Dataset Information

Combining shrinkage and sparsity in conjugate vector autoregressive models.

ABSTRACT: Conjugate priors allow for fast inference in large dimensional vector autoregressive (VAR) models. But at the same time, they introduce the restriction that each equation features the same set of explanatory variables. This paper proposes a straightforward means of postprocessing posterior estimates of a conjugate Bayesian VAR to effectively perform equation-specific covariate selection. Compared with existing techniques using shrinkage alone, our approach combines shrinkage and sparsity in both the VAR coefficients and the error variance-covariance matrices, greatly reducing estimation uncertainty in large dimensions while maintaining computational tractability. We illustrate our approach by means of two applications. The first application uses synthetic data to investigate the properties of the model across different data-generating processes, and the second application analyzes the predictive gains from sparsification in a forecasting exercise for U.S. data.

SUBMITTER: Hauzenberger N

PROVIDER: S-EPMC8048898 | biostudies-literature | 2021 Apr-May

REPOSITORIES: biostudies-literature

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Publications

Combining shrinkage and sparsity in conjugate vector autoregressive models.

Hauzenberger Niko N Huber Florian F Onorante Luca L

Journal of applied econometrics (Chichester, England) 20210113 3

Conjugate priors allow for fast inference in large dimensional vector autoregressive (VAR) models. But at the same time, they introduce the restriction that each equation features the same set of explanatory variables. This paper proposes a straightforward means of postprocessing posterior estimates of a conjugate Bayesian VAR to effectively perform equation-specific covariate selection. Compared with existing techniques using shrinkage alone, our approach combines shrinkage and sparsity in both ...[more]

PMID: 33888936

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Project description:BackgroundIn the analysis of effects by cell treatment such as drug dosing, identifying changes on gene network structures between normal and treated cells is a key task. A possible way for identifying the changes is to compare structures of networks estimated from data on normal and treated cells separately. However, this approach usually fails to estimate accurate gene networks due to the limited length of time series data and measurement noise. Thus, approaches that identify changes on regulations by using time series data on both conditions in an efficient manner are demanded.MethodsWe propose a new statistical approach that is based on the state space representation of the vector autoregressive model and estimates gene networks on two different conditions in order to identify changes on regulations between the conditions. In the mathematical model of our approach, hidden binary variables are newly introduced to indicate the presence of regulations on each condition. The use of the hidden binary variables enables an efficient data usage; data on both conditions are used for commonly existing regulations, while for condition specific regulations corresponding data are only applied. Also, the similarity of networks on two conditions is automatically considered from the design of the potential function for the hidden binary variables. For the estimation of the hidden binary variables, we derive a new variational annealing method that searches the configuration of the binary variables maximizing the marginal likelihood.ResultsFor the performance evaluation, we use time series data from two topologically similar synthetic networks, and confirm that our proposed approach estimates commonly existing regulations as well as changes on regulations with higher coverage and precision than other existing approaches in almost all the experimental settings. For a real data application, our proposed approach is applied to time series data from normal Human lung cells and Human lung cells treated by stimulating EGF-receptors and dosing an anticancer drug termed Gefitinib. In the treated lung cells, a cancer cell condition is simulated by the stimulation of EGF-receptors, but the effect would be counteracted due to the selective inhibition of EGF-receptors by Gefitinib. However, gene expression profiles are actually different between the conditions, and the genes related to the identified changes are considered as possible off-targets of Gefitinib.ConclusionsFrom the synthetically generated time series data, our proposed approach can identify changes on regulations more accurately than existing methods. By applying the proposed approach to the time series data on normal and treated Human lung cells, candidates of off-target genes of Gefitinib are found. According to the published clinical information, one of the genes can be related to a factor of interstitial pneumonia, which is known as a side effect of Gefitinib.

Dataset Information

Combining shrinkage and sparsity in conjugate vector autoregressive models.

Publications

Combining shrinkage and sparsity in conjugate vector autoregressive models.

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