scholarly journals shinyBN: an online application for interactive Bayesian network inference and visualization

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Jiajin Chen ◽  
Ruyang Zhang ◽  
Xuesi Dong ◽  
Lijuan Lin ◽  
Ying Zhu ◽  
...  
Keyword(s):  
Bayesian Networks ◽  
Bayesian Network ◽  
Network Inference ◽  
Graphical Model ◽  
Disease Risk ◽  
External Validation ◽  
Easy Method ◽  
Online Application ◽  
Link Type ◽  
Research Fields

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.

Bayesian Networks

2011 ◽  
pp. 89-93 ◽  
Author(s):  
Ahmad Bashir ◽  
Latifur Khan ◽  
Mamoun Awad
Keyword(s):  
Neural Networks ◽  
Bayesian Networks ◽  
Bayesian Network ◽  
Decision Trees ◽  
Graphical Model ◽  
Conditional Probabilities ◽  
Rule Bases

A Bayesian network is a graphical model that finds probabilistic relationships among variables of a system. The basic components of a Bayesian network include a set of nodes, each representing a unique variable in the system, their inter-relations, as indicated graphically by edges, and associated probability values. By using these probabilities, termed conditional probabilities, and their interrelations, we can reason and calculate unknown probabilities. Furthermore, Bayesian networks have distinct advantages compared to other methods, such as neural networks, decision trees, and rule bases, which we shall discuss in this paper.

Learning Bayesian Networks

2011 ◽  
pp. 315-321
Author(s):  
Marco F. Ramoni ◽  
Paola Sebastiani
Keyword(s):  
Probability Distribution ◽  
Bayesian Networks ◽  
Bayesian Network ◽  
Graphical Models ◽  
Graphical Model ◽  
Joint Probability ◽  
Joint Probability Distribution ◽  
Probabilistic Graphical Model ◽  
Conditional Probability Distribution ◽  
Statistics And Probability

Born at the intersection of artificial intelligence, statistics, and probability, Bayesian networks (Pearl, 1988) are a representation formalism at the cutting edge of knowledge discovery and data mining (Heckerman, 1997). Bayesian networks belong to a more general class of models called probabilistic graphical models (Whittaker, 1990; Lauritzen, 1996) that arise from the combination of graph theory and probability theory, and their success rests on their ability to handle complex probabilistic models by decomposing them into smaller, amenable components. A probabilistic graphical model is defined by a graph, where nodes represent stochastic variables and arcs represent dependencies among such variables. These arcs are annotated by probability distribution shaping the interaction between the linked variables. A probabilistic graphical model is called a Bayesian network, when the graph connecting its variables is a directed acyclic graph (DAG). This graph represents conditional independence assumptions that are used to factorize the joint probability distribution of the network variables, thus making the process of learning from a large database amenable to computations. A Bayesian network induced from data can be used to investigate distant relationships between variables, as well as making prediction and explanation, by computing the conditional probability distribution of one variable, given the values of some others.

System Reliability Evaluation Using Bayesian Networks

2013 ◽  
Vol 756-759 ◽  
pp. 2457-2461
Author(s):  
Lin Ying Liu ◽  
Qin Sun ◽  
Yao Wang
Keyword(s):  
Bayesian Networks ◽  
Bayesian Network ◽  
System Reliability ◽  
Network Inference ◽  
Fault Tree ◽  
Reliability Evaluation ◽  
Flow Chart ◽  
Inference Algorithms ◽  
Network Method ◽  
Bayesian Network Inference

Bayesian network method for system reliability evaluation which is based on a Bayesian network that transformed from a fault tree has gotten much attention these years. After a brief introduction to the method how to transform a fault tree into a Bayesian network, the paper elaborates the Bayesian network inference algorithms. The paper focuses on the way how the inference algorithms can be applied to the practice of system reliability evaluation and designs a systematic flow chart used to evaluate system reliability in a Bayesian network way. The experiment demonstrates the feasibility of the systematic flow chart.

scholarly journals Controlling false discoveries in Bayesian gene networks with lasso regression p-values

2018 ◽  
Author(s):  
Lingfei Wang ◽  
Tom Michoel
Keyword(s):  
Bayesian Networks ◽  
Gene Networks ◽  
Network Inference ◽  
Supplementary Information ◽  
Lasso Regression ◽  
Link Type ◽  
False Discovery ◽  
Systematic Biases ◽  
Empirical Tests ◽  
False Discoveries

AbstractMotivationBayesian networks can represent directed gene regulations and therefore are favored over co-expression networks. However, hardly any Bayesian network study concerns the false discovery control (FDC) of network edges, leading to low accuracies due to systematic biases from inconsistent false discovery levels in the same study.ResultsWe design four empirical tests to examine the FDC of Bayesian networks from three p-value based lasso regression variable selections — two existing and one we originate. Our method, lassopv, computes p-values for the critical regularization strength at which a predictor starts to contribute to lasso regression. Using null and Geuvadis datasets, we find that lassopv obtains optimal FDC in Bayesian gene networks, whilst existing methods have defective p-values. The FDC concept and tests extend to most network inference scenarios and will guide the design and improvement of new and existing methods. Our novel variable selection method with lasso regression also allows FDC on other datasets and questions, even beyond network inference and computational biology.AvailabilityLassopv is implemented in R and freely available at https://github.com/lingfeiwang/lassopv and https://cran.r-project.org/[email protected] informationSupplementary data are available at Bioinformatics online.

Learning Bayesian Networks

2011 ◽  
pp. 674-677
Author(s):  
Marco F. Ramoni ◽  
Paola Sebastiani
Keyword(s):  
Probability Distribution ◽  
Bayesian Networks ◽  
Bayesian Network ◽  
Graphical Models ◽  
Graphical Model ◽  
Joint Probability ◽  
Joint Probability Distribution ◽  
Probabilistic Graphical Model ◽  
Conditional Probability Distribution ◽  
Statistics And Probability

Born at the intersection of artificial intelligence, statistics, and probability, Bayesian networks (Pearl, 1988) are a representation formalism at the cutting edge of knowledge discovery and data mining (Heckerman, 1997). Bayesian networks belong to a more general class of models called probabilistic graphical models (Whittaker, 1990; Lauritzen, 1996) that arise from the combination of graph theory and probability theory, and their success rests on their ability to handle complex probabilistic models by decomposing them into smaller, amenable components. A probabilistic graphical model is defined by a graph, where nodes represent stochastic variables and arcs represent dependencies among such variables. These arcs are annotated by probability distribution shaping the interaction between the linked variables. A probabilistic graphical model is called a Bayesian network, when the graph connecting its variables is a directed acyclic graph (DAG). This graph represents conditional independence assumptions that are used to factorize the joint probability distribution of the network variables, thus making the process of learning from a large database amenable to computations. A Bayesian network induced from data can be used to investigate distant relationships between variables, as well as making prediction and explanation, by computing the conditional probability distribution of one variable, given the values of some others.

Learning Bayesian Networks

2011 ◽  
pp. 1124-1128
Author(s):  
Marco F. Ramoni ◽  
Paola Sebastiani
Keyword(s):  
Probability Distribution ◽  
Bayesian Networks ◽  
Bayesian Network ◽  
Graphical Models ◽  
Graphical Model ◽  
Joint Probability ◽  
Joint Probability Distribution ◽  
Probabilistic Graphical Model ◽  
Conditional Probability Distribution ◽  
Statistics And Probability

Born at the intersection of artificial intelligence, statistics, and probability, Bayesian networks (Pearl, 1988) are a representation formalism at the cutting edge of knowledge discovery and data mining (Heckerman, 1997). Bayesian networks belong to a more general class of models called probabilistic graphical models (Whittaker, 1990; Lauritzen, 1996) that arise from the combination of graph theory and probability theory, and their success rests on their ability to handle complex probabilistic models by decomposing them into smaller, amenable components. A probabilistic graphical model is defined by a graph, where nodes represent stochastic variables and arcs represent dependencies among such variables. These arcs are annotated by probability distribution shaping the interaction between the linked variables. A probabilistic graphical model is called a Bayesian network, when the graph connecting its variables is a directed acyclic graph (DAG). This graph represents conditional independence assumptions that are used to factorize the joint probability distribution of the network variables, thus making the process of learning from a large database amenable to computations. A Bayesian network induced from data can be used to investigate distant relationships between variables, as well as making prediction and explanation, by computing the conditional probability distribution of one variable, given the values of some others.

A Probabilistic Trust Model for Cloud Services Using Bayesian Networks

2021 ◽  
Author(s):  
Mihan Hosseinnezhad ◽  
Mohammad Abdollahi Azgomi ◽  
Mohammad Reza Ebrahimi Dishabi
Keyword(s):  
Cloud Computing ◽  
Bayesian Networks ◽  
Bayesian Network ◽  
Graphical Model ◽  
Service Providers ◽  
Estimation Error ◽  
Cloud Service ◽  
Trust Model ◽  
Cloud Services

Abstract With the rapid adoption of cloud computing in the industry, there has been a significant challenge in managing trust between cloud service providers and service consumers. In fact, trust management in cloud computing has become very challenging given the urgent need for cloud service requesters to choose efficient, trustworthy and non-risky services. One of the most important factors that can be considered in the trust or distrust of a service by the applicant is the different quality of services related to the service. Therefore, approaches are needed to assess the trustworthiness of cloud services with respect to the values ​​of their Quality of Service (QoS). Given the uncertainty that exists for cloud services, it is more realistic to model their QoS parameters as random variables and also consider different dependencies between them. In this paper, a new trust model for cloud services is proposed using Bayesian networks. Bayesian network is a probabilistic graphical model that can be used as one of the best methods to control uncertainty. Using Bayesian network makes it possible to infer more accurate QoS values ​​will which leads to the selection of highly trustworthy services by several cloud service requesters. The results of the experiments show that the proposed trust model is highly accurate and significantly reduces the estimation error.

Application of Bayesian Network in Safety Evaluation of Metro Construction

2013 ◽  
Vol 838-841 ◽  
pp. 1463-1468
Author(s):  
Xiang Ke Liu ◽  
Zhi Shen Wang ◽  
Hai Liang Wang ◽  
Jun Tao Wang
Keyword(s):  
Bayesian Networks ◽  
Bayesian Network ◽  
Posterior Probability ◽  
Fault Tree ◽  
Fault Tree Analysis ◽  
Safety Evaluation ◽  
Tree Analysis ◽  
Tunnel Blasting ◽  
Better Than

The paper introduced the Bayesian networks briefly and discussed the algorithm of transforming fault tree into Bayesian networks at first, then regarded the structures impaired caused by tunnel blasting construction as a example, introduced the built and calculated method of the Bayesian networks by matlab. Then assumed the probabilities of essential events, calculated the probability of top event and the posterior probability of each essential events by the Bayesian networks. After that the paper contrast the characteristics of fault tree analysis and the Bayesian networks, Identified that the Bayesian networks is better than fault tree analysis in safety evaluation in some case, and provided a valid way to assess risk in metro construction.

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