fricative vowels are known to somewhat resemble alveolopalatal fricative consonants in their tongue-palate constriction patterns and fricative noise production targets (Ling, 2009). Ultrasound tongue imaging was used to characterize the typical fricative vowel and alveolopalatal fricative consonant productions of 43 Sūzhōu Chinese speakers./nAnalysis reveals that most Sūzhōu Chinese speakers typically use a single tongue posture uniformly across the fricative vowels and consonants examined, while a minority of speakers deviate from uniformity to an idiosyncratic extent. The extent to which a speaker deviates from a uniform strategy is shown to be unrelated to demographic characteristics and language ability in Sūzhōu Chinese and Standard Chinese. This pattern at the population level suggests that "speaker-side" factors, such as articulatory reuse, are primarily responsible for shaping the "synchronic pool of variation" (Ohala, 1989) for this set of Sūzhōu Chinese segments.

Advisor: Johnson, Keith A
The role of Stem Cell Factor in recovery from neurological injury

Stroke, Alzheimer's Disease, and other neurological pathologies are not only among the leading causes of death in the United States but also account for a huge portion of national healthcare expenditure (National Center for Health Statistics, 2016 report). Advancing our understanding of the bodily response to neural injury and the mechanisms that might be used to prevent or heal that injury is of paramount importance. This dissertation is a presentation of work aimed at understanding the molecular cascades that govern regeneration after neural injury using the olfactory neuroepithelium (OE) - one of the few locations in the adult where such regeneration is naturally able to occur - as a model./nThroughout the human lifespan, the OE is continually subject to chemotoxic and mechanical insult. Remarkably, the epithelium has the ability to fully regenerate all cell types, both neurons and supporting cells after minor or extensive injury. Understanding the biological regulation that allows for this regeneration serves two purposes: One, these mechanisms may be usefully employed in the development of translational methods for treating neurological diseases. Two, the cells and stem cells of the OE constitute a rich potential source of cells for possible transplantation in translational approaches to pathologies where neural death has occurred. In this dissertation, we evaluated the functional importance of the Stem Cell Factor growth factor (SCF) and C-Kit, the receptor tyrosine kinase SCF binds to, in neural regeneration./nThe regenerative capability of the human epithelium is faithfully recapitulated by the murine OE, making it an ideal model of the human system for use in researching regenerative mechanisms. Using transgenic mouse models, we examined the expression of SCF and C-Kit in the OE via a combination of molecular imaging and single-cell transcriptional sequencing, and we discovered that SCF is expressed by all sustentacular (SUS) supporting cells and all horizontal basal stem cells, both in the uninjured and in the injured/regenerating OE. C-Kit is expressed by a large fraction of the globose basal cells, a population which is heterogeneous and consists both of stem and committed progenitor cells, and some microvillous cells, a population which is the subject of much current research. Interestingly, during regeneration after experimentally induced injury, the majority of cells express SCF or C-Kit. These striking expression patterns led us to look for deficits in SCF knock-out transgenic mice with the hope of better understanding the function of this growth factor. We found that SCF is critical to production of normal numbers of neurons and microvillous cells during regeneration. Extensive assessment of the expression patterns and impact of the ablation of SCF function in the OE led us to a novel understanding of the role of this growth factor/receptor pair in neural recovery after injury: SCF is critical for OE stem cells to make neuronal fate decisions during regeneration from injury.

Advisor: Ngai, John