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Identification of activation of transcription factors from microarray data /Kossenkov, Andrei. T̈ozeren, Aydin. January 2007 (has links)
Thesis (Ph. D.)--Drexel University, 2007. / Includes abstract and vita. Includes bibliographical references (leaves 103-115).
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Statistical mechanical models for image processing16 October 2001 (has links) (PDF)
No description available.
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Team behavior recognition using dynamic bayesian networksGaitanis, Konstantinos 31 October 2008 (has links)
Cette thèse de doctorat analyse les concepts impliqués dans la prise de décisions de groupes d'agents et applique ces concepts dans la création d'un cadre théorique et pratique qui permet la reconnaissance de comportements de groupes.
Nous allons présenter une vue d'ensemble de la théorie de l'intention, étudiée dans le passé par quelques grands théoriciens comme Searle, Bratmann et Cohen, et nous allons montrer le lien avec des recherches plus récentes dans le domaine de la reconnaissance de comportements.
Nous allons étudier les avantages et inconvénients des techniques les plus avancées dans ce domaine et nous allons créer un nouveau modèle qui représente et détecte les comportements de groupes. Ce nouveau modèle s'appelle Multiagent-Abstract Hidden Markov mEmory Model (M-AHMEM) et résulte de la fusion de modèles déjà existants, le but étant de créer une approche unifiée du problème. La plus grande partie de cette thèse est consacrée à la présentation détaillée du M-AHMEM et de l'algorithme responsable de la reconnaissance de comportements.
Notre modèle sera testé sur deux applications différentes : l'analyse gesturale humaine et la fusion multimodale des données audio et vidéo. A travers ces deux applications, nous avançons l'argument qu'un ensemble de données constitué de plusieurs variables corrélées peut être analysé efficacement sous un cadre unifié de reconnaissance de comportements. Nous allons montrer que la corrélation entre les différentes variables peut être modélisée comme une coopération ayant lieu à l'intérieur d'une équipe et que la reconnaissance de comportements constitue une approche moderne de classification et de reconnaissance de patrons.
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Essays on Aggregation and Cointegration of Econometric ModelsSilvestrini, Andrea 02 June 2009 (has links)
This dissertation can be broadly divided into two independent parts. The first three chapters analyse issues related to temporal and contemporaneous aggregation of econometric models. The fourth chapter contains an application of Bayesian techniques to investigate whether the post transition fiscal policy of Poland is sustainable in the long run and consistent with an intertemporal budget constraint.
Chapter 1 surveys the econometric methodology of temporal aggregation for a wide range of univariate and multivariate time series models.
A unified overview of temporal aggregation techniques for this broad class of processes is presented in the first part of the chapter and the main results are summarized. In each case, assuming to know the underlying process at the disaggregate frequency, the aim is to find the appropriate model for the aggregated data. Additional topics concerning temporal aggregation of ARIMA-GARCH models (see Drost and Nijman, 1993) are discussed and several examples presented. Systematic sampling schemes are also reviewed.
Multivariate models, which show interesting features under temporal aggregation (Breitung and Swanson, 2002, Marcellino, 1999, Hafner, 2008), are examined in the second part of the chapter. In particular, the focus is on temporal aggregation of VARMA models and on the related concept of spurious instantaneous causality, which is not a time series property invariant to temporal aggregation. On the other hand, as pointed out by Marcellino (1999), other important time series features as cointegration and presence of unit roots are invariant to temporal aggregation and are not induced by it.
Some empirical applications based on macroeconomic and financial data illustrate all the techniques surveyed and the main results.
Chapter 2 is an attempt to monitor fiscal variables in the Euro area, building an early warning signal indicator for assessing the development of public finances in the short-run and exploiting the existence of monthly budgetary statistics from France, taken as "example country".
The application is conducted focusing on the cash State deficit, looking at components from the revenue and expenditure sides. For each component, monthly ARIMA models are estimated and then temporally aggregated to the annual frequency, as the policy makers are interested in yearly predictions.
The short-run forecasting exercises carried out for years 2002, 2003 and 2004 highlight the fact that the one-step-ahead predictions based on the temporally aggregated models generally outperform those delivered by standard monthly ARIMA modeling, as well as the official forecasts made available by the French government, for each of the eleven components and thus for the whole State deficit. More importantly, by the middle of the year, very accurate predictions for the current year are made available.
The proposed method could be extremely useful, providing policy makers with a valuable indicator when assessing the development of public finances in the short-run (one year horizon or even less).
Chapter 3 deals with the issue of forecasting contemporaneous time series aggregates. The performance of "aggregate" and "disaggregate" predictors in forecasting contemporaneously aggregated vector ARMA (VARMA) processes is compared. An aggregate predictor is built by forecasting directly the aggregate process, as it results from contemporaneous aggregation of the data generating vector process. A disaggregate predictor is a predictor obtained from aggregation of univariate forecasts for the individual components of the data generating vector process.
The econometric framework is broadly based on Lütkepohl (1987). The necessary and sufficient condition for the equality of mean squared errors associated with the two competing methods in the bivariate VMA(1) case is provided. It is argued that the condition of equality of predictors as stated in Lütkepohl (1987), although necessary and sufficient for the equality of the predictors, is sufficient (but not necessary) for the equality of mean squared errors.
Furthermore, it is shown that the same forecasting accuracy for the two predictors can be achieved using specific assumptions on the parameters of the VMA(1) structure.
Finally, an empirical application that involves the problem of forecasting the Italian monetary aggregate M1 on the basis of annual time series ranging from 1948 until 1998, prior to the creation of the European Economic and Monetary Union (EMU), is presented to show the relevance of the topic. In the empirical application, the framework is further generalized to deal with heteroskedastic and cross-correlated innovations.
Chapter 4 deals with a cointegration analysis applied to the empirical investigation of fiscal sustainability. The focus is on a particular country: Poland. The choice of Poland is not random. First, the motivation stems from the fact that fiscal sustainability is a central topic for most of the economies of Eastern Europe. Second, this is one of the first countries to start the transition process to a market economy (since 1989), providing a relatively favorable institutional setting within which to study fiscal sustainability (see Green, Holmes and Kowalski, 2001). The emphasis is on the feasibility of a permanent deficit in the long-run, meaning whether a government can continue to operate under its current fiscal policy indefinitely.
The empirical analysis to examine debt stabilization is made up by two steps.
First, a Bayesian methodology is applied to conduct inference about the cointegrating relationship between budget revenues and (inclusive of interest) expenditures and to select the cointegrating rank. This task is complicated by the conceptual difficulty linked to the choice of the prior distributions for the parameters relevant to the economic problem under study (Villani, 2005).
Second, Bayesian inference is applied to the estimation of the normalized cointegrating vector between budget revenues and expenditures. With a single cointegrating equation, some known results concerning the posterior density of the cointegrating vector may be used (see Bauwens, Lubrano and Richard, 1999).
The priors used in the paper leads to straightforward posterior calculations which can be easily performed.
Moreover, the posterior analysis leads to a careful assessment of the magnitude of the cointegrating vector. Finally, it is shown to what extent the likelihood of the data is important in revising the available prior information, relying on numerical integration techniques based on deterministic methods.
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Essays in Dynamic MacroeconometricsBañbura, Marta 26 June 2009 (has links)
The thesis contains four essays covering topics in the field of macroeconomic forecasting.
The first two chapters consider factor models in the context of real-time forecasting with many indicators. Using a large number of predictors offers an opportunity to exploit a rich information set and is also considered to be a more robust approach in the presence of instabilities. On the other hand, it poses a challenge of how to extract the relevant information in a parsimonious way. Recent research shows that factor models provide an answer to this problem. The fundamental assumption underlying those models is that most of the co-movement of the variables in a given dataset can be summarized by only few latent variables, the factors. This assumption seems to be warranted in the case of macroeconomic and financial data. Important theoretical foundations for large factor models were laid by Forni, Hallin, Lippi and Reichlin (2000) and Stock and Watson (2002). Since then, different versions of factor models have been applied for forecasting, structural analysis or construction of economic activity indicators. Recently, Giannone, Reichlin and Small (2008) have used a factor model to produce projections of the U.S GDP in the presence of a real-time data flow. They propose a framework that can cope with large datasets characterised by staggered and nonsynchronous data releases (sometimes referred to as “ragged edge”). This is relevant as, in practice, important indicators like GDP are released with a substantial delay and, in the meantime, more timely variables can be used to assess the current state of the economy.
The first chapter of the thesis entitled “A look into the factor model black box: publication lags and the role of hard and soft data in forecasting GDP” is based on joint work with Gerhard Rünstler and applies the framework of Giannone, Reichlin and Small (2008) to the case of euro area. In particular, we are interested in the role of “soft” and “hard” data in the GDP forecast and how it is related to their timeliness.
The soft data include surveys and financial indicators and reflect market expectations. They are usually promptly available. In contrast, the hard indicators on real activity measure directly certain components of GDP (e.g. industrial production) and are published with a significant delay. We propose several measures in order to assess the role of individual or groups of series in the forecast while taking into account their respective publication lags. We find that surveys and financial data contain important information beyond the monthly real activity measures for the GDP forecasts, once their timeliness is properly accounted for.
The second chapter entitled “Maximum likelihood estimation of large factor model on datasets with arbitrary pattern of missing data” is based on joint work with Michele Modugno. It proposes a methodology for the estimation of factor models on large cross-sections with a general pattern of missing data. In contrast to Giannone, Reichlin and Small (2008), we can handle datasets that are not only characterised by a “ragged edge”, but can include e.g. mixed frequency or short history indicators. The latter is particularly relevant for the euro area or other young economies, for which many series have been compiled only since recently. We adopt the maximum likelihood approach which, apart from the flexibility with regard to the pattern of missing data, is also more efficient and allows imposing restrictions on the parameters. Applied for small factor models by e.g. Geweke (1977), Sargent and Sims (1977) or Watson and Engle (1983), it has been shown by Doz, Giannone and Reichlin (2006) to be consistent, robust and computationally feasible also in the case of large cross-sections. To circumvent the computational complexity of a direct likelihood maximisation in the case of large cross-section, Doz, Giannone and Reichlin (2006) propose to use the iterative Expectation-Maximisation (EM) algorithm (used for the small model by Watson and Engle, 1983). Our contribution is to modify the EM steps to the case of missing data and to show how to augment the model, in order to account for the serial correlation of the idiosyncratic component. In addition, we derive the link between the unexpected part of a data release and the forecast revision and illustrate how this can be used to understand the sources of the
latter in the case of simultaneous releases. We use this methodology for short-term forecasting and backdating of the euro area GDP on the basis of a large panel of monthly and quarterly data. In particular, we are able to examine the effect of quarterly variables and short history monthly series like the Purchasing Managers' surveys on the forecast.
The third chapter is entitled “Large Bayesian VARs” and is based on joint work with Domenico Giannone and Lucrezia Reichlin. It proposes an alternative approach to factor models for dealing with the curse of dimensionality, namely Bayesian shrinkage. We study Vector Autoregressions (VARs) which have the advantage over factor models in that they allow structural analysis in a natural way. We consider systems including more than 100 variables. This is the first application in the literature to estimate a VAR of this size. Apart from the forecast considerations, as argued above, the size of the information set can be also relevant for the structural analysis, see e.g. Bernanke, Boivin and Eliasz (2005), Giannone and Reichlin (2006) or Christiano, Eichenbaum and Evans (1999) for a discussion. In addition, many problems may require the study of the dynamics of many variables: many countries, sectors or regions. While we use standard priors as proposed by Litterman (1986), an
important novelty of the work is that we set the overall tightness of the prior in relation to the model size. In this we follow the recommendation by De Mol, Giannone and Reichlin (2008) who study the case of Bayesian regressions. They show that with increasing size of the model one should shrink more to avoid overfitting, but when data are collinear one is still able to extract the relevant sample information. We apply this principle in the case of VARs. We compare the large model with smaller systems in terms of forecasting performance and structural analysis of the effect of monetary policy shock. The results show that a standard Bayesian VAR model is an appropriate tool for large panels of data once the degree of shrinkage is set in relation to the model size.
The fourth chapter entitled “Forecasting euro area inflation with wavelets: extracting information from real activity and money at different scales” proposes a framework for exploiting relationships between variables at different frequency bands in the context of forecasting. This work is motivated by the on-going debate whether money provides a reliable signal for the future price developments. The empirical evidence on the leading role of money for inflation in an out-of-sample forecast framework is not very strong, see e.g. Lenza (2006) or Fisher, Lenza, Pill and Reichlin (2008). At the same time, e.g. Gerlach (2003) or Assenmacher-Wesche and Gerlach (2007, 2008) argue that money and output could affect prices at different frequencies, however their analysis is performed in-sample. In this Chapter, it is investigated empirically which frequency bands and for which variables are the most relevant for the out-of-sample forecast of inflation when the information from prices, money and real activity is considered. To extract different frequency components from a series a wavelet transform is applied. It provides a simple and intuitive framework for band-pass filtering and allows a decomposition of series into different frequency bands. Its application in the multivariate out-of-sample forecast is novel in the literature. The results indicate that, indeed, different scales of money, prices and GDP can be relevant for the inflation forecast.
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The Maximum Minimum Parents and Children AlgorithmPetersson, Mikael January 2010 (has links)
Given a random sample from a multivariate probability distribution p, the maximum minimum parents and children algorithm locates the skeleton of the directed acyclic graph of a Bayesian network for p provided that there exists a faithful Bayesian network and that the dependence structure derived from data is the same as that of the underlying probability distribution. The aim of this thesis is to examine the consequences when one of these conditions is not fulfilled. There are some circumstances where the algorithm works well even if there does not exist a faithful Bayesian network, but there are others where the algorithm fails. The MMPC tests for conditional independence between the variables and assumes that if conditional independence is not rejected, then the conditional independence statement holds. There are situations where this procedure leads to conditional independence being accepted that contradict conditional dependence relations in the data. This leads to edges being removed from the skeleton that are necessary for representing the dependence structure of the data.
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Bayesian Gaussian Graphical models using sparse selection priors and their mixturesTalluri, Rajesh 2011 August 1900 (has links)
We propose Bayesian methods for estimating the precision matrix in Gaussian graphical models. The methods lead to sparse and adaptively shrunk estimators of the precision matrix, and thus conduct model selection and estimation simultaneously. Our methods are based on selection and shrinkage priors leading to parsimonious parameterization of the precision (inverse covariance) matrix, which is essential in several applications in learning relationships among the variables. In Chapter I, we employ the Laplace prior on the off-diagonal element of the precision matrix, which is similar to the lasso model in a regression context. This type of prior encourages sparsity while providing shrinkage estimates. Secondly we introduce a novel type of selection prior that develops a sparse structure of the precision matrix by making most of the elements exactly zero, ensuring positive-definiteness.
In Chapter II we extend the above methods to perform classification. Reverse-phase protein array (RPPA) analysis is a powerful, relatively new platform that allows for high-throughput, quantitative analysis of protein networks. One of the challenges that currently limits the potential of this technology is the lack of methods that allows for accurate data modeling and identification of related networks and samples. Such models may improve the accuracy of biological sample classification based on patterns of protein network activation, and provide insight into the distinct biological relationships underlying different cancers. We propose a Bayesian sparse graphical modeling approach motivated by RPPA data using selection priors on the conditional relationships in the presence of class information. We apply our methodology to an RPPA data set generated from panels of human breast cancer and ovarian cancer cell lines. We demonstrate that the model is able to distinguish the different cancer cell types more accurately than several existing models and to identify differential regulation of components of a critical signaling network (the PI3K-AKT pathway) between these cancers. This approach represents a powerful new tool that can be used to improve our understanding of protein networks in cancer.
In Chapter III we extend these methods to mixtures of Gaussian graphical models for clustered data, with each mixture component being assumed Gaussian with an adaptive covariance structure. We model the data using Dirichlet processes and finite mixture models and discuss appropriate posterior simulation schemes to implement posterior inference in the proposed models, including the evaluation of normalizing constants that are functions of parameters of interest which are a result of the restrictions on the correlation matrix. We evaluate the operating characteristics of our method via simulations, as well as discuss examples based on several real data sets.
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Calibration of parameters for the Heston model in the high volatility period of marketMaslova, Maria January 2008 (has links)
The main idea of our work is the calibration parameters for the Heston stochastic volatility model. We make this procedure by using the OMXS30 index from the NASDAQ OMX Nordic Exchange Market. We separate our data into the stable period and high-volatility period on this Nordic Market. Deviation detection problem are solved using the Bayesian analysis of change-points. We estimate parameters of the Heston model for each of periods and make some conclusions.
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Traffic Analysis Attacks in Anonymity Networks : Relationship Anonymity-Overhead Trade-offVuković, Ognjen, Dán, György, Karlsson, Gunnar January 2013 (has links)
Mix networks and anonymity networks provide anonymous communication via relaying, which introduces overhead and increases the end-to-end message delivery delay. In practice overhead and delay must often be low, hence it is important to understand how to optimize anonymity for limited overhead and delay. In this work we address this question under passive traffic analysis attacks, whose goal is to learn the traffic matrix. For our study, we use two anonymity networks: MCrowds, an extension of Crowds, which provides unbounded communication delay and Minstrels, which provides bounded communication delay. We derive exact and approximate analytical expressions for the relationship anonymity for these systems. Using MCrowds and Minstrels we show that, contrary to intuition, increased overhead does not always improve anonymity. We investigate the impact of the system's parameters on anonymity, and the sensitivity anonymity to the misestimation of the number of attackers. / <p>QC 20130522</p>
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Dependent evidence in reasoning with uncertaintyLing, Xiaoning 06 December 1990 (has links)
The problem of handling dependent evidence is an important practical issue for
applications of reasoning with uncertainty in artificial intelligence. The existing solutions
to the problem are not satisfactory because of their ad hoc nature, complexities, or
limitations.
In this dissertation, we develop a general framework that can be used for extending
the leading uncertainty calculi to allow the combining of dependent evidence. The leading
calculi are the Shafer Theory of Evidence and Odds-likelihood-ratio formulation of Bayes
Theory. This framework overcomes some of the disadvantages of existing approaches.
Dependence among evidence from dependent sources is assigned dependence
parameters which weight the shared portion of evidence. This view of dependence leads
to a Decomposition-Combination method for combining bodies of dependent evidence.
Two algorithms based on this method, one for merging, the other for pooling a sequence
of dependent evidence, are developed. An experiment in soybean disease diagnosis is
described for demonstrating the correctness and applicability of these methods in a
domain of the real world application. As a potential application of these methods, a
model of an automatic decision maker for distributed multi-expert systems is proposed.
This model is a solution to the difficult problem of non-independence of experts. / Graduation date: 1991
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