1,651 research outputs found
Gene regulatory network inference by point-based Gaussian approximation filters incorporating the prior information
Examinar a ampliação do uso de TICs por organizações sociais e governamentais na gestĂŁo da cidade Ă© o objetivo do presente estudo. Nossa intenção Ă© entender de que forma as tecnologias da informação e comunicação podem ser uma via alternativa que redefine as relações entre Estado e sociedade, substituindo polĂticas urbanas tradicionais por formas colaborativas de interação dos atores sociais. Entre os resultados alcançados pela pesquisa, Ă© possĂvel destacar a elaboração de uma metodologia capaz de mapear os princĂpios de organização, articulação, conexĂŁo e interação que constituem a existĂŞncia de redes tecnossociais. A aplicação da metodologia nas cidades do Rio de Janeiro e de SĂŁo Paulo demonstrou indicadores, gráficos e práticas polĂticas. A análise desses dados revela como as redes se constituem por uma arquitetura mĂłvel, fluĂda, flexĂvel, organizadas em torno de polĂticas comuns de ação e formadas por uma identidade coletiva que aproxima os atores das redes tecnossociais. Os princĂpios que mediam esta coesĂŁo sĂŁo de compartilhamento, confiança e solidariedade, que redefinem as formas da organização do poder em direção a alternativas de organização polĂtica e desenvolvimento social
Gene regulatory network inference by point-based Gaussian approximation filters incorporating the prior information
The extended Kalman filter (EKF) has been applied to inferring gene regulatory networks. However, it is well known that the EKF becomes less accurate when the system exhibits high nonlinearity. In addition, certain prior information about the gene regulatory network exists in practice, and no systematic approach has been developed to incorporate such prior information into the Kalman-type filter for inferring the structure of the gene regulatory network. In this paper, an inference framework based on point-based Gaussian approximation filters that can exploit the prior information is developed to solve the gene regulatory network inference problem. Different point-based Gaussian approximation filters, including the unscented Kalman filter (UKF), the third-degree cubature Kalman filter (CKF3), and the fifth-degree cubature Kalman filter (CKF5) are employed. Several types of network prior information, including the existing network structure information, sparsity assumption, and the range constraint of parameters, are considered, and the corresponding filters incorporating the prior information are developed. Experiments on a synthetic network of eight genes and the yeast protein synthesis network of five genes are carried out to demonstrate the performance of the proposed framework. The results show that the proposed methods provide more accurate inference results than existing methods, such as the EKF and the traditional UKF
Simulation based sequential Monte Carlo methods for discretely observed Markov processes
Parameter estimation for discretely observed Markov processes is a
challenging problem. However, simulation of Markov processes is straightforward
using the Gillespie algorithm. We exploit this ease of simulation to develop an
effective sequential Monte Carlo (SMC) algorithm for obtaining samples from the
posterior distribution of the parameters. In particular, we introduce two key
innovations, coupled simulations, which allow us to study multiple parameter
values on the basis of a single simulation, and a simple, yet effective,
importance sampling scheme for steering simulations towards the observed data.
These innovations substantially improve the efficiency of the SMC algorithm
with minimal effect on the speed of the simulation process. The SMC algorithm
is successfully applied to two examples, a Lotka-Volterra model and a
Repressilator model.Comment: 27 pages, 5 figure
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Bayesian Inference for Genomic Data Analysis
High-throughput genomic data contain gazillion of information that are influenced by the complex biological processes in the cell. As such, appropriate mathematical modeling frameworks are required to understand the data and the data generating processes. This dissertation focuses on the formulation of mathematical models and the description of appropriate computational algorithms to obtain insights from genomic data.
Specifically, characterization of intra-tumor heterogeneity is studied. Based on the total number of allele copies at the genomic locations in the tumor subclones, the problem is viewed from two perspectives: the presence or absence of copy-neutrality assumption. With the presence of copy-neutrality, it is assumed that the genome contains mutational variability and the three possible genotypes may be present at each genomic location. As such, the genotypes of all the genomic locations in the tumor subclones are modeled by a ternary matrix. In the second case, in addition to mutational variability, it is assumed that the genomic locations may be affected by structural variabilities such as copy number variation (CNV). Thus, the genotypes are modeled with a pair of (Q + 1)-ary matrices. Using the categorical Indian buffet process (cIBP), state-space modeling framework is employed in describing the two processes and the sequential Monte Carlo (SMC) methods for dynamic models are applied to perform inference on important model parameters.
Moreover, the problem of estimating gene regulatory network (GRN) from measurement with missing values is presented. Specifically, gene expression time series data may contain missing values for entire expression values of a single point or some set of consecutive time points. However, complete data is often needed to make inference on the underlying GRN. Using the missing measurement, a dynamic stochastic model is used to describe the evolution of gene expression and point-based Gaussian approximation (PBGA) filters with one-step or two-step missing measurements are applied for the inference. Finally, the problem of deconvolving gene expression data from complex heterogeneous biological samples is examined, where the observed data are a mixture of different cell types. A statistical description of the problem is used and the SMC method for static models is applied to estimate the cell-type specific expressions and the cell type proportions in the heterogeneous samples
Graph Signal Processing: Overview, Challenges and Applications
Research in Graph Signal Processing (GSP) aims to develop tools for
processing data defined on irregular graph domains. In this paper we first
provide an overview of core ideas in GSP and their connection to conventional
digital signal processing. We then summarize recent developments in developing
basic GSP tools, including methods for sampling, filtering or graph learning.
Next, we review progress in several application areas using GSP, including
processing and analysis of sensor network data, biological data, and
applications to image processing and machine learning. We finish by providing a
brief historical perspective to highlight how concepts recently developed in
GSP build on top of prior research in other areas.Comment: To appear, Proceedings of the IEE
Modeling Gene Regulatory Networks from Time Series Data using Particle Filtering
This thesis considers the problem of learning the structure of gene regulatory networks using gene expression time series data. A more realistic scenario where the state space model representing a gene network evolves nonlinearly is considered while a linear model is assumed for the microarray data. To capture the nonlinearity, a particle filter based state estimation algorithm is studied instead of the contemporary linear approximation based approaches. The parameters signifying the regulatory relations among various genes are estimated online using a Kalman filter. Since a
particular gene interacts with a few other genes only, the parameter vector is expected to be sparse. The state estimates delivered by the particle filter and the observed
microarray data are then fed to a LASSO based least squares regression operation, which yields a parsimonious and efficient description of the regulatory network by setting the irrelevant coefficients to zero. The performance of the aforementioned algorithm is compared with Extended Kalman filtering (EKF), employing Mean Square Error as fidelity criterion using synthetic data and real biological data. Extensive computer simulations illustrate that the particle filter based gene network inference algorithm outperforms EKF and therefore, it can serve as a natural framework for
modeling gene regulatory networks
Inference of gene regulatory networks from genome-wide knockout fitness data
Motivation: Genome-wide fitness is an emerging type of high-throughput biological data generated for individual organisms by creating libraries of knockouts, subjecting them to broad ranges of environmental conditions, and measuring the resulting clone-specific fitnesses. Since fitness is an organism-scale measure of gene regulatory network behaviour, it may offer certain advantages when insights into such phenotypical and functional features are of primary interest over individual gene expression. Previous works have shown that genome-wide fitness data can be used to uncover novel gene regulatory interactions, when compared with results of more conventional gene expression analysis. Yet, to date, few algorithms have been proposed for systematically using genome-wide mutant fitness data for gene regulatory network inference. Results: In this article, we describe a model and propose an inference algorithm for using fitness data from knockout libraries to identify underlying gene regulatory networks. Unlike most prior methods, the presented approach captures not only structural, but also dynamical and non-linear nature of biomolecular systems involved. A state–space model with non-linear basis is used for dynamically describing gene regulatory networks. Network structure is then elucidated by estimating unknown model parameters. Unscented Kalman filter is used to cope with the non-linearities introduced in the model, which also enables the algorithm to run in on-line mode for practical use. Here, we demonstrate that the algorithm provides satisfying results for both synthetic data as well as empirical measurements of GAL network in yeast Saccharomyces cerevisiae and TyrR–LiuR network in bacteria Shewanella oneidensis
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