Benchmarking dynamic Bayesian network structure learning algorithms (original) (raw)

Non-stationary dynamic Bayesian networks

Neural Information Processing Systems, 2008

A principled mechanism for identifying conditional dependencies in time-series data is provided through structure learning of dynamic Bayesian networks (DBNs). An important assumption of 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 models called non-stationary dynamic Bayesian networks, 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. 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.

Learning the structure of dynamic Bayesian networks from time series and steady state measurements

Machine Learning, 2008

Dynamic Bayesian networks (DBN) are a class of graphical models that has become a standard tool for modeling various stochastic time-varying phenomena. In many applications, the primary goal is to infer the network structure from measurement data. Several efficient learning methods have been introduced for the inference of DBNs from time series measurements. Sometimes, however, it is either impossible or impractical to collect time series data, in which case, a common practice is to model the non-time series observations using static Bayesian networks (BN). Such an approach is obviously sub-optimal if the goal is to gain insight into the underlying dynamical model. Here, we introduce Bayesian methods for the inference of DBNs from steady state measurements. We also consider learning the structure of DBNs from a combination of time series and steady state measurements. We introduce two different methods: one that is based on an approximation and another one that provides exact computation. Simulation results demonstrate that dynamic network structures can be learned to an extent from steady state measurements alone and that inference from a combination of steady state and time series data has the potential to improve learning performance relative to the inference from time series data alone.

Learning Dynamic Bayesian Network Structures from Data

2003

Dynamic Bayesian networks (DBNs) are graphical models to represent stochastic processes. This dissertation investigates the use of DBNs to predict patient outcomes based on temporal data, the effectiveness of DBNs on nonstationary multivariate time series data, and the assumptions on the parametric nature of DBNs along with two related hypotheses: (1) Given the assumption that the dataset was generated by stationary and first-order Markov processes, patient-specific DBNs, each of which models a single patient, would predict patient mortality more accurately than DBNs that model an entire patient population. (2) The predictive performances of patient-specific DBNs would improve by relaxing the stationary and first-order Markov assumptions.

Dynamic Bayesian Network Modeling, Learning, and Inference: A Survey

IEEE Access, 2021

Since the introduction of Dynamic Bayesian Networks (DBNs), their efficiency and effectiveness have increased through the development of three significant aspects: (i) modeling, (ii) learning and (iii) inference. However, no reviews of the literature have been found that chronicle their importance and development over time. The aim of this study is to provide a systematic review of the literature that details the evolution and advancement of DBNs, focusing in the period 1997–2019 that emphasize the aspects of modeling, learning and inference. While the literature presents temporal event networks, knowledge encapsulation, relational and time varying representations as the four predominant DBN modeling approaches, this work groups them as essential techniques within DBNs and help practitioners by associating each to various challenge that arise in pattern discovery and prediction in dynamic processes. Regarding learning, the predominant methods mainly focus on scoring with greedy sear...

Learning Dynamic Bayesian Networks from Multivariate Time Series with Changing Dependencies

2003

Many examples exist of multivariate time series where dependencies between variables change over time. If these changing dependencies are not taken into account, any model that is learnt from the data will average over the different dependency structures. Paradigms that try to explain underlying processes and observed events in multivariate time series must explicitly model these changes in order to allow non-experts to analyse and understand such data. In this paper we have developed a method for generating explanations in multivariate time series that takes into account changing dependency structure. We make use of a dynamic Bayesian network model with hidden nodes. We introduce a representation and search technique for learning such models from data and test it on synthetic time series and real-world data from an oil refinery, both of which contain changing underlying structure. We compare our method to an existing EM-based method for learning structure. Results are very promising for our method and we include sample explanations, generated from models learnt from the refinery dataset.

Learning the structure of Bayesian Networks: A quantitative assessment of the effect of different algorithmic schemes

Complexity

One of the most challenging tasks when adopting Bayesian Networks (BNs) is the one of learning their structure from data. This task is complicated by the huge search space of possible solutions, and by the fact that the problem is NP-hard. Hence, full enumeration of all the possible solutions is not always feasible and approximations are often required. However, to the best of our knowledge, a quantitative analysis of the performance and characteristics of the different heuristics to solve this problem has never been done before. For this reason, in this work, we provide a detailed comparison of many different state-of-the-arts methods for structural learning on simulated data considering both BNs with discrete and continuous variables, and with different rates of noise in the data. In particular, we investigate the performance of different widespread scores and algorithmic approaches proposed for the inference and the statistical pitfalls within them.

Advanced non-homogeneous dynamic Bayesian network models for statistical analyses of time series data

2019

Non-homogeneous dynamic Bayesian network models (NH-DBNs) have become popular statistical tools for analyzing time series data in order to infer the relationships between units from the data. We consider those models where a set of changepoints is employed to divide the data into disjoint segments. The changepoints are time points in which after them the general trend of the data changes. Thereafter, data within each segment are modeled with linear regression model. Some segments might be rather short and including only a few data points. Statistical inference in short segments with just a few (insufficient) data may lead to wrong conclusions. This, indeed, calls for models which make use of information sharing among segments. Recently, models with different coupling mechanisms between segments have been introduced. The main shortcoming of these models are that they cannot deal with time series data in which some parameters are dissimilar (uncoupled) over segments. Another scenario ...

An Efficient Bayesian Network Structure Learning Strategy

New Generation Computing, 2016

This paper addresses the problem of efficiently finding an optimal Bayesian network structure for maximizing the posterior probability. In particular, we focus on the B& B strategy to save the computational effort associated with finding the largest score. To make the search more efficient, we need a tighter upper bound so that the current score can exceed it more easily. We find two upper bounds and prove that they are tighter than the existing one (Campos and Ji, J Mach Learn Res 12(3):663-689, 2011). Finally, we demonstrate that the proposed two bounds render the search to be much more efficient using the Alarm and Insurance data sets. For example, the search is twice to three times faster for n ¼ 100 and almost twice faster for n ¼ 500. We also experimentally verify that the overhead due to replacing the existing pruning rule by the proposed one is negligible.

Non-stationary continuous dynamic Bayesian networks

Neural Information Processing Systems, 2009

Dynamic Bayesian networks have been applied widely to reconstruct the structure of regulatory processes from time series data. The standard approach is based on the assumption of a homogeneous Markov chain, which is not valid in many realworld scenarios. Recent research efforts addressing this shortcoming have considered undirected graphs, directed graphs for discretized data, or over-flexible models that lack any information sharing among time series segments. In the present article, we propose a non-stationary dynamic Bayesian network for continuous data, in which parameters are allowed to vary among segments, and in which a common network structure provides essential information sharing across segments. Our model is based on a Bayesian multiple change-point process, where the number and location of the change-points is sampled from the posterior distribution.

Improving nonhomogeneous dynamic Bayesian networks with sequentially coupled parameters

Statistica Neerlandica

In systems biology, nonhomogeneous dynamic Bayesian networks (NH-DBNs) have become a popular modeling tool for reconstructing cellular regulatory networks from postgenomic data. In this paper, we focus our attention on NH-DBNs that are based on Bayesian piecewise linear regression models. The new NH-DBN model, proposed here, is a generalization of an earlier proposed model with sequentially coupled network interaction parameters. Unlike the original model, our novel model possesses segment-specific coupling parameters, so that the coupling strengths between parameters can vary over time. Thereby, to avoid model overflexibility and to allow for some information exchange among time segments, we globally couple the segment-specific coupling (strength) parameters by a hyperprior. Our empirical results on synthetic and on real biological network data show that the new model yields better network reconstruction accuracies than the original model.