VictorJuiz/thesis huggingface dataset:
On String-Similarity Estimation Problems

In this thesis, we study two widely used measures of string similarity: edit distance and dynamic time warping (DTW). We investigate alignment algorithms, metric embeddings, fast (approximation) algorithms, and communication complexity.
Results on Edit Distance: Edit distance is a fundamental distance metric between strings with applications throughout computer science. While the problem of estimating edit distance has been studied extensively, the equally important question of producing an alignment (i.e., the sequence of edits) has received far less attention. Somewhat surprisingly, we show that any algorithm to estimate edit distance can be used in a black-box fashion to produce an approximate alignment of strings, with modest loss in approximation factor and small loss in run time. Plugging in a previous result, we obtain an alignment that is a $(\log n)^{O(1/\varepsilon^2)}$ approximation in time $\tilde{O}(n^{1 + \varepsilon})$.
Closely related to the study of approximation algorithms is the study of metric embeddings. We present three results which together demonstrate the effectiveness of min-hash techniques in designing edit distance embeddings: (1) An embedding from Ulam distance (edit distance over permutations) to Hamming space that matches the best known distortion of $O(\log n)$ and also implicitly encodes sequences of edits; (2) Given an upper bound $K$ on edit distance, we show that embeddings of edit distance into Hamming space with distortion $f(n)$ can be modified in a black-box fashion to give distortion $O(f(\operatorname{poly}(K)))$ for a class of periodic-free strings; (3) A randomized dimension-reduction map with contraction $c$ and asymptotically optimal expected distortion $O(c)$, improving on a previous result.
Results on Dynamic Time Warping: In the second half of the thesis, we turn our attention to dynamic time warping (DTW), a close cousin of edit distance whose primary applications are as a similarity measure between time series.
We present the first strongly subquadratic algorithm for DTW in the low-distance regime. Our algorithm runs in time $O(n \cdot \dtw(x, y))$ for $x$ and $y$ of length $n$ over an arbitrary metric. Building on this, we present an approximation algorithm for $\dtw$ over an arbitrary $2$-hierarchically well-separated tree metric, providing a $\alpha$-approximation in time $\tilde{O}(n^2/\alpha)$. Additionally, we obtain the first approximation algorithm for edit distance to work over an arbitrary metric space, providing an $\alpha$-approximation in time $\tilde{O}(n^2 / \alpha)$, with high probability.
Finally, we provide near tight bounds on the one-way communication complexity of DTW -- an upper bound of $\tilde{O}(n / \alpha)$ bits for efficiently computing an $\alpha$-approximation of DTW between strings of length $n$, and a lower bound of $\Omega(n / \alpha)$ bits for the same problem.

Keywords:  Department of Computer Science
Stanford School of Engineering
Department of Computer Science
Algorithm
Edit Distance
Approximation Algorithm
Embedding
Thesis
Advisor: Charikar Moses
On the efficient analysis and sampling of mutant free energy landscapes

Molecular dynamics (MD) simulations are a computational technique capable of providing detailed atomic level understanding of molecular processes. They do this by numerically solving the microscopic interactions that govern these processes. Akin to a "computational microscope", MD simulations are used to predict and understand these protein free-energy landscapes. Given simulations from related mutant proteins, MD simulations could even predict the atomic level effects of mutations. These mutations might be oncogenic thereby increasing cell proliferation or they might abrogate an inhibitors' binding affinity or they might be completely benign. A structural and quantitative model for these mutations would be invaluable in both understanding the system and potentially designing personal therapeutics. However, MD simulations are very computationally expensive to converge and it is not immediately obvious how to compare multiple mutant simulations to one another in a statistically significant and efficient manner. In this thesis, I describe methods for analyzing and sampling mutant free energy landscapes. The first few chapters are dedicated towards building Markov state models (MSMs) for multiple protein kinases using milliseconds of aggregate simulation data. Currently, these are some of the largest kinase simulation datasets ever recorded. The latter chapters present several methodological advances on how to more efficiently predict mutational effects using a combination of enhanced sampling simulations and existing MSMs. This thesis attempts to merge the fields of Machine learning, enhanced sampling, and Markov state modeling for the efficient analysis and sampling of protein mutation landscapes.

Keywords: Chemistry.
Advisor: Martinez Todd J. (Todd Joseph)
Pande Vijay 
Frank C. W.
On the threshing floor : roadblocks and the policing of everyday life in Zimbabwe

Between 2012 and 2017, the Zimbabwean government dispatched police officers to mount roadblocks on the country's major roads and many of the minor ones. What had once been a ten-minute drive to work or to drop children off at school could now become an hour-long series of negotiations with the police officers who manned the roadblocks, in a country with no militias and no armed conflict. This dissertation presents a close examination of encounters at the roadblocks. Taking roadblocks as a key site of citizen/state engagement in the crisis era, it asks how people's conceptions of mobility, of governance, and of citizenship are expressed and transformed in the face of unrelenting policing. Emerging in the wake of staggering economic and sociopolitical crisis, roadblocks are central the state's performance of itself as such. Yet, as police and policed come together to negotiate the rituals of inspection, forms of sociality arise at the roadblock that prompt a different kind of understanding of citizenship, and challenge neat distinctions between police and policed. The dissertation is based on 21 months of ethnographic fieldwork I conducted in Zimbabwe - on the road, driving around in combis, buses, cars and trucks with motorists while they were stopped and inspected - as well as at police stations, government buildings, and other spaces in which the terms of everyday life are negotiated.

Keywords: Anthropology.
Advisor: Ferguson James
Ebron Paulla A.
Malkki Liisa H. (Liisa Helena) 
Tambar Kabir
Online sellers' offline environment : implications for platform strategy

How does a seller's local environment affect their behavior on digital platforms? The digitization of the economy has drastically lowered the costs of data storage, access, and transmission. Leveraging digital technologies, platform companies such as Amazon and Airbnb have created online marketplaces that have extended an unprecedented level of market access to individual entrepreneurs, whom we often refer to as sellers. Much of the existing research on digital platforms shows that platforms can dictate sellers' behavior through a variety of reward and punishment mechanisms, e.g., search ranking algorithms and surge pricing. However, a great amount of variation in sellers' behavior can be attributed to factors in their local environment -- factors outside the platform's control. Upon closer examination, one may realize that local factors could potentially explain many perplexing seller actions faced by platforms and their engineers. For instance, why do Uber drivers protest surge pricing? Why do e-commerce sellers continue to sell counterfeit products despite strict regulation? Why do Airbnb hosts refuse to interact with users even with algorithms rewarding host-user interactions? In this dissertation, I argue that factors such as sellers' cultural customs, local interactions, and perception of the law may serve to explain many of their behavioral patterns. These factors strongly affect sellers' behavior on digital platforms. Their behavior, in turn, influences a platform's growth trajectory and contains major social implications. Therefore, it is important for both platform designers and policymakers to pay attention to sellers' heterogeneous local environments in order to anticipate sellers' behavior, create appropriate designs, and devise sound policy.

Keywords: Management Science and Engineering.
Advisor: Eesley Charles 
Eisenhardt Kathleen M. 
Katila Riitta
Optical Kerr effect studies of hydrogen bonding and phase behavior in aqueous binary mixtures

The behavior of molecules in condensed phases involves complex considerations to fully describe the microscopic structure and dynamics. This is particularly interesting in complex liquids with inherent heterogeneity and in binary mixtures where the competition between the interactions between similar and dissimilar species greatly affects the microstructures of the liquid. The ubiquity of aqueous binary mixtures necessitates their study, particularly because the unique properties of water often manifests anomalously in the physical properties of binary mixtures. These changes in physical properties are the result of structural changes at the molecular level. In this thesis, the dynamical results from optical heterodyne-detected optical Kerr effect (OHD-OKE) experiments are reported for a series of aqueous binary mixtures. OHD-OKE is a nonresonant pump probe technique in which the bulk orientational dynamics of a liquid are measured via the time-dependent birefringence induced in the sample by an optical pulse. The OHD-OKE setup used in this thesis has the ability to measure dynamics over seven decades of time and eight decades of signal, which is an incredible window for a single experimental technique. Ultrafast pulses, which are necessary to have sufficient resolution, are generated by a Ti:Sapphire oscillator/regenerative amplifier. Multiple techniques including heterodyne detection and phase cycling are used to improve signal to noise, particularly at long time when signals are small. The theory behind OHD-OKE and a description of the experimental setup are given here. In addition to dynamical information, microstructural changes can be extracted from OHD-OKE data using the Debye Stokes Einstein (DSE) equation. The specific structures can be elucidated using complementary techniques. The remainder of the thesis is devoted to the aqueous binary mixtures of interest and the results from OHD-OKE and complementary techniques. First, a protic ionic liquid is compared to its aprotic analogue in order to better understand the role of hydrogen bonding in ionic liquids at various hydration levels. This work is further expanded to ionic liquids of varying chain lengths and anions in order to provide a deeper understanding of hydrophilicity and water saturation in ionic liquids. Finally, the anomalous phase behavior of the nicotine/water binary system is studied in order to elucidate the dynamics and microstructures associated with the lower critical solution temperature.

Keywords: Chemistry.
Advisor: Fayer Michael D. 
Bent Stacey 
Dai Hongjie
Optimization and decision-making under uncertainty

We consider several online and repeated decision problems with uncertainty features in resource allocation, energy storage management and internet advertising using worst-case and stochastic models. In the first part, we use worst-case models to design and analyze online algorithms that make irrevocable decisions without any future information. In the online resource allocation problem, a seller allocates items that can be produced at non-decreasing marginal costs per unit to buyers arriving in an online fashion. The objective is to maximize the social welfare which is the sum of the buyers' values less the total production cost. We then consider the energy storage management problem motivated by applications of energy storage networks in smart grids. Given renewable power supplies that generate power unpredictably, a grid operator wants to route power from these online power supplies to offline consumer demands using storage units subject to decay factors. The objective is to maximize the total utility of satisfied demands less the total production cost of routed power. In the second part, we consider the problems of budget management and contract design in internet advertising using stochastic models where a publisher allocates ad impressions given distributional information of advertisers' private valuations. In the budget management problem, the publisher manages advertisers' budgets on their behalf and adjusts allocations and payments such that the advertisers' cumulative expenditures are at most their budgets. Our goal is to study various budget management mechanisms on the bases of the publisher's profit, advertisers' utilities, incentive compatibility properties and uniqueness and stability of an equilibrium notion. For the contract design problem for selling online display advertisements, the publisher wants to sell ad impressions by bundling them via contracts before selling via auctions. The publisher wants to design a sequence of contracts that yields the maximum revenue, where advertisers are assigned priorities and buy bundles of impressions that are not yet purchased by those with higher priorities. Our contributions are both theoretical and empirical. We develop new algorithms and mechanisms with near optimality guarantees and provide characterizations of optimal solutions. We also provide empirical studies based on real datasets to validate our theoretical findings and derive further insights.

Advisor: Charikar Moses 
Saberi Amin 
Valiant Gregory
Optimization of CO2 Storage Systems with Constrained Bottom-Hole Pressure Injection

Of concern with CO2 storage in underground aquifers is the potential leakage of mobile CO2 into the regions above or surrounding the storage site. In this study, we perform an optimization study to minimize the mass of mobile CO2 at the top of the formation at the end of a typical CO2 storage project. We define and solve a comprehensive optimization problem involving well placement and control, along with appropriate constraints. The computations are performed within Stanford's Unified Optimization Framework.
We consider two different storage aquifer models - a channelized aquifer and an aquifer characterized by multi-Gaussian statistics. For both models, we perform a heuristic sensitivity study to estimate the required pore volume of the region surrounding the storage aquifer such that the bottom-hole pressure constraint is not violated. We consider different injection scenarios by varying the number of CO2 injection wells. Optimizations are performed using a combination of particle swarm optimization (PSO) and mesh adaptive direct search (MADS). Multiple runs are conducted to account for the stochastic nature of the optimizations. The sensitivity of the optimized objective to the number of injection wells is assessed for both models. We observe a 45% decrease in the objective function value as the number of wells is increased from one to four for the channelized aquifer model. For the Gaussian model, the corresponding decrease in the objective function value is 33%. We also perform a study to determine the minimum pore volume of the surrounding region that allows for a feasible injection strategy (in terms of maximum bottom-hole pressure), for each of the injection scenarios in both of the aquifer models. We observe that with four injection wells, a surrounding region of pore volume 17 times that of the storage aquifer is required for the channelized model, and 10 times that of the storage aquifer is required for the Gaussian model.

Keywords:  Energy Resources Engineering
School of Earth Energy &amp; Environmental Sciences
Optimization
CO2 Storage
CCS
Thesis
Advisor: Durlofsky Louis J.
Organothiol manipulation of copper for advanced electronics [electronic resource]

Organothiol manipulation of inorganic conductive materials like copper provides a powerful synthetic route towards low-dimensional technologically important materials with atomically well-defined structures. Two examples from my research are presented in this thesis dissertation to demonstrate how organothiol chemistry can be leveraged to manipulate copper for a two-dimensional (2D) interface and for a one-dimensional (1D) nanowire construct for advanced electronics. In the first example, the application of a hybrid layer containing organothiol at a 2D copper surface is demonstrated in which the hybrid layer manipulates the surface copper-oxide. The presence of defective copper-oxide remains a challenge for device technologies owing to its detrimental effects on the adhesion and stress-migration. Here we show a rapid, single-step, and organic-solvent-free thin-film deposition process that is capable of simultaneously reducing the weak copper-oxide while forming a densely connected copper/hybrid interface. A marked 9-fold improvement in interfacial adhesion is reported, along with a substantially suppressed copper stress-migration behavior during in-situ isothermal stress-relaxation experiments. The enhanced copper/hybrid interfacial adhesion and the improved copper stress-migration performance are attributed to the partial reduction of the ∼2 nm native Cu2O layer as demonstrated via atomic-resolution transmission electron microscopy. The hybrid-layer strategy we developed is expected to be effective in not only being a promising candidate for adhesion improvement to copper, but in promoting copper stress- and the related electro-migration performance. In the second example, I demonstrate the synthesis of 1D core-shell nanowires that have electrically conductive inorganic cores and insulating organic shells. Core-shell nanowires are synthesized via a facile solution process, leveraging the strong chemical interaction between organothiol molecular precursors and copper. Electronic properties of nanowires are characterized via electrochemical impedance spectroscopy, and elemental compositions are determined via x-ray photoelectron spectroscopy. Atomic arrangements inside the core-shell nanowires are unraveled via high-resolution x-ray diffraction in conjunction with molecular dynamic and density functional theory computations. Transmission electron microscopy provides a glimpse into the core-shell nanowire structure. We demonstrate, via this combinatorial approach, the exact atomic arrangement inside ultrathin nanowires comprising of only 5 inorganic atoms in the cross-section. The nanowires' unique electronic properties and our complete understanding of their atomically well-defined structures make them promising candidates for use in the next generation advanced electronics which are constantly seeking conductive features of diminishingly small size.

Keywords: Materials Science and Engineering.
Advisor: Dauskardt R. H. (Reinhold H.) primary advisor. Thesis advisor
Melosh Nicholas A. advisor. Thesis advisor
Salleo Alberto
"Out from behind this mask" : persona in African American poetry, 1830-1930

This dissertation examines the processes of African American poetry from the nineteenth century through modernism. Through original archival work, research on print cultures, and close formal analysis, it uncovers the contexts of production and reception in George Moses Horton's antislavery protest, Adah Isaacs Menken's neglected free verse, Paul Laurence Dunbar's metapoetic labor, and Jean Toomer's didactic meditations. These four chapters are grounded on a new framework for poetic identity that retheorizes the function of the poetic speaker, or persona, which gives a poem its central identity. Historically, persona has functioned as a masking device and marks an enduring problem in lyric theory that tends to conflate the identity of the poet with his/her constructed poetic identities. Persona in African American Poetry uses this conflation to explain something fundamental about black poetic expression: if the guiding principle and conventional wisdom of African American literary studies tends toward binaries—between authenticity and imitation, or white standards and black discourse—this dissertation shows, contrariwise, how black poets actually turned to more complicated stances and multiple identities. Persona in African American Poetry thus addresses the politics of canonization, recovering personae that have been excluded from criticism and pedagogy because they often contradict and complicate our understanding of a "racially authentic" black literature.

Advisor: Fishkin Shelley Fisher 
Jones Gavin Roger
Greene Roland
Overcoming challenges to incorporation of inertial sensors in an epitaxial encapsulation process

This work presents a deep investigation of one of the primary challenges to fabricating high performance inertial sensors - stiction. We begin with a summary of what stiction is, and a review of some of the past work understanding this problem and ways to over come it. We continue with a discussion of how the problem manifests itself in the Stanford Epi-Seal process, and the particular considerations of this problem. Our work begins with an experimental investigation of the process and in-use stiction problems in our devices. We develop design guidelines to assist future designers based upon the results of the experiments. Furthermore, we investigate the causes of stiction, and suggest ways in which the baseline process stiction may be improved in future work. A result of this investigation is a more formal understanding of stiction, and a reliable set of test structures and processes. We utilize the methodologies developed in the first experimental section, along with the test procedures to develop anti-stiction solutions. We first examine the common anti-stiction solutions, and determine that they are not applicable to the epi-seal process. Instead we thoroughly investigate mechanical structures which help dramatically reduce the stiction. We also develop models of the device behavior and adhesion which help us extend our understanding of stiction and make predictive assessments in the future. The epi-seal process presents an interesting platform for harsh environment devices. We examine the behavior of the principal failure mode (stiction) at high temperatures and under high-g shock inertial impacts. We demonstrate the suitability of the devices, and investigate some surprising results that emerge. We also investigate some other device parameters under these conditions. Lastly, we describe some of the high-speed, time-domain measurement systems used to collect the data used throughout this work. We briefly discuss the operational principle of several typical MEMS characterization tools, and outline the benefits and limitations. We compare these to data analysis techniques in the time domain, and show how many of the same techniques are used, but with different constraints.

Keywords: Mechanical Engineering.
Advisor: Kenny Thomas William 
Senesky Debbie 
Tang Sindy (Sindy K.Y.)