Data Analysis with Bayesian Networks: A Bootstrap Approach Nir Friedman, Moises Goldszmidt, and Abraham Wyner, UAI99.

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Data Analysis with Bayesian Networks: A Bootstrap Approach Nir Friedman, Moises Goldszmidt, and Abraham Wyner, UAI99

Abstract Confidence on learned Bayesian networks  Edges How can we believe that the presence of an edge is true?  Markov blankets The Markov blanket of a variable is true?  Order relations The variable Y is ancestor of the variable X? Especially for small datasets, this problem is so crucial. Efron’s Bootstrap approach was used in this paper.

Sparse datasets An application of Bayesian networks to molecular biology Thousands of attributes and at most hundreds of samples How can we separate the measurable “signal” from the “noise”?

Learning Bayesian networks Given data D, find the network structure with high score.  Bde score and MDL score Search space is so large.  Exponential order Greedy hill-climbing with restart can be used.

Partially Directed Acyclic Graphs (PDAGs) The network structure with directed and undirected edges.  The undirected edge allows both directions. X – Y represents both X  Y and Y  X.  In the case that both directions have the same score, we only have to allow both directions in the network. The accurate causal relationship can not be guaranteed by the dataset.

The Confidence Level of Features in the Network Edges, Markov blankets, and order relations  Above quantity can be regarded as the probability of the feature f’s presence in the Bayesian network induced from the samples of size N.

Non-Parametric Bootstrap For i = 1, 2, …, m  Re-sample, with replacement, N instances from D. Denote the resulting dataset by D i.  Apply the learning procedure on D i to induce a network structure For each feature of interest, define

Parametric Bootstrap Induce a network B from D For i = 1, 2, …, m  Sample N instances from B. Denote the resulting dataset by D i.  Apply the learning procedure on D i to induce a network structure For each feature of interest, define

Empirical Evaluation Synthetic datasets from alarm, gene, text networks were used. N = 100, 250, 500, 1000 Bootstrap sampling size was 10 and the number of re- sampling, m was 100.

Results on the Alarm Network

Threshold Setting The appropriate threshold setting is due to the problem domain.  0.8 was best to the alarm network and 0.65 was best to the text network.

Robust features Order relations and Markov blankets were robust to small dataset, but edges were sensitive to the sample size.

The Comparison of Parametric and Non- Parametric Bootstrap

Bootstrap for Network Induction Some constraints according to the threshold values from bootstrapping.

Conclusions The bootstrap estimates are quite cautious. Features induce with high confidence are rarely false positive. The Markov blanket and partial ordering amongst variables are more robust than the existence of edges.