VictorJuiz/thesis huggingface dataset:
Estimation in exponential families with unknown normalizing constant [electronic resource]

Exponential families of probability measures has been a subject of considerable interest in Statistics, both in theoretical and applied areas. One of the problems that frequently arise in such models is that the normalizing constant is not known in closed form. Also numerical computation of the normalizing constant is infeasible because the size of the underlying space is huge. As such, carrying out inferential procedures becomes challenging. In this thesis, the main object of study is some specific examples of exponential families on graphs and permutations, where the normalizing constant is hard to compute. Using large deviation results asymptotic estimates of the normalizing constant is obtained, and methods to estimate the normalizing constant are developed. In the case of graphs, this analysis gives some insight into the phenomenon of "degeneracy" observed in empirical studies in social science literature. In the case of permutations, this analysis is used to show the consistency of pseudo-likelihood.

Keywords: Statistics.
Advisor: Diaconis Persi primary advisor. Thesis advisor
Chatterjee Sourav advisor. Thesis advisor
Dembo Amir advisor. Thesis advisor
Evaluating software in environmental conflict resolution [electronic resource] : the role of MarineMap in coastal planning and decision making in California

Environmental managers and planners have become increasingly enthusiastic about the potential of collaborative technology such as decision support tools (DSTs) to improve environmental decision-making processes. Discussions about technology, however, rarely recognize the range of ways software can influence users' thinking and social dynamics in decision-making processes, in part because there are few empirical studies of processes that integrated technology tools. This mixed-methods study—which draws on data from approximately 60 semi-structured interviews, an online survey, the applications' log files, and videotaped meeting archives—examines how the geospatial DST MarineMap influenced participants' experiences during the implementation of California's Marine Life Protection Act (MLPA), producing a network of marine protected areas (MPAs) along the California Coast. More broadly, it argues for the importance of empirically observing how tools functioned and provides suggestions for evaluating software in environmental decision making. Overall, this research suggests that software should not be considered an objective source of information, but an active shaper of process dynamics. Implications include the need to evaluate tools as well as processes and the need for those implementing decision making processes to pay attention to the role software is playing.

Advisor: Ardoin Nicole M. (Nicole Michele) primary advisor. Thesis advisor
Martinez Janet K. primary advisor. Thesis advisor
Caldwell Margaret R.
White Richard
Evolution and coordination of gene expression through RNA-protein interactions [electronic resource]

Reprogramming of a gene's expression pattern by acquisition or loss of sequences recognized by specific regulatory RNA binding proteins has the potential to be a major mechanism in the evolution of biological regulatory programs. Systematic study of orthologous Puf3 proteins across eukaryotes revealed that the RNA binding specificity is highly conserved, yet the identity and functional commonalities of their RNA targets have extensively diverged. We identified six eukaryotic lineages within which RNA targets of Puf3 orthologs have been conserved over 250-500 million years of evolution. Focusing on Puf proteins and their targets across 80 fungi, we were able to construct a parsimonious model for their evolutionary history. This history entails changes in the number of Puf genes, modifications in the RNA binding specificity of the Puf proteins, and extensive and coordinated changes in the Puf targets and, in one remarkable case, switching of hundreds of mRNA targets from Puf3 to Puf4. Binding of Puf3 to more than 200 RNAs whose protein products are predominantly involved in the production and organization of mitochondrial complexes pre-dates the origin of budding yeasts and filamentous fungi and was maintained throughout the evolution of budding yeast. In filamentous fungi, more than 150 of the ancestral Puf3 targets were gained en masse by Puf4, with one lineage maintaining both Puf3 and Puf4 as regulators and another lineage losing Puf3 as a regulator of these RNAs. Gene expression profiling and sequence analysis suggest that the regulatory consequences of Puf4 in filamentous fungi are distinct from that of Puf3 for this set of RNAs in budding yeast. In filamentous fungi, Puf4 broadened its target set to include mitochondrial genes involved in the tricarboxylic acid (TCA) cycle among other functions, and Puf3 targets in these fungi diversified, notably gaining interactions with the mRNAs encoding the electron transport chain (ETC) complex I. These and many other changes involving just this handful of Puf proteins in fungi strongly support their role in coordinating gene expression through "RNA operons" and indicate an extensive involvement of RNA binding proteins and their RNA targets in the adaptation and reprogramming of gene expression. The timing and nature of these changes are distinct from those observed at the level of transcriptional control, suggesting that RNA-protein interactions provide an additional and rich infrastructure from which gene expression can be reconfigured. Beyond the static pictures of extant gene expression programs of currently employed model organisms, identifying the changes in gene expression programs throughout evolution will provide a unique window into the make-up, logic, and malleability of gene expression, ultimately contributing to our understanding of and ability to engineer this program.

Keywords: Biochemistry.
Advisor: Brown Patrick O'Reilly
Herschlag Daniel primary advisor. Thesis advisor
Straight Aaron
Yeh Ellen advisor. Thesis advisor
The evolution of genetic and epigenetic diversity in changing environments [electronic resource]

The production and maintenance of genetic and phenotypic diversity under temporally fluctuating selection has been a major focus of study in population genetics for more than five decades. In this thesis, I use analytical and computational models to gain insight into the relative roles of genetic and epigenetic diversity in adaptation to changing selection. The different chapters provide complimentary perspectives on the signatures of environmental volatility in the patterns of variation. Chapter 2 explores the evolution of epigenetic variation and its role in adaptation under changing selection pressures. Chapter 3 investigates the effect of recombination on the geometric mean principle under different environmental regimens and fitness landscapes. Two chapters of this thesis, Chapter 4 and Chapter 5 explore the evolution of phenotypic switching, a phenomenon widely documented in viruses, yeast and bacteria, where offspring can express a phenotype different from those of their parents. These chapters highlight the interplay of spatial and temporal environmental variability, offering new insights into how migration can influence the evolution of stochastic switching rates, epigenetic inheritance, and sources of phenotypic variation. Chapter 6 compares and contrasts how fluctuating selection shapes the rates of recombination, mutation and migration, highlighting surprising similarities in their evolutionary dynamics to changing selection. This chapter offers new insights into the role of the environmental duration, shape and randomness in predicting the long-term evolutionary advantage of the forces of recombination, mutation and migration. The models and analyses presented here provide a more complete understanding of the role of genetic and epigenetic diversity in adaptation to changing selection pressures.

Keywords: Biology.
Advisor: Feldman Marcus W. primary advisor. Thesis advisor
Fisher Daniel C.
Tuljapurkar Shripad
Exact simulation of jump-diffusions [electronic resource]

This thesis treats the problems of exact simulation and parameter inference for jump-diffusion processes. It has two parts. The first part develops a method for the exact simulation of a skeleton, a hitting time and other functionals of a one-dimensional jump-diffusion with state-dependent drift, volatility, jump intensity and jump size. The method requires the drift function to be C1, the volatility function to be C2, and the jump intensity function to be locally bounded. No further structure is imposed on these functions. The method leads to unbiased simulation estimators of security prices, transition densities, hitting probabilities, and other quantities. Numerical results illustrate its features. The second part develops and analyzes likelihood estimators for the parameters of a discretely-observed jump diffusion. We consider the case when the transition density of the process admits an expansion in terms of an infinite series. A randomization technique leads to an unbiased Monte Carlo estimator of the transition density and the likelihood function. We provide conditions under which resulting likelihood estimators are consistent and asymptotically normal. The method avoids the second-order bias of conventional discretization-based estimators. Unlike the estimators based directly on the density expansion, we do not require high-frequency observations. Numerical results confirm the method's properties.

Keywords: Management Science and Engineering.
Advisor: Giesecke Kay primary advisor. Thesis advisor
Glynn Peter W. advisor. Thesis advisor
Owen Art B. advisor. Thesis advisor
Experiments in environment and development [electronic resource]

Farmers are necessary agents in global efforts to conserve the environment now that croplands and pastures together constitute the largest terrestrial system on Earth. Accordingly, multimillion-dollar Payments for Environmental Services (PES) programs that subsidize farmers for conservation are gaining traction around the world. But whereas the history and theory of PES is already established, empirical evidence of its effectiveness in delivering additional and equitable conservation is still sparse. I empirically study additionality and equity of PES using data from a large-scale randomized experiment in Uganda, which I pair with a time series of Landsat satellite imagery. I find that farmers who participate in PES have significantly more photosynthetic vegetation and less non-photosynthetic vegetation on their farms as compared to farmers in the control group. I also find that participation rates among farmers are generally equitable across wealth quintiles. I then examine the factors that explain PES participation by eliciting individual trust and time preferences using a battery of behavioral experiments. I find the first evidence that farmers who exhibit a preference for proximate gains - present-biased preferences - are much more likely to participate in PES than those who show time-consistent or future-biased preferences, holding everything else constant. Finally, I extract substantive and methodological lessons from my first two studies, alongside similar investigations, so that decision makers in other developing countries have a road map for designing randomized experiments that rigorously examine conservation and development interventions.

Advisor: Field Christopher B. primary advisor. Thesis advisor
Ortolano Leonard primary advisor. Thesis advisor
Mooney Harold A. advisor. Thesis advisor
Sprenger Charles
Exploiting geometric information in camera networks [electronic resource]

Ubiquitous cameras have been widely deployed on smart phones and in smart environments. Because of the richness of the visual data that they provide, the key challenges are organizing and extracting useful information from the cameras. This dissertation explores different applications utilizing geometric information in camera networks to understand the visual data. These applications include image retrieval, image organization, tracking and detection. We first present a key point selection algorithm based on geometric consistency across images. Using selected key points can significantly reduce the length of the inverted index without hurting retrieval performance. Then we show a new compact image descriptor for large scale image search. Our proposed descriptor is an extension of Vector of Locally Aggregated Descriptors (VLAD) that incorporates weak geometry information into the current framework. We demonstrate the efficiency of our method where we achieve the state-of-the-art performance on existing benchmarks. We then propose an image organization algorithm based on constraints across two domains. By solving the co-clustering problem using the alternative optimization, the algorithm exhibits the state-of-the art performance on two datasets. After that we present a real time non-rigid face tracking system deployed in smart offices based on geometric constraints on facial landmarks, which analyzes behaviors of the computer user and helps avoid potential health issues. At last, we present an occupancy detection system deployed in a smart environment which utilizes a set of filters and the geometric consistency from multiple cameras to improve the accuracy of detections.

Keywords: Electrical Engineering.
Advisor: Aghajan Hamid K.
Poon Ada Shuk Yan
Özgür Ayfer advisor. Thesis advisor
Exploration of the regulatory networks of hybrid two-component systems in the model gut symbiont Bacteroides thetaiotaomicron [electronic resource]

This dissertation describes the regulatory capabilities of hybrid two-component systems in the model gut bacteria Bacteroides thetaiotaomicron. These unique proteins are important for carbohydrate sensing and consumption in the Bacteroides, but the full extent of their regulatory networks has not been previously explored. We created a chimeric hybrid two-component system that fused the well-characterized sensing domain of one, BT1754, to the uncharacterized regulatory domain of another, BT0366. We then used the BT1754 ligand, fructose, to functionally activate BT0366. Using genome-wide transcriptional profiling, we discovered that BT0366 both upregulates adjacent genes associated with the degradation of the plant polysaccharide arabinan, but also downregulates distal genes involved in mucin consumption. Using Chromatin Immunoprecipitation with high throughput sequencing, we then found that BT0366 binds directly to the genomic loci it helps regulate. Next, we developed tools for live-cell fluorescent microscopy of Bacteroides thetaiotaomicron in order to allow us to describe the physical positioning of hybrid two-component systems and their partnering molecules. This dissertation both describes regulatory activities of hybrid two-component systems in this common gut microbe and also provides tools for further study of subcellular localization in Bacteroides species.

Keywords: Microbiology and Immunology.
Advisor: Sonnenburg Justin
Amieva Manuel advisor. Thesis advisor
Huang Kerwyn Casey
Theriot Julie advisor. Thesis advisor
Exploring abstract interfaces in system-on-chip integration [electronic resource]

Modern mobile devices are marvels of computation. They can encode high-definition video, processing and compressing over 350MB/s of image data in real time. They have no trouble driving displays with as much resolution as a full laptop, and smart-phone manufacturers boast of running games with ``console quality'' graphics. Mobile devices pack all of this computational power into a 1-2W hand-held package by integrating a number of specialized hardware accelerators (IP) along with conventional CPU and GPUs in a system-on-chip (SoC). Unfortunately, creating these specialized systems is becoming increasingly expensive. Since hardware accelerators come from a number of different sources and design cycles, different accelerator blocks will often contain incompatible hardware interfaces. Therefore, a large portion of SoC design cost comes in the form of designers manually interfacing each accelerator into a system. This work includes everything from building custom logic to wire up a block, to developing the drivers and API needed to take advantage of the hardware. My research focuses on generating these interfaces, including the physical hardware used to tie IP blocks into a system and the associated software collateral. Leveraging recent trends such as High Level Synthesis and other hardware ``generator'' methodologies, I propose an IP interface abstraction and parameterization designed to describe the interface of most current IP blocks. By encoding this knowledge at a higher-level of abstraction, I am able to construct and demonstrate a hardware generator that maps an interface protocol description into synthesizable register transfer language (RTL), and that can automatically create hardware bridges between different interconnect standards. To ease the integration of the next generation of IP blocks---blocks that are automatically generated based off of user specification---I propose a set of interface primitives. When integrated into an IP generator, these primitives can automatically generate an interface that my interface system can tie to the rest of the system. I also demonstrate how the information stored in these types of primitives can be used to automatically generate a low-level software driver that manages access to the IP blocks. Finally, I show how the simulation environment provided with an IP generator can be used to provide a domain appropriate application programming interface (API) to drive the software. Using an image signal processor generator as my platform, I demonstrate the construction of a map between the simulation software and hardware driver that enables a full one-button flow from algorithm development to applications running on specialized hardware within a working system.

Keywords: Electrical Engineering.
Advisor: Horowitz Mark (Mark Alan) primary advisor. Thesis advisor
Kozyrakis Christoforos
Richardson Stephen
Exploring the complexity of pathway-level evolution [electronic resource]

This thesis explores how genes evolve together as integrated systems. In Chapter 1, I present conceptual background on the field of complexity and its relevance to this topic. Chapter 2 discusses theoretical work analyzing expected levels of divergence and polymorphism in the simple case of a linear metabolic pathway. Chapters 3 through 5 are gene-specific evolutionary studies in which I analyze the glycolytic enzymes phosphofructokinase, aldolase, and enolase in molecular functional terms. These gene-specific studies will contribute to a forthcoming empirical analysis of glycolysis at the pathway level.

Keywords: Biology.
Advisor: Watt Ward B. primary advisor. Thesis advisor
Feldman Marcus W. advisor. Thesis advisor
Fraser Hunter B. advisor. Thesis advisor
Extensions of Bayesian sequential partitioning for multivariate density estimation [electronic resource]

Density estimation is a fundamental problem in statistic, which can be used as a building block in statistical methods such as classification. Traditional approaches, such as the kernel method, have yielded accurate results when dealing with a moderate amount of data in a low dimensional space, but may perform poorly in higher dimension. Bayesian sequential partitioning (BSP) was proposed to overcome the drawback of traditional methods by applying scalable algorithms to estimate the probability density in higher dimension. The resulting estimate is a piecewise constant function supported on a partition that is learned from the data. In this work, two extensions/enhancements of BSP are proposed to broaden the area of its application. First, a smoothed version of the estimate is obtained by optimizing over a tensor-spline expansion of the log-density condition on the partition learned by BSP. Second, we develop a version of BSP that uses oriented cuts to produce non-rectangular partitions. By allowing more options to build the partition, our estimate is made invariant to the direction of data point distribution. Our numerical experiments show that the resulting estimate can achieve better approximation to the true density compared to standard BSP.

Keywords: Electrical Engineering.
Advisor: Wong Wing Hung primary advisor. Thesis advisor
Duchi John advisor. Thesis advisor
Gill John T.
False discovery rate control for spatial data [electronic resource]

In many modern applications the aim of the statistical analysis is to identify `interesting' or `differentially behaved' regions from noisy spatial measurements. From a statistical standpoint the task is both to identify a collection of regions which are likely to be non-null, and to associate to this collection a measure of uncertainty. Viewing this task as a large scale multiple testing problem, we present methods for controlling the clusterwise false discovery rate, defined as the expected fraction of reported regions that are in truth null. Our methods extend the recent work of Siegmund, Zhang, and Yakir (2011), and can be applied whenever the high level excursions of the noise process are well approximated by a (potentially inhomogeneous) Poisson process. Borrowing ideas from the Poisson clumping heuristic literature, we show that the widely used pointwise procedure generally fails to control the clusterwise FDR. We also present a general framework for incorporating various measures of cluster significance into the clusterwise false discovery control procedure. We show that incorporating cluster size can result in a significant increase in power.

Keywords: Statistics.
Advisor: Candès Emmanuel J. (Emmanuel Jean) primary advisor. Thesis advisor
Tibshirani Robert primary advisor. Thesis advisor
Siegmund David
Far From Black and White: The role of Race on Mother’s views of Emotional Intelligence Development in Children

This study aims to discover whether parental views of appropriate emotional expression and management development in children are affected by subculture within the US. Currently, many public and private educational institutions are devoting resources towards creating and implementing emotional intelligence curricula. Since the norms for emotional expression vary among cultures, it important to identify possible inconsistencies between curricula used at school and parental teachings in children’s homes. An understanding of whether racial or cultural backgrounds are a pertinent factor could be used to ensure compatibility between school and home. Data were collected through in-depth structured in person interviews with eighteen parents of children from two distinct self-identified cultural groups, Black parents of Black children age five to twelve and White parents of White children age five to twelve. Commonalities and differences were found between the two groups. Both groups of parents believed that children must learn to control their emotions just as they must learn to control their behavior, valued the emotional comfortableness of their children and viewed the ability to identify emotions in his or her self and in others as essential for their children to develop. It was also found that parents of Black children preferred their children to manage and express emotions in a more limited manner. This was in contrast to the views of parents of White children. Therefore, this study found a correlation between culture and parental views of appropriate emotional expression and management development in children.

Keywords: emotional intelligence
culture
race
children
Thesis
Advisor: Stipek Deborah
Cohen Geoff