Yes / Bayesian statistical inference relies on the posterior distribution. Depending on the model, the posterior can be more or less difficult to derive. In recent years, there has been a lot of interest in complex settings where the likelihood is analytically intractable. In such situations, approximate Bayesian computation (ABC) provides an attractive way of carrying out Bayesian inference. For obtaining reliable posterior estimates however, it is important to keep the approximation errors small in ABC. The choice of an appropriate set of summary statistics plays a crucial role in this effort. Here, we report the development of a new algorithm that is based on least angle regression for choosing summary statistics. In two population genetic examples, the performance of the new algorithm is better than a previously proposed approach that uses partial least squares. / Higher Education Commission (HEC), College Deanship of Scientific Research, King Saud University, Riyadh Saudi Arabia - research group project RGP-VPP-280.

No description available.

Processos estocásticos complexos são muitas vezes utilizados em modelagem, com o intuito de capturar uma maior proporção das principais características dos sistemas biológicos. A descrição do comportamento desses sistemas tem sido realizada por muitos amostradores baseados na distribuição a posteriori de Monte Carlo. Modelos probabilísticos que descrevem esses processos podem levar a funções de verossimilhança computacionalmente intratáveis, impossibilitando a utilização de métodos de inferência estatística clássicos e os baseados em amostragem por meio de MCMC. A Computação Bayesiana Aproximada (ABC) é considerada um novo método de inferência com base em estatísticas de resumo, ou seja, valores calculados a partir do conjunto de dados (média, moda, variância, etc.). Essa metodologia combina muitas das vantagens da eficiência computacional de processos baseados em estatísticas de resumo com inferência estatística bayesiana uma vez que, funciona bem para pequenas amostras e possibilita incorporar informações passadas em um parâmetro e formar uma priori para análise futura. Nesse trabalho foi realizada uma comparação entre os métodos de estimação, clássico, bayesiano e ABC, para estudos de simulação de modelos simples e para análise de dados de dinâmica populacional. Foram implementadas no software R as distâncias modular e do máximo como alternativas de função distância a serem utilizadas no ABC, além do algoritmo ABC de rejeição para equações diferenciais estocásticas. Foi proposto sua utilização para a resolução de problemas envolvendo modelos de interação populacional. Os estudos de simulação mostraram melhores resultados quando utilizadas as distâncias euclidianas e do máximo juntamente com distribuições a priori informativas. Para os sistemas dinâmicos, a estimação por meio do ABC apresentou resultados mais próximos dos verdadeiros bem como menores discrepâncias, podendo assim ser utilizado como um método alternativo de estimação. / Complex stochastic processes are often used in modeling in order to capture a greater proportion of the main features of natural systems. The description of the behavior of these systems has been made by many Monte Carlo based samplers of the posterior distribution. Probabilistic models describing these processes can lead to computationally intractable likelihood functions, precluding the use of classical statistical inference methods and those based on sampling by MCMC. The Approxi- mate Bayesian Computation (ABC) is considered a new method for inference based on summary statistics, that is, calculated values from the data set (mean, mode, variance, etc.). This methodology combines many of the advantages of computatio- nal efficiency of processes based on summary statistics with the Bayesian statistical inference since, it works well for small samples and it makes possible to incorporate past information in a parameter and form a prior distribution for future analysis. In this work a comparison between, classical, Bayesian and ABC, estimation methods was made for simulation studies considering simple models and for data analysis of population dynamics. It was implemented in the R software the modular and maxi- mum as alternative distances function to be used in the ABC, besides the rejection ABC algorithm for stochastic differential equations. It was proposed to use it to solve problems involving models of population interaction. The simulation studies showed better results when using the Euclidean and maximum distances together with informative prior distributions. For the dynamic systems, the ABC estimation presented results closer to the real ones as well as smaller discrepancies and could thus be used as an alternative estimation method.

Processos estocásticos complexos são muitas vezes utilizados em modelagem, com o intuito de capturar uma maior proporção das principais características dos sistemas biológicos. A descrição do comportamento desses sistemas tem sido realizada por muitos amostradores baseados na distribuição a posteriori de Monte Carlo. Modelos probabilísticos que descrevem esses processos podem levar a funções de verossimilhança computacionalmente intratáveis, impossibilitando a utilização de métodos de inferência estatística clássicos e os baseados em amostragem por meio de MCMC. A Computação Bayesiana Aproximada (ABC) é considerada um novo método de inferência com base em estatísticas de resumo, ou seja, valores calculados a partir do conjunto de dados (média, moda, variância, etc.). Essa metodologia combina muitas das vantagens da eficiência computacional de processos baseados em estatísticas de resumo com inferência estatística bayesiana uma vez que, funciona bem para pequenas amostras e possibilita incorporar informações passadas em um parâmetro e formar uma priori para análise futura. Nesse trabalho foi realizada uma comparação entre os métodos de estimação, clássico, bayesiano e ABC, para estudos de simulação de modelos simples e para análise de dados de dinâmica populacional. Foram implementadas no software R as distâncias modular e do máximo como alternativas de função distância a serem utilizadas no ABC, além do algoritmo ABC de rejeição para equações diferenciais estocásticas. Foi proposto sua utilização para a resolução de problemas envolvendo modelos de interação populacional. Os estudos de simulação mostraram melhores resultados quando utilizadas as distâncias euclidianas e do máximo juntamente com distribuições a priori informativas. Para os sistemas dinâmicos, a estimação por meio do ABC apresentou resultados mais próximos dos verdadeiros bem como menores discrepâncias, podendo assim ser utilizado como um método alternativo de estimação. / Complex stochastic processes are often used in modeling in order to capture a greater proportion of the main features of natural systems. The description of the behavior of these systems has been made by many Monte Carlo based samplers of the posterior distribution. Probabilistic models describing these processes can lead to computationally intractable likelihood functions, precluding the use of classical statistical inference methods and those based on sampling by MCMC. The Approxi- mate Bayesian Computation (ABC) is considered a new method for inference based on summary statistics, that is, calculated values from the data set (mean, mode, variance, etc.). This methodology combines many of the advantages of computatio- nal efficiency of processes based on summary statistics with the Bayesian statistical inference since, it works well for small samples and it makes possible to incorporate past information in a parameter and form a prior distribution for future analysis. In this work a comparison between, classical, Bayesian and ABC, estimation methods was made for simulation studies considering simple models and for data analysis of population dynamics. It was implemented in the R software the modular and maxi- mum as alternative distances function to be used in the ABC, besides the rejection ABC algorithm for stochastic differential equations. It was proposed to use it to solve problems involving models of population interaction. The simulation studies showed better results when using the Euclidean and maximum distances together with informative prior distributions. For the dynamic systems, the ABC estimation presented results closer to the real ones as well as smaller discrepancies and could thus be used as an alternative estimation method.

Mathematical and computational epidemiological models are important tools in efforts to combat the spread of infectious diseases. The models can be used to predict further progression of an epidemic and for assessing potential countermeasures to control disease spread. In the proposal of models (when data is available), one needs parameter estimation methods. In this thesis, likelihood-less Bayesian inference methods are concerned. The data and the model originate from the spread of a verotoxigenic Escherichia coli in the Swedish cattle population. In using the SISE3 model, which is an extension of the susceptible-infected-susceptible model with added environmental pressure and three age categories, two different methods were employed to give an estimated posterior: Approximate Bayesian Computations and Synthetic Likelihood Markov chain Monte Carlo. The mean values of the resulting posteriors were close to the previously performed point estimates, which gives the conclusion that Bayesian inference on a nation scaled SIS-like network is conceivable.

No description available.

Natural history models for breast cancer describe the unobservable disease progression. These models can either be fitted using likelihood-based estimation to data on individual tumour characteristics, or calibrated to fit statistics at a population level. Likelihood-based inference using individual level data has the advantage of ensuring model parameter identifiability. However, the likelihood function can be computationally heavy to evaluate or even intractable. In this thesis likelihood-free estimation using Approximate Bayesian Computation (ABC) will be explored. The main objective is to investigate whether ABC can be used to fit models to data collected in the presence of mammography screening. As a background, a literature review of ABC is provided. As a first step an ABC-MCMC algorithm is constructed for two simple models both describing populations in absence of mammography screening, but assuming different functional forms of tumour growth. The algorithm is evaluated for these models in a simulation study using synthetic data, and compared with results obtained using likelihood-based inference. Later, it is investigated whether ABC can be used for the models in presence of screening. The findings of this thesis indicate that ABC is not directly applicable to these models. However, by including a sub-model for tumour onset and assuming that all individuals in the population have the same screening attendance it was possible to develop an ABC-MCMC algorithm that carefully takes individual level data into consideration in the estimation procedure. Finally, the algorithm was tested in a simple simulation study using synthetic data. Future research is still needed to evaluate the statistical properties of the algorithm (using extended simulation) and to test it on observational data where previous estimates are available for reference. / Natural history models för bröstcancer är statistiska modeller som beskriver det dolda sjukdomsförloppet. Dessa modeller brukar antingen anpassas till data på individnivå med likelihood-baserade metoder, eller kalibreras mot statistik för hela populationen. Fördelen med att använda data på individnivå är att identifierbarhet hos modellparametrarna kan garanteras. För dessa modeller händer det dock att det är beräkningsintensivt eller rent utav omöjligt att evaluera likelihood-funktionen. Huvudsyftet med denna uppsats är att utforska huruvida metoden Approximate Bayesian Computation (ABC), som används för skattning av statistiska modeller där likelihood-funktionen inte är tillgänglig, kan implementeras för en modell som beskriver bröstcancer hos individer som genomgår mammografiscreening. Som en del av bakgrunden presenteras en sammanfattning av modern ABC-forskning. Metoden består av två delar. I den första delen implementeras en ABC-MCMC algoritm för två enklare modeller. Båda dessa modeller beskriver tumörtillväxten hos individer som ej genomgår mammografiscreening, men modellerna antar olika typer av tumörtillväxt. Algoritmen testades i en simulationsstudie med syntetisk data genom att jämföra resultaten med motsvarande från likelihood-baserade metoder. I den andra delen av metoden undersöks huruvida ABC är kompatibelt med modeller för bröstcancer hos individer som genomgår screening. Genom att lägga till en modell för uppkomst av tumörer och göra det förenklande antagandet att alla individer i populationen genomgår screening vid samma ålder, kunde en ABC-MCMC algoritm utvecklas med hänsyn till data på individnivå. Algoritmen testades sedan i en simulationsstudie nyttjande syntetisk data. Framtida studier behövs för att undersöka algoritmens statistiska egenskaper (genom upprepad simulering av flera dataset) och för att testa den mot observationell data där tidigare parameterskattningar finns tillgängliga.

Cette thèse se décompose en deux parties. Dans un premier temps nous nous intéressons à la sélection bayésienne de variables dans un modèle probit mixte.L'objectif est de développer une méthode pour sélectionner quelques variables pertinentes parmi plusieurs dizaines de milliers tout en prenant en compte le design d'une étude, et en particulier le fait que plusieurs jeux de données soient fusionnés. Le modèle de régression probit mixte utilisé fait partie d'un modèle bayésien hiérarchique plus large et le jeu de données est considéré comme un effet aléatoire. Cette méthode est une extension de la méthode de Lee et al. (2003). La première étape consiste à spécifier le modèle ainsi que les distributions a priori, avec notamment l'utilisation de l'a priori conventionnel de Zellner (g-prior) pour le vecteur des coefficients associé aux effets fixes (Zellner, 1986). Dans une seconde étape, nous utilisons un algorithme Metropolis-within-Gibbs couplé à la grouping (ou blocking) technique de Liu (1994) afin de surmonter certaines difficultés d'échantillonnage. Ce choix a des avantages théoriques et computationnels. La méthode développée est appliquée à des jeux de données microarray sur le cancer du sein. Cependant elle a une limite : la matrice de covariance utilisée dans le g-prior doit nécessairement être inversible. Or il y a deux cas pour lesquels cette matrice est singulière : lorsque le nombre de variables sélectionnées dépasse le nombre d'observations, ou lorsque des variables sont combinaisons linéaires d'autres variables. Nous proposons donc une modification de l'a priori de Zellner en y introduisant un paramètre de type ridge, ainsi qu'une manière de choisir les hyper-paramètres associés. L'a priori obtenu est un compromis entre le g-prior classique et l'a priori supposant l'indépendance des coefficients de régression, et se rapproche d'un a priori précédemment proposé par Gupta et Ibrahim (2007).Dans une seconde partie nous développons deux nouvelles méthodes MCMC basées sur des populations de chaînes. Dans le cas de modèles complexes ayant de nombreux paramètres, mais où la vraisemblance des données peut se calculer, l'algorithme Equi-Energy Sampler (EES) introduit par Kou et al. (2006) est apparemment plus efficace que l'algorithme classique du Parallel Tempering (PT) introduit par Geyer (1991). Cependant, il est difficile d'utilisation lorsqu'il est couplé avec un échantillonneur de Gibbs, et nécessite un stockage important de valeurs. Nous proposons un algorithme combinant le PT avec le principe d'échanges entre chaînes ayant des niveaux d'énergie similaires dans le même esprit que l'EES. Cette adaptation appelée Parallel Tempering with Equi-Energy Moves (PTEEM) conserve l'idée originale qui fait la force de l'algorithme EES tout en assurant de bonnes propriétés théoriques et une utilisation facile avec un échantillonneur de Gibbs.Enfin, dans certains cas complexes l'inférence peut être difficile car le calcul de la vraisemblance des données s'avère trop coûteux, voire impossible. De nombreuses méthodes sans vraisemblance ont été développées. Par analogie avec le Parallel Tempering, nous proposons une méthode appelée ABC-Parallel Tempering, basée sur la théorie des MCMC, utilisant une population de chaînes et permettant des échanges entre elles. / This thesis is divided into two main parts. In the first part, we propose a Bayesian variable selection method for probit mixed models. The objective is to select few relevant variables among tens of thousands while taking into account the design of a study, and in particular the fact that several datasets are merged together. The probit mixed model used is considered as part of a larger hierarchical Bayesian model, and the dataset is introduced as a random effect. The proposed method extends a work of Lee et al. (2003). The first step is to specify the model and prior distributions. In particular, we use the g-prior of Zellner (1986) for the fixed regression coefficients. In a second step, we use a Metropolis-within-Gibbs algorithm combined with the grouping (or blocking) technique of Liu (1994). This choice has both theoritical and practical advantages. The method developed is applied to merged microarray datasets of patients with breast cancer. However, this method has a limit: the covariance matrix involved in the g-prior should not be singular. But there are two standard cases in which it is singular: if the number of observations is lower than the number of variables, or if some variables are linear combinations of others. In such situations we propose to modify the g-prior by introducing a ridge parameter, and a simple way to choose the associated hyper-parameters. The prior obtained is a compromise between the conditional independent case of the coefficient regressors and the automatic scaling advantage offered by the g-prior, and can be linked to the work of Gupta and Ibrahim (2007).In the second part, we develop two new population-based MCMC methods. In cases of complex models with several parameters, but whose likelihood can be computed, the Equi-Energy Sampler (EES) of Kou et al. (2006) seems to be more efficient than the Parallel Tempering (PT) algorithm introduced by Geyer (1991). However it is difficult to use in combination with a Gibbs sampler, and it necessitates increased storage. We propose an algorithm combining the PT with the principle of exchange moves between chains with same levels of energy, in the spirit of the EES. This adaptation which we are calling Parallel Tempering with Equi-Energy Move (PTEEM) keeps the original idea of the EES method while ensuring good theoretical properties and a practical use in combination with a Gibbs sampler.Then, in some complex models whose likelihood is analytically or computationally intractable, the inference can be difficult. Several likelihood-free methods (or Approximate Bayesian Computational Methods) have been developed. We propose a new algorithm, the Likelihood Free-Parallel Tempering, based on the MCMC theory and on a population of chains, by using an analogy with the Parallel Tempering algorithm.