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Description
The ability to design high performance buildings has acquired great importance in recent years due to numerous federal, societal and environmental initiatives. However, this endeavor is much more demanding in terms of designer expertise and time. It requires a whole new level of synergy between automated performance prediction with the human capabilities to perceive, evaluate and ultimately select a suitable solution. While performance prediction can be highly automated through the use of computers, performance evaluation cannot, unless it is with respect to a single criterion. The need to address multi-criteria requirements makes it more valuable for a designer to know the "latitude" or "degrees of freedom" he has in changing certain design variables while achieving preset criteria such as energy performance, life cycle cost, environmental impacts etc. This requirement can be met by a decision support framework based on near-optimal "satisficing" as opposed to purely optimal decision making techniques. Currently, such a comprehensive design framework is lacking, which is the basis for undertaking this research. The primary objective of this research is to facilitate a complementary relationship between designers and computers for Multi-Criterion Decision Making (MCDM) during high performance building design. It is based on the application of Monte Carlo approaches to create a database of solutions using deterministic whole building energy simulations, along with data mining methods to rank variable importance and reduce the multi-dimensionality of the problem. A novel interactive visualization approach is then proposed which uses regression based models to create dynamic interplays of how varying these important variables affect the multiple criteria, while providing a visual range or band of variation of the different design parameters. The MCDM process has been incorporated into an alternative methodology for high performance building design referred to as Visual Analytics based Decision Support Methodology [VADSM]. VADSM is envisioned to be most useful during the conceptual and early design performance modeling stages by providing a set of potential solutions that can be analyzed further for final design selection. The proposed methodology can be used for new building design synthesis as well as evaluation of retrofits and operational deficiencies in existing buildings.
ContributorsDutta, Ranojoy (Author) / Reddy, T Agami (Thesis advisor) / Runger, George C. (Committee member) / Addison, Marlin S. (Committee member) / Arizona State University (Publisher)
Created2013
Description
The technology expansion seen in the last decade for genomics research has permitted the generation of large-scale data sources pertaining to molecular biological assays, genomics, proteomics, transcriptomics and other modern omics catalogs. New methods to analyze, integrate and visualize these data types are essential to unveil relevant disease mechanisms. Towards these objectives, this research focuses on data integration within two scenarios: (1) transcriptomic, proteomic and functional information and (2) real-time sensor-based measurements motivated by single-cell technology. To assess relationships between protein abundance, transcriptomic and functional data, a nonlinear model was explored at static and temporal levels. The successful integration of these heterogeneous data sources through the stochastic gradient boosted tree approach and its improved predictability are some highlights of this work. Through the development of an innovative validation subroutine based on a permutation approach and the use of external information (i.e., operons), lack of a priori knowledge for undetected proteins was overcome. The integrative methodologies allowed for the identification of undetected proteins for Desulfovibrio vulgaris and Shewanella oneidensis for further biological exploration in laboratories towards finding functional relationships. In an effort to better understand diseases such as cancer at different developmental stages, the Microscale Life Science Center headquartered at the Arizona State University is pursuing single-cell studies by developing novel technologies. This research arranged and applied a statistical framework that tackled the following challenges: random noise, heterogeneous dynamic systems with multiple states, and understanding cell behavior within and across different Barrett's esophageal epithelial cell lines using oxygen consumption curves. These curves were characterized with good empirical fit using nonlinear models with simple structures which allowed extraction of a large number of features. Application of a supervised classification model to these features and the integration of experimental factors allowed for identification of subtle patterns among different cell types visualized through multidimensional scaling. Motivated by the challenges of analyzing real-time measurements, we further explored a unique two-dimensional representation of multiple time series using a wavelet approach which showcased promising results towards less complex approximations. Also, the benefits of external information were explored to improve the image representation.
ContributorsTorres Garcia, Wandaliz (Author) / Meldrum, Deirdre R. (Thesis advisor) / Runger, George C. (Thesis advisor) / Gel, Esma S. (Committee member) / Li, Jing (Committee member) / Zhang, Weiwen (Committee member) / Arizona State University (Publisher)
Created2011
Description
Today's competitive markets force companies to constantly engage in the complex task of managing their demand. In make-to-order manufacturing or service systems, the demand of a product is shaped by price and lead times, where high price and lead time quotes ensure profitability for supplier, but discourage the customers from placing orders. Low price and lead times, on the other hand, generally result in high demand, but do not necessarily ensure profitability. The price and lead time quotation problem considers the trade-off between offering high and low prices and lead times. The recent practices in make-to- order manufacturing companies reveal the importance of dynamic quotation strategies, under which the prices and lead time quotes flexibly change depending on the status of the system. In this dissertation, the objective is to model a make-to-order manufacturing system and explore various aspects of dynamic quotation strategies such as the behavior of optimal price and lead time decisions, the impact of customer preferences on optimal decisions, the benefits of employing dynamic quotation in comparison to simpler quotation strategies, and the benefits of coordinating price and lead time decisions. I first consider a manufacturer that receives demand from spot purchasers (who are quoted dynamic price and lead times), as well as from contract customers who have agree- ments with the manufacturer with fixed price and lead time terms. I analyze how customer preferences affect the optimal price and lead time decisions, the benefits of dynamic quo- tation, and the optimal mix of spot purchaser and contract customers. These analyses necessitate the computation of expected tardiness of customer orders at the moment cus- tomer enters the system. Hence, in the second part of the dissertation, I develop method- ologies to compute the expected tardiness in multi-class priority queues. For the trivial single class case, a closed formulation is obtained. For the more complex multi-class case, numerical inverse Laplace transformation algorithms are developed. In the last part of the dissertation, I model a decentralized system with two components. Marketing department determines the price quotes with the objective of maximizing revenues, and manufacturing department determines the lead time quotes to minimize lateness costs. I discuss the ben- efits of coordinating price and lead time decisions, and develop an incentivization scheme to reduce the negative impacts of lack of coordination.
ContributorsHafizoglu, Ahmet Baykal (Author) / Gel, Esma S (Thesis advisor) / Villalobos, Jesus R (Committee member) / Mirchandani, Pitu (Committee member) / Keskinocak, Pinar (Committee member) / Runger, George C. (Committee member) / Arizona State University (Publisher)
Created2012
Description
Rapid advance in sensor and information technology has resulted in both spatially and temporally data-rich environment, which creates a pressing need for us to develop novel statistical methods and the associated computational tools to extract intelligent knowledge and informative patterns from these massive datasets. The statistical challenges for addressing these massive datasets lay in their complex structures, such as high-dimensionality, hierarchy, multi-modality, heterogeneity and data uncertainty. Besides the statistical challenges, the associated computational approaches are also considered essential in achieving efficiency, effectiveness, as well as the numerical stability in practice. On the other hand, some recent developments in statistics and machine learning, such as sparse learning, transfer learning, and some traditional methodologies which still hold potential, such as multi-level models, all shed lights on addressing these complex datasets in a statistically powerful and computationally efficient way. In this dissertation, we identify four kinds of general complex datasets, including "high-dimensional datasets", "hierarchically-structured datasets", "multimodality datasets" and "data uncertainties", which are ubiquitous in many domains, such as biology, medicine, neuroscience, health care delivery, manufacturing, etc. We depict the development of novel statistical models to analyze complex datasets which fall under these four categories, and we show how these models can be applied to some real-world applications, such as Alzheimer's disease research, nursing care process, and manufacturing.
ContributorsHuang, Shuai (Author) / Li, Jing (Thesis advisor) / Askin, Ronald (Committee member) / Ye, Jieping (Committee member) / Runger, George C. (Committee member) / Arizona State University (Publisher)
Created2012
Description
Functional or dynamic responses are prevalent in experiments in the fields of engineering, medicine, and the sciences, but proposals for optimal designs are still sparse for this type of response. Experiments with dynamic responses result in multiple responses taken over a spectrum variable, so the design matrix for a dynamic response have more complicated structures. In the literature, the optimal design problem for some functional responses has been solved using genetic algorithm (GA) and approximate design methods. The goal of this dissertation is to develop fast computer algorithms for calculating exact D-optimal designs.
First, we demonstrated how the traditional exchange methods could be improved to generate a computationally efficient algorithm for finding G-optimal designs. The proposed two-stage algorithm, which is called the cCEA, uses a clustering-based approach to restrict the set of possible candidates for PEA, and then improves the G-efficiency using CEA.
The second major contribution of this dissertation is the development of fast algorithms for constructing D-optimal designs that determine the optimal sequence of stimuli in fMRI studies. The update formula for the determinant of the information matrix was improved by exploiting the sparseness of the information matrix, leading to faster computation times. The proposed algorithm outperforms genetic algorithm with respect to computational efficiency and D-efficiency.
The third contribution is a study of optimal experimental designs for more general functional response models. First, the B-spline system is proposed to be used as the non-parametric smoother of response function and an algorithm is developed to determine D-optimal sampling points of a spectrum variable. Second, we proposed a two-step algorithm for finding the optimal design for both sampling points and experimental settings. In the first step, the matrix of experimental settings is held fixed while the algorithm optimizes the determinant of the information matrix for a mixed effects model to find the optimal sampling times. In the second step, the optimal sampling times obtained from the first step is held fixed while the algorithm iterates on the information matrix to find the optimal experimental settings. The designs constructed by this approach yield superior performance over other designs found in literature.
First, we demonstrated how the traditional exchange methods could be improved to generate a computationally efficient algorithm for finding G-optimal designs. The proposed two-stage algorithm, which is called the cCEA, uses a clustering-based approach to restrict the set of possible candidates for PEA, and then improves the G-efficiency using CEA.
The second major contribution of this dissertation is the development of fast algorithms for constructing D-optimal designs that determine the optimal sequence of stimuli in fMRI studies. The update formula for the determinant of the information matrix was improved by exploiting the sparseness of the information matrix, leading to faster computation times. The proposed algorithm outperforms genetic algorithm with respect to computational efficiency and D-efficiency.
The third contribution is a study of optimal experimental designs for more general functional response models. First, the B-spline system is proposed to be used as the non-parametric smoother of response function and an algorithm is developed to determine D-optimal sampling points of a spectrum variable. Second, we proposed a two-step algorithm for finding the optimal design for both sampling points and experimental settings. In the first step, the matrix of experimental settings is held fixed while the algorithm optimizes the determinant of the information matrix for a mixed effects model to find the optimal sampling times. In the second step, the optimal sampling times obtained from the first step is held fixed while the algorithm iterates on the information matrix to find the optimal experimental settings. The designs constructed by this approach yield superior performance over other designs found in literature.
ContributorsSaleh, Moein (Author) / Pan, Rong (Thesis advisor) / Montgomery, Douglas C. (Committee member) / Runger, George C. (Committee member) / Kao, Ming-Hung (Committee member) / Arizona State University (Publisher)
Created2015
Description
The recent technological advances enable the collection of various complex, heterogeneous and high-dimensional data in biomedical domains. The increasing availability of the high-dimensional biomedical data creates the needs of new machine learning models for effective data analysis and knowledge discovery. This dissertation introduces several unsupervised and supervised methods to help understand the data, discover the patterns and improve the decision making. All the proposed methods can generalize to other industrial fields.
The first topic of this dissertation focuses on the data clustering. Data clustering is often the first step for analyzing a dataset without the label information. Clustering high-dimensional data with mixed categorical and numeric attributes remains a challenging, yet important task. A clustering algorithm based on tree ensembles, CRAFTER, is proposed to tackle this task in a scalable manner.
The second part of this dissertation aims to develop data representation methods for genome sequencing data, a special type of high-dimensional data in the biomedical domain. The proposed data representation method, Bag-of-Segments, can summarize the key characteristics of the genome sequence into a small number of features with good interpretability.
The third part of this dissertation introduces an end-to-end deep neural network model, GCRNN, for time series classification with emphasis on both the accuracy and the interpretation. GCRNN contains a convolutional network component to extract high-level features, and a recurrent network component to enhance the modeling of the temporal characteristics. A feed-forward fully connected network with the sparse group lasso regularization is used to generate the final classification and provide good interpretability.
The last topic centers around the dimensionality reduction methods for time series data. A good dimensionality reduction method is important for the storage, decision making and pattern visualization for time series data. The CRNN autoencoder is proposed to not only achieve low reconstruction error, but also generate discriminative features. A variational version of this autoencoder has great potential for applications such as anomaly detection and process control.
The first topic of this dissertation focuses on the data clustering. Data clustering is often the first step for analyzing a dataset without the label information. Clustering high-dimensional data with mixed categorical and numeric attributes remains a challenging, yet important task. A clustering algorithm based on tree ensembles, CRAFTER, is proposed to tackle this task in a scalable manner.
The second part of this dissertation aims to develop data representation methods for genome sequencing data, a special type of high-dimensional data in the biomedical domain. The proposed data representation method, Bag-of-Segments, can summarize the key characteristics of the genome sequence into a small number of features with good interpretability.
The third part of this dissertation introduces an end-to-end deep neural network model, GCRNN, for time series classification with emphasis on both the accuracy and the interpretation. GCRNN contains a convolutional network component to extract high-level features, and a recurrent network component to enhance the modeling of the temporal characteristics. A feed-forward fully connected network with the sparse group lasso regularization is used to generate the final classification and provide good interpretability.
The last topic centers around the dimensionality reduction methods for time series data. A good dimensionality reduction method is important for the storage, decision making and pattern visualization for time series data. The CRNN autoencoder is proposed to not only achieve low reconstruction error, but also generate discriminative features. A variational version of this autoencoder has great potential for applications such as anomaly detection and process control.
ContributorsLin, Sangdi (Author) / Runger, George C. (Thesis advisor) / Kocher, Jean-Pierre A (Committee member) / Pan, Rong (Committee member) / Escobedo, Adolfo R. (Committee member) / Arizona State University (Publisher)
Created2018
Description
Modern intelligent transportation systems (ITS) make driving more efficient, easier, and safer. Knowledge of real-time traffic conditions is a critical input for operating ITS. Real-time freeway traffic state estimation approaches have been used to quantify traffic conditions given limited amount of data collected by traffic sensors. Currently, almost all real-time estimation methods have been developed for estimating laterally aggregated traffic conditions in a roadway segment using link-based models which assume homogeneous conditions across multiple lanes. However, with new advances and applications of ITS, knowledge of lane-based traffic conditions is becoming important, where the traffic condition differences among lanes are recognized. In addition, most of the current real-time freeway traffic estimators consider only data from loop detectors. This dissertation develops a bi-level data fusion approach using heterogeneous multi-sensor measurements to estimate real-time lane-based freeway traffic conditions, which integrates a link-level model-based estimator and a lane-level data-driven estimator.
Macroscopic traffic flow models describe the evolution of aggregated traffic characteristics over time and space, which are required by model-based traffic estimation approaches. Since current first-order Lagrangian macroscopic traffic flow model has some unrealistic implicit assumptions (e.g., infinite acceleration), a second-order Lagrangian macroscopic traffic flow model has been developed by incorporating drivers’ anticipation and reaction delay. A multi-sensor extended Kalman filter (MEKF) algorithm has been developed to combine heterogeneous measurements from multiple sources. A MEKF-based traffic estimator, explicitly using the developed second-order traffic flow model and measurements from loop detectors as well as GPS trajectories for given fractions of vehicles, has been proposed which gives real-time link-level traffic estimates in the bi-level estimation system.
The lane-level estimation in the bi-level data fusion system uses the link-level estimates as priors and adopts a data-driven approach to obtain lane-based estimates, where now heterogeneous multi-sensor measurements are combined using parallel spatial-temporal filters.
Experimental analysis shows that the second-order model can more realistically reproduce real world traffic flow patterns (e.g., stop-and-go waves). The MEKF-based link-level estimator exhibits more accurate results than the estimator that uses only a single data source. Evaluation of the lane-level estimator demonstrates that the proposed new bi-level multi-sensor data fusion system can provide very good estimates of real-time lane-based traffic conditions.
Macroscopic traffic flow models describe the evolution of aggregated traffic characteristics over time and space, which are required by model-based traffic estimation approaches. Since current first-order Lagrangian macroscopic traffic flow model has some unrealistic implicit assumptions (e.g., infinite acceleration), a second-order Lagrangian macroscopic traffic flow model has been developed by incorporating drivers’ anticipation and reaction delay. A multi-sensor extended Kalman filter (MEKF) algorithm has been developed to combine heterogeneous measurements from multiple sources. A MEKF-based traffic estimator, explicitly using the developed second-order traffic flow model and measurements from loop detectors as well as GPS trajectories for given fractions of vehicles, has been proposed which gives real-time link-level traffic estimates in the bi-level estimation system.
The lane-level estimation in the bi-level data fusion system uses the link-level estimates as priors and adopts a data-driven approach to obtain lane-based estimates, where now heterogeneous multi-sensor measurements are combined using parallel spatial-temporal filters.
Experimental analysis shows that the second-order model can more realistically reproduce real world traffic flow patterns (e.g., stop-and-go waves). The MEKF-based link-level estimator exhibits more accurate results than the estimator that uses only a single data source. Evaluation of the lane-level estimator demonstrates that the proposed new bi-level multi-sensor data fusion system can provide very good estimates of real-time lane-based traffic conditions.
ContributorsZhou, Zhuoyang (Author) / Mirchandani, Pitu (Thesis advisor) / Askin, Ronald (Committee member) / Runger, George C. (Committee member) / Zhou, Xuesong (Committee member) / Arizona State University (Publisher)
Created2015
Description
In species with highly heteromorphic sex chromosomes, the degradation of one of the sex chromosomes can result in unequal gene expression between the sexes (e.g., between XX females and XY males) and between the sex chromosomes and the autosomes. Dosage compensation is a process whereby genes on the sex chromosomes achieve equal gene expression which prevents deleterious side effects from having too much or too little expression of genes on sex chromsomes. The green anole is part of a group of species that recently underwent an adaptive radiation. The green anole has XX/XY sex determination, but the content of the X chromosome and its evolution have not been described. Given its status as a model species, better understanding the green anole genome could reveal insights into other species. Genomic analyses are crucial for a comprehensive picture of sex chromosome differentiation and dosage compensation, in addition to understanding speciation.
In order to address this, multiple comparative genomics and bioinformatics analyses were conducted to elucidate patterns of evolution in the green anole and across multiple anole species. Comparative genomics analyses were used to infer additional X-linked loci in the green anole, RNAseq data from male and female samples were anayzed to quantify patterns of sex-biased gene expression across the genome, and the extent of dosage compensation on the anole X chromosome was characterized, providing evidence that the sex chromosomes in the green anole are dosage compensated.
In addition, X-linked genes have a lower ratio of nonsynonymous to synonymous substitution rates than the autosomes when compared to other Anolis species, and pairwise rates of evolution in genes across the anole genome were analyzed. To conduct this analysis a new pipeline was created for filtering alignments and performing batch calculations for whole genome coding sequences. This pipeline has been made publicly available.
In order to address this, multiple comparative genomics and bioinformatics analyses were conducted to elucidate patterns of evolution in the green anole and across multiple anole species. Comparative genomics analyses were used to infer additional X-linked loci in the green anole, RNAseq data from male and female samples were anayzed to quantify patterns of sex-biased gene expression across the genome, and the extent of dosage compensation on the anole X chromosome was characterized, providing evidence that the sex chromosomes in the green anole are dosage compensated.
In addition, X-linked genes have a lower ratio of nonsynonymous to synonymous substitution rates than the autosomes when compared to other Anolis species, and pairwise rates of evolution in genes across the anole genome were analyzed. To conduct this analysis a new pipeline was created for filtering alignments and performing batch calculations for whole genome coding sequences. This pipeline has been made publicly available.
ContributorsRupp, Shawn Michael (Author) / Wilson Sayres, Melissa A (Thesis advisor) / Kusumi, Kenro (Committee member) / DeNardo, Dale (Committee member) / Arizona State University (Publisher)
Created2016
Description
Study of canine cancer’s molecular underpinnings holds great potential for informing veterinary and human oncology. Sporadic canine cancers are highly abundant (~4 million diagnoses/year in the United States) and the dog’s unique genomic architecture due to selective inbreeding, alongside the high similarity between dog and human genomes both confer power for improving understanding of cancer genes. However, characterization of canine cancer genome landscapes has been limited. It is hindered by lack of canine-specific tools and resources. To enable robust and reproducible comparative genomic analysis of canine cancers, I have developed a workflow for somatic and germline variant calling in canine cancer genomic data. I have first adapted a human cancer genomics pipeline to create a semi-automated canine pipeline used to map genomic landscapes of canine melanoma, lung adenocarcinoma, osteosarcoma and lymphoma. This pipeline also forms the backbone of my novel comparative genomics workflow.
Practical impediments to comparative genomic analysis of dog and human include challenges identifying similarities in mutation type and function across species. For example, canine genes could have evolved different functions and their human orthologs may perform different functions. Hence, I undertook a systematic statistical evaluation of dog and human cancer genes and assessed functional similarities and differences between orthologs to improve understanding of the roles of these genes in cancer across species. I tested this pipeline canine and human Diffuse Large B-Cell Lymphoma (DLBCL), given that canine DLBCL is the most comprehensively genomically characterized canine cancer. Logistic regression with genes bearing somatic coding mutations in each cancer was used to determine if conservation metrics (sequence identity, network placement, etc.) could explain co-mutation of genes in both species. Using this model, I identified 25 co-mutated and evolutionarily similar genes that may be compelling cross-species cancer genes. For example, PCLO was identified as a co-mutated conserved gene with PCLO having been previously identified as recurrently mutated in human DLBCL, but with an unclear role in oncogenesis. Further investigation of these genes might shed new light on the biology of lymphoma in dogs and human and this approach may more broadly serve to prioritize new genes for comparative cancer biology studies.
Practical impediments to comparative genomic analysis of dog and human include challenges identifying similarities in mutation type and function across species. For example, canine genes could have evolved different functions and their human orthologs may perform different functions. Hence, I undertook a systematic statistical evaluation of dog and human cancer genes and assessed functional similarities and differences between orthologs to improve understanding of the roles of these genes in cancer across species. I tested this pipeline canine and human Diffuse Large B-Cell Lymphoma (DLBCL), given that canine DLBCL is the most comprehensively genomically characterized canine cancer. Logistic regression with genes bearing somatic coding mutations in each cancer was used to determine if conservation metrics (sequence identity, network placement, etc.) could explain co-mutation of genes in both species. Using this model, I identified 25 co-mutated and evolutionarily similar genes that may be compelling cross-species cancer genes. For example, PCLO was identified as a co-mutated conserved gene with PCLO having been previously identified as recurrently mutated in human DLBCL, but with an unclear role in oncogenesis. Further investigation of these genes might shed new light on the biology of lymphoma in dogs and human and this approach may more broadly serve to prioritize new genes for comparative cancer biology studies.
ContributorsSivaprakasam, Karthigayini (Author) / Dinu, Valentin (Thesis advisor) / Trent, Jeffrey (Thesis advisor) / Hendricks, William (Committee member) / Runger, George C. (Committee member) / Arizona State University (Publisher)
Created2018
Description
Accounting for over a third of all emerging and re-emerging infections, viruses represent a major public health threat, which researchers and epidemiologists across the world have been attempting to contain for decades. Recently, genomics-based surveillance of viruses through methods such as virus phylogeography has grown into a popular tool for infectious disease monitoring. When conducting such surveillance studies, researchers need to manually retrieve geographic metadata denoting the location of infected host (LOIH) of viruses from public sequence databases such as GenBank and any publication related to their study. The large volume of semi-structured and unstructured information that must be reviewed for this task, along with the ambiguity of geographic locations, make it especially challenging. Prior work has demonstrated that the majority of GenBank records lack sufficient geographic granularity concerning the LOIH of viruses. As a result, reviewing full-text publications is often necessary for conducting in-depth analysis of virus migration, which can be a very time-consuming process. Moreover, integrating geographic metadata pertaining to the LOIH of viruses from different sources, including different fields in GenBank records as well as full-text publications, and normalizing the integrated metadata to unique identifiers for subsequent analysis, are also challenging tasks, often requiring expert domain knowledge. Therefore, automated information extraction (IE) methods could help significantly accelerate this process, positively impacting public health research. However, very few research studies have attempted the use of IE methods in this domain.
This work explores the use of novel knowledge-driven geographic IE heuristics for extracting, integrating, and normalizing the LOIH of viruses based on information available in GenBank and related publications; when evaluated on manually annotated test sets, the methods were found to have a high accuracy and shown to be adequate for addressing this challenging problem. It also presents GeoBoost, a pioneering software system for georeferencing GenBank records, as well as a large-scale database containing over two million virus GenBank records georeferenced using the algorithms introduced here. The methods, database and software developed here could help support diverse public health domains focusing on sequence-informed virus surveillance, thereby enhancing existing platforms for controlling and containing disease outbreaks.
This work explores the use of novel knowledge-driven geographic IE heuristics for extracting, integrating, and normalizing the LOIH of viruses based on information available in GenBank and related publications; when evaluated on manually annotated test sets, the methods were found to have a high accuracy and shown to be adequate for addressing this challenging problem. It also presents GeoBoost, a pioneering software system for georeferencing GenBank records, as well as a large-scale database containing over two million virus GenBank records georeferenced using the algorithms introduced here. The methods, database and software developed here could help support diverse public health domains focusing on sequence-informed virus surveillance, thereby enhancing existing platforms for controlling and containing disease outbreaks.
ContributorsTahsin, Tasnia (Author) / Gonzalez, Graciela (Thesis advisor) / Scotch, Matthew (Thesis advisor) / Runger, George C. (Committee member) / Arizona State University (Publisher)
Created2019