# An Introduction to Reversible Jump MCMC for Bayesian Networks, with Application

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1 An Introduction to Reversible Jump MCMC for Bayesian Networks, with Application, CleverSet, Inc. STARMAP/DAMARS Conference Page 1

2 The research described in this presentation has been funded by the U.S. Environmental Protection Agency through the STAR Cooperative Agreement #CR to Colorado State University. It has not been subjected to the Agency s review and therefore does not necessarily reflect the views of the Agency, and no official endorsement should be inferred. STARMAP/DAMARS Conference Page 2

3 Introduction Bayesian Networks Bayesian Networks (BNs) are a method for representing complex multivariate probability distributions. Graphical Structure: Directed Acyclic Graph Each node represents a variable An edge represents an association between two variables Parametrical Model: Multivariate Gaussian Data are independent, multivariate Gaussian Parameters are multivariate Gaussian Marginal distribution of each node (variable) is a multiple regression STARMAP/DAMARS Conference Page 3

4 Introduction Bayesian Networks D B C A Important point: despite the arrows, BNs represent a probability distribution and do not imply causations, only associations. STARMAP/DAMARS Conference Page 4

5 Introduction Reversible Jump Markov chain Monte Carlo MCMC is a method for simulating a probability distribution that cannot be directly simulated. MCMC is often used for model selection, especially in very large model spaces. RJMCMC is a type of MCMC that allows for dimensional changes in the probability distribution being simulated. RJMCMC can be used for model selection in cases where dimensionality may change, such as: ARIMA time series models Gaussian Mixtures STARMAP/DAMARS Conference Page 5

6 RJMCMC for BNs RJMCMC is suited to searching for BNs because: A change in the graphical structure of a BN results in a change in the number of parameters The number of possible structures of BNs increases super-exponentially in the number of variables. STARMAP/DAMARS Conference Page 6

7 RJMCMC for BNs How it works: RJMCMC randomly walks around the space of possible model structures by changing one edge at a time called structural learning. At each step in its walk, all of the model parameters are updated called parametrical learning. At the end, you have a list of all of the model structures it visited at each step and their corresponding set of parameters. STARMAP/DAMARS Conference Page 7

8 Example: MAHA-MAIA Subset of numerical data taken from the MAHA-MAIA study. Six variables chosen, with help of a domain expert: Insect IBI - Insect Index of Biotic Integrity Sediment Disturbance - A log-scale metric of excess grain-size diameter Environmental disturbance - Combined percentages of disturbance (urban, agricultural, and mining disturbances) ph Natural logarithm of nutrients (maximum of either N or P) Natural logarithm of slightly translated Acid Neutralizing Capacity STARMAP/DAMARS Conference Page 8

9 Example: MAHA-MAIA Implementation notes To avoid numerical issues, variables were standardized. Three graphical structures are presented: The structure with the maximum posterior probability, The average model, which gives us a sense of the likelihood of an association between pairs of variables, A reference model obtained from the package TETRAD IV. + s and - s, derived from the learned parameters, denote the type of quantitative association between variables. STARMAP/DAMARS Conference Page 9

10 Example: MAHA-MAIA Maximum posterior probability structure Disturbance + - Nutrients Sediment + Bug_IBI ANC ph STARMAP/DAMARS Conference Page 10

11 Example: MAHA-MAIA Posterior probabilities of all visited structures Posterior Probability Max Prob = STARMAP/DAMARS Conference Page 11

12 Example: MAHA-MAIA Average structure Note: edges with posterior probability <.3 not shown Disturbance Nutrients Sediment Bug_IBI ph 1 ANC STARMAP/DAMARS Conference Page 12

13 Example: MAHA-MAIA Structure discovered by TETRAD IV Note: undirected edge on right can be oriented either direction Disturbance Nutrients Sediment Bug_IBI ANC Phstvl STARMAP/DAMARS Conference Page 13

14 Example: MAHA-MAIA Discussion The + s and - s seem reasonable, and the structures agree, but the direction of the edges from Bug IBI seem to preclude a causal interpretation. Recall that BNs encode a joint probability distribution and don t necessarily suggest a causal relation. Try again, but remove models from consideration that include edges emanating from Bug IBI. STARMAP/DAMARS Conference Page 14

15 Example: MAHA-MAIA (2) Maximum posterior probability structure + Nutrients ANC + + Disturbance - Sediment - ph + - Bug_IBI STARMAP/DAMARS Conference Page 15

16 Example: MAHA-MAIA (2) Posterior probabilities of all visited structures Posterior Probability Max Prob = STARMAP/DAMARS Conference Page 16

17 Example: MAHA-MAIA (2) Average structure Note: edges with posterior probability <.3 not shown ph 1, + ANC 0.986, , - 1, + Bug_IBI Nutrients 0.438, , - 1, + Sediment 0.337, - Disturbance STARMAP/DAMARS Conference Page 17

18 Example: MAHA-MAIA (2) Structure discovered by TETRAD IV Disturbance Sediment Nutrients Bug_IBI ANC ph STARMAP/DAMARS Conference Page 18

19 Conclusion Finding an optimal BN that fits data is known to be a very hard problem (NP-hard, in fact), making heuristic algorithms a necessity. Though many of these algorithms are much faster than RJMCMC, increases in computing power and programming refinements are making its lack of speed less of an issue. Furthermore, other methods lack the unique strengths of RJMCMC: Posterior edge probabilities give a measure of the likelihood of association Combined structure discovery and parameter learning Fully Bayesian solution STARMAP/DAMARS Conference Page 19

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