VictorJuiz/thesis huggingface dataset:
Algorithmic market design [electronic resource]

This thesis consists of two essays that exploit algorithmic techniques to solve two matching market design problems. The first essay introduces a simple benchmark model of dynamic matching in networked markets, where agents arrive and depart stochastically and the network of acceptable transactions among agents forms a random graph. The main insight of our analysis is that waiting to thicken the market can be substantially more important than increasing the speed of transactions. We also show that naive local algorithms that maintain market thickness by choosing the right time to match agents, but do not exploit global network structure, can perform very close to optimal algorithms. Finally, our analysis asserts that having information about agents' departure times is highly valuable. To elicit agents' departure times when it is private, we design an incentive-compatible continuous-time dynamic mechanism without transfers. The second essay extends the scope of random allocation mechanisms, in which the mechanism first identifies a feasible "expected allocation" and then implements it by randomizing over nearby feasible integer allocations. Previous literature had shown that the cases in which this is possible are sharply limited. We show that if some of the feasibility constraints can be treated as goals rather than hard constraints then, subject to weak conditions that we identify, any expected allocation that satisfies all the constraints and goals can be implemented by randomizing among nearby integer allocations that satisfy all the hard constraints exactly and the goals at least approximately. We show that by adding ex post utility goals to random serial dictatorship, we can construct a strategy-proof mechanism with the same ex ante utility that is nearly ex post fair.

Keywords: Economics.
Advisor: Milgrom Paul R. (Paul Robert)
Jackson Matthew O. advisor. Thesis advisor
Roth Alvin E.
Algorithms for decoding cancer genomes [electronic resource] : phylogenetic inference and haplotype assembly

The field of cancer genomics is expanding rapidly due to major advancements in the sequencing technologies. Only a decade ago, the cost and limited throughput of DNA sequencing made the study of cancer genome alterations at base-pair resolution infeasible. Today, whole-genome sequencing of tumor populations is commonplace. Cancer evolves through cycles of cell damage and a series of clonal expansions, marking the genome with new alterations along the way. To unravel the life history of cancer genomes, new computational methods are needed to take advantage of the wealth of whole genome sequence data now available. In this dissertation, I first describe my work developing computational methods for studying the role of early neoplasias in breast cancer evolution and show how these methods can reveal robust clonal lineages and identify cancer progenitor mutations. Next, I describe a probabilistic approach for haplotype reconstruction of an invasive breast carcinoma genome using long DNA fragments from Moleculo sequencing technology. I show how cancer-specific aneuploidies can be leveraged to achieve megabase-length haplotypes with high accuracy. Finally, I demonstrate applications of phase information for detecting false somatic variant calls, and for identifying and phasing segmental duplications.

Advisor: Batzoglou Serafim primary advisor. Thesis advisor
Dill David L. advisor. Thesis advisor
Sidow Arend advisor. Thesis advisor
Algorithms for unsymmetric cone optimization and an implementation for problems with the exponential cone [electronic resource]

Symmetric cone optimization subsumes linear optimization, second-order cone optimization, and semidefinite optimization. It is of interest to extend the algorithmic developments of symmetric cone optimization into the realm of unsymmetric cones. We analyze the theoretical properties of some algorithms for unsymmetric cone problems. We show that they achieve excellent worst-case iteration bounds while not necessarily being practical to implement. Using lessons from this analysis and inspired by the Mehrotra predictor-corrector algorithm, we extend the homogeneous implementation ECOS to handle problems modeled with Cartesian products of the positive orthant, second-order cones, and the exponential cone, and we empirically validate its efficiency.

Advisor: Saunders Michael
Ye Yinyu primary advisor. Thesis advisor
Gerritsen Margot (Margot G.) advisor. Thesis advisor
An Engineering Student's Autoethnography: Preparing Engineering Students to Work on Taboo Topics in the Service of Communities

Engineers create and implement technologies that provide solutions to some of the most pressing problems in the world today. Engineering education, or the formal training of engineering students, is integral in preparing these engineers to go out into an increasingly globalized world. It has become crucial that engineers are prepared for a wide array of situations outside of a purely technical role. From this, comes a need to bridge the gap between engineering education theory and practice, and study of whether these types of interactions, between engineering students and international communities, are worthwhile and equitable for both parties. This paper uses autoethnography as a method to analyze and distill a framework for preparing engineering students working on what are considered to be “taboo” topics in international development context.
Looking at engineering students working on international development projects in sanitation and hygiene stresses the importance of the framework with which one approaches the issue: working with the community, rather than working for them (Hariharan 2011). The metrics of assessment are twofold: first, global preparedness, or “the readiness to engage and effectively operate under uncertainty in different cultural contexts to address engineering problems” and second, global competency, or “development of one’s skills and attitudes in successfully interacting with persons of diverse backgrounds” (Streiner et al., 2014) have recently been brought forward into the discussion. This paper, through the methodology of autoethnography, will use skills derived from these two metrics of global preparedness and global competency to understand how an engineering student, the author of this thesis, worked with an community on a taboo topic.

Keywords: Graduate School of Education
Engineering Education
Taboo
Gujarat
Thesis
Advisor: Wotipka Christine Min
Willinsky John
Naim Kamran
An Evaluation of the Analogy Between Nuclear and Cyber Deterrence

The nuclear-cyber deterrence analogy is a popular and controversial comparison to make in American military, policymaking, and academic circles. Leaders in the field, many of who grew up during the Cold War, often draw the parallel to make sense of the impacts of strategic cyber weapons. Analogizing strategic cyber weapons to nuclear weapons has a powerful surface allure; these weapons have intercontinental range, near instantaneous delivery, and a growing potential for destructiveness. In particular, applying nuclear deterrence frameworks to cyberspace is appealing because it promises a way to mitigate a serious emerging threat. However, the analogy is flawed. Nuclear weapons represent a revolution in military affairs that developed into a strategic deterrent because of its unique characteristics. These characteristics include the sheer destructiveness of a single nuclear weapon, the assuredness of that destruction, and the debate over how to use nuclear weapons. Strategic cyber weapons have neither matured as a revolution in military affairs nor developed the characteristics and debate over their use to the same extent as nuclear weapons. Therefore, at this point, it is not possible to make the nuclear-cyber deterrence analogy and basing policy on the assumption that the analogy is correct is erroneous and potentially even dangerous. In the future, as the world becomes more cyber-dependent and the technology of strategic cyber weapons develops, it may be possible that the analogy will become more credible, at which point it will be necessary to re-evaluate it.

Keywords: CISAC
Strategic Cyber Weapons
Nuclear Weapons
Deterrence
Revolution in Military Affairs
Center for International Security and Cooperation
Thesis
Advisor: Blacker Coit D.
An Investigation of Mysterious Oscillations in Black Hole Accretion Disks

We give an overview of the physics and observational signatures of accretion disks surrounding black holes. By observing the hot, accreting matter falling into the black hole, astronomers have discovered broad peaks in the X-ray power spectral densities of these objects known as quasi-periodic oscillations (QPOs). We detail this phenomenon and discuss various theoretical models proposed to explain it. We also present results on the role of the magnetic fields on normal mode trapping in the disk. Finally, while most QPOs have been observed in stellar mass black hole binaries ($M\sim 1-100 \,M_{\odot}$), we will also elaborate on the observational signatures of super-massive ($M\sim 10^6 - 10^{10} M_{\odot}$) black holes in active galactic nuclei (AGN) and the possibility of using optical power spectra to hunt for QPOs.

Keywords:  Department of Physics
black holes - accretion disks
accretion - active galactic nuclei
AGN - quasi-periodic oscillations
QPO - X-rays: binaries
Thesis
Advisor: Wagoner Robert
Blandford Roger
Analog circuit start-up behavior analysis [electronic resource] : an interval arithmetic based approach

Analysis of electronic circuit start-up behavior is an interesting problem from both theoretical and practical viewpoints. Although the introduction of ternary logic has effectively solved the problem for digital circuits, we have not seen a similar solution for analog circuits. This work introduces a new method that efficiently solves this problem for small analog circuits. The proposed method treats electronic circuits as non-linear dynamical systems. Particularly, we introduce a novel reformulation of the dynamical systems theory and use this new framework to investigate the relationship between a circuit's start-up behavior and its DC solutions. These theoretical considerations culminate in a rigorous (i.e. non-heuristic) algorithm that effectively reduces the original problem into an equation solving problem. The practical side of our work is concerned with solving the resulting equations. In general, finding the complete solution set of a system of algebraical (i.e. non-differential) equations is an NP-hard problem, but some approaches do work well for certain types of problems. Our method uses an interval arithmetic based branch-and-bound algorithm that is known to be effective for solving equations with smooth non-linearities. We further enhanced this algorithm by incorporating (1) a novel affine relaxation procedure, (2) a graph based constraint propagation technique, and (3) a novel graph-decomposition algorithm to improve the scalability of the proposed method. With these improvements, the proposed method easily handles circuits with dozens of state variables.

Keywords: Electrical Engineering.
Advisor: Horowitz Mark
Murmann Boris advisor. Thesis advisor
Osgood Brad advisor. Thesis advisor
Analysis and design of shrouded turbines [electronic resource]

A shrouded wind turbine consists of a rotor that is enclosed within an aerodynamically shaped flow-accelerating device. This work aims to improve the theoretical knowledge of shrouded turbines and to establish a better understanding of the underlying aerodynamics. A cost-effective tool is developed and utilized to improve the design of shrouded turbines. Specifically, the aerodynamics of such a system is investigated using a range of modeling fidelities and a technique for rapid design is also developed and used to demonstrate considerable gains in power extraction.

Keywords: Aeronautics and Astronautics.
Advisor: Alonso Juan José
Duraisamy Karthikeyan
Iaccarino Gianluca advisor. Thesis advisor
Lele Sanjiva K. (Sanjiva Keshava)
Analysis and modeling of large-scale systems [electronic resource] : taxis and social polling

Technological advances in transportation have fundamentally revolutionized the way people live and move. The foundational blocks of technology are: (i) cheap and fine-grained sensors of movement, (ii) a ubiquitous communication network for collecting data from the sensors, (iii) a cloud-based platform for storing, processing and analyzing the movement data, and (iv) a high penetration of smart phones over which to offer novel transportation-based services. Thus, in a short span of time, the way people commute in public transit or hire car systems has changed dramatically; the way packages and food is delivered is changing; and even the travel and leisure industry is being disrupted. These massive societal trends have also generated many interesting technical challenges, notably in terms of "a big data system for things that move". In this thesis, we describe the challenges of collecting and processing real-world movement data from a large-scale network of vehicles and passengers. We then describe a big data system and algorithms for healing noisy real-world data and then processing, analyzing and visualizing it. While we have made use of such a system for our analysis, our key contribution is a methodology for modeling large-scale movement processes based on data. Using these models we are able to answer questions such as: What factors affect the operation of a large-scale transportation network? What factors limit the efficiency of a large-scale transportation network and how can the efficiency be improved? We consider the above questions in the context of data from New York City yellow taxicab rides for 2013, which has over 170 million trips from a fleet of more than 14,000 taxis. From an analysis of the data we obtain, in addition to insights about the operation of the taxi fleet, the following: (i) correlations between taxi operation and cultural activities in the city, (ii) economic reasons for shift change times, (iii) the impact of severe weather on travel in the city, and (iv) the impact of congestion on taxi trips. Using our modeling framework, we consider methods of enhancing the efficiency of the taxi system in terms of reducing idle time for the taxis and, hence, using a smaller number of vehicles for handling the same number of rides. We obtain a network-flow based model for reassigning trips to taxis which reduces the number of taxis required to fulfill all trips in a city. One finding of our model is that only 72% of yellow taxicabs are necessary to finish all observed trips in New York City, following the same schedule of pickups and drop-offs. Furthermore, after investigating trips reassigned by our model, we discover patterns which provide useful insights into possible directions of improvement for the current taxi system.

Advisor: Prabhakar Balaji
Bayati Mohsen advisor. Thesis advisor
Katti Sachin
Analysis of genomic variants for investigating the genetic etiology of disease [electronic resource]

The study of genomic variation within human populations is critical for elucidating the genetic factors that contribute to disease. Identifying and characterizing the genetic architecture of disease advances clinical care by facilitating the development of novel diagnostic tools, the identification of new therapeutic targets, and the practice of personalized treatment for genetic syndromes. The massive volume of genetic data generated by modern genotyping technologies, combined with the informatics challenges of filtering and interpreting these noisy measurements, represent significant obstacles to genomic research. These technical issues necessitate the development of computationally efficient methodologies that leverage raw genotype data for the comparative genomic analysis of complex phenotypes across human subpopulations. In this dissertation, I describe my contributions towards the biomedical study of genetic syndromes using high-throughput genotyping technologies. First, I discuss methods for studying the genome evolution of pre-malignant cancer lesions during progression to breast cancer. Second, I describe algorithms for performing highly accurate variant validation in genomic studies using next generation sequencing. Finally, I present methods for identifying novel disease susceptibility loci in complex diseases using identity by descent mapping in large case-control cohorts.

Keywords: Biomedical Informatics.
Advisor: Batzoglou Serafim primary advisor. Thesis advisor
Pritchard Jonathan (Jonathan K.) advisor. Thesis advisor
Sidow Arend advisor. Thesis advisor
Angle-Resolved Photoemission Spectroscopic Study of Cuprate Fermiology in Bilayer Bismuth Strontium Calcium Copper Oxide

Twenty-nine years have passed since the discovery of high-transition-temperature (Tc) superconductivity, yet no microscopic theory has successfully explained this remarkable phenomenon. Unlike conventional superconductivity where an energy gap opens at the Fermi level as we cool below Tc, high-Tc superconductivity in cuprates is accompanied by a mysterious pseudogap regime, where an energy gap is observed even above Tc. Both the nature of pseudogap and its effect on such high Tc are poorly understood, so this thesis work aims to probe the pseudogap and its relationship with high-Tc superconductivity, using angle-resolved photoemission spectroscopy (ARPES). We focus on the part of the phase diagram for bilayer Bi-Sr-Ca-Cu-O (Bi2212) near a putative quantum critical point (QCP), where pseudogap is believed to emerge from superconductivity at T = 0 K. Results have verified the phase competition between pseudogap and superconductivity. Data also support a conjectured reentrant phase boundary under the superconducting dome. In addition, we discover a robust gap suppression near antinodal momenta at T << Tc, whose origin is not pseudogap; rather, the suppression is either an intrinsic signature of d-wave superconductivity or is related to a novel order near the QCP. Close to this critical doping, we also observe no ARPES signature of particle-hole symmetry breaking by the pseudogap. The above findings provide important new insights of superconductivity, pseudogap and possibly new ground-state orders near the QCP.

Keywords:  Department of Physics
ARPES
high-Tc superconductivity
cuprate Fermiology
Bi2212
energy gap
d-wave superconductivity
pseudogap
quantum critical point
antinodal gap suppression
particle-hole symmetry
crystal growth
Thesis
Advisor: Shen Zhi-Xun
Fisher Ian R.
The animal city [electronic resource] : remaking human and animal lives in America, 1820-1910

"The Animal City: Remaking Human and Animal Lives in America, 1820-1910" examines the important role of animals in nineteenth century American cities and traces the transformation of urban animal populations and human relationships with animals into the twentieth century. In so doing, it also examines larger social, cultural, political, legal, and economic change. American cities were once full of a variety of domesticated, semi-domesticated, and undomesticated species of animals. By the early twentieth century, however, the range of human-animal relationships and the geography of certain animal populations in cities were utterly transformed. This project seeks to understand what happened in those intervening decades and to recover the lost worlds of urban animal life and human-animal relations. Animal policy became a major form of governmental regulation in the lives of urban Americans in the nineteenth century, effected through new laws and new means of enforcement. Ideas of sanitation, refinement, and morality shaped animal policy profoundly, bolstered by the development of public health agencies, law enforcement, and the spread of early forms of urban zoning. Understanding nineteenth century urban animal policy also helps explain certain aspects of urban development and environmental inequalities into the twentieth century and up to the present. Many cities continue to show the invisible scars of this environmental history of animal regulation and exclusion. In some ways this is also the story of an emerging chasm between consumers and the animals they consume. Urban residents in nineteenth century America experienced the disappearance of livestock alongside the growth of pet ownership and pet culture. Together, the layers of change in urban animal populations in nineteenth century America marked notable remaking of human and animal life.

Keywords: History.
Advisor: White Richard
Frank Zephyr L.
Winterer Caroline
Aperiodic plasmonics [electronic resource] : manipulating light with nanostructured groove arrays on metallic surfaces

In the age of computers, there has been growing interest in many areas of science and engineering to use numerical techniques to explore problems that are mathematically or analytically intractable. In photonics specifically, there is a desire to design and realize non-periodic nanophotonic structures that outperform their periodic counterparts. One major obstacle to this goal is the necessity to solve the computationally expensive Maxwell's equations repeatedly over a vast parameter space. Here, we will apply the technique of numerical optimization to design aperiodic plasmonic nanostructures. Plasmonics, the study of driven collective oscillations of free electrons in metals, provides for optical modes with subwavelength footprints and is a promising compromise between the small world of electronics and the fast world of photonics. It is well known that nanostructured grooves and slits on a metallic surface are very strong generators and scatterers of surface plasmons, yet the geometries involved make exact analytical solutions impossible. The first step toward designing aperiodic plasmonic groove structures is to identify the fundamental building block of such structures, the metal-air groove, and simplify its mathematical representation so that calculations can be performed very quickly. After the building blocks are described in sufficient detail, the next step is the mathematical model that relates the individual building blocks together in a complete structure. We develop a computation strategy based on a transfer matrix model that can be used to calculate the plasmonic scattering properties of a number of closely spaced grooves to acceptable accuracy with extreme speed. Having characterized the building blocks and the model that glues them together, we apply these results, together with an optimization procedure, to design interesting aperiodic plasmonic groove structures. We first demonstrate a unidirectional launcher of surface plasmons from normally incident light with an extinction ratio of 55 to 1 using only five grooves. The unidirectional launcher is a great starting point due to its simplicity -- relatively few grooves are needed and there is only one operational wavelength, and yet the parameter space is already large enough to necessitate numerical optimization. Building on top of these results, we will conclude with an investigation of structures that split light into specific regions depending on their wavelength. This thesis demonstrates the ability to control the scattering and localization of plasmons using very few carefully chosen scattering elements, and the work presented here can be harnessed to design the next generation of subwavelength photonic devices.

Keywords: Electrical Engineering.
Advisor: Brongersma Mark L. primary advisor. Thesis advisor
Fan Shanhui
Vuckovic Jelena advisor. Thesis advisor