VictorJuiz/thesis huggingface dataset:
Fast Algorithms for Interior Point Methods

Interior point methods (IPM) are first introduced as an efficient polynomial time algorithm to solve linear programs. Since then, they have enjoyed success in general convex optimization with the introduction of self-concordant barriers, replacing the ellipsoid method as the optimizer of choice in many settings. As compared to the ellipsoid method, interior point methods boast a better runtime complexity due to its $O(\sqrt{n})$ iteration complexity, where each iteration requires a linear system solve for the Newton step computation. This implies a naive $O(n^{0.5+\omega})$ total runtime for IPMs, where $\omega$ is the exponent of matrix multiplication./nIn a recent breakthrough work, [Cohen, Lee, Song'18] showed that we can solve linear programs in the IPM framework in current matrix multiplication time $\widetilde{O}(n^{\omega})$, implying that linear programs are computationally not much harder than matrix inversion. In this thesis, we extend this result to general Empirical Risk Minimization (ERM), showing that many convex optimization problems can be solved as efficiently as matrix inversion./nSpecifically, many convex problems in machine learning and computer science share the same form:/n\begin{align*}/n\min_{x} \sum_{i} f_i( A_i x + b_i),/n\end{align*}/nwhere $f_i$ are convex functions on $\R^{n_i}$ with constant $n_i$, $A_i \in \R^{n_i \times d}$, $b_i \in \R^{n_i}$ and $\sum_i n_i = n$. This problem generalizes linear programming and we give an algorithm that runs in time/n\begin{align*}/nO^* ( ( n^{\omega} + n^{2.5 - \alpha/2} + n^{2+ 1/6} ) \log (1 / \delta) )/n\end{align*}/nwhere $\alpha$ is the dual exponent of matrix multiplication, and $\delta$ is the relative accuracy, and $O^*$ hides sub-polynomial terms. Note that the runtime has only a log dependence on the condition numbers or other data dependent parameters and these are captured in $\delta$. For the current bound $\omega \sim 2.38$ and $\alpha \sim 0.31$, our runtime $O^* ( n^{\omega} \log (n / \delta))$ matches the current best for solving a dense least squares regression problem, which is a special case of the problem we consider. Very recently, [Alman'18] proved that all the current known techniques can not give a better $\omega$ below $2.168$, which is larger than our $2+1/6$./nOur algorithm proposes two novel concepts, which can be of independent interest :\/n$\bullet$ We give a robust deterministic central path method, whereas the previous central path is a stochastic central path which updates weights by a random sparse vector. \/n$\bullet$ We propose an efficient data-structure to maintain the central path of interior point methods even when the weights update vector is dense.

Advisor: Srivastava, Nikhil
Rao, Satish
Optimality Theory and the Semiotic Triad: A New Approach for Songwriting, Sound Recording, and Artistic Analysis

Songwriters have always taken full advantage of the ‘artistic license’ offered them by their listeners. This dissertation investigates the freedoms and limitations of artistic license by examining language in the musical environment. This dissertation uses Optimality Theory as its method of analysis together with Peircean Semiotics. The OT analysis includes examples from both English and German and investigates the musical environment on syntactic, morphological, and phonological levels. The dissertation also explores the potential impact that songs can have on spoken language by considering the differences between modifications and innovations in songwriting. Additionally, I examine the roles iconicity and arbitrariness play in art and pop culture. As evolving principles of the Sign, iconicity and arbitrariness interact with one another in an overlapping manner, thus producing new innovations in art and language. These new innovations are then conventionalized, creating a new layer upon which more innovations take place. The fractal nature of this process adds credence to the reproductive nature of Peirce’s Triad. Lastly, this dissertation applies Peirce’s Triad to the art form of sound recording to shed light on that creative process and is then applied for an analysis of dissimilar musical genres to add further explication on the differing expectations of those musical genes.

Advisor: Rauch, Irmengard
The conserved herpesviral kinase ORF36 activates B2 retrotransposons during murine gammaherpesvirus infection

Nearly half of the human genome is composed of sequence encoding for elements known as retrotransposons. Although these non-coding RNA elements were initially considered to be “junk,” the last few decades have brought about a new appreciation for the importance of retrotransposons as dynamic players in a variety of host pathways. In Chapter I, I review the evolution of retrotransposons, and their architecture in mammalian genomes. I focus on the Short Interspersed Nuclear Elements (SINEs), a class of retrotransposon derived from host RNA polymerase III (RNAPIII)-transcribed genes. I describe their transcription by RNAPIII, as well as their functional relevance pre- and post-transcriptionally. I introduce B2 SINEs, a prominent murine SINE often used as a model to study SINE biology. These elements are highly induced during times of cellular stress, such as that caused by viral infection. Murine gammaherpesvirus 68 (MHV68) leads to a dramatic upregulation of B2 SINEs, which can influence viral gene transcription. In Chapter II, I present our investigation of the pathway to induction of B2 SINEs by MHV68 during infection, and our finding of the conserved herpesvirus kinase ORF36 as being able to induce these elements independently. In Chapter III, I discuss attempts to elucidate the functional relevance of B2 SINEs induced during infection. I describe an RNA-sequencing experiment done to examine changes in global transcription in the presence or absence of B2 SINEs during infection, as well as an experimental method to isolate B2 ncRNAs induced during infection, for potential use in downstream functional applications. In Chapter IV, I discuss perspectives on the presented data, and future directions for continued elucidation of the link between ORF36 and B2 SINE induction, as well as future directions for studying the functional relevance of induced elements. This study highlights the important role that retrotransposons, in particular SINE elements, play in host and viral pathways, and provides the first description of a herpesviral ORF that is able to induce these elements.

Advisor: Glaunsinger, Britt A
"Buy, Reade, Regard": Learning to Sing and Play through the Printed Page in Early Modern England

Abstract/n“Buy, Reade, Regard”:/nLearning to Sing and Play through the Printed Page in Early Modern England/nby/nMargaret E. Jones/nDoctor of Philosophy in Music/nDesignated Emphasis in Renaissance and Early Modern Studies/nUniversity of California, Berkeley/nProfessor Davitt Moroney, Chair/nIn 1676 Thomas Mace reluctantly laid the lute to rest in Musick’s Monument. The “monument” in question was built both for the lute and for the styles of music that had been popular earlier in the century during what is often called the golden age of English lute music. Mace’s complaints about the fate of the lute in part were a reaction to the stylistic changes sweeping across England at the time. However, the ways music circulated – specifically the circulation of printed instruction books and manuscripts among musical amateurs – also played major roles in these ongoing changes to music-making, leading ultimately to the demise of the lute as a solo instrument. Musick’s Monument was the culmination of a trend in music publishing that began in the 1590s, where music publishers increased their output of music instruction books to respond to a growing market of rising merchant-class amateurs and students at universities. Several of these books – and in particular Thomas Robinson’s The Schoole of Musicke (1603) – complicate the intersections between instrumental and vocal music instruction by using the lute itself as an instructor for the voice. The dual-materiality of these lesson books – that is primarily the ways they encourage physical interactions with instruments, and secondarily the physical presence, format, and layouts of the books themselves – encouraged readers to use them in specific ways. At times the layout of duets positioned readers around a single book; at other times the books even encouraged their own dismantling in order to be used./nThis dissertation traces the development of music-book publishing for self-taught amateurs. It recasts narratives about early modern music education to place greater emphasis on historical students as empowered readers, teachers and thinkers maneuvering within complex social and political realities. It also shows the variety of skills covered in self-instruction books and the ways these books use the same lute tablature to teach both playing and singing. It examines these books through a critical bibliographic lens, tracing the intersections between physical objects, the people that used them, and the music they contained. Ultimately, I contend that these instruction books and the self-guided study they encouraged were instrumental in the development of educational institutions that continue to develop into the present.

Advisor: Moroney, Davitt
Modern Methods of Radio Astronomy Signal Detection with Case Studies in Epoch of Reionization, Fast Radio Bursts and Search for Extraterrestrial Intelligence

Modern radio astronomy has brought forth an era of data explosion. With advances in instrumentation and computational power, new host of algorithms for data analysis become possible and necessary. Techniques of data reduction and interference rejection are crucial to signal detection for a wide range of scientific questions. In 21\,cm cosmology, a faint and diffuse signal from primordial hydrogen requires extracting every last bit of sensitivity from the instruments. In search of fast radio burst and signals of extra-terrestrial technology we need to sort through large volumes of data while effectively distinguishing candidate signals from noise and interference. Overcoming these challenges requires novel intuition of the experiments as well as applications of state-of-the art methods of statistics./nRedundant arrays are a kind of interferometers designed to detect the 21cm power spectrum. The spectrum itself is naturally linked to the square of the visibilities, giving rise to a set of theoretical formulations that skips the need for forming images. Such formulation, however, does not naturally include all sensitivity of the interferometer. Thus in this thesis we develop a technique to complete this formulation and provide the remaining sensitivities./n/nFast radio bursts (FRB) are a type of millisecond-duration transient signal seen in spectrograms with a quadratically dispersed shape. At the time of the writing of this thesis, the physical nature of the sources is yet unknown. One of the repeating sources is FRB121102. Using deep learning, we detect the most number of signals from FRB121102 during a single observation. The 93 pulses provide new wealth of statistical properties, most notably periodicity. Whether the emission is periodic provides an insightful look on the nature of the source. With our novel method of periodicity search, we show that the received pulses are likely not periodic with any period longer than 10 milliseconds./n/nRadio frequency search for extraterrestrial intelligence (SETI) is one of the most open-ended questions in astronomy. With properties of the candidate signal unknown, SETI needs intelligent methods that automatically extracts information from large volumes of data. In parallel with new developments in radio astronomy, machine learning techniques, in particular deep learning has successfully revolutionized applications in computer vision, speech processing, text processing, and signal processing. In this thesis, we demonstrate a range of data processing techniques, with focus on deep learning, to signal detection in SETI. We showcase a blind detection for repeating signals, a semi-supervised representation learning framework, as well as a generative model for anomaly detection and interference rejection.

Advisor: de Pater, Imke
Phage Wars: the molecular interactions underlying the arms race between a lytic bacteriophage and epidemic Vibrio cholerae

Viruses infect all living organisms, and in response, hosts have had to adapt to the constant threat of viral infection. The interactions between viruses and their hosts shape the evolutionary trajectory of both entities over time. Phages, which are viruses that infect bacteria, are the most prevalent infectious agents and can vastly outnumber their bacterial hosts in a given environment. One such target of phage predation is the pathogen Vibrio cholerae, which can be co-isolated with phages both from cholera patient stool samples, as well as from aquatic reservoirs in regions where cholera is endemic. Analysis of the phages that are shed in cholera patient stools indicates that one phage, ICP1, is the most dominant phage that infects epidemic V. cholerae, at least in Bangladesh. In response to the constant threat of infection, epidemic V. cholerae has acquired an anti-phage island, referred to as PLE, that specifically blocks ICP1 infection. Here, we use the interactions between ICP1 and V. cholerae PLE as a model system to examine the molecular interactions between a virulent phage and its bacterial host. Using natural isolates enables us to comprehend the ways in which this molecular arms race has influenced the evolution of both ICP1 and epidemic V. cholerae. In the first chapter, we identify the molecular specificity of the PLE response to ICP1 during infection, demonstrating that this anti-phage island is highly evolved to activate only in response to the dominant phage ICP1. In the second chapter, we identify additional ICP1-PLE molecular interactions that facilitate PLE escape from ICP1-mediated host takeover processes. In the third chapter, we examine the ICP1-encoded CRISPR-Cas adaptive immune system that is specifically deployed to processively degrade PLE and allow for ICP1 to productively infect the PLE (+) V. cholerae host. Overall, the work presented here updates our understanding of the mechanisms by which anti-phage islands, such as PLE, have the capacity to exploit their predatory phage to mobilize and influence the evolution of pathogenic populations.

Advisor: Seed, Kimberley D
Many-Body Quantum Dynamics and Non-Equilibrium Phases of Matter

Isolated, many-body quantum systems, evolving under their intrinsic dynamics, exhibit a multitude of exotic phenomena and raise foundational questions about statistical mechanics. A flurry of theoretical work has been devoted to understanding how these systems reach thermal equilibrium in the absence of coupling to an external bath and, when thermalization does not occur, investigating the emergent non-equilibrium phases of matter. With the advent of synthetic quantum systems, such as ultra-cold atoms in optical lattices or trapped ions, these questions are no longer academic and can be directly studied in the laboratory. This dissertation explores the non-equilibrium phenomena that stem from the interplay between interactions, disorder, symmetry, topology, and external driving./nFirst, we study how strong disorder, leading to many-body localization, can arrest the heating of a Floquet system and stabilize symmetry-protected topological order that does not have a static analogue. We analyze its dynamical and entanglement properties, highlight its duality to a discrete time crystal, and propose an experimental implementation in a cold-atom setting./nQuenched disorder and the many-body localized state are crucial ingredients in protecting macroscopic quantum coherence. We explore the stability of many-body localization in two and higher dimensions and analyze its robustness to rare regions of weak disorder./nWe then study a second example of non-thermal behavior, namely integrability. We show that a class of random spin models, realizable in systems of atoms coupled to an optical cavity, gives rise to a rich dynamical phase diagram, which includes regions of integrability, classical chaos, and of a novel integrable structure whose conservation laws are reminiscent of the integrals of motion found in a many-body localized phase./nThe third group of disordered, non-ergodic systems we consider, spin glasses, have fascinating connections to complexity theory and the hardness of constraint satisfaction. We define a statistical ensemble that interpolates between the classical and quantum limits of such a problem and show that there exists a sharp boundary separating satisfiable and unsatisfiable phases.

Advisor: Altman, Ehud
Invisible Illegality: The Double Bind of Being Asian and Undocumented

How do undocumented young adults of Asian origin, namely those who can “pass” as documented, navigate their everyday lives?  More broadly, how do racial discourses shape pathways of incorporation for undocumented young adults?  Undocumented immigrants of Asian origin occupy a unique social location in the United States because what “illegal” conjures in the American consciousness is not what “Asian” looks like. On one hand, they live in a context where they are primarily racialized as non-threatening “model minorities” leading to perceptions of success, achievement, and docility. Simultaneously, however, they also carry the burden of their criminalized undocumented immigration status. This status, and both the stigma and burden that come with it, is invisible. Not only is legal status undetectable to the naked eye, unlike race or gender, but Asians do not fall into the racial imagery of an “illegal immigrant” that is conflated with “Mexican.” Living in the United States as someone who is Asian and undocumented is, in essence, a double-edged sword./nDrawing on a comparative analysis of in-depth interviews with 63 undocumented Asian and Latinx young adults from California, in addition to two years of intermittent participant observation at community-based organizations, events, and workshops serving the undocumented population, I shed light on the ways in which illegality, the everyday experience of living with undocumented status, is refracted through the prism of racialization in the United States. My findings reveal that 1.5-generation undocumented Asian immigrants experience what I call invisible illegality. Race operates to simultaneously shield Asian undocumented young adults from and expose them to the precarious nature of their immigration status, and this varies across institutional and relational contexts. Relative to their Latinx counterparts, Asian undocumented immigrants experience advantages such as greater physical security since they are less vulnerable to racial profiling and ICE raids. However, being a camouflaged minority within the undocumented population results in their exclusion from a collective identity of illegality that, for many, rests on shared race-based narratives of being Latino. Such exclusion results in intensified feelings of shame and a sense of isolation both within their ethnoracial community and the broader undocumented community. It also hinders access to formal and informal supports in civil society. The unique nexus of being Asian and undocumented thus leads to a delicate position of invisible illegality that is produced by multiple co-constitutive processes of racialization./n /nBy unraveling how the intersection of race and undocumented status uniquely shapes the burdens of illegality of undocumented young adults of Asian origin, Invisible Illegality has sobering implications beyond an understanding of diverse trajectories of illegality. It exposes the ways in which the racialization of immigrant communities is a powerful mechanism that cements broader inequalities in U.S. society.

Advisor: Bloemraad, Irene
Classical Nonparametric Hypothesis Tests with Applications in Social Good

Hypothesis testing has come under fire in the past decade as misuses have become increas- ingly visible. It is common to use tests whose assumptions don’t reflect how the data were collected, and editorial policies of many journals reward “p-hacking” by setting the arbitrary threshold of 0.05 to determine whether a result merits publication. In fact, properly designed hypothesis tests are an invaluable tool for inference and decision-making. Classical nonparametric tests, once reserved for problems that could be worked out with pencil and paper or approximated asymptotically, can now be applied to complex datasets with the help of modern computing power. This dissertation tailors some nonparametric tests to modern applications for social good./nPermutation tests are a class of hypothesis tests for data that involve random (or plausibly random) assignment. The parametric assumptions for common tests, like the t-test and linear regression, may not hold for randomized experiments; in contrast, the assumptions of permutation tests are implied by the experimental design. But off-the-shelf permutation tests are not a panacea: tests must be tailored to fit the experimental design, and there are subtle numerical issues with implementing the tests in software. We construct permutation tests and software to address particular questions in randomized and natural experiments, including identifying what, if anything, student evaluations of teaching measure, and whether voting machines malfunctioned in Georgia’s November 2018 election./nRisk-limiting post-election audits (RLAs) have existed for a decade, but have not been adopted widely, in part due to logistical hurdles. This thesis uses classical nonparametric techniques, including Fisher’s combination method and Wald’s sequential probability ratio test, to build new RLA methods that accommodate the idiosyncratic logistics of statewide elections. A new, more flexible method for using stratified samples in RLAs makes it easier and more efficient to audit elections conducted on heterogeneous voting equipment. This thesis also develops an RLA method based on Bernoulli sampling, which allows ballots to be audited “in parallel” across precincts on Election Day. The RLA method for stratified samples of ballots was piloted in Michigan to study its performance in the face of real-world constraints.

Advisor: Stark, Philip B
Unlocking Design Reuse with Hardware Compiler Frameworks

Emerging applications from the edge to the cloud are constantly increasing demand for energy efficient and performant computation. While specialized hardware can meet these power and performance goals, the high non-reoccurring engineering (NRE) costs of designing, testing, and verifying custom hardware severely hinders its supply. Hardware construction languages such as Chisel enable hardware designers to write parameterized hardware libraries which increase design reuse by turning NRE effort into reusable solutions for future specialized chips. This thesis introduces FIRRTL, Chisel’s hardware compiler framework, which enables automatic and custom RTL-transformations including logic optimization and design instrumentation. In addition, this thesis proposes an aspect-oriented-inspired paradigm, Colla-Gen, as a mechanism to improve design collateral reuse (e.g. physical design floorplanning or verification instrumentation), which forms another large portion of chip NRE costs.

Advisor: Bachrach, Jonathan
Asanovic, Krste