VictorJuiz/thesis huggingface dataset:
Identifying and Resolving Entities in Text

When automated systems attempt to deal with unstructured text, a key subproblem is identifying the relevant actors in that text---answering the "who" of the narrative being presented. This thesis is concerned with developing tools to solve this NLP subproblem, which we call entity analysis. We focus on two tasks in particular: first, coreference resolution, which consists of within-document identification of entities, and second, entity linking, which involves identifying each of those entities with an entry in a knowledge base like Wikipedia./nOne of the challenges of coreference is that it requires dealing with many different linguistic phenomenon: constraints in reference resolution arise from syntax, semantics, discourse, and pragmatics. This diversity of effects to handle makes it difficult to build effective learning-based coreference resolution systems rather than relying on handcrafted features. We show that a set of simple features inspecting surface lexical properties of a document is sufficient to capture a range of these effects, and that these can power an efficient, high-performing coreference system./nOur analysis of our base coreference system shows that some examples can only be resolved successfully by exploiting world knowledge or deeper knowledge of semantics. Therefore, we turn to the task of entity linking and tackle it not in isolation, but instead jointly with coreference. By doing so, our coreference module can draw upon knowledge from a resource like Wikipedia, and our entity linking module can draw on information from multiple mentions of the entity we are attempting to resolve. Our joint model of these tasks, which additionally models semantic types of entities, gives strong performance across the board and shows that effectively exploiting these interactions is a natural way to build better NLP systems./nHaving developed these tools, we show that they can be useful for a downstream NLP task, namely automatic summarization. We develop an extractive and compressive automatic summarization system, and argue that one deficiency it has is its inability to use pronouns coherently in generated summaries, as we may have deleted content that contained a pronoun's antecedent. Our entity analysis machinery allows us to place constraints on summarization that guarantee pronoun interpretability: each pronoun must have a valid antecedent included in the summary or it must be expanded into a reference that makes sense in isolation. We see improvements in our system's ability to produce summaries with coherent pronouns, which suggests that deeper integration of various parts of the NLP stack promises to yield better systems for text understanding.

Advisor: Klein, Dan
Pilot Zones: The New Urban Environment of Twentieth Century Britain

In the last third of the twentieth century, Britain underwent an urban transformation that was faster and more profound than any since the industrial revolution. Modernist housing schemes became gated communities. State managed shopping precincts became private out-of-town shopping malls. Derelict docklands became “enterprise zones” for fostering the financial service industry. A material world built from concrete began to give way to a world made of steel and glass. Using material from archives across Britain this dissertation discusses the role played by cities in producing, reflecting, and normalizing Britain’s post-social democratic settlement. The phrase “pilot zones” refers to the five spaces that act as case studies for this dissertation. The first of these two were policies. Enterprise zones, created by the Conservative government in 1981, were miniature tax havens in inner city areas, while National Garden Festivals were ambitious, state-directed garden shows in derelict urban areas that aimed to attract capital for urban redevelopment. The remaining three case studies — housing estates, shopping malls, and business parks — are built forms with histories that spanned much of the twentieth century. This dissertation looks at how they were privatized and re-imagined. Pilot zones created an environment that made particular political outcomes possible – and shut others down. The dissertation shows that the material basis for the privatized and securitized landscape of British cities at the millennium was assembled much earlier in the century for reasons that cannot be reduced to either structural economic change or the machinations of high politics. The built environment offers a new way of thinking about the sources of the culture and politics of the postwar period, one that not only avoids a dependence on the overly narrow and parochial term “Thatcherism”, but also is more tangible and accessible than the increasingly theistic term “neoliberalism.” Although Britain is the primary focus of my research, the dissertation uncovers many instances of transnational exchange or cooperation, either in ideas, policies, or techniques, particularly with the US and Hong Kong.

Advisor: Vernon, James
Evaluating the impact of support services on health and behavioral outcomes among adolescent mothers and their children in Mexico and Chile

Globally, 16 million children, about 11% of all births, are born to women aged 15 to 19 each year. Young mothers and their children bear a heavier burden of poor health and social outcomes compared to families in which the mother began childbearing later in life. The majority of teenage births occur in low- and middle-income countries. However, most research on interventions to improve outcomes among teenage mothers and their children is completed in high-income, Western countries. The social, economic and cultural contexts surrounding adolescent pregnancy and parenthood vary widely across countries. As a result, it is important to assess whether programs and policies that appear effective in high-income, Western countries maintain their effectiveness in other settings, where the majority of early childbearing occurs./nThe goal of this dissertation is to identify programs and policies that improve outcomes for adolescent mothers and their children. The first paper explores what it means to be an adolescent mother in rural Mexico by comparing indicators of socioeconomic status, maternal wellbeing and parenting practices of adolescent and older mothers, documenting social perceptions of young motherhood, and understanding young mothers’ perceptions of motherhood using quantitative and qualitative methods. The second paper uses a cluster-randomized controlled trial of a parenting education program, Educación Inical, in Mexico to assess whether the estimated effect of the parenting program on parenting behaviors and child cognitive development varies by the age at which the mother began childbearing. The final paper explores the association between having a child in center-based child care and parenting stress and child behavior among adolescent mothers and their children in Chile./nThe studies presented here find no evidence of improved outcomes among adolescent parents or their children of a parenting education program or center-based child care support. As such, interventions that have shown promise in Western countries and among populations not limited by age at first birth may not be easily transferable to young mothers in other settings. This research highlights an important gap in understanding how best to support adolescent mothers and their children. These studies also point to the need for research that clarifies adolescent mothers’ sources of adversity and opportunity in varying cultural, social and economic settings in order to appropriately target programs and policies. Additionally, it is critical that research on the impact of programs and policies that are hypothesized to improve outcomes for adolescent mothers and their children take place in locations where the majority of adolescent pregnancy and parenting occurs. Understanding what works to improve outcomes for adolescent mothers and their children across a range of contexts is necessary to meet the needs of millions of families who reside outside of where the evidence base has traditionally focused.

Advisor: Fernald, Lia CH
Repetitive Novelty: Italian Opera in Paris and London in the 1830s and 1840s

My dissertation connects music, politics, and society by focusing on the cultural life of the Théâtre Italien in Paris and the King’s Theatre in London. I claim that a culture of “repetitive novelty” emerged at the Italian opera houses as a means of managing the gap between the reality of a fractured, rapidly changing society and the ideals of a stable political and social situation. I argue that the need to stabilize rapid change was a particular civic imperative in Paris after the July Revolution and in London after the Reform Act of 1832. The worrying success of a repetitive work, the proliferation of ways to enjoy a celebrity, or the struggle of audience members to belong to an elite crowd all required people in Paris and London to reconcile their experiences of disorienting pace and change. My dissertation explores the ways in which politics pervaded social and fashionable life and the ways elite opera goers experienced, celebrated, and resisted change. The first chapter addresses the composition of the audience at the Théâtre Italien, drawing on archival documents written by opera-goers in combination with newspaper articles written about opera-goers. In the following chapter, I examine what these audiences listened to and saw in order to explore what the experience of repeated spectacles meant to them. My third chapter concerns the sheet music and objects that people bought to remember performances, which I use to open up the range of meaning that one opera singer could have in a burgeoning celebrity culture. Each of these chapters draws on a broad understanding of politics, which I treat as more than mere state governance and top-down official policy, but as something lived and experienced. I argue that the politics of intimate relations and the politics of music must be examined through texts and objects that provide glimpses into everyday life: letters bargaining for better seats, gifts between friends, gossip columns, and reviews of the twentieth performance of an opera. These ephemera, far from eschewing politics, supply the key to understanding a new and quietistic kind of modern political life.

Advisor: Smart, Mary Ann
Pseudoalignment for metagenomic and metatranscriptomic read assignment

The first step in many metagenomic and metatranscriptomic analysis workflows is assigning high-throughput sequencing reads to specific strains or transcripts, providing the basis for identification and later quantification. However, the high degree of similarity between the sequences of many strains and genes makes it difficult to assign reads at the lowest level of taxonomy, and reads are typically assigned to more general taxonomic levels where they are unambiguous. Recent developments in RNA-Seq analysis have found direct-match k-mer based methods to be extremely accurate and fast when comparing sequenced RNA-Seq reads to transcriptomes. While similar methods have been used in metagenomics before now, none are highly accurate at distinguishing similar strains, and none have been applied to metatranscriptomic data. We explore connections between metagenomic and metatranscriptomic read assignment and the quantification of transcripts from RNA-Seq data to develop novel methods for rapid and accurate quantification of microbiome strains and transcripts./nWe find that the recent idea of pseudoalignment introduced in the RNA-Seq context is highly applicable in the metagenomics and metatranscriptomics settings as well. When coupled with the Expectation-Maximization (EM) algorithm, reads can be assigned far more accurately and quickly than is currently possible with state of the art software, making it possible and practical for the first time to analyze abundances of individual genomes in metagenomics and metatranscriptomics projects.

Advisor: Pachter, Lior
Engineering Biomaterials and Biomolecules for Vascular Regeneration

Tissue engineering and regenerative medicine is a multidisciplinary field that combines the knowledge and technologies of biology, materials, chemistry and medicine among others. Within the realm of tissue repair and regeneration, vascular reconstruction, in particular, is influenced by both biophysical and biochemical cues and it is critical to fully understand how these cues interact with the physiological microenvironment. In this dissertation, we demonstrated how host vascular regenerative potential can be harnessed by optimizing vascular grafts from both the biomaterial and biochemical perspectives. We utilized and optimized electrospinning technology to create microfibrous vascular grafts. We showed that incorporating a fast degrading polymer into the vascular grafts effectively enhances cell infiltration without majorly compromising its mechanical and structural properties. Our in vivo data suggests that although the optimized vascular graft was able to induce the initiation of vascular regeneration, the process was accelerated and enhanced with the help of biochemical cues presented in the form of stromal cell-derived factor-1α (SDF-1α). In the presence of chemokine SDF-1α, the vascular grafts demonstrated better wall remodeling and long-term patency. This observation again highlights the significance of both biomaterial and biochemical effects. While the vascular grafts in our studies might recruit inflammatory cells, calcification which is a destructive complication typically associated with inflammatory response was not observed. The final part of this dissertation details our efforts in using protein engineering to broaden the biological application of SDF-1α by introducing a free cysteine residue on its C-terminus. We showed that the cysteine-modified SDF-1α exhibits a bioactivity different from its unmodified counterpart, the underlying mechanism of which needs to be elucidated in future studies. Taken together, this work is expected to provide insights into optimization of vascular graft platforms for broad therapeutic applications.

Advisor: Li, Song
A Multiscale Micromophic Molecular Dynamics: Theory and Applications

Multiscale simulation is a long standing dream in computational physics and materials. The motivation is natural: each single-scale model has its deficiencies. For example, microscale models such as Molecular Dynamics are limited to size in space and time; macroscale models such as Finite Element Method find difficulty recovering some fundamental physical phenomena such as materials defects. Simulations across scales are challenging because quantities in different scales have distinct properties. Mechanism needs to be harnessed to translate the information. Cross-scale communication is a typical two-way message passing: bottom-up and top down. Bottom-up approach is relatively straightforward, where statistical theory or homogenization is used to collect lower-scale information and interpret it in higher levels. On the other hand, top-down approach requires physical insights. Specifically, in a mechanical system, top-down message passing can be the response of the molecular system when macroscale boundary conditions such as distributed load are enforced. In this work, we reveal an intrinsic multiscale structure in solid materials. A “supercell” is introduced as a cluster of particles. Compare with “material point” in continuum mechanics, the “supercell” has internal degrees of freedom, which makes it equivalent to molecular systems. By introducing different force fields, we derive the dynamical equations for the different scales in the structure. The systematic multiscale framework solves the issue of top-down message passing by including quantities from different scales and connecting them in a uniform dynamical framework. We discuss the technical aspects in implementing the theory, i.e. constraints of the variables, integrators and temperature control. Numerical example of phase transition are presented to validate the theory, including bulk Nickel lattice under displacement and traction boundary conditions and Nickel nanowire with traction. Furthermore, based on the developed multiscale theory, we establish a computational model to achieve efficiency in realistic multiscale simulations. The model includes three parts: atomistic region, macro region and transition zone. Atomistic region is where physical details are desired and is simulated by Molecular Dynamics. Macro region only concerns macroscale deformable behaviors of solid materials, which can be calculated by various models depending on the problem of interests. We choose state-based peridynamics in this work as a demonstration. The essential part is the transition zone which is responsible for translating messages across different domains. The “supercell” developed in the previous theory is employed as a transition element to carry those different messages. With solid theoretic foundation, the cross-scale message translation is clearly characterized. We also construct a filter to solve the issue of high-frequency wave reflection. Examples of 1-D and 2-D wave propagations are presented to demonstrate the procedure of cross-scale transition and the effect of the filter.

Advisor: Li, Shaofan
Building Algebra One Giant Step at a Time: Toward a Reverse-Scaffolding Pedagogical Approach for Fostering Subjective Transparency Through Engineering Levels of Interaction With a Technological Learning Environment

The project brings together and studies the intersection of three ‘big’ ideas from educational research and practice. Firstly, this project is built on the constructivist assumption that meaningful learning occurs when students interact with educational materials that occasion problem solving and reflection. Secondly, this project elaborates on the theoretical construct of transparency by tracking its subjective development. Finally, the project reexamines the notion of scaffolding – the socio-cultural idea that novices receive expert intervention in the form of supports until mastery is achieved – specifically scaffolding that enables an authentic discovery- based learning experience. This work occurs within the context of early algebra. The story of learning algebra in schools is often told as the challenge of progressing from arithmetic to algebra. A main character in this story is the “=” sign or, rather, students’ evolving meanings for this sign (Herscovics & Linchevski, 1996). The balance metaphor is undoubtedly the most common visualization of algebraic propositions. Still, students’ persistent difficulty in transitioning from arithmetic to algebra suggests that the balance metaphor may not be the ideal method for building transparency for a relational understanding of equations (Jones, Inglis, Gilmore, & Evans, 2013). Therefore, this study investigates an alternative approach. Using a technological-enabled constructivist learning activity, Giant Steps for Algebra, students construct models of realistic narratives. As they build a virtual model of a problem situation, students discover technical principles for assuring the model’s fidelity to the situation. These construction heuristics, are precisely the conceptual foundations of algebra, and the activity’s situated intermediary learning objectives (SILOs). To enable to gradual development of transparency for Giant Steps, at each interaction level, the student discovers a SILO, and then the technology takes over by automatizing that SILO, thus freeing the student for further discovery. This activity architecture is called reverse scaffolding, because the tools relieve learners from performing what they know to do, as opposed to what they do not know to do. In a quasi-experimental evaluation study (Grades 4 & 9; n=40), reverse-scaffolding students outperformed baseline students, for whom the technical features were pre-automatized upfront, on measures of transparency for the SILOs. I thus conclude that discovery-based learning activities are advantageous, and that reverse-scaffolding technological activities can level the gradual development of subjective transparency.

Advisor: Abrahamson, Dor
Participation of retinal glucagonergic amacrine cells in the regulation of eye growth and refractive error: evidence from neurotoxins and in vivo immunolesioning

Growth is one of the fundamental characteristics of biological systems. The study of eye growth regulation presents an interesting window that allows for the investigation of the role of the visual environment on internal processes. We now know that there is an intricate circuitry within the eye, independent of higher brain processes, that controls the growth of the eye but more needs to be elucidated about these local regulatory circuits. An improved understanding of this circuitry is critical to developing new therapies for abnormalities in eye growth regulation such as myopia, which is impacting more and more individuals around the world each day and in its more severe from, is linked to potentially blinding ocular complications./n/nThe role of retinal glucagon, a neuropeptide, in the regulation of eye growth and refractive error has attracted the interest of researchers over the past 15 years yet there remain many unresolved questions. The research described in this dissertation aimed to elucidate the respective roles in eye growth regulation of specific subpopulations of retinal glucagonergic amacrine cells, which have been the subject of much speculation as the source of inhibitory growth signals, i.e. stop signals, yet not thoroughly investigated./nThe approach taken to investigate this problem is to ablate glucagonergic amacrine cells in vivo using different neurotoxins, and to examine how this affects the sign-dependent circuitry of eye growth regulation. In addition, with the advent of advancements in high resolution imaging and electrophysiology, we were able to characterize the effects of these neurotoxins on the region-specific and time-sensitive changes in the structure and function of the living retina./nThat the inhibitory response induced by imposed myopic defocus remains intact, in spite of total ablation of glucagon cells (Chapter 5) or elimination of the peripheral glucagon cells (Chapter 3) and other unintended adverse retina effects, compared to findings from previous studies involving QUIS (Chapter 2) of this thesis, is a novel finding. These results point to the same conclusion that glucagon cells themselves are not responsible for the decoding of the sign of optical defocus, but appear to have a role in fine-tuning of compensatory growth responses. The results of our experiments also suggest that the choroid may serve as an intermediate relay, and the altered anterior chamber development raise the further possibility that retina-derived growth modulatory factors also regulate the anterior segment, perhaps reaching this more remote site by diffusion forward through the vitreous chamber or via the uvea.

Advisor: Wildsoet, Christine F