Dissertations / Theses on the topic 'Singular-Value Decomposition (SVD)'
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Ek, Christoffer. "Singular Value Decomposition." Thesis, Linnéuniversitetet, Institutionen för datavetenskap, fysik och matematik, DFM, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-21481.
Full textDigital information transmission is a growing field. Emails, videos and so on are transmitting around the world on a daily basis. Along the growth of using digital devises there is in some cases a great interest of keeping this information secure. In the field of signal processing a general concept is antenna transmission. Free space between an antenna transmitter and a receiver is an example of a system. In a rough environment such as a room with reflections and independent electrical devices there will be a lot of distortion in the system and the signal that is transmitted might, due to the system characteristics and noise be distorted. System identification is another well-known concept in signal processing. This thesis will focus on system identification in a rough environment and unknown systems. It will introduce mathematical tools from the field of linear algebra and applying them in signal processing. Mainly this thesis focus on a specific matrix factorization called Singular Value Decomposition (SVD). This is used to solve complicated inverses and identifying systems. This thesis is formed and accomplished in collaboration with Combitech AB. Their expertise in the field of signal processing was of great help when putting the algorithm in practice. Using a well-known programming script called LabView the mathematical tools were synchronized with the instruments that were used to generate the systems and signals.
Jolly, Vineet Kumar. "Activity Recognition using Singular Value Decomposition." Thesis, Virginia Tech, 2006. http://hdl.handle.net/10919/35219.
Full textMaster of Science
Renkjumnong, Wasuta. "SVD and PCA in Image Processing." Digital Archive @ GSU, 2007. http://digitalarchive.gsu.edu/math_theses/31.
Full textHaque, S. M. Rafizul. "Singular Value Decomposition and Discrete Cosine Transform based Image Watermarking." Thesis, Blekinge Tekniska Högskola, Avdelningen för för interaktion och systemdesign, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:bth-5269.
Full textPhone number: +88041730212
Kaufman, Jason R. "Digital video watermarking using singular value decomposition and two-dimensional principal component analysis." Ohio : Ohio University, 2006. http://www.ohiolink.edu/etd/view.cgi?ohiou1141855950.
Full textBrown, Michael J. "SINGULAR VALUE DECOMPOSITION AND 2D PRINCIPAL COMPONENT ANALYSIS OF IRIS-BIOMETRICS FOR AUTOMATIC HUMAN IDENTIFICATION." Ohio University / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1149187904.
Full textChu, Yue. "SVD-BAYES: A SINGULAR VALUE DECOMPOSITION-BASED APPROACH UNDER BAYESIAN FRAMEWORK FOR INDIRECT ESTIMATION OF AGE-SPECIFIC FERTILITY AND MORTALITY." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1609638415015896.
Full textCampbell, Kathlleen. "Extension of Kendall's tau Using Rank-Adapted SVD to Identify Correlation and Factions Among Rankers and Equivalence Classes Among Ranked Elements." Diss., Temple University Libraries, 2014. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/284578.
Full textPh.D.
The practice of ranking objects, events, and people to determine relevance, importance, or competitive edge is ancient. Recently, the use of rankings has permeated into daily usage, especially in the fields of business and education. When determining the association among those creating the ranks (herein called sources), the traditional assumption is that all sources compare a list of the same items (herein called elements). In the twenty-first century, it is rare that any two sources choose identical elements to rank. Adding to this difficulty, the number of credible sources creating and releasing rankings is increasing. In statistical literature, there is no current methodology that adequately assesses the association among multiple sources. We introduce rank-adapted singular value decomposition (R-A SVD), a new method that uses Kendall's tau as the underlying correlation method. We begin with (P), a matrix of data ranks. The first step is to factor the covariance matrix (K) as follows: K = cov(P) = V D^2 V Here, (V) is an orthonormal basis for the rows that is useful in identifying when sources agree as to the rank order and specifically which sources. D is a diagonal of eigenvalues. By analogy with singular value decomposition (SVD), we define U^* as U^* = PVD^(-1) The diagonal matrix, D, provides the factored eigenvalues in decreasing order. The largest eigenvalue is used to assess the overall association among the sources and is a conservative unbiased method comparable to Kendall's W. Anderson's test determines whether this association is significant and also identifies other significant eigenvalues produced by the covariance matrix.. Using Anderson's test (1963) we identify the a significantly large eigenvalues from D. When one or more eigenvalues is significant, there is evidence that the association among the sources is significant. Focusing on the a corresponding vectors of V specifically identifies which sources agree. In cases where more than one eigenvalue is significant, the $a$ significant vectors of V provide insight into factions. When more than one set of sources is in agreement, each group of agreeing sources is considered a faction. In many cases, more than one set of sources will be in agreement with one another but not necessarily with another set of sources; each group that is in agreement would be considered a faction. Using the a significant vectors of U^* provides different but equally important results. In many cases, the elements that are being ranked can be subdivided into equivalence classes. An equivalence class is defined as subpopulations of ranked elements that are similar to one another but dissimilar from other classes. When these classes exist, U^* provides insight as to how many classes and which elements belong in each class. In summary, the R-A SVD method gives the user the ability to assess whether there is any underlying association among multiple rank sources. It then identifies when sources agree and allows for more useful and careful interpretation when analyzing rank data.
Temple University--Theses
Idrees, Zunera, and Eliza Hashemiaghjekandi. "Image Compression by Using Haar Wavelet Transform and Singualr Value Decomposition." Thesis, Linnéuniversitetet, Institutionen för datavetenskap, fysik och matematik, DFM, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-11467.
Full textGunyan, Scott Nathan. "An Examination into the Statistics of the Singular Vectors for the Multi-User MIMO Wireless Channel." Diss., CLICK HERE for online access, 2004. http://contentdm.lib.byu.edu/ETD/image/etd539.pdf.
Full textKoski, Antti E. "Rapid frequency estimation." Worcester, Mass. : Worcester Polytechnic Institute, 2006. http://www.wpi.edu/Pubs/ETD/Available/etd-032806-165036/.
Full textKeywords: DSS; ECM; SVD; Singular Value Decomposition; rapid frequency estimation; frequency estimation. Includes bibliographical references (leaves 174-177).
Odedo, Victor. "High resolution time reversal (TR) imaging based on spatio-temporal windows." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/high-resolution-time-reversal-tr-imaging-based-on-spatiotemporal-windows(f0589f73-901f-4de2-9886-7045b7f6cfd4).html.
Full textBrundin, Michelle, Peter Morris, Gustav Åhlman, and Emil Rosén. "Implementation av webbsida för rekommendationssystem med användaruppbyggd databas." Thesis, Uppsala universitet, Institutionen för teknikvetenskaper, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-175489.
Full textSvoboda, Pavel. "Vyhledávání osob ve fotografii." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2009. http://www.nusl.cz/ntk/nusl-236716.
Full textKučaidze, Artiom. "Tinklalapio navigavimo asociacijų analizės ir prognozavimo modelis." Master's thesis, Lithuanian Academic Libraries Network (LABT), 2009. http://vddb.library.lt/obj/LT-eLABa-0001:E.02~2008~D_20090908_201802-74260.
Full textIn this document we develop a model for analyzing and predicting the scent of a web site, which is based on information foraging theory. The goal of this model is to simulate potential web page users and their information foraging paths having specific information needs. Model is being developed combining LSA, SVD algorithms and correlation values calculations. LSA algorithm is used for creating semantic spaces and correlation values are user in statistics. Together they provide possibility to analyze word‘s semantic similarity. Primary problems of web navigation are described in this document. These problems can occur for users while creating the scent of a web site. User can face with concurrency between links problem, wrong sense link problem and unfamiliar link problem. In this document we demonstrate how model recognizes and analyzes these problems.
Samadi, Afshin. "Large Scale Solar Power Integration in Distribution Grids : PV Modelling, Voltage Support and Aggregation Studies." Doctoral thesis, KTH, Elektriska energisystem, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-154602.
Full textThe Doctoral Degrees issued upon completion of the programme are issued by Comillas Pontifical University, Delft University of Technology and KTH Royal Institute of Technology. The invested degrees are official in Spain, the Netherlands and Sweden, respectively. QC 20141028
Golub, Frank. "An Estimation Technique for Spin Echo Electron Paramagnetic Resonance." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1372095953.
Full textAkkari, Samy. "Contrôle d'un système multi-terminal HVDC (MTDC) et étude des interactions entre les réseaux AC et le réseau MTDC." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLC069/document.
Full textHVDC transmission systems are largely used worldwide, mostly in the form of back-to-back and point-to-point HVDC, using either thyristor-based LCC or IGBT-based VSC. With the recent deployment of the INELFE HVDC link between France and Spain, and the commissioning in China of a three-terminal HVDC transmission system using Modular Multilevel Converters (MMCs), a modular design of voltage source converters, the focus of the scientific community has shifted onto the analysis and control of MMC-based HVDC transmission systems. In this thesis, the average value models of both a standard 2-level VSC and an MMC are proposed and the most interesting difference between the two converter technologies -the control of the stored energy in the MMC- is emphasised and explained. These models are then linearised, expressed in state-space form and validated by comparing their behaviour to more detailed models under EMT programs. Afterwards, these state-space representations are used in the modelling of HVDC transmission systems, either point-to-point or Multi-Terminal HVDC (MTDC). A modal analysis is performed on an HVDC link, for both 2-level VSCs and MMCs. The modes of these two systems are specifed and compared and the independent control of the DC voltage and the DC current in the case of an MMC is illustrated. This analysis is extended to the scope of a 5-terminal HVDC system in order to perform a stability analysis, understand the origin of the system dynamics and identify the dominant DC voltage mode that dictates the DC voltage response time. Using the Singular Value Decomposition method on the MTDC system, the proper design of the voltage-droop gains of the controllers is then achieved so that the system operation is ensured within physical constraints, such as the maximum DC voltage deviation and the maximum admissible current in the power electronics. Finally, a supplementary droop "the frequency-droop control" is proposed so that MTDC systems also participate to the onshore grids frequency regulation. However, this controller interacts with the voltage-droop controller. This interaction is mathematically quantified and a corrected frequency-droop gain is proposed. This control is then illustrated with an application to the physical converters of the Twenties project mock-up
Jalboub, Mohamed K. "Investigation of the application of UPFC controllers for weak bus systems subjected to fault conditions. An investigation of the behaviour of a UPFC controller: the voltage stability and power transfer capability of the network and the effect of the position of unsymmetrical fault conditions." Thesis, University of Bradford, 2012. http://hdl.handle.net/10454/5699.
Full textLibyan Government
Reninger, Pierre-Alexandre. "Méthodologie d'analyse de levés électromagnétiques aéroportés en domaine temporel pour la caractérisation géologique et hydrogéologique." Phd thesis, Université d'Orléans, 2012. http://tel.archives-ouvertes.fr/tel-00802341.
Full textJalboub, Mohamed. "Investigation of the application of UPFC controllers for weak bus systems subjected to fault conditions : an investigation of the behaviour of a UPFC controller : the voltage stability and power transfer capability of the network and the effect of the position of unsymmetrical fault conditions." Thesis, University of Bradford, 2012. http://hdl.handle.net/10454/5699.
Full textBelica, Michal. "Metody sumarizace dokumentů na webu." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2013. http://www.nusl.cz/ntk/nusl-236386.
Full textAyvazyan, Vigen. "Etude de champs de température séparables avec une double décomposition en valeurs singulières : quelques applications à la caractérisation des propriétés thermophysiques des matérieux et au contrôle non destructif." Thesis, Bordeaux 1, 2012. http://www.theses.fr/2012BOR14671/document.
Full textInfrared thermography is a widely used method for characterization of thermophysical properties of materials. The advent of the laser diodes, which are handy, inexpensive, with a broad spectrum of characteristics, extend metrological possibilities of infrared cameras and provide a combination of new powerful tools for thermal characterization and non destructive evaluation. However, this new dynamic has also brought numerous difficulties that must be overcome, such as high volume noisy data processing and low sensitivity to estimated parameters of such data. This requires revisiting the existing methods of signal processing, adopting new sophisticated mathematical tools for data compression and processing of relevant information.New strategies consist in using orthogonal transforms of the signal as a prior data compression tools, which allow noise reduction and control over it. Correlation analysis, based on the local cerrelation study between partial derivatives of the experimental signal, completes these new strategies. A theoretical analogy in Fourier space has been performed in order to better understand the «physical» meaning of modal approaches.The response to the instantaneous point source of heat, has been revisited both numerically and experimentally. By using separable temperature fields, a new inversion technique based on a double singular value decomposition of experimental signal has been introduced. In comparison with previous methods, it takes into account two or three-dimensional heat diffusion and therefore offers a better exploitation of the spatial content of infrared images. Numerical and experimental examples have allowed us to validate in the first approach our new estimation method of longitudinal thermal diffusivities. Non destructive testing applications based on the new technique have also been introduced.An old issue, which consists in determining the initial temperature field from noisy data, has been approached in a new light. The necessity to know the thermal diffusivities of an orthotropic medium and the need to take into account often three-dimensional heat transfer, are complicated issues. The implementation of the double singular value decomposition allowed us to achieve interesting results according to its ease of use. Indeed, modal approaches are statistical methods based on high volume data processing, supposedly robust as to the measurement noise
Yang, Shun-Lin, and 楊順霖. "Development of TFT-LCD Automatic mura Inspection Using Singular Value Decomposition (SVD)." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/qbc62y.
Full text國立臺北科技大學
自動化科技研究所
95
A novel TFT-LCD defect inspection algorithm is proposed for automatic detection of Macro defect (mura) based on background reconstruction concept. Efficient and accurate surface defect detection on TFT LCD panels has become extremely crucial to success of LCD panel manufacturing. Detecting mura defects in a LCD panel can be difficult due to non-uniform brightness background and slightly different brightness levels between the defect region and the background. As such, a singular value decomposition (SVD) based background reconstruction algorithm is developed to establish the background image without mixing mura defects. To extract mura defects, an adaptive threshold strategy is then employed to separate defects from the background image. Through some experimental tests on real mura defects, it was verified that the proposed algorithm has a superior capability for detecting mura defects. The method of detecting mura defects in this article is divided into three stages. In the first stage, SVD is used to separate the detecting image into two singular vector matrix and a diagonal matrix call singular value matrix, that include images energy. The second stage we recontruct the background image without mura defects using the largest singular value. The third stage, we sgment the defect image using the maximum entropy threshold method and expect to minimize the overkill rate of defects.We deployed the mura measurement index call semu of SEMI to measure the quantification of mura and use it to eliminate the ghost defects. At the same time, there exist some noises to be filtered away from the result when the background image is reconstructed in SVD method.To overcome this proplem,this paper proposed a modification method for SVD singular vector and experimented on natual mura defect inspection. Experimental results mura defects can be detected successfull and efficiently.
Mcneill, Daniel Kyle. "Evolutionary and Iterative Training of Recurrent Neural Networks via the Singular Value Decomposition." Doctoral thesis, 2021. http://hdl.handle.net/11589/216712.
Full textThis work examines the use of the singular value decomposition (SVD) from linear algebra as a tool for the analysis of neural networks, as well as its use to speed up or even limit learning (to prevent over-fitting or maintain stability, for example) and as the basis for iterative and evolutionary learning algorithms. What we present here are methods of taking the inherent structure of the transformation into account — even while using evolutionary methods — using the singular value decomposition. Of course, preserving some structure of the transformations is not completely new — whether this means preserving sparseness or some type of invariance, as in the shift invariance of a convolutional layer. The methods we present allow us to train recurrent neural networks for a variety of problems with changes through time, including price prediction, predictive maintenance and model identification, and automatic control. Our method does not rely on back propagation and can be used in either supervised or unsupervised settings. Further, our models can be easily initialized by using either domain knowledge or (linear) least squares to “pre-program” the model and begin optimization in an area of the solution space likely to yield results. Finally, given a neural network previously trained in one domain, our models and methods allow the reuse and quick retraining for a similar domain, by preserving the inherent structure of the transformation at the heart of the neural network.
Chiang, Tse-Yu, and 江則佑. "Abbe-SVD: Compact Abbe’s Kernel Generation for Microlithography Aerial Image Simulation using Singular-Value Decomposition Method." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/17771551777073303525.
Full text國立臺灣大學
電子工程學研究所
96
At the present days, the key and critical part of industrial IC manufacture is the optical lithography technology which can duplicate the design patterns on the mask onto wafer by light exposure. However, when the mask patterns are too small which are approaching light wave length, the image quality and resolution on the wafer are getting worse owing to diffraction effect. Therefore, some necessary resolution enhancement techniques are proposed with remarkable skills and algorithms, and need to be verified by simulations or experimental results. The most direct and accurate simulation is the imaging of patterns on wafer. Accurate imaging simulation can show exposed and unexposed regions after photolithography by computer. Existing commercial and academic OPC simulators which compute in frequency domain with Abbe''s method applied on partial coherent light source take several days for computation with hundreds of computers working together at the same time. Hence, we propose to generate a compact Abbe''s kernel for microlithography aerial image simulation using singular-value decomposition method. The advantages of this approach are as follows: First, since not all the Abbe''s kernels have critical effects on aerial image, we can eliminate them to generate a compact one with SVD. Therefore, we can speed up simulation time, and furthermore keep the accuracy user specified. Second, with advanced concentric circles source discretization, equivalent kernels with higher precision is produced. Finally, we can use compact Abbe''s kernel to build LUT to speed up simulation time. In this thesis, we introduce some basic knowledge of optical lithography in chapter 1 and some coherent light in optics with analytical solution in chapter 2. Then, partially coherent light concept, advanced illumination aperture and Abbe''s method are introduced in chapter 3 and our Abbe-SVD algorithm and advanced source discretization will also be derived. Experimental result and some comparisons will be shown in chapter 4 and finally conclusion will be made in chapter 5.
Chiang, Tse-Yu. "Abbe-SVD: Compact Abbe's Kernel Generation for Microlithography Aerial Image Simulation using Singular-Value Decomposition Method." 2008. http://www.cetd.com.tw/ec/thesisdetail.aspx?etdun=U0001-2306200804053500.
Full textSukkari, Dalal. "High Performance Polar Decomposition on Manycore Systems and its application to Symmetric Eigensolvers and the Singular Value Decomposition." Diss., 2019. http://hdl.handle.net/10754/652466.
Full textHinga, Mark Brandon. "Using parallel computation to apply the singular value decomposition (SVD) in solving for large Earth gravity fields based on satellite data." Thesis, 2004. http://hdl.handle.net/2152/1190.
Full textHinga, Mark Brandon Tapley Byron D. "Using parallel computation to apply the singular value decomposition (SVD) in solving for large Earth gravity fields based on satellite data." 2004. http://wwwlib.umi.com/cr/utexas/fullcit?p3143269.
Full textAtemnkeng, Tabi Rosy Christy. "Estimation of Longevity Risk and Mortality Modelling." Master's thesis, 2022. http://hdl.handle.net/10362/135573.
Full textPrevious mortality models failed to account for improvements in human mortality rates thus in general, human life expectancy was underestimate. Declining mortality and increasing life expectancy (longevity) profoundly alter the population age distribution. This demographic transition has received considerable attention on pension and annuity providers. Concerns have been expressed about the implications of increased life expectancy for government spending on old-age support. The goal of this paper is to lay out a framework for measuring, understanding, and analyzing longevity risk, with a focus on defined pension plans. Lee-Carter proposed a widely used mortality forecasting model in 1992. The study looks at how well the Lee-Carter model performed for female and male populations in the selected country (France) from 1816 to 2018. The Singular Value Decomposition (SVD) method is used to estimate the parameters of the LC model. The mortality table then assesses future improvements in mortality and life expectancy, taking into account mortality assumptions, to see if pension funds and annuity providers are exposed to longevity risk. Mortality assumptions are predicted death rates based on a mortality table. The two types of mortality are mortality at birth and mortality in old age. Longevity risk must be effectively managed by pension and annuity providers. To mitigate this risk, pension providers must factor in future improvements in mortality and life expectancy, as mortality rates tend to decrease over time. The findings show that failing to account for future improvements in mortality results in an expected provision shortfall. Protection mechanisms and policy recommendations to manage longevity risk can help to mitigate the financial impact of an unexpected increase in longevity.
Šikorský, Tomáš. "Studium chirálních vlastností supramolekulárních komplexů." Master's thesis, 2011. http://www.nusl.cz/ntk/nusl-296381.
Full textSuresh, V. "Image Structures For Steganalysis And Encryption." Thesis, 2010. http://etd.iisc.ernet.in/handle/2005/2273.
Full textCarrelli, David John. "Utilising Local Model Neural Network Jacobian Information in Neurocontrol." Thesis, 2006. http://hdl.handle.net/10539/1815.
Full textIn this dissertation an efficient algorithm to calculate the differential of the network output with respect to its inputs is derived for axis orthogonal Local Model (LMN) and Radial Basis Function (RBF) Networks. A new recursive Singular Value Decomposition (SVD) adaptation algorithm, which attempts to circumvent many of the problems found in existing recursive adaptation algorithms, is also derived. Code listings and simulations are presented to demonstrate how the algorithms may be used in on-line adaptive neurocontrol systems. Specifically, the control techniques known as series inverse neural control and instantaneous linearization are highlighted. The presented material illustrates how the approach enhances the flexibility of LMN networks making them suitable for use in both direct and indirect adaptive control methods. By incorporating this ability into LMN networks an important characteristic of Multi Layer Perceptron (MLP) networks is obtained whilst retaining the desirable properties of the RBF and LMN approach.
Joshi, Champa. "Understanding Spatio-Temporal Variability and Associated Physical Controls of Near-Surface Soil Moisture in Different Hydro-Climates." Thesis, 2013. http://hdl.handle.net/1969.1/149547.
Full textΤρικοίλης, Ιωάννης. "Εύρεση γεωμετρικών χαρακτηριστικών ερυθρών αιμοσφαιρίων από εικόνες σκεδασμένου φωτός." Thesis, 2010. http://nemertes.lis.upatras.gr/jspui/handle/10889/3696.
Full textIn this thesis we study and implement methods of estimating the geometrical features of the human red blood cell from a set of simulated light scattering images produced by a He-Ne laser beam at 632.8 μm. Ιn first chapter an introduction to the properties and the characteristics of red blood cells are presented. Furthermore, we describe various abnormalities of erythrocytes and the until now used ways of detection. In second chapter the properties of electromagnetic radiation and the light scattering problem of EM radiation from human erythrocytes are presented. The third chapter consists of two parts. In first part we analyse the theory of neural networks and we describe the radial basis function neural network. Then, we describe the theoritical and mathematical background of the methods that we use for feature extraction which are Singular Value Decomposition (SVD), Angular Radial Transform and Gabor filters. In second part the solution of the inverse problem of light scattering is described. We present the methodology of the solution process in which we implement a Singular Value Decomposition approach, a shape descriptor with Angular Radial Transform and a homogenous texture descriptor which uses Gabor filters for the estimation of the geometrical characteristics and a RBF neural network for the classification of the erythrocytes. In the forth and last chapter the described methods are evaluated and we summarise the experimental results and conclusions that were extracted from this thesis.
LANTERI, ALESSANDRO. "Novel methods for Intrinsic dimension estimation and manifold learning." Doctoral thesis, 2016. http://hdl.handle.net/11573/905425.
Full textGhous, Hamid. "Building a robust clinical diagnosis support system for childhood cancer using data mining methods." Thesis, 2016. http://hdl.handle.net/10453/90061.
Full textProgress in understanding core pathways and processes of cancer requires thorough analysis of many coding and noncoding regions of the genome. Data mining and knowledge discovery have been applied to datasets across many industries, including bioinformatics. However, data mining faces a major challenge in its application to bioinformatics: the diversity and dimensionality of biomedical data. The term ‘big data’ was applied to the clinical domain by Yoo et al. (2014), specifically referring to single nucleotide polymorphism (SNP) and gene expression data. This research thesis focuses on three different types of data: gene-annotations, gene expression and single nucleotide polymorphisms. Genetic association studies have led to the discovery of single genetic variants associated with common diseases. However, complex diseases are not caused by a single gene acting alone but are the result of complex linear and non-linear interactions among different types of microarray data. In this scenario, a single gene can have a small effect on disease but cannot be the major cause of the disease. For this reason there is a critical need to implement new approaches which take into account linear and non-linear gene-gene and patient-patient interactions that can eventually help in diagnosis and prognosis of complex diseases. Several computational methods have been developed to deal with gene annotations, gene expressions and SNP data of complex diseases. However, analysis of every gene expression and SNP profile, and finding gene-to-gene relationships, is computationally infeasible because of the high-dimensionality of data. In addition, many computational methods have problems with scaling to large datasets, and with overfitting. Therefore, there is growing interest in applying data mining and machine learning approaches to understand different types of microarray data. Cancer is the disease that kills the most children in Australia (Torre et al., 2015). Within this thesis, the focus is on childhood Acute Lymphoblastic Leukaemia. Acute Lymphoblastic Leukaemia is the most common childhood malignancy with 24% of all new cancers occurring in children within Australia (Coates et al., 2001). According to the American Cancer Society (2016), a total of 6,590 cases of ALL have been diagnosed across all age groups in USA and the expected deaths are 1,430 in 2016. The project uses different data mining and visualisation methods applied on different types of biological data: gene annotations, gene expression and SNPs. This thesis focuses on three main issues in genomic and transcriptomic data studies: (i) Proposing, implementing and evaluating a novel framework to find functional relationships between genes from gene-annotation data. (ii) Identifying an optimal dimensionality reduction method to classify between relapsed and non-relapsed ALL patients using gene expression. (iii) Proposing, implementing and evaluating a novel feature selection approach to identify related metabolic pathways in ALL This thesis proposes, implements and validates an efficient framework to find functional relationships between genes based on gene-annotation data. The framework is built on a binary matrix and a proximity matrix, where the binary matrix contains information related to genes and their functionality, while the proximity matrix shows similarity between different features. The framework retrieves gene functionality information from Gene Ontology (GO), a publicly available database, and visualises the functional related genes using singular value decomposition (SVD). From a simple list of gene-annotations, this thesis retrieves features (i.e Gene Ontology terms) related to each gene and calculates a similarity measure based on the distance between terms in the GO hierarchy. The distance measures are based on hierarchical structure of Gene Ontology and these distance measures are called similarity measures. In this framework, two different similarity measures are applied: (i) A hop-based similarity measure where the distance is calculated based on the number of links between two terms. (ii) An information-content similarity measure where the similarity between terms is based on the probability of GO terms in the gene dataset. This framework also identifies which method performs better among these two similarity measures at identifying functional relationships between genes. Singular value decomposition method is used for visualisation, having the advantage that multiple types of relationships can be visualised simultaneously (gene-to-gene, term-to-term and gene-to-term) In this thesis a novel framework is developed for visualizing patient-to-patient relationships using gene expression values. The framework builds on the random forest feature selection method to filter gene expression values and then applies different linear and non-linear machine learning methods to them. The methods used in this framework are Principal Component Analysis (PCA), Kernel Principal Component Analysis (kPCA), Local Linear Embedding (LLE), Stochastic Neighbour Embedding (SNE) and Diffusion Maps. The framework compares these different machine learning methods by tuning different parameters to find the optimal method among them. Area under the curve (AUC) is used to rank the results and SVM is used to classify between relapsed and non-relapsed patients. The final section of the thesis proposes, implements and validates a framework to find active metabolic pathways in ALL using single nucleotide polymorphism (SNP) profiles. The framework is based on the random forest feature selection method. A collected dataset of ALL patient and healthy controls is constructed and later random forest is applied using different parameters to find highly-ranked SNPs. The credibility of the model is assessed based on the error rate of the confusion matrix and kappa values. Selected high ranked SNPs are used to retrieve metabolic pathways related to ALL from the KEGG metabolic pathways database. The methodologies and approaches presented in this thesis emphasise the critical role that different types of microarray data play in understanding complex diseases like ALL. The availability of flexible frameworks for the task of disease diagnosis and prognosis, as proposed in this thesis, will play an important role in understanding the genetic basis to common complex diseases. This thesis contributes to knowledge in two ways: (i) Providing novel data mining and visualisation frameworks to handle biological data. (ii) Providing novel visualisations for microarray data to increase understanding of disease.
Pani, Jagdeep. "Provable Methods for Non-negative Matrix Factorization." Thesis, 2016. http://hdl.handle.net/2005/2739.
Full text