Learning Dynamic Bayesian Networks Research Articles

Dynamic Bayesian network structure learning based on an improved bacterial foraging optimization algorithm

With the rapid development of artificial intelligence and data science, Dynamic Bayesian Network (DBN), as an effective probabilistic graphical model, has been widely used in many engineering fields. And swarm intelligence algorithm is an optimization algorithm based on natural selection with the characteristics of distributed, self-organization and robustness. By applying the high-performance swarm intelligence algorithm to DBN structure learning, we can fully utilize the algorithm's global search capability to effectively process time-based data, improve the efficiency of network generation and the accuracy of network structure. This study proposes an improved bacterial foraging optimization algorithm (IBFO-A) to solve the problems of random step size, limited group communication, and the inability to maintain a balance between global and local searching. The IBFO-A algorithm framework comprises four layers. First, population initialization is achieved using a logistics-sine chaotic mapping strategy as the basis for global optimization. Second, the activity strategy of a colony foraging trend is constructed by combining the exploration phase of the Osprey optimization algorithm. Subsequently, the strategy of bacterial colony propagation is improved using a "genetic" approach and the Multi-point crossover operator. Finally, the elimination-dispersal activity strategy is employed to escape the local optimal solution. To solve the problem of complex DBN learning structures due to the introduction of time information, a DBN structure learning method called IBFO-D, which is based on the IBFO-A algorithm framework, is proposed. IBFO-D determines the edge direction of the structure by combining the dynamic K2 scoring function, the designed V-structure orientation rule, and the trend activity strategy. Then, according to the improved reproductive activity strategy, the concept of "survival of the fittest" is applied to the network candidate solution while maintaining species diversity. Finally, the global optimal network structure with the highest score is obtained based on the elimination-dispersal activity strategy. Multiple tests and comparison experiments were conducted on 10 sets of benchmark test functions, two non-temporal and temporal data types, and six data samples of two benchmark 2T-BN networks to evaluate and analyze the optimization performance and structure learning ability of the proposed algorithm under various data types. The experimental results demonstrated that IBFO-A exhibits good convergence, stability, and accuracy, whereas IBFO-D is an effective approach for learning DBN structures from data and has practical value for engineering applications.

Learning dynamic Bayesian networks from time-dependent and time-independent data: Unraveling disease progression in Amyotrophic Lateral Sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease causing patients to quickly lose motor neurons. The disease is characterized by a fast functional impairment and ventilatory decline, leading most patients to die from respiratory failure. To estimate when patients should get ventilatory support, it is helpful to adequately profile the disease progression. For this purpose, we use dynamic Bayesian networks (DBNs), a machine learning model, that graphically represents the conditional dependencies among variables. However, the standard DBN framework only includes dynamic (time-dependent) variables, while most ALS datasets have dynamic and static (time-independent) observations. Therefore, we propose the sdtDBN framework, which learns optimal DBNs with static and dynamic variables. Besides learning DBNs from data, with polynomial-time complexity in the number of variables, the proposed framework enables the user to insert prior knowledge and to make inference in the learned DBNs. We use sdtDBNs to study the progression of 1214 patients from a Portuguese ALS dataset. First, we predict the values of every functional indicator in the patients’ consultations, achieving results competitive with state-of-the-art studies. Then, we determine the influence of each variable in patients’ decline before and after getting ventilatory support. This insightful information can lead clinicians to pay particular attention to specific variables when evaluating the patients, thus improving prognosis. The case study with ALS shows that sdtDBNs are a promising predictive and descriptive tool, which can also be applied to assess the progression of other diseases, given time-dependent and time-independent clinical observations.

Learning Dynamic Bayesian Networks structure based on a new hybrid K2-Bat learning algorithm

ABSTRACT The temporal dimension makes it difficult and complex to learn the Dynamic Bayesian Networks structure for huge search space. We propose a new hybrid K2-Bat algorithm to learn the structure of Dynamic Bayesian Networks. This work contains two optimal strategies: an ordering-based algorithm INOK2 to learn initial network structure and an adaptive binary bat algorithm to learn transition network structure. Based on the requirement of K2 algorithm for prior knowledge, a fitness function is built to quantitatively score node order in INOK2. The initial population is generated by the node block sequence constructed by directional support tree. A dynamic learning factor, inverted mutation s`node sequence to improve the global searching ability and the convergence speed. Then, the optimal initial network structure can be obtained. In addition, an improved binary bat algorithm is proposed to improve the development behavior of bat algorithm by using dynamic selection strategy in transitional network learning. Finally, experiments on four well-known benchmark problems are performed. The results show that the proposed algorithm can successfully learn the structure of Dynamic Bayesian Networks without prior knowledge, and balance solutions quality and computational effort.

A learning method for dynamic Bayesian network structures using a multi-objective particle swarm optimizer

In this article, we present a multi-objective discrete particle swarm optimizer (DPSO) for learning dynamic Bayesian network (DBN) structures. The proposed method introduces a hierarchical structure consisting of DPSOs and a multi-objective genetic algorithm (MOGA). Groups of DPSOs find effective DBN sub-network structures and a group of MOGAs find the whole of the DBN network structure. Through numerical simulations, the proposed method can find more effective DBN structures, and can obtain them faster than the conventional method.

GlobalMIT: learning globally optimal dynamic bayesian network with the mutual information test criterion

Dynamic Bayesian networks (DBN) are widely applied in modeling various biological networks including the gene regulatory network (GRN). Due to the NP-hard nature of learning static Bayesian network structure, most methods for learning DBN also employ either local search such as hill climbing, or a meta stochastic global optimization framework such as genetic algorithm or simulated annealing. This article presents GlobalMIT, a toolbox for learning the globally optimal DBN structure from gene expression data. We propose using a recently introduced information theoretic-based scoring metric named mutual information test (MIT). With MIT, the task of learning the globally optimal DBN is efficiently achieved in polynomial time. The toolbox, implemented in Matlab and C++, is available at http://code.google.com/p/globalmit. vinh.nguyen@monash.edu; madhu.chetty@monash.edu Supplementary data is available at Bioinformatics online.

Learning Non-Stationary Dynamic Bayesian Networks

Learning dynamic Bayesian network structures provides a principled mechanism for identifying conditional dependencies in time-series data. An important assumption of traditional DBN structure learning is that the data are generated by a stationary process, an assumption that is not true in many important settings. In this paper, we introduce a new class of graphical model called a non-stationary dynamic Bayesian network, in which the conditional dependence structure of the underlying data-generation process is permitted to change over time. Non-stationary dynamic Bayesian networks represent a new framework for studying problems in which the structure of a network is evolving over time. Some examples of evolving networks are transcriptional regulatory networks during an organism's development, neural pathways during learning, and traffic patterns during the day. We define the non-stationary DBN model, present an MCMC sampling algorithm for learning the structure of the model from time-series data under different assumptions, and demonstrate the effectiveness of the algorithm on both simulated and biological data.

Predicting Project Velocity in XP Using a Learning Dynamic Bayesian Network Model

Bayesian networks, which can combine sparse data, prior assumptions and expert judgment into a single causal model, have already been used to build software effort prediction models. We present such a model of an extreme programming environment and show how it can learn from project data in order to make quantitative effort predictions and risk assessments without requiring any additional metrics collection program. The model's predictions are validated against a real world industrial project, with which they are in good agreement.

Learning dynamic Bayesian network models via cross-validation

We study cross-validation as a scoring criterion for learning dynamic Bayesian network models that generalize well. We argue that cross-validation is more suitable than the Bayesian scoring criterion for one of the most common interpretations of generalization. We confirm this by carrying out an experimental comparison of cross-validation and the Bayesian scoring criterion, as implemented by the Bayesian Dirichlet metric and the Bayesian information criterion. The results show that cross-validation leads to models that generalize better for a wide range of sample sizes.

Studying the Conditions for Learning Dynamic Bayesian Networks to Discover Genetic Regulatory Networks

Learning regulatory interactions between genes from microarray measurements presents one of the major challenges in functional genomics. This article studies the suitability of learning dynamic Bayesian networks under realistic experimental settings. Through extensive artificial-data experiments, it is investigated how the performance of discovering the true interactions depends on varying data conditions. These experiments show that the performance most strongly deteriorates when the connectivity of the original network increases, and more than a proportional increase in the number of samples is needed to compensate for this. Furthermore, it was found that a lower performance is achieved when the original network size becomes larger, but this decrease can be greatly reduced with increased computational effort. Finally, it is shown that the performance of the search algorithm benefits more from a larger number of restarts rather than from the use of more sophisticated search strategies.

Studying the Conditions for Learning Dynamic Bayesian Networks to Discover Genetic Regulatory Networks

Studying the Conditions for Learning Dynamic Bayesian Networks to Discover Genetic Regulatory Networks

Evolutionary learning of dynamic probabilistic models with large time lags

In this paper, we explore the automatic explanation of multivariate time series (MTS) through learning dynamic Bayesian networks (DBNs). We have developed an evolutionary algorithm which exploits certain characteristics of MTS in order to generate good networks as quickly as possible. We compare this algorithm to other standard learning algorithms that have traditionally been used for static Bayesian networks but are adapted for DBNs in this paper. These are extensively tested on both synthetic and real-world MTS for various aspects of efficiency and accuracy. By proposing a simple representation scheme, an efficient learning methodology, and several useful heuristics, we have found that the proposed method is more efficient for learning DBNs from MTS with large time lags, especially in time-demanding situations. © 2001 John Wiley & Sons, Inc.