The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data

BMC Bioinformatics

Research Article

Junbai Wang¹ 

[1] Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, 0310, Montebello, Oslo, Norway;

关键词: Prior Assumption;    Bayesian Hierarchical Model;    Bayesian Neural Network;    Regularization Constant;    Computational Time Cost;   

DOI  :  10.1186/1471-2105-11-412

 received in 2009-12-05, accepted in 2010-08-04,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundTo further understand the implementation of hyperparameters re-estimation technique in Bayesian hierarchical model, we added two more prior assumptions over the weight in BayesPI, namely Laplace prior and Cauchy prior, by using the evidence approximation method. In addition, we divided hyperparameter (regularization constants α of the model) into multiple distinct classes based on either the structure of the neural networks or the property of the weights.ResultsThe newly implemented BayesPI was tested on both synthetic and real ChIP-based high-throughput datasets to identify the corresponding protein binding energy matrices. The results obtained were encouraging: 1) there was a minor effect on the quality of predictions when prior assumptions over the weights were altered (e.g. the prior probability distributions to the weights and the number of classes to the hyperparameters) in BayesPI; 2) however, there was a significant impact on the computational speed when tuning the weight prior in the model: for example, BayesPI with a Laplace weight prior achieved the best performance with regard to both the computational speed and the prediction accuracy.ConclusionsFrom this study, we learned that it is absolutely necessary to try different prior assumptions over the weights in Bayesian hierarchical model to design an efficient learning algorithm, though the quality of the final results may not be associated with such changes. In future, the evidence approximation method can be an alternative to Monte Carlo methods for computational implementation of Bayesian hierarchical model.

【 授权许可】

CC BY   
© Wang; licensee BioMed Central Ltd. 2010