利用贝叶斯网络分析基因表达数据

利用基因表达数据提出一种新的网络模型—贝叶斯网络,发现基因的互作.一个贝叶斯网络是多变量联合概率分布的有向图模型,表示变量间的条件独立属性.首先我们阐明贝叶斯网络如何表示基因间的互作,然后介绍从基因芯片数据学习贝叶斯网络的方法.     

Arc refractor methods for adaptive importance sampling on large Bayesian networks under evidential reasoning

Approximate Bayesian inference by importance sampling derives probabilistic statements from a Bayesian network, an essential part of evidential reasoning with the network and an important aspect of many Bayesian methods. A critical problem in importance sampling on Bayesian networks is the selection of a good importance function to sample a network’s prior and posterior probability distribution. The initially optimal importance functions eventually start deviating from the optimal function when sampling a network’s posterior distribution given evidence, even when adaptive methods are used that adjust an importance function to the evidence by learning. In this article we propose a new family of Refractor Importance Sampling (RIS) algorithms for adaptive importance sampling under evidential reasoning. RIS applies “arc refractors” to a Bayesian network by adding new arcs and refining the conditional probability tables. The goal of RIS is to optimize the importance function for the posterior distribution and reduce the error variance of sampling. Our experimental results show a significant improvement of RIS over state-of-the-art adaptive importance sampling algorithms.     

A PC algorithm variation for ordinal variables

Bayesian networks are graphical models that represent the joint distribution of a set of variables using directed acyclic graphs. The graph can be manually built by domain experts according to their knowledge. However, when the dependence structure is unknown (or partially known) the network has to be estimated from data by using suitable learning algorithms. In this paper, we deal with a constraint-based method to perform Bayesian networks structural learning in the presence of ordinal variables. We propose an alternative version of the PC algorithm, which is one of the most known procedures, with the aim to infer the network by accounting for additional information inherent to ordinal data. The proposal is based on a nonparametric test, appropriate for ordinal variables. A comparative study shows that, in some situations, the proposal discussed here is a slightly more efficient solution than the PC algorithm.     

Inference of an oscillating model for the yeast cell cycle

High-throughput techniques allow measurement of hundreds of cell components simultaneously. The inference of interactions between cell components from these experimental data facilitates the understanding of complex regulatory processes. Differential equations have been established to model the dynamic behavior of these regulatory networks quantitatively. Usually traditional regression methods for estimating model parameters fail in this setting, since they overfit the data. This is even the case, if the focus is on modeling subnetworks of, at most, a few tens of components. In a Bayesian learning approach, this problem is avoided by a restriction of the search space with prior probability distributions over model parameters.This paper combines both differential equation models and a Bayesian approach. We model the periodic behavior of proteins involved in the cell cycle of the budding yeast Saccharomyces cerevisiae, with differential equations, which are based on chemical reaction kinetics. One property of these systems is that they usually converge to a steady state, and lots of efforts have been made to explain the observed periodic behavior. We introduce an approach to infer an oscillating network from experimental data. First, an oscillating core network is learned. This is extended by further components by using a Bayesian approach in a second step. A specifically designed hierarchical prior distribution over interaction strengths prevents overfitting, and drives the solutions to sparse networks with only a few significant interactions.We apply our method to a simulated and a real world dataset and reveal main regulatory interactions. Moreover, we are able to reconstruct the dynamic behavior of the network.     

Learning Bayesian networks from datasets joining continuous and discrete variables

The current paper addresses two problems observed in structure learning applications to computational biology.The first one is dealing with mixed data. Most optimization criteria for learning algorithms are applicable to either discrete or continuous data. Mixed datasets are usually handled by discretization of continuous data, which often leads to the loss of information. In order to address this problem, we adapted discrete scoring functions to continuous data. Consequently, the same score is used to both types of variables, and the network structure may be learned from mixed data directly.The second problem is the control of the type I error level. Usually, learning algorithms output a network that is the best according to some optimization criteria, but the reliability of particular relationships represented by this network is unknown. We address this problem by allowing the user to specify the expected error level and adjusting the parameters of the scoring criteria to this level.     

Computational learning of the conditional phase-type (C-Ph) distribution

This paper presents a new algorithm for learning the structure of a special type of Bayesian network. The conditional phase-type (C-Ph) distribution is a Bayesian network that models the probabilistic causal relationships between a skewed continuous variable, modelled by the Coxian phase-type distribution, a special type of Markov model, and a set of interacting discrete variables. The algorithm takes a data set as input and produces the structure, parameters and graphical representations of the fit of the C-Ph distribution as output. The algorithm, which uses a greedy-search technique and has been implemented in MATLAB, is evaluated using a simulated data set consisting of 20,000 cases. The results show that the original C-Ph distribution is recaptured and the fit of the network to the data is discussed.     

Parameter estimation and model selection for mixtures of truncated exponentials

Bayesian networks with mixtures of truncated exponentials (MTEs) support efficient inference algorithms and provide a flexible way of modeling hybrid domains (domains containing both discrete and continuous variables). On the other hand, estimating an MTE from data has turned out to be a difficult task, and most prevalent learning methods treat parameter estimation as a regression problem. The drawback of this approach is that by not directly attempting to find the parameter estimates that maximize the likelihood, there is no principled way of performing subsequent model selection using those parameter estimates. In this paper we describe an estimation method that directly aims at learning the parameters of an MTE potential following a maximum likelihood approach. Empirical results demonstrate that the proposed method yields significantly better likelihood results than existing regression-based methods. We also show how model selection, which in the case of univariate MTEs amounts to partitioning the domain and selecting the number of exponential terms, can be performed using the BIC score.     

Finding the needles in the haystack: efficient intelligence processing

As a result of communication technologies, the main intelligence challenge has shifted from collecting data to efficiently processing it so that relevant, and only relevant, information is passed on to intelligence analysts. We consider intelligence data intercepted on a social communication network. The social network includes both adversaries (eg terrorists) and benign participants. We propose a methodology for efficiently searching for relevant messages among the intercepted communications. Besides addressing a real and urgent problem that has attracted little attention in the open literature thus far, the main contributions of this paper are two-fold. First, we develop a novel knowledge accumulation model for intelligence processors, which addresses both the nodes of the social network (the participants) and its edges (the communications). Second, we propose efficient prioritization algorithms that utilize the processor’s accumulated knowledge. Our approach is based on methods from graphical models, social networks, random fields, Bayesian learning, and exploration/exploitation algorithms.     

Imprecise probability models for learning multinomial distributions from data. Applications to learning credal networks

This paper considers the problem of learning multinomial distributions from a sample of independent observations. The Bayesian approach usually assumes a prior Dirichlet distribution about the probabilities of the different possible values. However, there is no consensus on the parameters of this Dirichlet distribution. Here, it will be shown that this is not a simple problem, providing examples in which different selection criteria are reasonable. To solve it the Imprecise Dirichlet Model (IDM) was introduced. But this model has important drawbacks, as the problems associated to learning from indirect observations. As an alternative approach, the Imprecise Sample Size Dirichlet Model (ISSDM) is introduced and its properties are studied. The prior distribution over the parameters of a multinomial distribution is the basis to learn Bayesian networks using Bayesian scores. Here, we will show that the ISSDM can be used to learn imprecise Bayesian networks, also called credal networks when all the distributions share a common graphical structure. Some experiments are reported on the use of the ISSDM to learn the structure of a graphical model and to build supervised classifiers.     

An interactive approach for Bayesian network learning using domain/expert knowledge

Using domain/expert knowledge when learning Bayesian networks from data has been considered a promising idea since the very beginning of the field. However, in most of the previously proposed approaches, human experts do not play an active role in the learning process. Once their knowledge is elicited, they do not participate any more. The interactive approach for integrating domain/expert knowledge we propose in this work aims to be more efficient and effective. In contrast to previous approaches, our method performs an active interaction with the expert in order to guide the search based learning process. This method relies on identifying the edges of the graph structure which are more unreliable considering the information present in the learning data. Another contribution of our approach is the integration of domain/expert knowledge at different stages of the learning process of a Bayesian network: while learning the skeleton and when directing the edges of the directed acyclic graph structure.     

供应链网络可靠性的多层Bayes估计模型

对供应链网络可靠性进行界定和分析,以节点企业间的协同为基础,得到可靠度计算模型,以此为依据采集实证样本无失效运行的数据.根据供应链网络可靠性统计特性,建立一种多层Bayes估计方法,应用于样本可靠性评估中.在估计失效率的基础上,对供应链网络可靠度进行估计,对仿真结果进行分析,显示多层Bayes估计方法应用效果较好,精确度高,反映了参数不确定性对供应链网络可靠性的影响,能够较好地解决依据无失效数据判定供应链网络可靠性水平的问题.     

On the semi-discretization of optimal control problems for networks of elastic strings: global optimality systems and domain decomposition

We consider a star-graph as an examplary network, with elastic strings stretched along the edges. The network is allowed to perform out-of-the plane displacements. We consider such networks as being controlled at its simple nodes via Dirichlet conditions. The objective is to steer given initial data to final target data in a given time T with minimal control costs. This problem is discussed in the continuous as well as in the discrete case. We discuss an iterative domain decomposition technique and its discrete analogue. We prove convergence and show some numerical results.     

A Bayesian record linkage model incorporating relational data

In this article, we introduce a novel Bayesian approach for linking multiple social networks in order to discover the same real world person having different accounts across networks. In particular, we develop a latent model that allows us to jointly characterize the network and linkage structures relying on both relational and profile data. In contrast to other existing approaches in the machine learning literature, our Bayesian implementation naturally provides uncertainty quantification via posterior probabilities for the linkage structure itself or any function of it. Our findings clearly suggest that our methodology can produce accurate point estimates of the linkage structure even in the absence of profile information, and also, in an identity resolution setting, our results confirm that including relational data into the matching process improves the linkage accuracy. We illustrate our methodology using real data from popular social networks such as Twitter , Facebook , and YouTube .     

Learning continuous time Bayesian network classifiers

Streaming data are relevant to finance, computer science, and engineering while they are becoming increasingly important to medicine and biology. Continuous time Bayesian network classifiers are designed for analyzing multivariate streaming data when time duration of event matters. Structural and parametric learning for the class of continuous time Bayesian network classifiers are considered in the case where complete data is available. Conditional log-likelihood scoring is developed for structural learning on continuous time Bayesian network classifiers. Performance of continuous time Bayesian network classifiers learned when combining conditional log-likelihood scoring and Bayesian parameter estimation are compared with that achieved by continuous time Bayesian network classifiers when learning is based on marginal log-likelihood scoring and to that achieved by dynamic Bayesian network classifiers. Classifiers are compared in terms of accuracy and computation time. Comparison is based on numerical experiments where synthetic and real data are used. Results show that conditional log-likelihood scoring combined with Bayesian parameter estimation outperforms marginal log-likelihood scoring. Conditional log-likelihood scoring becomes even more effective when the amount of available data is limited. Continuous time Bayesian network classifiers outperform in terms of computation time and accuracy dynamic Bayesian network on synthetic and real data sets.     

Bayesian MAP model selection of chain event graphs

Chain event graphs are graphical models that while retaining most of the structural advantages of Bayesian networks for model interrogation, propagation and learning, more naturally encode asymmetric state spaces and the order in which events happen than Bayesian networks do. In addition, the class of models that can be represented by chain event graphs for a finite set of discrete variables is a strict superset of the class that can be described by Bayesian networks. In this paper we demonstrate how with complete sampling, conjugate closed form model selection based on product Dirichlet priors is possible, and prove that suitable homogeneity assumptions characterise the product Dirichlet prior on this class of models. We demonstrate our techniques using two educational examples.     

An optimization-based approach for the design of Bayesian networks

Bayesian networks model conditional dependencies among the domain variables, and provide a way to deduce their interrelationships as well as a method for the classification of new instances. One of the most challenging problems in using Bayesian networks, in the absence of a domain expert who can dictate the model, is inducing the structure of the network from a large, multivariate data set. We propose a new methodology for the design of the structure of a Bayesian network based on concepts of graph theory and nonlinear integer optimization techniques.     

Learning Bayesian network classifiers by risk minimization

Bayesian networks (BNs) provide a powerful graphical model for encoding the probabilistic relationships among a set of variables, and hence can naturally be used for classification. However, Bayesian network classifiers (BNCs) learned in the common way using likelihood scores usually tend to achieve only mediocre classification accuracy because these scores are less specific to classification, but rather suit a general inference problem. We propose risk minimization by cross validation (RMCV) using the 0/1 loss function, which is a classification-oriented score for unrestricted BNCs. RMCV is an extension of classification-oriented scores commonly used in learning restricted BNCs and non-BN classifiers. Using small real and synthetic problems, allowing for learning all possible graphs, we empirically demonstrate RMCV superiority to marginal and class-conditional likelihood-based scores with respect to classification accuracy. Experiments using twenty-two real-world datasets show that BNCs learned using an RMCV-based algorithm significantly outperform the naive Bayesian classifier (NBC), tree augmented NBC (TAN), and other BNCs learned using marginal or conditional likelihood scores and are on par with non-BN state of the art classifiers, such as support vector machine, neural network, and classification tree. These experiments also show that an optimized version of RMCV is faster than all unrestricted BNCs and comparable with the neural network with respect to run-time. The main conclusion from our experiments is that unrestricted BNCs, when learned properly, can be a good alternative to restricted BNCs and traditional machine-learning classifiers with respect to both accuracy and efficiency.     

Solving regression problem with complementary neural networks and an adjusted averaging technique

This research deals with complementary neural networks (CMTNN) for the regression problem. Complementary neural networks consist of a pair of neural networks called truth neural network and falsity neural network, which are trained to predict truth and falsity outputs, respectively. In this paper, a novel adjusted averaging technique is proposed in order to enhance the result obtained from the basic CMTNN. We test our proposed technique based on the classical benchmark problems including housing, concrete compressive strength, and computer hardware data sets from the UCI machine learning repository. We also realize our technique to the porosity prediction problem based on well log data set obtained from practical field data in the oil and gas industry. We found that our proposed technique provides better performance when compared to the traditional CMTNN, backpropagation neural network, and support vector regression with linear, polynomial, and radial basis function kernels.     

<Emphasis Type="Italic">Graph_sampler</Emphasis>: a simple tool for fully Bayesian analyses of DAG-models

Bayesian networks (BNs) are widely used graphical models usable to draw statistical inference about directed acyclic graphs. We presented here Graph_sampler a fast free C language software for structural inference on BNs. Graph_sampler uses a fully Bayesian approach in which the marginal likelihood of the data and prior information about the network structure are considered. This new software can handle both the continuous as well as discrete data and based on the data type two different models are formulated. The software also provides a wide variety of structure prior which can depict either the global or local properties of the graph structure. Now based on the type of structure prior selected, we considered a wide range of possible values for the prior making it either informative or uninformative. We proposed a new and much faster jumping kernel strategy in the Metropolis–Hastings algorithm. The source C code distributed is very compact, fast, uses low memory and disk storage. We performed out several analyses based on different simulated data sets and synthetic as well as real networks to discuss the performance of Graph_sampler.