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shinyBN: an online application for interactive Bayesian network inference and visualization
BMC Bioinformatics volume 20, Article number: 711 (2019)
Abstract
Background
High-throughput technologies have brought tremendous changes to biological domains, and the resulting high-dimensional data has also posed enormous challenges to computational science. A Bayesian network is a probabilistic graphical model represented by a directed acyclic graph, which provides concise semantics to describe the relationship between entities and has an independence assumption that is suitable for sparse omics data. Bayesian networks have been broadly used in biomedical research fields, including disease risk assessment and prognostic prediction. However, the inference and visualization of Bayesian networks are unfriendly to the users lacking programming skills.
Results
We developed an R/Shiny application, shinyBN, which is an online graphical user interface to facilitate the inference and visualization of Bayesian networks. shinyBN supports multiple types of input and provides flexible settings for network rendering and inference. For output, users can download network plots, prediction results and external validation results in publication-ready high-resolution figures.
Conclusion
Our user-friendly application (shinyBN) provides users with an easy method for Bayesian network modeling, inference and visualization via mouse clicks. shinyBN can be used in the R environment or online and is compatible with three major operating systems, including Windows, Linux and Mac OS. shinyBN is deployed at https://jiajin.shinyapps.io/shinyBN/. Source codes and the manual are freely available at https://github.com/JiajinChen/shinyBN.
Background
Bayesian networks have become one of the most commonly used models for the modeling and reasoning of uncertain systems. In the biomedical field, Bayesian networks are successfully applied to assess the risk of disease and explore the relationship between genotypes and phenotypes [1, 2]. However, the inference and visualization of Bayesian networks is not user friendly. SMILE (Structural Modeling, Inference, and Learning Engine) is a causal discovery engine [3] and is easily embedded into the other tools, such as jSMILE, a Java implementation of SMILE, and rSMILE, an R package connecting to jSMILE [4]. However, since SMILE has been shifted from open license to commercial version (product brand: GeNIe), rSMILE and jSMILE are no longer maintained. BayesianNetwork, an R/Shiny web widget to construct Bayesian network [5], while the connections between nodes are nondirectional, and only one predictor variable can be considered for outcome inference which hinders its application in real-word medical studies. In addition, there are some commercial products for Bayesian network analysis which require complex installation (Table 1). To solve these inconveniences, we developed shinyBN, an online tool based on R and Shiny for interactive inference and visualization of Bayesian network, incorporating multiple types of inputs, flexible parameter settings, and multiple combinations of outcomes.
Implementation
Overview of shinyBN
shinyBN was developed with five R packages:
bnlearn for structure learning and parameter training [6];
gRain for network inference [7];
visNetwork for network visualization [8];
pROC for plotting receiver operating characteristic (ROC) curves [9];
rmda for plotting the decision curve analysis (DCA);
and was further wrapped by R/Shiny, a framework to build interactive web applications by R [10]. By using these packages, shinyBN could construct the Bayesian network by the uploaded structural information from Excel file or R object, learning the Bayesian network by individual data, visualize and customize the network illustration, and implement the network for outcome inference. A flow chart of the proposed shinyBN is shown in Fig. 1. shinyBN is compatible with three major operating systems and popular browsers (Additional file 2).
The flow chart of the proposed shinyBN application
Network input
shinyBN supports three types of input:
Microsoft Excel file, which has network structural information and properties of the nodes (size, color, shape) and edges (color, width and line type);
bnlearn output object that embeds Bayesian network (class bn or bn.fit);
csv file with individual data for Bayesian network structure learning and parameter training. The data is an N × M matrix with discrete data, where N is the number of observables and M is the number of the features (nodes).
Network construction
Bayesian network constructions are performed using the methods in the bnlearn R package [6]. Users can select constraint-based algorithms, score-based algorithms or hybrid algorithms to train the network structure and incorporate structural priors by setting whitelists (included in the graph) and blacklists (excluded from the graph), and the bootstrap approach is supported in shinyBN as well [11]. Parameter estimation via either maximum likelihood estimation or the Bayesian method is supported in shinyBN. The structure information (nodes, edges) of constructed network can be further extracted for visualization using visNetwork. The network can be directly transformed to class grain that met the requirement of the input for gRain package and perform inference.
Network visualization
Network visualizations are based on the visNetwork R package using vis.js JavaScript library [8]. Once the input is uploaded to the server, a visualization of the network with default settings is automatically rendered. The properties of the nodes and edges can be modified by changing the corresponding settings. Node color can be defined individually, by color palettes that meet scientific journal requirements, or by the dominant colors automatically extracted from the uploaded picture. The widths of the connections can be defined manually or corresponding to the strength of the probabilistic relationships. For a better presentation, graph layouts can be modified by the default layouts or, conveniently, by mouse drag and drop. A high-resolution network graph can be downloaded from shinyBN.
Outcome inference
Inferences are performed using the junction tree algorithm in gRain R package [7]. It transforms a Bayesian network model into a tree, combines the efficiency of belief propagation and the sum-product method to allow the efficient computation of posterior probabilities.
By selecting the nodes of interest as outcomes, defining the factors (nodes) as predictive variables, setting the values accordingly as evidence, the predicted results will be displayed in a bar plot or a probabilistic table. Marginal and joint prediction results for multiple outcomes can be output. In addition, shinyBN supports external validation sets uploaded for batch inference and outputs the inference results, an ROC curve, a DCA curve and other evaluation indices. Publication-ready high-resolution figures can be downloaded from shinyBN.
Timing evaluation
The performance of the application largely depends on the configurations of the computer. In order to improve the performance, the shiny server is upgraded with 8GB of RAM. We evaluated the timing of shinyBN by using several publicly accessible networks with different number of nodes (Table 2).
Results
Real data application
Stroke is a severe complication of sickle cell anemia (SCA) that can cause permanent brain damage and even death. By integrating 108 SNPs from 39 candidate genes and clinical characteristics from 1398 individuals with SCA, Sebastiani et al. constructed a Bayesian network to predict the risk of stroke, which achieved an excellent accuracy of 98.2% [1].
First, the network model was replicated using the information from the original study and uploaded to shinyBN. Size and color of nodes and width of edges could be modified for a better presentation. In the example, the color of the nodes for the clinical characteristics was set to pink, and the color of the Markov blanket for stroke, which directly associated with stroke, was set to yellow. The layout of network was manually adjusted by the mouse drag and drop (Fig. 2). By setting the evidence for some candidate gene loci, the predicted probabilities for stroke are displayed in a table and a bar plot (Additional file 3). The network can be downloaded as an HTML file for high-resolution figures or in as an Excel file for network structures. Furthermore, we simulated random data from the stroke Bayesian network with a missing rate of 40% for each variable and then uploaded it to the server as a pseudo external validation set. The ROC plot (Additional file 4) and the DCA plot (Additional file 5) were displayed, and the batch inference results were download as a comma-separated values file.
The stroke network rendered by shinyBN
Conclusions
In conclusion, we developed an online application, shinyBN, to construct and illustrate a Bayesian network with high scalability. shinyBN supports multiple types of input and provides flexible settings for network rendering and inference. A real data application confirms that the Bayesian network can be used for omics data modeling. By integrating several packages, shinyBN is a practical pipeline for Bayesian network modeling, inference and visualization.
Availability and requirements
Project name: shinyBN.
Project home page: https://github.com/JiajinChen/shinyBN
Operating system(s):
For R users, any platform for which the R software is implemented;
For online users, any platform with compatible browser.
Programming language: R
Other requirements: Shiny
License: Apache License 2.0
Any restrictions to use by non-academics: None
Availability of data and materials
The proposed shinyBN is deployed at https://jiajin.shinyapps.io/shinyBN/. Source codes and manual are freely available at https://github.com/JiajinChen/shinyBN and Additional file 1. The R scripts to construct the stroke network are included as Additional file 6. The testing files for users are included as Additional file 7.
Abbreviations
- API:
-
Application programming interface
- DCA:
-
Decision curve analysis
- HTML:
-
HyperText Markup Language
- ROC:
-
Receiver operating characteristic
- SCA:
-
Sickle cell anemia
- SMILE:
-
Structural modeling, inference, and learning engine
- SNP:
-
Single nucleotide polymorphism
References
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Acknowledgements
The authors thank the contributors of the cited R packages.
Funding
This work has been supported by the National Key Research and Development Program of China (2016YFE0204900 to F.C.), the National Natural Science Foundation of China (81530088 to F.C., 81973142 to Y.W.), the US National Institutes of Health (CA209414, CA092824, and ES000002 to D.C.C.). The funding sponsors had no role in study design, collection, analysis and interpretation of data, or preparation of the manuscript.
Author information
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Contributions
JC wrote the codes and the manuscript. YW and FC conceived the idea and designed the software. DCC revised the manuscript critically. RZ, XD and LL optimized the code. YZ and JH extensively tested the application. All authors read and approved the final manuscript.
Corresponding authors
Correspondence to Yongyue Wei or Feng Chen.
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Cite this article
Chen, J., Zhang, R., Dong, X. et al. shinyBN: an online application for interactive Bayesian network inference and visualization. BMC Bioinformatics 20, 711 (2019). https://doi.org/10.1186/s12859-019-3309-0
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Keywords
- Bayesian network
- Visualization
- Inference
- Online tool
- R package
