VictorJuiz/thesis huggingface dataset:
Precise-first models for incorporating global constraints in coreference resolution [electronic resource]

Coreference resolution, the task of finding all textual mentions that refer to the same real-world entity, is crucial for many natural language processing applications, including information extraction, question answering, and summarization. Previous research has shown the importance of a rich feature space that models lexical, syntactic, semantic, pragmatic, and discourse phenomena. Incorporating this varied information during the resolution process is a key factor in high performance coreference resolution. This dissertation introduces a simple scaffolding framework that deploys strong features through tiers of models that perform significantly better than a single-pass model. The sieve architecture applies a battery of deterministic coreference models one at a time from highest to lowest precision, each model building on the previous model's cluster output. The approach makes use of global information through an entity-centric model that encourages the sharing of features across all mentions that point to the same real-world entity. I also show that this precise-first architecture can be applied to a statistical as well as rule-based classification. Replacing the rule-based sieves with a hybrid system, using a precise-first sequence of (supervised) statistical coreference resolution models in the same framework leads to state-of-the-art performance in coreference resolution. Finally, I show how this hybrid classifier can be made faster and with a smaller memory footprint to widen its practical applicability. Compared to the extensive work on entity coreference, the related problem of event coreference remains relatively under-explored, with minimal work on how entity and event coreference can be considered jointly on an open domain. I introduce a novel coreference resolution system that models entities and events jointly. The iterative method cautiously constructs clusters of entity and event mentions using linear regression to model cluster merge operations. As clusters are built, information flows between entity and event clusters through features that model semantic role dependencies. My system handles nominal and verbal events as well as entities, and the joint formulation allows information from event coreference to help entity coreference, and vice versa. All the approaches presented in the dissertation rely on two high-level insights: incorporating both local and global information effectively in coreference resolution, and using this information in a precise-first manner, allowing high-precision information to propagate throughout the system.

Keywords: Electrical Engineering.
Advisor: Jurafsky Dan
Garcia-Molina Hector advisor. Thesis advisor
Manning Christopher D. advisor. Thesis advisor
Widrow Bernard
Precisely localized guidance signals instruct dendrite branching and morphogenesis [electronic resource]

The establishment of a complex, cell type-specific dendritic arbor is crucial for many neurons to receive the appropriate inputs from their receptive fields and to properly function within a neural circuit. However, the immense complexity of dendrite morphology has made it far more challenging to study than the pathfinding of a single axon. In the model nematode Caenorhabditis elegans, the sensory neuron PVD establishes stereotypical, highly-branched dendrite morphology. Using genetic approaches, we identified a novel ligand-receptor complex of membrane adhesion molecules that is both necessary and sufficient to instruct spatially restricted growth and branching of PVD dendrites. The ligand complex SAX-7/L1CAM and MNR-1 function at defined locations in the surrounding hypodermal tissue, while DMA-1 and HPO-30/Claudin act as cognate co-receptors in PVD. Mutations in this complex lead to dramatic defects in the formation, stabilization, and organization of the dendritic arbor. Ectopic expression of SAX-7 and MNR-1 generates a predictable, unnaturally patterned dendritic tree in a DMA-1 and HPO-30 dependent manner. Both in vivo and in vitro experiments indicate that these molecules function as a ligand-receptor complex to instruct dendrite morphogenesis. Similar to developing axons, growing dendrites also encounter intermediate targets marked by guidance signals but must switch their response upon arrival so that they can move away and complete the next stage of development. During the development of wild-type PVD neurons, dendrites bypass a zone of high level SAX-7 without responding to the signal. We found that in mutants lacking KPC-1, a C. elegans Furin homolog, dendrites fail to escape from this intermediate target but are trapped in the area. Further analysis revealed that KPC-1 down-regulates the level of the branching receptor DMA-1 on dendrites by targeting it to late endosomes. In a kpc-1 mutant, the level of DMA-1 is abnormally high on dendrites, resulting in trapping of dendrites at locations where a high level of SAX-7 is present. Thus, precise regulation of guidance receptors creates flexibility of responses to guidance signals and is critical for neuronal morphogenesis. In summary, we identified a pair of skin-derived, precisely localized guidance molecules that instruct dendrite morphogenesis and their cognate neuronal receptors, as well as an intracellular mechanism that regulates membrane targeting of the dendritic receptor to ensure that signalling happens at the right place and right time.

Keywords: Biology.
Advisor: Shen Kang
Clandinin Thomas R. (Thomas Robert)
Luo Liqun
Prickle and spiny-legs isoforms of the prickle locus control the direction of tissue planar polarization through both microtubule dependent and independent mechanisms [electronic resource]

Planar cell polarity (PCP) signaling directs the alignment of cells within the plane of the tissue perpendicular to the apicobasal axis. In PCP signaling in flies, a group of proteins known as the core module polarizes each cell and communicates that polarity to neighboring cells to create local areas of alignment. Alone, the core module has no mechanism for sensing the axis of the tissue; however, the core module may be able to interpret global directional signals that can specify tissue axes including those from Fat, Dachsous, and Four-jointed. Identifying and understanding the mechanistic links between these global and core signals is an important goal in the field of PCP signaling. The prickle locus in flies produces multiple protein isoforms including Prickle (Pk) and Spiny-legs (Sple). Pk and Sple are part of the core module, but they are required in mutually exclusive tissues. Further, swapping which isoform is expressed in a given tissue reverses the direction of tissue polarity. This makes Pk and Sple interesting candidates for molecules that could allow the core module to interpret tissue wide signals thereby linking the direction of core module polarization to the tissue axis. Here, I use the developing wing and abdominal epithelia of the fly as model systems to investigate the cell biological mechanisms underlying the ability of Pk and Sple to determine the direction of tissue polarization. I show that in some tissues Pk and Sple specify the direction of tissue polarity by differentially controlling the polarity of an apical microtubule (MT) network. In other tissues, Pk and Sple control the direction of tissue polarity without affecting MT polarity. I explore the tissue-wide signals that provide directional cues in all of these tissues and discuss both MT dependent and independent mechanisms that Pk and Sple may use to interpret various global signals.

Keywords: Genetics.
Advisor: Axelrod Jeffrey (Jeffrey David)
Fuller Margaret T.
Lipsick Joseph Steven
Stearns Tim advisor. Thesis advisor
Probabilistic models for understanding regulation of translation [electronic resource]

The process of translation, whereby RNA is converted to protein, is an essential biosynthetic process requiring a large fraction of the cell's resources. However, our understanding of the regulatory mechanisms at this stage of gene expression is limited. Recent high-throughput experimental techniques and our development of probabilistic models for their analysis have allowed us to better explore translation efficiency, codon preferences, and mRNA secondary structure, as well as the interplay between these factors. In this work, we first present a queuing-theory-based probabilistic model for ribosome profiling data to extract robust estimates of protein synthesis rates and translation rates per codon, which can vary across individual genes. We use this model to show that local rates and translation efficiency are not affected by manipulations of tRNA abundance in physiological conditions in yeast; this reverses the direction of causality previously assumed to hold. Instead, we propose that initiation sequence signals, such as mRNA structure, could drive translation. To further understand varying translation rates, we also apply this model to human cells and present results on allele-specific ribosome pausing. Second, we delve deeper into RNA structure, which is important more broadly throughout the pipeline of protein expression and in many aspects of regulation control. However, accurately determining RNA structure at large scale is difficult with only experimental data or algorithmic methods. We present a conditional log-linear model that can incorporate information from multiple structure probing assays, and, although limited by the data quality, improves prediction accuracy over leading algorithms. Our method can also be used to derive new insight into biological processes influenced by RNA structure, such as translation.

Advisor: Koller Daphne primary advisor. Thesis advisor
Batzoglou Serafim advisor. Thesis advisor
Weissman Jonathan advisor. Thesis advisor
Problems in change-point detection [electronic resource]

This thesis discusses two projects about change-point detection problems. The first part of the thesis focuses on the comparison between the higher-criticism and the Berk-Jones statistics, both of which belong to an optimal sub-class among a larger class of statistics for testing Gaussian mixture models. Despite the asymptotic equivalence in the power, we heuristically compare the power of them by considering the rejection regions under nite sample settings, followed by numerical simulations that verify the argument. We deduce and prove the approximate formula for the tail probabilities of these two statistics, with which one can efficiently determine the threshold for any specific significance level (that is, the probability of getting a false positive). A slight generation of the derivation provides the formula for computing the power of both statistics under Gaussian mixture alternatives. Besides, we explore two applications of the problem: construction of a lower confidence bound for the proportion of the false null hypothesis and copy number variation detection in aligned DNA sequences. The second project is concerned with change-point detection in a stochastic process. The project is motivated by the Chernobyl disaster, which occurred in 1986. The general scientific question was whether radioactive fallout from the disaster had an impact on human health, specifically the viability of human fetuses, in southern Germany. Professor H. R. Lerche of the University of Freiburg provided data from 1980/01/01 to 1996/12/31 on live births and still births in several regions of southern Germany. We model the probability of stillbirths with a logistic model, and test if there is a change-point in the intercept after the accident. We derive approximations for the overall p-value of the test statistic by two different methods and compare them with numerical experiments to assess their performance. Finally we apply out method to the data, which do not provide sufficient evidence to infer an impact of the accident, in agreement with the results of previous studies.

Keywords: Statistics.
Advisor: Siegmund David
Lai T. L. advisor. Thesis advisor
Walther Guenther advisor. Thesis advisor
Profilin 1, stress granules, and ALS pathogenesis [electronic resource]

Amyotrophic lateral sclerosis (ALS), or Lou Gehrig's disease, is the most common adult-onset motor neuron disease. Upper and lower motor neurons mysteriously begin to degenerate in ALS patients resulting in muscle weakness rapidly progressing to paralysis and death within only a few years. There has been an explosion in the knowledge of the genetic causes of ALS in the last decade and pathogenic mechanisms are emerging (Chapter 1). In this dissertation I have attempted to contribute to the understanding of ALS mechanisms with the ultimate goal of helping to halt or slow the disease. With experiments in yeast and mammalian cells, I have discovered a novel role for the ALS-linked actin-binding protein profilin 1 in cellular stress granules and showed that ALS- linked profilin 1 mutant proteins have altered stress granule dynamics (Chapter 2). Profilin 1 now joins a growing list of ALS-linked proteins that transit into stress granules. Interestingly, many stress granule proteins are also observed in the neuropathology of ALS motor neurons. Stress granules have been proposed to act as crucibles of ALS pathogenesis, but their composition has been notably difficult to fully identify. Here I present a comprehensive literature review of all reports that have discovered stress granule-associated proteins (Appendix) and my progress towards the development of an unbiased method to determine the proteome of stress granules using an enzymatic tagging strategy in live human cells (Chapter 3). Finally, noncoding DNA repeat expansions in the C9orf72 gene were recently identified as the largest known cause of ALS to date. Here I present negative results from a genetic analysis in several hundred ALS patients and healthy controls of noncoding repetitive DNA regions in candidate genes known to cause other neurological and neuromuscular diseases. The lack of association with ALS in these genes suggests that they do not contribute to ALS pathogenesis (Chapter 4). Together, these experiments and results support the hypothesis that stress granules are intimately linked to ALS pathogenesis and provide a path forward towards further understanding of the role of stress granule biology in the normal cellular stress response and how their dysfunction might contribute to disease.

Advisor: Gitler Aaron D. primary advisor. Thesis advisor
Reimer Richard J. advisor. Thesis advisor
Wang Xinnan
Wyss-Coray Anton advisor. Thesis advisor
Programs that work [electronic resource] : mathematics teacher preparation programs in Japan, the United States, and Finland

This study examines successful and internationally renowned mathematics teacher training programs in Japan, the United States, and Finland. Using interview data from program instructors, prospective mathematics teachers, and program directors, as well as from my own experiences as a teacher and researcher in each of these countries, I examine themes in mathematics teacher education are consistent across these three cultural contexts, namely the relationship between theory and practice, authenticity, and the goals of mathematics teaching. In addition, I examine themes unique to each context, such as juku (Japan), English Language Learners (the United States), and equity versus elitism (Finland). I also look at the themes of relationships and expectations that are reflected in my personal account of learning to teach in Japan, the United States, and Finland. Despite recent emphasis on reform teaching methods, such as those proposed by the National Council of Teachers of Mathematics, and drastic reforms in the last decade through policies such as No Child Left Behind and Race to the Top, the United States continues to fall further behind in international comparisons of mathematics achievement. Believing that problems do exist within the American educational system, educational research leaders have pointed to the continued educational success of nations such as Finland and Japan in order to learn what features of these high-performing systems might be components for success. While there is great value in international comparisons, this viewpoint ignores high-performing programs in the United States and ignores the fact that not all overseas programs are equal. I argue that the exemplary cases are the most valuable, including the case of well-established programs in the United States as well.

Keywords: Education.
Advisor: Goldman Shelley
Boaler Jo
Lotan Rachel A. advisor. Thesis advisor
McDermott Ray (Raymond Patrick)
Propagation phenomena in reaction-advection-diffusion equations [electronic resource]

Reaction-advection-diffusion (RAD) equations are a class of non-linear parabolic equations which are used to model a diverse range of biological, physical, and chemical phenomena. Originally introduced in the early twentieth century as a model for population dynamics, they have been used in recent years in diverse contexts including climate change, criminal behavior, and combustion. These equations are characterized by the combination of three behaviors: spreading, stirring, and growth/decay. The main focus of mathematical research into RAD equations over the past century has been in characterizing the propagation of solutions. Indeed, these equations are characterized by the invasion of an unstable state by a stable state at a constant rate (for instance, the invasion of empty space by a population until the environmental carrying capacity is reached). In general, this can be characterized by the existence, uniqueness, and stability of traveling wave solutions, or solutions with a fixed profile which move at a constant speed in time. In general, the speed and shape of these traveling waves gives us the speed with which the stable state invades the unstable state. This thesis assumes the following trajectory, investigating two specific RAD equations: the Fisher-KPP equation, used in population dynamics, and a coupled reactive-Boussinesq system, used to model combustion in a fluid. For the former equation, we prove results regarding the precise spreading rate, and for the latter equation, we prove an existence result for a special solution that generalizes the traveling wave. In the first part of this thesis, we prove two results quantifying the precise speed of spreading for solutions to the Cauchy problem of the Fisher-KPP equation. The first of these results, concerning localized initial data, provides intuition for a lower order term obtained non-rigorously in. Specifically, we prove a quantitative convergence-to-equilibrium result in a related model, which has been used as a close approximation of the Fisher-KPP equation. The second of these results, concerning non-localized initial data and building on the work of Hamel and Roques, quantifies the super-linear in time spreading of the population. Here we compute the highest order term in the spreading for a broad class of initial data. In the second part of this thesis, we look at a coupled system that models combustion in a fluid, and we prove a qualitative propagation result. Unlike classical models, this relatively new system accounts for the effect of advection induced by the buoyancy force that results from the evolution of the temperature. Essentially, this means that we take into account the phenomenon that ``hot air rises.'' We exhibit a generalized traveling wave solution of this system, called a pulsating front, in two-dimensional periodic domains. To our knowledge, this is the first result regarding the existence of ``pulsating fronts'' in a coupled system.

Keywords: Mathematics.
Advisor: Ryzhik Leonid primary advisor. Thesis advisor
Menz Georg
Papanicolaou George advisor. Thesis advisor
Prospects for alternative fuels in heavy-duty diesel engines with sootless emissions [electronic resource]

The emission of carbonaceous particulate matter (soot) from work-producing devices is a global problem. Direct-injection, compression-ignited (Diesel) engines are a source of soot emissions that are problematic because they are mobile and operate regularly within populated regions. The subsequent effect on air quality is a serious health concern due to their small size and potential penetrability within the human body through the lungs. Furthermore, their contribution to atmospheric aerosols has a significantly negative effect on the environment. The problem with Diesel engine combustion is primarily a function of the fuel properties and subsequent combustion kinetics. The attraction of No.~2 Diesel fuel is that it is easily autoignitable, and for a typical direct-injection, compression-ignited engine this is a desirable quality. By employing a high-temperature combustion strategy, however, a host of alternative fuels become viable. This work addresses the prospects for using non-traditional fuels within a direct-injection, compression-ignited engine. A number of alternative fuels are identified as having potential, namely methanol, ethanol, butanol, dimethyl ether, synthesis gas, and methane (as a surrogate for natural gas). These are attractive because they are either oxygenated (and rely less on ambient gas entrainment) or gaseous (and can turbulently mix with ease). The combustion behavior of each fuel is examined by two means: First, a simple and well-controlled apparatus allows single-jet combustion to be imaged with a high-frame-rate, color digital camera. Second, a computationally efficient, quasi-dimensional jet model is used to explore each fuel with a detailed chemical mechanism, and includes a multi-step soot model. Once each fuel is examined independently, a subset are identified as forming too much soot such that their use within a production engine would emit levels above the EPA regulation standard. Two separate soot reduction methods are then explored within this work: dilution of the fuel with water, and dilution of the ambient gas with exhaust gas species. For each strategy, images are obtained that provide direct evidence of reduced soot formation. The jet model is then examined in detail to gain deeper insight into the potential mechanisms leading to the observed soot reduction.

Keywords: Mechanical Engineering.
Advisor: Edwards C. F. (Christopher Francis) primary advisor. Thesis advisor
Lutz Andrew E. (Andrew Edward) advisor. Thesis advisor
Wang Hai