Constraint-based Learning Algorithms Research Articles

Constraint-Based Bayesian Network Structure Learning using Uncertain Experts’ Knowledge

Exploiting experts' knowledge can significantly increase the quality of the Bayesian network (BN) structures produced by learning algorithms. However, in practice, experts may not be 100% confident about the opinions they provide. Worst, the latter can also be conflicting. Including such specific knowledge in learning algorithms is therefore complex. In the literature, there exist a few score-based algorithms that can exploit both data and the knowledge about the existence/absence of arcs in the BN. But, as far as we know, no constraint-based learning algorithm is capable of exploiting such knowledge. In this paper, we fill this gap by introducing the mathematical foundations for new independence tests including this kind of information. We provide a new constraint-based algorithm relying on these tests as well as experiments that highlight the robustness of our method and its benefits compared to other constraint-based learning algorithms.

Improving Bayesian network local structure learning via data-driven symmetry correction methods

Learning the structure of a Bayesian network (BN) from data is NP-hard. To efficiently handle high-dimensional datasets, many BN local structure learning algorithms are proposed. These learning algorithms can be categorized into two types: constraint-based and score-based. These learning algorithms learn the local structures separately for each node. As a result, asymmetric pairs of neighbors and Markov blankets create conflicts between the local structures. To resolve the conflicts, symmetry correction is required. The commonly used AND-rule symmetry correction method, which simply drops nodes in asymmetric pairs from the neighbor sets and Markov blankets of both nodes, may result in loss of information in learning the BN. In this paper, we propose a hybrid framework that combines a local structure learning algorithm of a particular type (either constraint-based or score-based) with a data-driven symmetry correction method of the other type. The score-based symG method and the constraint-based symC method are proposed to be used in the hybrid framework. Empirical results show that performances of constraint-based learning algorithms are improved by using the proposed score-based symG method. Similarly, the performance of score-based local learning algorithm is better when symC is used, compared to using symG.

An improved constraint-based Bayesian network learning method using Gaussian kernel probability density estimator

Bayesian network has powerful expression and reasoning ability of uncertainty knowledge. At present, it is widely used in many fields, such as fault diagnosis, medical diagnosis and prediction, financial analysis and prediction, decision support, etc. How to construct the Bayesian network effectively is an important research problem in the area of data mining. The constraint-based learning algorithm is commonly used for the construction of Bayesian network (BNs), such as Fast Incremental Association (Fast-IAMB) and Max-Min Parents & Children (MMPC), etc. At present, the Chi square test and correlation coefficient are often used to calculate the correlation between variables in these algorithms. But the calculation accuracy of these methods is not high, thus to influence the effectiveness of the constraint-based BNs learning algorithms. On the basis of the entropy estimation approach of Gaussian kernel probability density estimator, this paper uses the (conditional) mutual information to calculate the correlation between different variables and thus to improve the learning accuracy of the constraint-based BNs learning algorithms. The concrete calculation process about the data type of discrete, continuous and mixed has been described separately. Experiment simulations on the Alarm network prove that our algorithm can improve the learning accuracy of the existing three kinds of constraint-based BNs learning algorithms without affecting the learning efficiency. It also has better learning effect when to process the concrete and continuous data with sparsity. The method in this work can be used to learn more accurate Bayesian network, and then served the research of artificial intelligence, expert system decision making, etc.

Bayesian Network Constraint-Based Structure Learning Algorithms: Parallel and Optimized Implementations in the bnlearn R Package

It is well known in the literature that the problem of learning the structure of Bayesian networks is very hard to tackle: Its computational complexity is super-exponential in the number of nodes in the worst case and polynomial in most real-world scenarios. Efficient implementations of score-based structure learning benefit from past and current research in optimization theory, which can be adapted to the task by using the network score as the objective function to maximize. This is not true for approaches based on conditional independence tests, called constraint-based learning algorithms. The only optimization in widespread use, backtracking, leverages the symmetries implied by the definitions of neighborhood and Markov blanket. In this paper we illustrate how backtracking is implemented in recent versions of the bnlearn R package, and how it degrades the stability of Bayesian network structure learning for little gain in terms of speed. As an alternative, we describe a software architecture and framework that can be used to parallelize constraint-based structure learning algorithms (also implemented in bnlearn) and we demonstrate its performance using four reference networks and two real-world data sets from genetics and systems biology. We show that on modern multi-core or multiprocessor hardware parallel implementations are preferable over backtracking, which was developed when single-processor machines were the norm.

Bayesian network modeling of Port State Control inspection findings and ship accident involvement

The paper utilizes Port State Control inspection data for discovering interactions between the numbers of various types of deficiencies found on ships and between the deficiencies and ship’s involvement in maritime traffic accidents and incidents. Bayesian network models for describing the dependencies of the inspection results, ship age, type, flag, accident involvement, and incidents reported by the Vessel Traffic Service are learned from the Finnish Port State Control data from 2009–2011, 2004–2010 Baltic Sea accident statistics and the reported Gulf of Finland Vessel Traffic Service incidents within 2004–2008. Two alternative Bayesian network algorithms are applied to the model construction. Further, additional models including a hidden variable which represents the complete system and its safety features and which links the accident and incident involvement and Port State Control findings are presented. Based on model-data fit comparisons and 10-fold cross-validation, a constraint-based learning algorithm NPC mainly outperforms the score-based algorithm repeated hill-climbing with random restarts. For the highest scoring models, mutual information and influence of evidence analyses are conducted in order to analyze which network variables and variable states are the most influential ones for determining the accident involvement. The analyses suggest that knowledge on ship type, the Port State Control inspection type and the number of structural conditions related deficiencies are among the ones providing the most information regarding accident involvement and the true state of the hidden system safety variable.

Revealing miRNA Regulation and miRNA Target Prediction Using Constraint-Based Learning

The past decades have witnessed advances in genomic technology; and this has allowed laboratories to generate vast amount of biological data, including microarray gene expression data. Effective analysis of the data helps in better understanding the mechanisms behind the complex behavior of the cell. Actually, a huge body of research focuses on the role of gene regulatory networks (GRNs) in controlling the cell. However, studying the heterogeneous interactions between mRNA and miRNA has received less attention. Fortunately, revealing the targets of miRNAs started to gain some consideration from the research community. Further, integrating mRNA gene expression and miRNA expression data is receiving more attention; the target is to understand the role of miRNA in regulating mRNA in different cell contexts; this could lead to predicting miRNA targets and constructing miRNA-mRNA interaction networks. On the other hand, we have already demonstrated the power of constraint-based learning as a promising technique to learn the structure of GRN , which are homogeneous in the sense that they contain one type of nodes, namely, genes. In this study, we extend our previous work to show how constraint-based learning can be effectively applied to tackle a more challenging problem, namely, to learn the structure of heterogeneous networks, like mRNA-miRNA network. In other words, to build the whole picture of the heterogeneous interactions, we used constraint-based learning algorithms which usually perform well on sparse graphs to predict the interactions within heterogeneous networks, namely, miRNA-mRNA interactions. We are able to achieve this by extending our PCPDPr algorithm, which works on homogeneous networks. The extended version named htrPCPDPr is capable of handling networks connecting two heterogeneous sets of nodes into a bipartite graph. This way, we propose a new learning mechanism to predict miRNA targets from expression profiles of both mRNA and miRNA, in addition to sequence-based prior knowledge about the interactions. The method has been applied to different set of genes related to the Alzheimer disease; the results reported in this paper demonstrate the novelty, applicability, and effectiveness of the proposed approach.