Partition function Proposal distribution Acceptance probability We only case the prior distribution for acceptance. Importance Sampling is also combined with MCMCMC. MCMCMC with Importance Sampling : Likelihood for configuration of a node n and its parents
Order MCMC It sample over total orders not over structures. A B C A B C A C B B C A B A C C A B C B A
Order MCMC It sample over total orders not over structures. Proposal move flipping two nodes of the previous order Computational limitations Using candidate sets S ets of parents with the highest scores in likelihood for each node Reduces the computation time.
Order MCMC Selection features We can extract the edges by approximating and averaging under the stationary distribution, where
Synthetical data 41 th to 50 th genes are not connected.
Synthetic data - MCMCMC with Importance Sampling has the best performance. - Order MCMC is the second. - Order MCMC is much faster than MCMCMC with Importance Sampling.
Synthetic data I changed one parameters for MCMC simulation. 1) Standard application (using standard parameters) 2) Change a noise value (Decrease noise value to 0.1) 3) Change a training data size (Decrease the size to 50) 4) Change the number of iterations (Increase the number to 50000) Standard parameters ( MCMC in Bayes Net Toolbox ) training data size:200, noise value:0.3, the number of iterations: 5000 (5000 samples and 5000 burn-ins)
Synthetic data Convergence 1) MCMC in BNT 2) MCMCMC Importance Sampling (IM) 3) MCMCMC Importance Sampling (ID) 4) Order MCMC 1 2 3 4 training set size : 200 noise : 0.3 5000 iterations.
Synthetic data MCMCMC (Burn-in# + Sample #) Left: 5000 + 5000 Right: 100000 + 100000 Acceptance ratios Left: MCMC in BNT, Right : Order MCMC Middle: MCMCMC with Importance Sampling
Diffuse large B cell lymphoma Data Data discretisation I used K-means algorithms to discretise gene expression levels f or each genes since the stationary level for each gene can be diff erent from others. ( up, down and normal ) Problem of this discretisation If there are too many noises, the noises can make fluctuations Finally, this method can not work well for gene3.
Diffuse large B cell lymphoma Data Comparison of convergence MCMC in BNT MCMCMC with Importance Sampling(ID) Order MCMC # of genes : 27 Training data size : 105 Iterations : 20000
Diffuse large B cell lymphoma Data Comparison of Acceptance Ratios The number of genes : 27, Training data size : 105, Iterations : 20000
Gene expression inoculated by viruses in susceptible Arabidopsis thaliana plants Viruses • Cucumber mosaic cucumovirus • Oil seed rape tobamovirus • Turnip vein clearing tobamovirus • Potato virus X potexvirus • Turnip mosaic potyvirus 1) 2) 3) 4) 5) 1DAI 2DAI 3DAI 4DAI 5DAI 7DAI Symptom occurs.
- Fall '19
- MCMC, Bayesian network, Directed acyclic graph
Other Related Materials
- of micro organisms that are unique to them Example Aminoglycosides include
- Port Of Los Angeles High
- CHEM 118C - Summer 2015
- Females XX both not being expressed one is shut down since it is packing 2
- University of Maryland
- BSCI 103 - Fall 2010
BSCI103- test 1
- A LuxI types of enzymes synthesize an effector molecule HSL bound by LuxR type
- University of British Columbia
- MICB 325 - Winter 2014
Prelim Topic 8 2015