Дисертації з теми "Computational methods for Complex Systems"
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Gravino, Pietro <1984>. "Novel investigation methods in Computational Social Dynamics and Complex Systems." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2015. http://amsdottorato.unibo.it/6765/.
Повний текст джерелаRen, Xuchun. "Novel computational methods for stochastic design optimization of high-dimensional complex systems." Diss., University of Iowa, 2015. https://ir.uiowa.edu/etd/1738.
Повний текст джерелаAbdullah, Rudwan Ali Abolgasim. "Intelligent methods for complex systems control engineering." Thesis, University of Stirling, 2007. http://hdl.handle.net/1893/257.
Повний текст джерелаGrill, Maximilian Josef [Verfasser], Wolfgang A. [Akademischer Betreuer] Wall, Wolfgang A. [Gutachter] Wall, and Philipp J. [Gutachter] Thurner. "Computational Models and Methods for Molecular Interactions of Deformable Fibers in Complex Biophysical Systems / Maximilian Josef Grill ; Gutachter: Wolfgang A. Wall, Philipp J. Thurner ; Betreuer: Wolfgang A. Wall." München : Universitätsbibliothek der TU München, 2020. http://d-nb.info/122267274X/34.
Повний текст джерелаLiu, Zifan. "Complex systems and health systems, computational challenges." Thesis, Versailles-St Quentin en Yvelines, 2015. http://www.theses.fr/2015VERS001V/document.
Повний текст джерелаThe eigenvalue equation intervenes in models of infectious disease prop- agation and could be used as an ally of vaccination campaigns in the ac- tions carried out by health care organizations. The epidemiological model- ing techniques can be considered by analogy, as computer viral propagation which depends on the underlying graph status at a given time. We point out PageRank as method to study the epidemic spread and consider its calcula- tion in the context of small-world phenomenon. A parallel implementation of multiple implicitly restarted Arnoldi method (MIRAM) is proposed for calculating dominant eigenpair of stochastic matrices derived from very large real networks. Their high damp- ing factor makes many existing algorithms less efficient, while MIRAM could be promising. We also propose in this thesis a parallel graph gen- erator that can be used to generate distributed synthesized networks that display scale-free and small-world structures. This generator could serve as a testbed for graph related algorithms. MIRAM is implemented within the framework of Trilinos, targeting big data and sparse matrices representing scale-free networks, also known as power law networks. Hypergraph partitioning approach is employed to minimize the communication overhead. The algorithm is tested on a nation wide cluster of clusters Grid5000. Experiments on very large networks such as twitter and yahoo with over 1 billion nodes are conducted. With our parallel implementation, a speedup of 27× is met compared to the sequential solver
Ahmadi, Adl Amin. "Computational Methods for Biomarker Identification in Complex Disease." Scholar Commons, 2015. http://scholarcommons.usf.edu/etd/5895.
Повний текст джерелаMiller, David J. Ghosh Avijit. "New methods in computational systems biology /." Philadelphia, Pa. : Drexel University, 2008. http://hdl.handle.net/1860/2810.
Повний текст джерелаGibson, Michael Andrew Bruck Jehoshua. "Computational methods for stochastic biological systems /." Diss., Pasadena, Calif. : California Institute of Technology, 2000. http://resolver.caltech.edu/CaltechETD:etd-05132005-154222.
Повний текст джерелаLe, Xuan Tuan. "Understanding complex systems through computational modeling and simulation." Thesis, Paris Sciences et Lettres (ComUE), 2017. http://www.theses.fr/2017PSLEP003.
Повний текст джерелаTraditional approaches are not sufficient, and sometimes impossible in dealing with complexity issues such as emergence, self-organization, evolution and adaptation of complex systems. As illustrated in this thesis by the practical work of the author in a real-life project, the spreading of infectious disease as well as interventions could be considered as difusion processes on complex networks of heterogeneous individuals in a society which is considered as a reactive system. Modeling of this system requires explicitly specifying of each individual’s behaviors and (re)actions, and transforming them into computational model which has to be flexible, reusable, and ease of coding. Statechart, typical for model-based programming, is a good solution that the thesis proposes. Bottom-up agent based simulation finds emergence episodes in what-if scenarios that change rules governing agent’s behaviors that requires agents to learn to adapt with these changes. Decision tree learning is proposed to bring more flexibility and legibility in modeling of agent’s autonomous decision making during simulation runtime. Our proposition for computational models such as agent based models are complementary to traditional ones, and in some case they are unique solutions due to legal, ethical issues
Safa, Issam I. "Towards Topological Methods for Complex Scalar Data." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1322457949.
Повний текст джерелаWu, Fei. "Parallel computational methods for constrained mechanical systems." Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/282561.
Повний текст джерелаVazquez, Montelongo Erik Antonio. "Computational Study of Intermolecular Interactions in Complex Chemical Systems." Thesis, University of North Texas, 2020. https://digital.library.unt.edu/ark:/67531/metadc1703283/.
Повний текст джерелаDing, Jiarui. "Computational methods for systems biology data of cancer." Thesis, University of British Columbia, 2016. http://hdl.handle.net/2429/58164.
Повний текст джерелаScience, Faculty of
Computer Science, Department of
Graduate
Rosario, Ricardo C. H. "Computational Methods for Feedback Control in Structural Systems." NCSU, 1998. http://www.lib.ncsu.edu/theses/available/etd-19981030-155600.
Повний текст джерелаNumerical methods, LQR control, an abstract formulation andreduced basis techniques for a system consisting of a thin cylindrical shellwith surface-mounted piezoceramic actuators are investigated.Donnell-Mushtari equations,modified to include Kelvin-Voigt damping and passive patch contributions,are used to model the system dynamics. The voltage-induced piezoceramicpatch contributions, used as input inthe control regime, enter the equations as externalforces and moments. Existence and uniqueness of solutions are demonstratedthrough variational and semigroup formulations of the system equations.The semigroup formulation is also used to establish theoretical controlresults and illustrate convergence of the finite dimensional controlsand Riccati operators.The spatial components of the state arediscretized using a Galerkin expansion resulting in an ordinarydifferential equation that can be readily marched in time by existingordinary differential equationsolvers.Full order approximation methods which employ standard basiselements such as cubic or linear splines result in large matrixdimensions rendering the system computationally expensive for real-timesimulations. To lessen on-line computational requirements, reducedbasis methods employing snapshots of the full order model as basisfunctions are investigated.As a first step in validating the model, a shell with obtainable analyticnatural frequencies and modes was considered. The derived frequenciesand modeswere then compared with numerical approximations using full order basisfunctions. Further testing on the static and dynamic performance of the fullorder model was carried out through the following steps:(i) choose true state solutions, (ii) solve for the forces in theequations that would lead to these known solutions, and (iii) comparenumerical results excited by the derived forces with the true solutions.Reduced order methods employing the Lagrange and theKarhunen-Loève proper orthogonal decomposition (POD)basis functions are implemented on the model. Finally, a statefeedback method was developed and investigated computationallyfor both the full order and reduced ordermodels.
Cong, Yang, and 丛阳. "Optimization models and computational methods for systems biology." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hub.hku.hk/bib/B47752841.
Повний текст джерелаpublished_or_final_version
Mathematics
Doctoral
Doctor of Philosophy
Raghothama, Jayanth. "Integrating Computational and Participatory Simulations for Design in Complex Systems." Doctoral thesis, KTH, Vårdlogistik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-208170.
Повний текст джерелаQC 20170602
Mey, Antonia S. J. S. "Trajectory ensemble methods for understanding complex stochastic systems." Thesis, University of Nottingham, 2013. http://eprints.nottingham.ac.uk/13368/.
Повний текст джерелаCastillo, Andrea R. (Andrea Redwing). "Assessing computational methods and science policy in systems biology." Thesis, Massachusetts Institute of Technology, 2009. http://hdl.handle.net/1721.1/51655.
Повний текст джерелаIncludes bibliographical references (p. 109-112).
In this thesis, I discuss the development of systems biology and issues in the progression of this science discipline. Traditional molecular biology has been driven by reductionism with the belief that breaking down a biological system into the fundamental biomolecular components will elucidate such phenomena. We have reached limitations with this approach due to the complex and dynamical nature of life and our inability to intuit biological behavior from a modular perspective [37]. Mathematical modeling has been integral to current system biology endeavors since detailed analysis would be invasive if performed on humans experimentally or in clinical trials [17]. The interspecies commonalities in systemic properties and molecular mechanisms suggests that certain behaviors transcend specie differentiation and therefore easily lend to generalizing from simpler organisms to more complex organisms such as humans [7, 17]. Current methodologies in mathematical modeling and analysis have been diverse and numerous, with no standardization to progress the discipline in a collaborative manner. Without collaboration during this formative period, successful development and application of systems biology for societal welfare may be at risk. Furthermore, such collaboration has to be standardized in a fundamental approach to discover generic principles, in the manner of preceding long-standing science disciplines. This study effectively implements and analyzes a mathematical model of a three-protein biochemical network, the Synechococcus elongatus circadian clock.
(cont.) I use mass action theory expressed in kronecker products to exploit the ability to apply numerical methods-including sensitivity analysis via boundary value formulation (BVP) and trapiezoidal integration rule-and experimental techniques-including partial reaction fitting and enzyme-driven activations-when mathematically modeling large-scale biochemical networks. Amidst other applicable methodologies, my approach is grounded in the law of mass action because it is based in experimental data and biomolecular mechanistic properties, yet provides predictive power in the complete delineation of the biological system dynamics for all future time points. The results of my research demonstrate the holistic approach that mass action method-ologies have in determining emergent properties of biological systems. I further stress the necessity to enforce collaboration and standardization in future policymaking, with reconsiderations on current stakeholder incentive to redirect academia and industry focus from new molecular entities to interests in holistic understanding of the complexities and dynamics of life entities. Such redirection away from reductionism could further progress basic and applied scientific research to embetter our circumstances through new treatments and preventive measures for health, and development of new strains and disease control in agriculture and ecology [13].
by Andrea R. Castillo.
S.M.in Technology and Policy
Elmansy, Dalia F. "Computational Methods to Characterize the Etiology of Complex Diseases at Multiple Levels." Case Western Reserve University School of Graduate Studies / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=case1583416431321447.
Повний текст джерелаWiltshire, Serge William. "On The Application Of Computational Modeling To Complex Food Systems Issues." ScholarWorks @ UVM, 2019. https://scholarworks.uvm.edu/graddis/1077.
Повний текст джерелаHenning, Peter Allen. "Computational Parameter Selection and Simulation of Complex Sphingolipid Pathway Metabolism." Thesis, Georgia Institute of Technology, 2006. http://hdl.handle.net/1853/16202.
Повний текст джерелаKartal, Elcin. "Metamodeling Complex Systems Using Linear And Nonlinear Regression Methods." Master's thesis, METU, 2007. http://etd.lib.metu.edu.tr/upload/2/12608930/index.pdf.
Повний текст джерелаYang, Chao. "ON PARTICLE METHODS FOR UNCERTAINTY QUANTIFICATION IN COMPLEX SYSTEMS." The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1511967797285962.
Повний текст джерелаOliver, John M. "Multi-objective optimisation methods applied to complex engineering systems." Thesis, Cranfield University, 2014. http://dspace.lib.cranfield.ac.uk/handle/1826/11707.
Повний текст джерелаLawrence, A. Raelene. "A computational investigation of inorganic systems using ab initio methods /." free to MU campus, to others for purchase, 2000. http://wwwlib.umi.com/cr/mo/fullcit?p9998495.
Повний текст джерелаDimova, Dilyana [Verfasser]. "Computational Methods Generating High-Resolution Views of Complex Structure-Activity Relationships / Dilyana Dimova." Bonn : Universitäts- und Landesbibliothek Bonn, 2014. http://d-nb.info/1052061044/34.
Повний текст джерелаBrocklebank, Denise. "Computational methods for genetic analysis of complex pedigrees : An application to Huntington's disease." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.531952.
Повний текст джерелаUapipatanakul, Sakchai. "Development of computational methods for conjugate heat transfer analysis in complex industrial applications." Thesis, University of Manchester, 2012. https://www.research.manchester.ac.uk/portal/en/theses/development-of-computational-methods-for-conjugate-heat-transfer-analysis-in-complex-industrial-applications(3910eec7-601d-4da1-8c08-854404bbba3a).html.
Повний текст джерелаJha, Sumit Kumar. "Model Validation and Discovery for Complex Stochastic Systems." Research Showcase @ CMU, 2010. http://repository.cmu.edu/dissertations/10.
Повний текст джерелаJiang, Hao, and 姜昊. "Construction and computation methods for biological networks." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hub.hku.hk/bib/B50662144.
Повний текст джерелаpublished_or_final_version
Mathematics
Doctoral
Doctor of Philosophy
Repiscak, Peter. "Computational chemistry for complex systems : open-shell molecules to conjugated organic materials." Thesis, Heriot-Watt University, 2017. http://hdl.handle.net/10399/3348.
Повний текст джерелаAlmaatouq, Abdullah Mohammed. "Complex systems and a computational social science perspective on the labor market." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104577.
Повний текст джерелаCataloged from PDF version of thesis.
Includes bibliographical references (pages 99-109).
Thesis: S.M.. Massachusetts Institute of Technology, Computation for Design and Optimization Program, 2016.
Labor market institutions are central for modern economies, and their polices can directly affect unemployment rates and economic growth. At the individual level, unemployment often has a detrimental impact on people's well-being and health. At the national level, high employment is one of the central goals of any economic policy, due to its close association with national prosperity. The main goal of this thesis is to highlight the need for frameworks that take into account the complex structure of labor market interactions. In particular, we explore the benefits of leveraging tools from computational social science, network science, and data-driven theories to measure the flow of opportunities and information in the context of the labor market. First, we investigate our key hypothesis, which is that opportunity/information flow through weak ties, and this is a key determinant of the length of unemployment. We then extend the idea of opportunity/information flow to clusters of other economic activities, where we expect the flow within clusters of related activities to be higher than within isolated activities. This captures the intuition that within related activities there are more "capitals" involved and that such activities require similar "capabilities." Therefore, more extensive clusters of economic activities should generate greater growth through exploiting the greater flow of opportunities and information. We quantify the opportunity/information flow using a complexity measure of two economic activities (i.e. jobs and exports).
by Abdullah Almaatouq.
S.M.
Botha, Paul Jacobus. "Detecting change in complex process systems with phase space methods." Thesis, Stellenbosch : University of Stellenbosch, 2006. http://hdl.handle.net/10019/508.
Повний текст джерелаZhao, Yang. "Computational Methods for Analyzing Chemical Graphs and Biological Networks." 京都大学 (Kyoto University), 2014. http://hdl.handle.net/2433/188864.
Повний текст джерелаBasudhar, Anirban. "Computational Optimal Design and Uncertainty Quantification of Complex Systems Using Explicit Decision Boundaries." Diss., The University of Arizona, 2011. http://hdl.handle.net/10150/201491.
Повний текст джерелаGuan, Jinyan. "Bayesian Generative Modeling of Complex Dynamical Systems." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/612950.
Повний текст джерелаMwanga, Alifas Yeko. "Reliability modelling of complex systems." Thesis, Pretoria : [s.n.], 2006. http://upetd.up.ac.za/thesis/available/etd-12142006-121528.
Повний текст джерелаAl-Haddad, Tristan Farris. "PerFORMance: Integrating Structural Feedback into Design Processes for Complex Surface-Active Form." Thesis, Available online, Georgia Institute of Technology, 2006, 2006. http://etd.gatech.edu/theses/available/etd-07102006-111810/.
Повний текст джерелаCasellas, Soler Josep. "Elucidating deactivation and reaction paths of photosensitive organic systems through computational methods." Doctoral thesis, Universitat Rovira i Virgili, 2016. http://hdl.handle.net/10803/386574.
Повний текст джерелаEsta tesis estudia computacionalmente los procesos que explican las propiedades fotoquímicas de ciertos compuestos orgánicos. Para ello se han usado métodos ab initio multiconfiguracionales, CASSCF y CASPT2, con los que se describe la topografía de las superficies de energía potencial de los estados de más baja energía y se localizan los caminos de reacción. Se ha estudiado primeramente el mecanismo de fotoisomerización del azobenzeno y su derivado, la fenilazopiridina. El mecanismo de reacción obtenido explica satisfactoriamente por qué el rendimiento cuántico de la isomerización depende de la excitación inicial y del grado de restricción de la rotación interna en estos sistemas. También se ha analizado un protocolo computacional para poder reproducir el espectro de absorción en disolución de sistemas flexibles, usando como ejemplo la fenilazopiridina. Se ha estudiado también la 9-fenilfenalenona. A diferencia del sistema del que deriva, la fenalenona, que presenta un alto rendimiento cuántico de sensitización de oxígeno singlete, el de la 9-fenilfenalenona es muy bajo. Se ha demostrado que eso se debe a que en el segundo la fotoexcitación produce la formación por ciclación de un fotoproducto metaestable que rápidamente revierte en el compuesto original. Este estudio ha supuesto un reto para los métodos computacionales empleados debido a su gran tamaño. Por último se ha estudiado el dehidroescualeno, un carotenoide que interviene en procesos de absorción de energía lumínica de organismos vegetales. El estudio determina la estructura de los estados excitados de baja energía y la influencia de la flexibilidad de este compuesto en las energías de estos estados. Se demuestra que la aproximación de utilizar sólo la conformación más simétrica proporciona buenos resultados a nivel cualitativo pero que, si se busca la reproducción cuantitativa de las observaciones experimentales, se debe tener en cuenta la flexibilidad molecular.
This thesis develops a computational work to study the processes that explain the photochemical properties of some organic compounds. Multiconfigurational ab initio methods, CASSCF and CASPT2 have been used to determine the topography of the potential energy surfaces of the low energy states and locate reaction paths. We have studied first the mechanism of photoisomerization of azobenzene and its derivative phenylazopyridine. The reaction mechanism obtained explains satisfactorily why the isomerization quantum yield depends on the initial excitation and on the degree of the restriction on the internal rotation of these systems. We have also analysed the performance of a computational protocol to reproduce the absorption spectrum of flexible systems in solution, using phenylazopyridine as target system. We have also studied 9-phenylphenalenone. Its parent system, phenalenone, shows a high quantum yield in the process of singlet oxygen sensitization, but the quantum yield of this phenyl derivate for the same process is very low. Our study shows that this difference is due to a side reaction induced by the initial photoexcitation, which produces a metastable photoproduct by cyclisation that turns back quickly to the initial reactant. This study has been a challenge for the computational methods used due to its big size. Finally, we have studied dehidrosqualene, a carotenoid involved in light harvesting processes in vegetables. Our study determines the structure of the low energy excited states and the influence of the flexibility of this compound in the energy of these states. We show that to use only the most symmetric conformation on this flexible compound to calculate the energy of the excited states, give results that qualitatively agree with the experimental observations but, if quantitative agreement is required, the molecular flexibility must be taken into account.
Russell, Gregory B. (Gregory Brian). "A systems analysis of complex software product development dynamics and methods." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/42371.
Повний текст джерелаThesis (S.M.)--Massachusetts Institute of Technology, System Design and Management Program, 2007.
Software development projects and products have long shouldered a reputation for missed deadlines, blown budgets, and low quality. Unfortunately, this negative reputation appears to be supported by more than just anecdotal evidence; quoting an industry study', respected software development expert and author Steve McConnell reports in his book Professional Software Development" that "Roughly 25 percent of all projects fail outright, and the typical project is 100 percent over budget at the point it's canceled." What's more, notes McConnell, "Fifty percent of projects are delivered late, over-budget, or with less functionality than desired." Exactly why software development projects and products have historically performed so poorly and with arguably little if any improvement over the past 40 years, however, is a subject on which there is less agreement. While blame often aligns along functional (product marketing and sales) versus technical (software development) lines, the increasing popularity of different and often contradictory software development methodologies seems to suggest that no real consensus exists within the software development community itself. The goal of this thesis is twofold: 1. To describe a set of key factors to consider when analyzing software processes 2. To outline an organizational framework that is optimized for implementing and managing software development practices
by Gregory B. Russell.
S.M.
Lekscha, Jaqueline Stefanie. "Complex systems methods for detecting dynamical anomalies in past climate variability." Doctoral thesis, Humboldt-Universität zu Berlin, 2020. http://dx.doi.org/10.18452/21047.
Повний текст джерелаStudying palaeoclimate proxy data from archives such as tree rings, lake sediments, speleothems, and ice cores using windowed recurrence network analysis offers the possibility to characterise dynamical anomalies in past climate variability. This thesis aims at developing a more reliable framework of windowed recurrence network analysis by comparing different phase space reconstruction approaches for non-uniformly sampled noisy data and by tackling the problem of increased numbers of false positive significant points when correlations within the analysis results can not be neglected. For this, different phase space reconstruction approaches are systematically compared and a generalised areawise significance test which implements a numerical estimation of the correlations within the analysis results is introduced. In particular, the test can be used to identify patches of possibly false positive significant points. The developed analysis framework is applied to detect and characterise dynamical anomalies in past climate variability in North and South America by studying four real-world palaeoclimatic time series from different archives. Furthermore, the question whether palaeoclimate proxy time series from different archives are equally well suited for tracking past climate dynamics with windowed recurrence network analysis is approached by using the framework of proxy system modelling. This thesis promotes the use of non-linear methods for analysing palaeoclimate proxy time series, provides a detailed assessment of potentials and limitations of windowed recurrence network analysis and identifies future research directions that can complement the obtained results and conclusions.
Sage, Aled. "Observation-driven configuration of complex software systems." Thesis, University of St Andrews, 2004. http://hdl.handle.net/10023/6479.
Повний текст джерелаRung, Johan. "Signals and Noise in Complex Biological Systems." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7862.
Повний текст джерелаGrabowicz, Przemyslaw Adam. "Complex networks approach to modeling online social systems. The emergence of computational social science." Doctoral thesis, Universitat de les Illes Balears, 2014. http://hdl.handle.net/10803/131220.
Повний текст джерелаLa presente tesis está dedicada a la descripción, análisis y modelado cuantitativo de sistemas complejos sociales en forma de redes sociales en internet. Mediante el uso de métodos y conceptos provenientes de ciencia de redes, análisis de redes sociales y minería de datos se descubren diferentes patrones estadísticos de los sistemas estudiados. Uno de los objetivos a largo plazo de esta línea de investigación consiste en hacer posible la predicción del comportamiento de sistemas complejos tecnológico-sociales, de un modo similar a la predicción meteorológica, usando inferencia estadística y modelado computacional basado en avances en el conocimiento de los sistemas tecnológico-sociales. A pesar de que el objeto del presente estudio son seres humanos, en lugar de los átomos o moléculas estudiados tradicionalmente en la física estadística, la disponibilidad de grandes bases de datos sobre comportamiento humano hace posible el uso de técnicas y métodos de física estadística. En el presente trabajo se utilizan grandes bases de datos provenientes de redes sociales en internet, se miden patrones estadísticos de comportamiento social, y se desarrollan métodos cuantitativos, modelos y métricas para el estudio de sistemas complejos tecnológico-sociales.
Balachandran, Libish Kalathil. "Computational workflow management for conceptual design of complex systems : an air-vehicle design perspective." Thesis, Cranfield University, 2007. http://dspace.lib.cranfield.ac.uk/handle/1826/5070.
Повний текст джерелаChow, Fung-kiu, and 鄒鳳嬌. "Modeling the minority-seeking behavior in complex adaptive systems." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B29367487.
Повний текст джерелаBelyaeva, Anastasiya. "Computational methods for analyzing and modeling gene regulation and 3D genome organization." Thesis, Massachusetts Institute of Technology, 2021. https://hdl.handle.net/1721.1/130828.
Повний текст джерелаCataloged from the official PDF of thesis.
Includes bibliographical references (pages 261-281).
Biological processes from differentiation to disease progression are governed by gene regulatory mechanisms. Currently large-scale omics and imaging data sets are being collected to characterize gene regulation at every level. Such data sets present new opportunities and challenges for extracting biological insights and elucidating the gene regulatory logic of cells. In this thesis, I present computational methods for the analysis and integration of various data types used for cell profiling. Specifically, I focus on analyzing and linking gene expression with the 3D organization of the genome. First, I describe methodologies for elucidating gene regulatory mechanisms by considering multiple data modalities. I design a computational framework for identifying colocalized and coregulated chromosome regions by integrating gene expression and epigenetic marks with 3D interactions using network analysis.
Then, I provide a general framework for data integration using autoencoders and apply it for the integration and translation between gene expression and chromatin images of naive T-cells. Second, I describe methods for analyzing single modalities such as contact frequency data, which measures the spatial organization of the genome, and gene expression data. Given the important role of the 3D genome organization in gene regulation, I present a methodology for reconstructing the 3D diploid conformation of the genome from contact frequency data. Given the ubiquity of gene expression data and the recent advances in single-cell RNA-sequencing technologies as well as the need for causal modeling of gene regulatory mechanisms, I then describe an algorithm as well as a software tool, difference causal inference (DCI), for learning causal gene regulatory networks from gene expression data.
DCI addresses the problem of directly learning differences between causal gene regulatory networks given gene expression data from two related conditions. Finally, I shift my focus from basic biology to drug discovery. Given the current COVID19 pandemic, I present a computational drug repurposing platform that enables the identification of FDA approved compounds for drug repurposing and investigation of potential causal drug mechanisms. This framework relies on identifying drugs that reverse the signature of the infection in the space learned by an autoencoder and then uses causal inference to identify putative drug mechanisms.
by Anastasiya Belyaeva.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Computational and Systems Biology Program
Huismann, Immo. "Computational fluid dynamics on wildly heterogeneous systems." TUDPress, 2018. https://tud.qucosa.de/id/qucosa%3A74002.
Повний текст джерелаChen, Wei. "A robust concept exploration method for configuring complex systems." Diss., Georgia Institute of Technology, 1995. http://hdl.handle.net/1853/20224.
Повний текст джерелаSurujon, Defne. "Computational approaches in infectious disease research: Towards improved diagnostic methods." Thesis, Boston College, 2020. http://hdl.handle.net/2345/bc-ir:109089.
Повний текст джерелаDue to overuse and misuse of antibiotics, the global threat of antibiotic resistance is a growing crisis. Three critical issues surrounding antibiotic resistance are the lack of rapid testing, treatment failure, and evolution of resistance. However, with new technology facilitating data collection and powerful statistical learning advances, our understanding of the bacterial stress response to antibiotics is rapidly expanding. With a recent influx of omics data, it has become possible to develop powerful computational methods that make the best use of growing systems-level datasets. In this work, I present several such approaches that address the three challenges around resistance. While this body of work was motivated by the antibiotic resistance crisis, the approaches presented here favor generalization, that is, applicability beyond just one context. First, I present ShinyOmics, a web-based application that allow visualization, sharing, exploration and comparison of systems-level data. An overview of transcriptomics data in the bacterial pathogen Streptococcus pneumoniae led to the hypothesis that stress-susceptible strains have more chaotic gene expression patterns than stress-resistant ones. This hypothesis was supported by data from multiple strains, species, antibiotics and non-antibiotic stress factors, leading to the development of a transcriptomic entropy based, general predictor for bacterial fitness. I show the potential utility of this predictor in predicting antibiotic susceptibility phenotype, and drug minimum inhibitory concentrations, which can be applied to bacterial isolates from patients in the near future. Predictors for antibiotic susceptibility are of great value when there is large phenotypic variability across isolates from the same species. Phenotypic variability is accompanied by genomic diversity harbored within a species. I address the genomic diversity by developing BFClust, a software package that for the first time enables pan-genome analysis with confidence scores. Using pan-genome level information, I then develop predictors of essential genes unique to certain strains and predictors for genes that acquire adaptive mutations under prolonged stress exposure. Genes that are essential offer attractive drug targets, and those that are essential only in certain strains would make great targets for very narrow-spectrum antibiotics, potentially leading the way to personalized therapies in infectious disease. Finally, the prediction of adaptive outcome can lead to predictions of future cross-resistance or collateral sensitivities. Overall, this body of work exemplifies how computational methods can complement the increasingly rapid data generation in the lab, and pave the way to the development of more effective antibiotic stewardship practices
Thesis (PhD) — Boston College, 2020
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology