VictorJuiz/thesis huggingface dataset:
Accountable Data Fusion and Privacy Preservation Techniques in Cyber-Physical Systems

With the deployment of large sensor-actuator networks, Cyber-Physical Systems (CPSs), such as smart buildings, smart grids, and transportation systems, are producing massive amounts of data often in different forms and quality. These data are in turn being used collectively to inform decision-making of the entities that engage with the CPSs. The impact of these systems on people's lives has led to a strong call for accountability of system decisions made based upon various data sources. The collection, analysis, and dissemination of these data also present a privacy risk that needs to be addressed./nThe first part of this dissertation focuses on accountable data fusion. We develop an online prediction framework that integrates dynamic sensor measurements with prior knowledge. The proposed framework facilitates reasoning about prediction confidence, which is crucial to making dependable decisions. We also move beyond predictive modeling to interpretable analytics by evaluating the influence of each data instance on the algorithmic outcome. We formalize the notion of ``data value,'' and provide efficient algorithms to compute it. This value notion not only enables us to better understand black-box predictions through the lens of training data, but allows for fair allocation of the profit generated from a prediction model that is built with data from cooperative entities. We further use the proposed value notion to develop an effective data sanitization mechanism, which screens off low-quality or even adversarial data instances from the training set./nIn the second part, we address the problem of incorporating privacy as an active engineering constraint into the CPS design and operation. We discuss a privacy metric inspired by information theory and provide algorithms to optimize the privacy mechanism for a given system or co-design the privacy mechanism and system control. In order to avoid unnecessary privacy-utility tradeoffs, we develop a framework to identify redundant data for specific decision-making processes. Furthermore, we present a privacy-preserving data publishing system, which can achieve improved data utility by optimizing the privacy mechanism according to the use of published data. While the algorithms and techniques introduced can be applied to many CPSs, we will mainly focus on the implications for smart buildings.

Advisor: Spanos, Costas
Outlyers: Maroons and Marronage in Eighteenth and Nineteenth-Century Literature

“Outlyers: Maroons and Marronage in Eighteenth and Nineteenth-Century Literature,” foregrounds an archival pursuit in which recovery is deprioritized. Crucial to this study is an archival paradox: Maroons absented themselves from the printed record, eschewed the position of author, only to be figured and represented by others who, expectedly, struggled with the depiction of a practice they could not know firsthand. The intentional erasure of “traces” by maroons was necessary to the successful practice of marronage. The project is organized around four “maroon objects”—the portrait, the fetish, the epaulette, and the hatchet—that recur in historical representations concerning maroons. These maroon objects mediate maroon subject and text./nMy first chapter, “Maroon Portraits,” examines the circulating narratives of La Mulâtresse Solitude of Guadeloupe. Solitude sits for a portrait that is continuously painted, as artists insist on producing visual images in tension with the long textual record that precedes them. Chapter Two, “Maroon Fetishes,” reads the proliferation of fetishes in Le Macandal by Marie Augustin and other iterations of the story of Haitian Maroon leader François Macandal. I read for the extension of belief in a fetish’s power to the realm of fiction and representation. In Chapter Three, “Maroon Epaulettes,” I examine how Victor Hugo, William Wells Brown and George Washington Cable work through the maroon’s military position in the context of slave revolution. Their depictions highlight the maroon practice of camouflage through the representation of military uniform, epaulettes in particular. The final chapter, “Maroon Hatchets,” examines the severing violence of the hatchet as employed by authors representing the earliest moments of marronage. The chapter reads works by Aimée Césaire, Victor Séjour and Martin Delany, who turn to formal innovations in their imaginings of the individual’s path to marronage.

Advisor: Best, Stephen
Design and Synthesis of Chemical Tools for Imaging Neuronal Activity

The ultimate goal of neuroscience is to correlate the activity of neurons and neuronal networks to higher order behaviors and cognition. This colossal task necessitates a variety of optical tools that can both measure and modulate neuronal activity. This dissertation describes the design, synthesis and characterization of a variety of such tools. In order to interrogate the electrical activity of neuronal circuits directly, we synthesized tetramethylrhodamine-based voltage reporters, or RhoVRs, that possess excitation and emission profiles in the green to orange region of the visible spectrum and use photoinduced electron transfer (PeT) as a trigger for voltage sensing. Two RhoVRs with particularly attractive photophysical properties were developed: RhoVR 1, which possessed the highest voltage sensitivity of any RhoVR (47% ΔF/F per 100 mV), and RhoVR(Me), a less sensitive (13% ΔF/F per 100 mV) but far brighter RhoVR (4-fold brighter than RhoVR 1). In order to facilitate the use of RhoVRs in complex tissues such as brain slice or in vivo, we developed genetically targetable RhoVRs using the HaloTag system (RhoVR-Halos). RhoVR-Halos maintained the fast kinetics and high sensitivities typical of RhoVRs (up to 34% ΔF/F per 100 mV) while labeling HaloTag expressing cells with high selectivity in culture, brain slice and in vivo. In addition, RhoVRs possess high two-photon cross sections (up to 190 GM), making them excellent candidates for two-photon voltage imaging. While voltage indicators allow for the study of fast voltage dynamics in real time, they necessitate very fast imaging speeds that are not well suited for mapping activity across large neuronal networks. In order to facilitate neuronal activity mapping, we developed a Ca2+ integrator MethylAzid-1 (MA-1). MA-1 acts as a coincidence detector for both light and Ca2+, allowing a temporally precise “snapshot” of [Ca2+] to be taken. MA-1 undergoes a 25 nm shift in absorbance upon chelation of Ca2+ (Kd = 270 nM) that allows for the selective photolysis of Ca2+-free MA-1 with 400 nm light. The extent of photolysis can be visualized post hoc through either “click chemistry” or the fluorogenic reduction of remaining MA-1. In addition to tools which report neuronal activity, we synthesized a new class of photocages based on 6-aminobenzofurans (BFCs) that can be used to selectively release caged compounds, such as neurotransmitters, upon irradiation with UV light. BFCs operate through a photo-induced elimination reaction that generates an extended azaquinone-methide from the excited state. Initial studies revealed BFCs are strong absorbers of UV/Violet light (λmax = 365 nm, ε = 30,000 M-1 cm-1) that readily photolyze (Φphotolysis up to 0.18) to release their caged cargo. Together, this work demonstrates the power of optical tools to study neuronal systems ranging from sub-cellular domains to large networks of neurons and lays the groundwork for their application in complex tissues such as brain slice or in vivo.

Advisor: Miller, Evan W
We Animals, We Cyborgs: Rethinking Anthropocentrism in Postwar Italian Literature

The challenge to anthropocentrism is at the core of critical animal studies, that draws from and contributes to the reflections of posthumanistic thought. By turning their attention from what are usually considered criteria to separate and place in a hierarchy human and nonhuman animals (most prominently, reason and language) to what they have in common, namely their embeddedness and materiality, the animal studies challenges at their very roots the humanistic ideals that dictate what a human beings are, how they look like, what their privileges are. As Cary Wolfe puts it, “underneath them all [human and nonhuman animals] [...] is a shared finitude, a shared ‘passivity’ [...] that runs directly counter to the liberal model of the subject as above all a creature of volition, autonomy, and agency” (Posthumanism 139). By shifting the focus from agency to vulnerability, animal studies seeks to transfigure a principle of exclusion into a common, constitutive ground on which to envision a new way of conceiving the relations among living beings./nIn this dissertation I analyze texts that reject, each in its own way, the neatness of the distinction between humanness and animality. Their four authors - Federigo Tozzi (1883-1920), Anna Maria Ortese (1914-1998), Primo Levi (1919-1987), and Paolo Volponi (1924-1994) - populate their pages with human characters who look at and interact with nonhuman animals as characters in their own right, and not as mere rhetorical and symbolic props or projections of human feelings, states of mind, or behaviors. The attitude of these writers and of (most of) their characters is born of the intuition of what all animals, human and non human, share - namely their finitude, their vulnerability, the thick, inescapable materiality of their bodies. In this intuition is the germ of a challenge to anthropocentrism through the implicit and sometimes explicit critique of the Cartesian paradigms of mind/body dualism and of the animal-machine, both based on the preeminence of reason as the criterion for the ontological superiority of (a selected few) human animals.

Advisor: Spackman, Barbara G
Ring-shaped and Dual-electrode Bimorph Piezoelectric Micromachined Ultrasonic Transducers

The potential widespread usages of ultrasonic transducer technology have inspired the development of microelectromechanical systems (MEMS)-based devices. The research presented in this dissertation focuses on enhancing the performance of piezoelectric micromachined ultrasonic transducers (PMUTs) by devising innovative design structures, analytically deriving models to understand and optimize performance, and using these findings to demonstrate PMUT-based systems with increased capabilities. The ring-shaped PMUT is firstly introduced as a high-performance PMUT architecture, which is demonstrated both analytically and experimentally to show several important advantages over traditional designs. Due to specific effects of acoustic interactions that have not been previously studied, an extremely wide bandwidth can be achieved with aptly defined ring-shaped PMUTs in liquid-coupled operation. Specifically, fabricated devices are measured to have a velocity bandwidth of up to 160\%, which is more than 60% greater than the highest bandwidth of any reported standalone PMUT and is tunable by altering device dimensions. PMUT arrays are used to demonstrate a new type of ultrasonic flow sensor that offers a robust, simple, and low-power chip-scale solution. The sensor operates in the pulse-echo mode to detect changes in flow with a measured sensitivity that is 286% of that for previously reported MUT-based flow meters, all without commanding any voltage over 5 V. The enhancement is a result of four unique features reported herein: (1) the high-sensitivity bimorph structure of the fabricated PMUTs; (2) the spatial separation between the transmitter and receiver transducer elements; (3) the high directivity of the transmitted acoustic pulse; and (4) the differential readout. Finally, arrays of PMUTs are also proposed for high intensity applications, beginning with the development of an equivalent circuit network model that accounts for the inter-transducer acoustic coupling and leads to practical design equations with interesting implications for the design of high-power arrays. The findings are corroborated by experimental results from several fabricated prototypes, which also use electronic phased array focusing to achieve acoustic outputs that demonstrate feasibility for many high-intensity applications, especially for those requiring small transducer sizes. The prototype device exhibits an output pressure as high as 3.2 kPa/V in standard transmission, which can be boosted to 12.2 kPa/V by applying phased array focusing at a depth of 2 mm. Furthermore, a linear relationship between focal pressure and applied voltage is observed with a maximum measured pressure of 187 kPa peak-to-peak, demonstrating feasibility to reach the intensity ranges required for medical operations in the future.

Advisor: Lin, Liwei
Trajectory Inference and Analysis in Single-Cell Genomics

I present a biological study of differentiating stem cells along with statistical and computational methods for the analysis of data from such studies. The motivating biological example comes from a study of steady-state tissue maintenance in the mouse olfactory epithelium, where we are interested in characterizing the transcriptional changes that drive cell fate decisions. This study uses single-cell RNA sequencing (scRNA-Seq) to quantify the transcriptional activity of hundreds of cells across thousands of genes. Analysis of such data requires an intensive computational pipeline. I present two novel tools designed to fit into such a pipeline: first, I present Slingshot, a method for modeling the developmental process and ordering cellular profiles along it; second, I present tradeR, a method for analyzing patterns of gene expression along such a developmental process and testing for meaningful differences. Together with existing tools, these methods can help us understand the molecular mechanics underlying such fundamental biological processes as organism development, tissue maintenance, and regeneration.

Advisor: Dudoit, Sandrine
A Localization Theorem for Derived Loop Spaces and Periodic Cyclic Homology

Motivated by a theorem in the K-theoretic setting relating the localization of K_0(X/T) over a closed point z \in Spec(K_0(BT)) to the Borel-Moore homology of the fixed points H.^{BM}(X^z; C), we prove an equivariant localization theorem for smooth quotient stacks by reductive groups G in the setting of derived loop spaces and periodic cyclic homology, realizing a Jordan decomposition of loops described by Ben-Zvi and Nadler. We show that the derived loop space L(X/G) is a family of twisted unipotent loop spaces over Aff(L(BG)) = G//G; more precisely, the fiber over a formal neighborhood of a semisimple orbit [z] \in G//G is the unipotent loop space of the classical fixed points with a twisted S^1-action. We further study the relationship between unipotent loop spaces and formal loop spaces, and prove that their Tate S^1-invariant functions are isomorphic. Applying a theorem of Bhatt identifying derived de Rham cohomology with Betti cohomology, we obtain an equivariant localization theorem for periodic cyclic homology in the smooth case, identifying the completion of HP(Perf(X/G)) at z \in G//G with the 2-periodic equivariant singular cohomology of the z-fixed points H*(X^z/G^z; k)((u)).

Advisor: Nadler, David
RF Transmitter Design for Large Antenna Array Applications

Recent advances in wireless technologies have enabled fast increase of mobile data traffic. In fact, mobile data traffic has grown 18-fold over the past 5 years. The rapid growing demand imposes a big near-far problem on our wireless network. Beamforming technique provides an opportunity to efficiently solve the near-far problem, by combining elements in an antenna array in such a way that signals at particular angles experience constructive interference while others experience destructive interference./nThis thesis focuses on the design of energy-efficient RF transmitters for large antenna array applications. In order to be energy-efficient, we should minimize the overhead power consumption. It makes the design challenging while minimizing out-of-band emissions and supporting multiple/reconfigurable bands as well as programmability in terms of performance (i.e., output power, noise figure, resolution, bandwidth, etc.), since any fixed frequency bandpass filters should be eliminated./nTo address these challenges, a mixer-last TX architecture is proposed, which uses current DACs to deliver charge directly to the 50 Ohm output RF load. Out-of-band emissions are reduced by digital oversampling, and the charging operation of a baseband capacitor./nUsing the proposed transmitter architectures, two chips were implemented. The first chip was fabricated in TSMC's 65nm CMOS technology. With a peak output power of 5.1dBm, the first chip consumes 49.2 mW and the measured noise floor at 40MHz offset is -155dBc/Hz. Realizing it is impossible to build a single transmitter that is power efficient under all applications, we developed a generator for our proposed TX architecture using Berkeley Analog Generator (BAG) framework. A generator captures the design methodology and is process portable. It could significantly lower the design cost so that different transmitters that are efficient for different design specifications can be generated.The second chip was generated by the generator and was fabricated in TSMC's 16nm CMOS technology. It consumes 5.14 mW at peak output power of -19.6 dBm. Compared with the first 65nm prototype, it is more power efficient in the output power range of less than -4 dBm.

Advisor: Alon, Elad
Negative capacitance and hyperdimensional computing for unconventional low-power computing

Properties that emerge from the collective behavior of constituents at different length scales can be exploited to reduce power consumption below conventional limits in computing. At the device level, ferroelectric-dielectric coupling ("negative capacitance") can reduce energy consumption below 1 / 2 CV^2 in capacitors. However, this effect is still not well understood. We construct a microscopic model and analyze energy flow from the perspective of Poynting’s theorem to clear up these misunderstandings. At the circuit level, high-dimensional distributed representations relax requirements on signal-to-noise ratio and supply voltage, and enable new architecture designs. Computing with these representations ("hyperdimensional computing") is natural for performing energy efficient cognitive computing at the application level. However, data in practice is always measured in some sort of representation, which may not be natural for hyperdimensional computing. We bridge this gap by proposing to use an approximation of the bispectrum to map data measured in practice into high-dimensional distributed representations for use with hyperdimensional computing.

Advisor: Salahuddin, Sayeef
A High-Density Carbon Fiber Neural Recording Array Technology: Design, Fabrication, Assembly, and Validation

Increasingly advanced tools are desired for understanding electrical activity in the brain, whether for basic neuroscience or clinically relevant brain-machine interfaces. Among the many classes of tools available, intracortical neural recording electrodes have the potential advantage of both high spatial and temporal resolution, and depending on the device can be suitable for either acute or chronic applications. To achieve the breadth of desirable characteristics for an acute neural recording array, including minimal adverse biological response, full-volume sampling, and scalability to a large number of recording electrodes, a new type of device must be developed. This dissertation presents significant steps toward such a device, demonstrating a high-density 32-channel carbon fiber microwire neural recording array capable of acute in vivo recording. De- parting from the in-plane architectural paradigm of conventional microwire-style neural recording arrays, an array substrate is microfabricated in silicon and 5 μm diameter carbon fiber monofil- aments are threaded through holes in that silicon substrate to create a two-dimensional array of carbon fiber recording electrodes that can, in principle, be scaled to an arbitrary number of record- ing electrodes. In addition to scalability, this device architecture affords electrode pitch four times finer than the state of the art among microwire recording arrays. The fine diameter of the carbon fibers affords both minimal cross-section and nearly three orders of magnitude greater lateral compliance compared to traditional tungsten microwires, with these features serving to minimize the adverse biological response of the implanted electrodes./nThe substrate microfabrication and array assembly processes are robust and repeatable, and with the introduction of a robotic system to automate the insertion of carbon fibers into the through- silicon vias with submicron precision, the processes are fundamentally scalable to an array with a large number of electrodes. A specially formulated isotropically conductive adhesive mechanically and electrically bonds the carbon fiber recording electrodes to the silicon substrate, and post- processing of both the adhesive and the recording sites serves to further lower the impedance for superior electrophysiological characteristics. Recording is demonstrated in the primary motor cortex of a rat, with single-unit action potentials being recorded on many channels. This carbon fiber microwire neural recording array is a promising technology for increasing information density while minimizing the adverse biological response in acute preparations, particularly in applications where microwire arrays are already commonplace.

Advisor: Maharbiz, Michel M
Pister, Kristofer SJ