Inferring cellular regulatory networks with Bayesian model averaging for linear regression (BMALR)
Abstract: Bayesian network and linear regression methods have been widely applied to reconstruct cellular regulatory networks. In this work, we propose a Bayesian model averaging for linear regression (BMALR) method to infer molecular interactions in biological systems. This method uses a new closed form solution to compute the posterior probabilities of the edges from regulators to the target gene within a hybrid framework of Bayesian model averaging and linear regression methods. We have assessed the performance of BMALR by benchmarking on both in silico DREAM datasets and real experimental datasets. The results show that BMALR achieves both high prediction accuracy and high computational efficiency across different benchmarks. A pre-processing of the datasets with the log transformation can further improve the performance of BMALR, leading to a new top overall performance. In addition, BMALR can achieve robust high performance in community predictions when it is combined with other competing methods. The proposed method BMALR is competitive compared to the existing network inference methods. Therefore, BMALR will be useful to infer regulatory interactions in biological networks. A free open source software tool for the BMALR algorithm is available at https://sites.google.com/site/bmalr4netinfer/
- Standort
-
Deutsche Nationalbibliothek Frankfurt am Main
- Umfang
-
Online-Ressource
- Sprache
-
Englisch
- Anmerkungen
-
Molecular BioSystems. 10, issue 8 (2014), 2023-2030 , DOI 10.1039/C4MB00053F, issn: 1742-2051
IN COPYRIGHT http://rightsstatements.org/page/InC/1.0 rs
- Klassifikation
-
Mathematik
- Ereignis
-
Veröffentlichung
- (wo)
-
Freiburg
- (wer)
-
Universität
- (wann)
-
2014
- Urheber
- Beteiligte Personen und Organisationen
-
Fakultät für Biologie
BIOSS Centre for Biological Signalling Studies
Albert-Ludwigs-Universität Freiburg
- DOI
-
10.1039/C4MB00053F
- URN
-
urn:nbn:de:bsz:25-freidok-122987
- Rechteinformation
-
Der Zugriff auf das Objekt ist unbeschränkt möglich.
- Letzte Aktualisierung
-
14.08.2025, 10:52 MESZ
Datenpartner
Deutsche Nationalbibliothek. Bei Fragen zum Objekt wenden Sie sich bitte an den Datenpartner.
Beteiligte
- Huang, Xun
- Zi, Zhike
- Fakultät für Biologie
- BIOSS Centre for Biological Signalling Studies
- Albert-Ludwigs-Universität Freiburg
- Universität
Entstanden
- 2014
Ähnliche Objekte (12)
Bayesian dynamic quantile model averaging
Model averaging for sparse seemingly unrelated regression using Bayesian networks among the errors
Inferring cellular networks – a review
Sovereign risk indices and Bayesian theory averaging
Model selection in Medical Research: A simulation study comparing Bayesian Model Averaging and Stepwise Regression
Bayesian semiparametric regression
Bayesian quantile regression
Bayesian quantile regression
Bayesian model averaging using power-expected-posterior priors
Inferring gene regression networks with model trees
A generalisation of the method of regression calibration and comparison with Bayesian and frequentist model averaging methods
Inferring neuronal functional connectivity using dynamic Bayesian networks
Bayesian dynamic quantile model averaging
Model averaging for sparse seemingly unrelated regression using Bayesian networks among the errors
Inferring cellular networks – a review
Sovereign risk indices and Bayesian theory averaging
Model selection in Medical Research: A simulation study comparing Bayesian Model Averaging and Stepwise Regression
Bayesian semiparametric regression
Bayesian quantile regression
Bayesian quantile regression
Bayesian model averaging using power-expected-posterior priors
Inferring gene regression networks with model trees
A generalisation of the method of regression calibration and comparison with Bayesian and frequentist model averaging methods
Inferring neuronal functional connectivity using dynamic Bayesian networks
Bayesian dynamic quantile model averaging
Model averaging for sparse seemingly unrelated regression using Bayesian networks among the errors
Inferring cellular networks – a review
Sovereign risk indices and Bayesian theory averaging
Model selection in Medical Research: A simulation study comparing Bayesian Model Averaging and Stepwise Regression
Bayesian semiparametric regression
Bayesian quantile regression
Bayesian quantile regression
Bayesian model averaging using power-expected-posterior priors
Inferring gene regression networks with model trees
A generalisation of the method of regression calibration and comparison with Bayesian and frequentist model averaging methods