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Using multi-step proposal distribution for improved MCMC convergence in Bayesian network structure learning
Springer Science and Business Media LLC - Tập 2015 - Trang 1-14 - 2015
Bayesian networks have become popular for modeling probabilistic relationships between entities. As their structure can also be given a causal interpretation about the studied system, they can be used to learn, for example, regulatory relationships of genes or proteins in biological networks and pathways. Inference of the Bayesian network structure is complicated by the size of the model structure...... hiện toàn bộ
A novel cost function to estimate parameters of oscillatory biochemical systems
Springer Science and Business Media LLC - Tập 2012 - Trang 1-17 - 2012
Oscillatory pathways are among the most important classes of biochemical systems with examples ranging from circadian rhythms and cell cycle maintenance. Mathematical modeling of these highly interconnected biochemical networks is needed to meet numerous objectives such as investigating, predicting and controlling the dynamics of these systems. Identifying the kinetic rate parameters is essential ...... hiện toàn bộ
A Hypothesis Test for Equality of Bayesian Network Models
Springer Science and Business Media LLC - Tập 2010 - Trang 1-11 - 2010
Bayesian network models are commonly used to model gene expression data. Some applications require a comparison of the network structure of a set of genes between varying phenotypes. In principle, separately fit models can be directly compared, but it is difficult to assign statistical significance to any observed differences. There would therefore be an advantage to the development of a rigorous ...... hiện toàn bộ
Learning directed acyclic graphs from large-scale genomics data
Springer Science and Business Media LLC - Tập 2017 - Trang 1-16 - 2017
In this paper, we consider the problem of learning the genetic interaction map, i.e., the topology of a directed acyclic graph (DAG) of genetic interactions from noisy double-knockout (DK) data. Based on a set of well-established biological interaction models, we detect and classify the interactions between genes. We propose a novel linear integer optimization program called the Genetic-Interactio...... hiện toàn bộ
A visual analytics approach for models of heterogeneous cell populations
Springer Science and Business Media LLC - Tập 2012 - Trang 1-13 - 2012
In recent years, cell population models have become increasingly common. In contrast to classic single cell models, population models allow for the study of cell-to-cell variability, a crucial phenomenon in most populations of primary cells, cancer cells, and stem cells. Unfortunately, tools for in-depth analysis of population models are still missing. This problem originates from the complexity o...... hiện toàn bộ
Incorporating prior knowledge induced from stochastic differential equations in the classification of stochastic observations
Springer Science and Business Media LLC - Tập 2016 - Trang 1-14 - 2016
In classification, prior knowledge is incorporated in a Bayesian framework by assuming that the feature-label distribution belongs to an uncertainty class of feature-label distributions governed by a prior distribution. A posterior distribution is then derived from the prior and the sample data. An optimal Bayesian classifier (OBC) minimizes the expected misclassification error relative to the pos...... hiện toàn bộ
Identifying Statistical Dependence in Genomic Sequences via Mutual Information Estimates
Springer Science and Business Media LLC - Tập 2007 Số 1 - Trang 1-11 - 2007
Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (DNA or RNA) that are statistically correlated. We develop a precise...... hiện toàn bộ
Phát hiện các gen tuần hoàn từ các biểu hiện gen được lấy mẫu không đồng đều: Nghiên cứu so sánh Dịch bởi AI
Springer Science and Business Media LLC - Tập 2008 - Trang 1-8 - 2008
Các phép đo biểu hiện gen bằng microarray theo chuỗi thời gian đã được sử dụng để phát hiện các gen liên quan đến chu kỳ tế bào. Do các ràng buộc trong thực nghiệm, hầu hết các quan sát từ microarray được thu thập thông qua việc lấy mẫu không đều. Trong bài báo này, ba phương pháp phân tích phổ phổ biến, cụ thể là Lomb-Scargle, Capon và ước lượng biên độ và pha cho dữ liệu thiếu (MAPES) được so sá...... hiện toàn bộ
#chuỗi thời gian #microarray #biểu hiện gen #Lomb-Scargle #Capon #ước lượng biên độ và pha #gen tuần hoàn
Origins of Stochasticity and Burstiness in High-Dimensional Biochemical Networks
Springer Science and Business Media LLC - Tập 2009 - Trang 1-14 - 2008
Two major approaches are known in the field of stochastic dynamics of intracellular biochemical networks. The first one places the focus of attention on the fact that many biochemical constituents vitally important for the network functionality may be present only in small quantities within the cell, and therefore the regulatory process is essentially discrete and prone to relatively big fluctuati...... hiện toàn bộ
Relations between the set-complexity and the structure of graphs and their sub-graphs
Springer Science and Business Media LLC - Tập 2012 - Trang 1-10 - 2012
We describe some new conceptual tools for the rigorous, mathematical description of the “set-complexity” of graphs. This set-complexity has been shown previously to be a useful measure for analyzing some biological networks, and in discussing biological information in a quantitative fashion. The advances described here allow us to define some significant relationships between the set-complexity me...... hiện toàn bộ
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