Learning Bayesian Networks That Enable Full Propagation of Evidence

This paper builds on recent developments in Bayesian network (BN) structure learning under the controversial assumption that the input variables are dependent. This assumption can be viewed as a learning constraint geared towards cases where the input variables are known or assumed to be dependent. It addresses the problem of learning multiple disjoint subgraphs that do not enable full propagation of evidence. This problem is highly prevalent in cases where the sample size of the input data is low with respect to the dimensionality of the model, which is often the case when working with real data. The paper presents a novel hybrid structure learning algorithm, called SaiyanH, that addresses this issue. The results show that this constraint helps the algorithm to estimate the number of true edges with higher accuracy compared to the state-of-the-art. Out of the 13 algorithms investigated, the results rank SaiyanH 4th in reconstructing the true DAG, with accuracy scores lower by 8.1% (F1), 10.2% (BSF), and 19.5% (SHD) compared to the top ranked algorithm, and higher by 75.5% (F1), 118% (BSF), and 4.3% (SHD) compared to the bottom ranked algorithm. Overall, the results suggest that the proposed algorithm discovers satisfactorily accurate connected DAGs in cases where other algorithms produce multiple disjoint subgraphs that often underfit the true graph

Bayesian network structure learning with causal effects in the presence of latent variables.

Latent variables may lead to spurious relationships that can be misinterpreted as causal relationships. In Bayesian Networks (BNs), this challenge is known as learning under causal insufficiency. Structure learning algorithms that assume causal insufficiency tend to reconstruct the ancestral graph of a BN, where bi-directed edges represent confounding and directed edges represent direct or ancestral relationships. This paper describes a hybrid structure learning algorithm, called CCHM, which combines the constraint-based part of cFCI with hill-climbing score-based learning. The score-based process incorporates Pearl s do-calculus to measure causal effects and orientate edges that would otherwise remain undirected, under the assumption the BN is a linear Structure Equation Model where data follow a multivariate Gaussian distribution. Experiments based on both randomised and well-known networks show that CCHM improves the state-of-the-art in terms of reconstructing the true ancestral graph

Learning Bayesian networks from demographic and health survey data.

Child mortality from preventable diseases such as pneumonia and diarrhoea in low and middle-income countries remains a serious global challenge. We combine knowledge with available Demographic and Health Survey (DHS) data from India, to construct Causal Bayesian Networks (CBNs) and investigate the factors associated with childhood diarrhoea. We make use of freeware tools to learn the graphical structure of the DHS data with score-based, constraint-based, and hybrid structure learning algorithms. We investigate the effect of missing values, sample size, and knowledge-based constraints on each of the structure learning algorithms and assess their accuracy with multiple scoring functions. Weaknesses in the survey methodology and data available, as well as the variability in the CBNs generated by the different algorithms, mean that it is not possible to learn a definitive CBN from data. However, knowledge-based constraints are found to be useful in reducing the variation in the graphs produced by the different algorithms, and produce graphs which are more reflective of the likely influential relationships in the data. Furthermore, valuable insights are gained into the performance and characteristics of the structure learning algorithms. Two score-based algorithms in particular, TABU and FGES, demonstrate many desirable qualities; a) with sufficient data, they produce a graph which is similar to the reference graph, b) they are relatively insensitive to missing values, and c) behave well with knowledge-based constraints. The results provide a basis for further investigation of the DHS data and for a deeper understanding of the behaviour of the structure learning algorithms when applied to real-world settings

Approximate learning of high dimensional Bayesian network structures via pruning of Candidate Parent Sets.

Score-based algorithms that learn Bayesian Network (BN) structures provide solutions ranging from different levels of approximate learning to exact learning. Approximate solutions exist because exact learning is generally not applicable to networks of moderate or higher complexity. In general, approximate solutions tend to sacrifice accuracy for speed, where the aim is to minimise the loss in accuracy and maximise the gain in speed. While some approximate algorithms are optimised to handle thousands of variables, these algorithms may still be unable to learn such high dimensional structures. Some of the most efficient score-based algorithms cast the structure learning problem as a combinatorial optimisation of candidate parent sets. This paper explores a strategy towards pruning the size of candidate parent sets, aimed at high dimensionality problems. The results illustrate how different levels of pruning affect the learning speed relative to the loss in accuracy in terms of model fitting, and show that aggressive pruning may be required to produce approximate solutions for high complexity problems

Simpson's Paradox and the implications for medical trials.

This paper describes Simpson's paradox, and explains its serious implications for randomised control trials. In particular, we show that for any number of variables we can simulate the result of a controlled trial which uniformly points to one conclusion (such as 'drug is effective') for every possible combination of the variable states, but when a previously unobserved confounding variable is included every possible combination of the variables state points to the opposite conclusion ('drug is not effective'). In other words no matter how many variables are considered, and no matter how 'conclusive' the result, one cannot conclude the result is truly 'valid' since there is theoretically an unobserved confounding variable that could completely reverse the result

Model of host-pathogen Interaction dynamics links In vivo optical imaging and immune responses

Tracking disease progression in vivo is essential for the development of treatments against bacterial infection. Optical imaging has become a central tool for in vivo tracking of bacterial population development and therapeutic response. For a precise understanding of in vivo imaging results in terms of disease mechanisms derived from detailed postmortem observations, however, a link between the two is needed. Here, we develop a model that provides that link for the investigation of Citrobacter rodentium infection, a mouse model for enteropathogenic Escherichia coli (EPEC). We connect in vivo disease progression of C57BL/6 mice infected with bioluminescent bacteria, imaged using optical tomography and X-ray computed tomography, to postmortem measurements of colonic immune cell infiltration. We use the model to explore changes to both the host immune response and the bacteria and to evaluate the response to antibiotic treatment. The developed model serves as a novel tool for the identification and development of new therapeutic interventions

Value of information analysis for interventional and counterfactual Bayesian networks in forensic medical sciences

Objectives: Inspired by real-world examples from the forensic medical sciences domain, we seek to determine whether a decision about an interventional action could be subject to amendments on the basis of some incomplete information within the model, and whether it would be worthwhile for the decision maker to seek further information prior to suggesting a decision

Risk assessment and risk management of violent reoffending among prisoners

“The final publication is available at Springer via http://dx.doi.org/10.1016/j.eswa.2015.05.025”