Granger causality vs. dynamic Bayesian network inference: a comparative study

Cunlu Zou, Katherine J Denby, Jianfeng Feng

Research output: Contribution to journalArticlepeer-review

Abstract

BACKGROUND: In computational biology, one often faces the problem of deriving the causal relationship among different elements such as genes, proteins, metabolites, neurons and so on, based upon multi-dimensional temporal data. Currently, there are two common approaches used to explore the network structure among elements. One is the Granger causality approach, and the other is the dynamic Bayesian network inference approach. Both have at least a few thousand publications reported in the literature. A key issue is to choose which approach is used to tackle the data, in particular when they give rise to contradictory results.

RESULTS: In this paper, we provide an answer by focusing on a systematic and computationally intensive comparison between the two approaches on both synthesized and experimental data. For synthesized data, a critical point of the data length is found: the dynamic Bayesian network outperforms the Granger causality approach when the data length is short, and vice versa. We then test our results in experimental data of short length which is a common scenario in current biological experiments: it is again confirmed that the dynamic Bayesian network works better.

CONCLUSION: When the data size is short, the dynamic Bayesian network inference performs better than the Granger causality approach; otherwise the Granger causality approach is better.

Original languageEnglish
Pages (from-to)122
JournalBMC Bioinformatics
Volume10
DOIs
Publication statusPublished - 24 Apr 2009

Keywords

  • Bayes Theorem
  • Computational Biology
  • Gene Expression Profiling
  • Oligonucleotide Array Sequence Analysis
  • Pattern Recognition, Automated

Cite this