accounting for model uncertainty via mcmc...
TRANSCRIPT
Accounting for Model Uncertainty via MCMC
Ricardo Sandes Ehlers
Departamento de Estatıstica
Universidade Federal do Parana
http://www.est.ufpr.br/∼ehlers
8th Brazilian Meeting on Bayesian Statistics March 26-29, 2006
8th Brazilian Meeting on Bayesian Statistics March 26-29, 2006
Examples
• choice of explanatory variables in regression (and its extensions);
• order selection in polynomial models;
• order specification in (S)ARIMA and regime swichting time series models;
“The number of things that you don’t know is one of the things that you don’t
know”.
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8th Brazilian Meeting on Bayesian Statistics March 26-29, 2006
Examples
• choice of explanatory variables in regression (and its extensions);
• order selection in polynomial models;
• order specification in (S)ARIMA and regime swichting time series models;
“The number of things that you don’t know is one of the things that you don’t
know”.
Model Selection
In real problems, model choice is typically subjetive resulting from the combination
of factors like
• quantitative measures,
• personal experience and
• costs.
Here we will talk about quantitative criteria.
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Bayesian Inference
Bayesian inference is based on Bayes theorem:
π(θ) ∝ L(y|θ) p(θ)
y: observed data and
θ: model parameters.
In words
posterior distribution ∝ likelihood× prior distribution.
We want to make inferences about a function g(θ) computing its posterior mean
Eπ[g(θ)] =
∫
g(θ)π(θ)dθ
typically analytically intractable.
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Markov chain Monte Carlo
We want to be able to generate θ1, . . . ,θm ∼ π(θ) (Target distribution)
defining transition densities P (θt,θt+1) of a Markov chain.
Given the realizations {θ(t), t = 0, 1, . . . } of a Markov chain that has π as equilibriumdistribution then, under certain conditions,
θ(t) t→∞−→ π(θ) and1
n
n∑
t=1
g(θ(t)i )
n→∞−→ Eπ(g(θi)) a.s.
Although the chain is dependent by definition the arithmetic mean of the chain
values is a consistent estimator of the theoretical mean.
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The Metropolis-Hastings Algorithm
Starting at θ0 at time (iteration) t = 0, at each iteration t = 1, 2, . . .
1. sample a candidate value φ ∼ q(·|θt).
2. sample u ∼ U(0, 1) and if
u ≤ min
{
1,π(φ)
π(θ)
q(φ|θt)
q(φ|θt)
}
set θt+1 = φ, otherwise set θt+1 = θt.
q is arbitrary but in practice ...
• q(φ|θt) = q(φ),
• q(φ|θt) = q(|φ− θt|),• q(φ|θt) symmetric.
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The Gibbs Sampler
The transition kernel is formed by complete conditional distributions
π(θi|θ−i) =π(θ)
∫
π(θ)dθi
, θ−i = (θ1, . . . , θi−1, θi+1, . . . , θd)′.
At each iteration we obtain a new value θ′ generating
θ′1 ∼ π(θ1|θ2, θ3, . . . , θd)
θ′2 ∼ π(θ2|θ′1, θ3, . . . , θd)...
θ′d ∼ π(θd|θ′1, θ′2, . . . , θ′d−1)
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The Toolbox
BUGS (Bayesian inference Using Gibbs Sampling): WinBUGS, GeoBUGS,
PKBUGS, OpenBUGS. (http://www.mrc-bsu.cam.ac.uk/bugs/)
You can run WinBUGS from Linux ! (http://www.est.ufpr.br/dicas)
JAGS (Just Another Gibbs Sampler). (www-fis.iarc.fr/∼martyn/software/jags).BOA (Bayesian Output Analysis Program). CODA (Convergence Diagnostics and
Output Analysis). R: R-CODA, mcmc, MCMCpack, bayesSurv, bayesm.
(http://www.est.ufpr.br/R).
More specific programs:
Nmix (Fortran): Bayesian analysis of univariate normal mixtures, implementing
Richardson and Green (1997).
AutoRJ (Fortran): automatic RJMCMC (Green, 2003)
Updated information: MCMC Preprint Service
(http://www.statslab.cam.ac.uk/∼mcmc).Ricardo Ehlers Model Uncertainty via MCMC 7
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Searching for the “Best” Model(s)
Supose that the numberM of alternative models is quite large.
E.g. linear model with 19 possible covariates: 219 = 524288 alternative models (with
no interations).
Enumerate, estimate and associate a measure fit and parsimony to each possible
model may not be the best strategy.
How to compare competing models?
How to make average inference using the competing models (or a subset of this)?
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Bayesian Approach
Supose we have k different modelsM1, . . . ,Mk
a prioriwe assign probabilities p(Mi) to each model.
For each model there is a vector of parameters θi ∈ Rni with:
• a likelihood given the observations p(y|θi,Mi)
• a prior distribution p(θi|Mi).
We obtain the posterior distribution of both models and their associated parameters
via Bayes theorem,
π(Mi,θi) ∝ p(y|θi,Mi) p(θi|Mi) p(Mi)
obtaining a sample from this posterior and counting the number of times each
model is visited by the chain.
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Bayesian Model Averaging
Hoeting, Madigan, Raftery and Volinsky (1999) Statistical Science 14, 382-401
LetM denote the set that indexes all entertained models. Assume that ∆ is an
outcome of interest well defined across models (e.g. a future value yt+k).
The posterior distribution for ∆ is
p(∆|y) =∑
i
p(∆|Mi,y)p(Mi|y)
for data y and posterior model probability
p(Mi|y) =p(y|Mi)p(Mi)
p(y)
where
p(y|Mi) =
∫
p(y|θi,Mi)p(θi|Mi)dθi
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Classical Approach
Model discrimination is based on comparison of information criteria, e.g.
Akaike (1974) AIC(θi,Mi) = −2 log p(y|θi,Mi) + 2ni
Schwartz (1978) BIC(θi,Mi) = −2 log p(y|θi,Mi) + ni log T
Ideally we should compare AIC (or BIC) weights
wi ∝ exp(−AIC(θi,Mi)/2)
∝ p(y|θi,Mi) exp(−ni).
The weights wi are proportional to the posterior model probabilities (in θi) with
priors
p(θi|Mi) ∝ constant and p(Mi) ∝ e−ni.
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Deviance Information Criterion
Spiegelhalter, Best, Carlin, and van der Linde (2002)
DIC(θi,Mi) = −2 log p(y|θi,Mi) + 2pD
= D + pD
where θi = E(θi|y), D = E(D(θi)|y) and pD = D −D(θi).
DIC is easily calculated during the chain simulations. If θ1i , . . . ,θ
mi is a sample from
π(θi) then
D ≈ 1
m
m∑
k=1
D(θki ) and D(θi) ≈ D
(
1
m
m∑
k=1
θki
)
WinBUGS version 1.4 computes DIC automatically.
Gelfand and Ghosh (1998) Utility rather than probability to guide model choice.
Dγ =γ
γ + 1
n∑
i=1
(µi − yi,obs)2 +
n∑
i=1
σ2i ,
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Example: Mapping Homicide Rates in Curitiba City
Silva, Mota, and Ehlers (2004) Data: Number of homicides in 2000 by district of
Curitiba city,
Yi|ei, ψi ∼ Poisson(eiψi), i = 1, . . . , n.
Model: Hierarchical Bayes with spatial component
ψi = exp(X ′iβ + θi + φi).
and covariate effects of: Median Income, Illiteracy, Households at risk.
Priors,
φi|φj, j 6= i ∼ N
(∑
j∈δiwijφj
∑
j∈δiwij
,1
τφ∑
j∈δiwij
)
(1)
β ∼ N(0, Iσ2β)
β0 ∼ U(−∞,∞)
τφ ∼ Γ(0.5, 0.0005)
τθ ∼ Γ(0.5, 0.0005)
θi ∼ N(0, 1/τθ)
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Table 1: DIC values and normalized DIC weights for each model from WinBugs with 30000 simula-
tions.
Model PD DIC weights
No spatial effect 43.728 274.556 0.0000
No covariates 33.292 261.888 0.0062
Illiteracy 18.978 252.448 0.6936
Household 63.434 292.265 0.0000
Income 29.812 259.717 0.0183
Income+Illiteracy 20.632 254.249 0.2819
Illiteracy+Household 61.703 285.940 0.0000
Income+Household 63.323 291.764 0.0000
Income+Illiteracy+Household 57.467 286.244 0.0000
We apply Occam’s razor principle Madigan and Raftery (1994) and use the more
parsimonious model.
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0.24 − 0.30.3 − 0.50.5 − 0.70.7 − 1.311.31 − 7.4
(a)
0.08 − 0.120.12 − 0.170.17 − 0.220.22 − 0.370.37 − 2.7
(b)
Figure 1: (a) and (b) Maps of relative risk point estimates and posterior standard deviation in the
Bayesian hierarchical model by district of Curitiba.
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Sample based AIC
Given a sample θ1i , . . . ,θ
mi ∼ π(θi|Mi) an obvious extension of the usual AIC is
EAIC = E [AIC(θi,Mi)|y] = D(θi,Mi) + 2ni or D(θi,Mi) + 2ni
Same for the EBIC = E [BIC(θi,Mi)|y].
We could use posterior medians or modes instead of posterior means?
What is the distance between values of these measures?
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Example: Autoregressive Models
AR(k) : yt =k∑
j=1
ajyt−j + ǫt, ǫt ∼ N(0, σ2ǫ )
Figure 2: 114 observations of base 10 logarithms minus the mean of the annual trappings of Canadian
lynx, 1821-1934.
0 20 40 60 80 100
-1.0
-0.5
0.00.5
1.0
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Table 4 in Brooks, S.P. (2002) Discussion to Spiegelhalter et al. (2002). AR(k) models for Lynx data.
k pD DIC EAIC EBIC π(k) wDIC
kwEAIC
kwEBIC
k
1 1.88 206.660 206.78 209.51 0.000 0.000 0.000 0.000
2 2.85 126.580 127.72 133.19 0.243 0.000 0.003 0.858
3 3.78 127.060 129.27 137.48 0.016 0.000 0.001 0.101
4 4.76 125.520 128.75 139.70 0.007 0.000 0.002 0.033
5 5.70 125.230 129.52 143.20 0.002 0.000 0.001 0.006
6 6.62 126.300 131.68 148.09 0.001 0.000 0.004 0.000
7 7.60 122.340 128.72 147.88 0.002 0.000 0.002 0.001
8 8.61 121.810 129.19 151.08 0.002 0.000 0.001 0.000
9 9.58 122.750 131.16 155.79 0.001 0.000 0.001 0.000
10 10.54 118.940 128.40 155.76 0.002 0.001 0.002 0.000
11 11.33 106.510 117.16 147.26 0.154 0.431 0.566 0.001
12 12.61 106.890 118.27 151.10 0.268 0.356 0.325 0.000
13 13.56 108.740 121.17 156.74 0.135 0.142 0.076 0.000
14 14.46 110.770 124.30 162.61 0.067 0.051 0.016 0.000
15 15.37 112.896 127.42 168.47 0.000 0.019 0.003 0.000
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Trans-dimensional Jumps
• Propose a jump from modelMi to modelMj w.p. rij,
• generate a vector u of dimension nj − ni from q(),
• set θj = fij(θi,u)where fij : Θi × Rnj−ni → Θj denotes a bijective function.
• Accept the jump w.p. min(1, A)where
A =π(θj,Mj)
π(θi,Mi)︸ ︷︷ ︸
target ratio
rjirij q(u)
∣∣∣∣
∂fij(θi,u)
∂(θi,u)
∣∣∣∣
︸ ︷︷ ︸
proposal ratio
Choice of proposal distribution q is crucial to cover model and parameter spaces.
When possible use the complete conditionals, or
approximations to the complete condicionals Brooks and Ehlers (2002)
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Possible Targets
Joint posterior distribution
π(Mi,θi) ∝ p(y|θi,Mi) p(θi|Mi) p(Mi).
Boltzmann Distribution
πT (θi,Mi) ∝ exp
(−g(θi,Mi)
T
)
.
MCMC + Simulated Annealing: Brooks, Friel, and King (2003)
MCMC + Genetic Algorithms: Ehlers and Ferreira (2005)
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ARIMAmodels
Ehlers and Brooks (2004) Reparameterization in terms of reciprocal roots of
characteristic polynomials
AR(I)MA(p, q) :k∏
i=1
(1 − λiL)yt =
q∏
j=1
(1 − δjL)ǫt, ǫt ∼ N(0, σ2).
Stationarity/Inversibility: |λi| < 1, i = 1, . . . , k and |δi| < 1, i = 1, . . . , q.
Possible jumps: Addition/Deletion of 1 real root or a pair of (conjugate) complex
roots.
Possible proposals: Truncated Normal, Beta-based, Logstica-based.
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Table 2: Model probabilities and proportion of correct model for a simulated AR(3).
Sample size
proposal 20 50 100 200 500 1000
Truncated normal 0.0092 0.0398 0.1074 0.2677 0.4565 0.5480
0.0000 0.1500 0.3500 0.6000 0.9000 0.9500
Beta-based 0.0096 0.0441 0.1059 0.2702 0.4812 0.5404
0.0000 0.1500 0.3500 0.6500 0.9500 0.9000
Logistic-based 0.0092 0.0414 0.1058 0.2628 0.4822 0.5436
0.0000 0.1500 0.3000 0.6000 0.9500 0.9000
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Figure 3: Southern oscillation index (SOI), 540 measurements taken between 1950-1995.
0 100 200 300 400 500
-8-6
-4-2
02
4
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Table 3: Posterior model order probabilities, 500,000 iterations after a 500,000 burn-in.
Proposal d (p, q) 0 1 2 3 4 5
Truncated normal 0 1 0.0000 0.2245 0.0518 0.0503 0.0398 0.0336
2 0.0024 0.0164 0.0556 0.0292 0.0249 0.0184
3 0.0111 0.0173 0.0374 0.0286 0.0247 0.0186
4 0.0130 0.0083 0.0178 0.0134 0.0140 0.0104
5 0.0200 0.0071 0.0148 0.0113 0.0103 0.0085
1 0 0.0000 0.0135 0.0089 0.0156 0.0147 0.0193
1 0.0000 0.0023 0.0042 0.0067 0.0078 0.0105
2 0.0001 0.0018 0.0032 0.0053 0.0067 0.0086
3 0.0004 0.0020 0.0024 0.0041 0.0042 0.0058
4 0.0004 0.0012 0.0024 0.0034 0.0050 0.0060
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ARModels with Logistic Smooth Transition
LSTAR(m, p1, . . . , pm): m regimes and pi lags in each regime.
yt = α′1x1,t + (α′
2x2,t − α′1x1,t) G1(yt−d, γ1, c1) + · · · +
(α′mxm,t − α′
m−1xm−1,t) Gm−1(yt−d, γm−1, cm−1) + ǫt, ǫt ∼ N(0, σ2ǫ )
where
Gi(yt−d, γi, ci) =1
1 + exp[−γi(yt−d − ci)], i = 1, . . . ,m− 1.
xj,t = (1, yt−1, . . . , yt−pj)
αj = (α0, α1, . . . , αpj) : AR coefficients
γi > 0 : smoothing parameters
ci : threshold parameters
Total number of parameters
k =∑m
j=1(1 + pj) + 2(m− 1) + 1
Lubrano (2000): m = 2, p1 = p2 = p known.
Lopes and Salazar (2006): m = 2, p1 = p2 = p unknown.
Ehlers (2005): m, p1, . . . , pm unknown.
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The joint posterior of (m, p1, . . . , pm,γ, c,α, σ2ǫ |y) is proportional to
p(y|m,p,γ, c,α, σ2ǫ ) p(c|m) p(γ|m) p(m) p(σ2
ǫ )m∏
j=1
p(pj|m) p(αj|pj).
Priors (Lubrano, 2000),
p(α1, σ2) ∝ 1/σ2 and αj|σ2
ǫ , γ∗ ∼ N(0, σ2
ǫ exp(γ∗)Ipj), j = 2, . . . ,m
where α′ = (α′1, . . . ,α
′m) and γ∗ = max{γ1, . . . , γm−1}.
σ2ǫ ∼ IG(a, b), a, b > 0.
p(c|m) =
(m− 1)!∏m−1
j=1 p(cj), c1 < c2 < · · · < cm−1,
0, otherwise
p(γ|m) =m−1∏
j=1
p(γj), γj ∼ Cauchy(0, σγ) truncated to γj > 0.
m ∼ U{1, . . . ,mmax} and pj ∼ U{1, . . . , pmax}, j = 1, . . . ,m.
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RJMCMC in LSTARModels
split/combine jumps: randomly choose between creating new regime or combining
2 existing ones.
Creating regimes
• sample j ∈ {1, . . . ,m− 1}
• c′j = cj − ǫ, c′j+1 = cj + ǫ, γ′j = γjτ , γ′j+1 = γj/τ
• sample α(m+1) from its complete conditional distribution.
Combining regimes
• randomly choose a pair of adjacent thresholds cj < cj+1
• c′j = (cj + cj+1)/2, γ′j =
√γjγj+1, ǫ = (cj+1 − cj)/2, τ =
√
γj/γj+1
• update the coefficients α(m−1)
Within-regime jumps
• randomly choose a regime j and propose new valor p′j for pj,
• update α(m) from its complete conditional.
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RJMCMC in LSTAR models
RJMCMC for LSTAR Models, Iterations= 50000 Burn-in= 25000 Thinning= 1
Time difference of 17.35 mins
1074 models visited out of 2366 candidates
splits combines births deaths
proposed 8379 4054 12440 12560
accepted 2049 2049 3208 3112
prob model m lags thres smoo sig2
1 0.2134 24 2 2 11 0 3.301 6.38 0.039
2 0.0493 25 2 2 12 0 3.215 5.67 0.040
3 0.0409 363 3 2 2 12 2.927 3.275 1.77 2.15 0.042
4 0.0374 11 2 1 11 0 3.149 5.32 0.041
5 0.0191 38 2 3 12 0 3.223 4.82 0.039
6 0.0188 155 2 12 12 0 3.128 2.86 0.039
7 0.0184 157 2 13 1 0 3.130 2.80 0.040
8 0.0183 26 2 2 13 0 3.133 4.04 0.039
9 0.0155 8 2 1 8 0 3.160 4.45 0.047
10 0.0144 9 2 1 9 0 3.201 3.36 0.047
11 0.0118 180 3 1 1 11 2.844 3.266 1.67 1.69 0.046
12 0.0113 181 3 1 1 12 2.977 3.296 1.64 1.87 0.042
13 0.0108 52 2 4 13 0 3.142 4.61 0.039
+ models with prob < 0.05*P(24)
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RJMCMC + Genetic Algorithms
E.g. Linear Models
E(Y ) = β0 + βj1xj1 + · · · + βjkxjk, k = 0, . . . , kmax
2kmax possible models with intercept.
If estimation requires little computational effort, we propose an effective and
semi-automatic method for model comparison.
Given a population of models Z = (z1, . . . , zM)where zij = 0, 1.
Propose a new population z′ via genetic operators (esp. mutation and crossover).
Accept the new population with probability,
min
(
1,exp{−BIC(z′)}exp{−BIC(z)}
P (z′, z)
P (z, z′)
)
where
P (z, z′) = Pr(proposing a jump from population z to z′)
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Crossover Move
Randomly choose a pair of individuals zi, zj and propose a new population as
follows,
1. randomly choose k ∈ {1, . . . , p− 1}
2. set z′i = (zi,1, . . . , zi,k−1, zj,k . . . , zj,p)
3. set z′j = (zj,1, . . . , zj,k−1, zi,k . . . , zi,p)
4. Accept this new population with probability min(1, A) where
A =exp(−BIC(z′
i) −BIC(z′j))
exp(−BIC(zi) −BIC(zj))
P (z′, z)
P (z, z′)
This updating scheme is repeated for all [M/2] pairs of individuals selected without
replacement from the population.
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Mutation Move
Either include a new regressor with probability w, or delete an existing one with
probability 1 − w.
Suppose we are now updating zi and an inclusion is proposed. Then,
1. randomly choose j ∈ J = {j : zij = 0} and set z′ij = 1
2. accepted this move w.p. min(1, A) where
A =exp(−BIC(z′
i))
exp(−BIC(zi))
w |J |(1 − w) (|J | + 1)
with J = {j : zij = 1} and |J | denotes the cardinality of J .
Likewise, if a deletion is proposed
1. choose j ∈ J and set z′ij = 0.
2. accept the move w.p. min(1, A−1).
This updating scheme is repeated for all individuals in the population.
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Simulated Data
50 observations with kmax= 19 (524288 candidate models). Output based on 2500
iterations (after 2500 burn-in) and a population of size 20.
Full enumeration GA-RJMCMC
weights model probs model
1 0.5974 10512 0.5928 10512
2 0.0451 11536 0.0497 26896
3 0.0427 26896 0.0464 11536
4 0.0371 43280 0.0413 43280
5 0.0299 272656 0.0330 11024
6 0.0288 11024 0.0295 272656
7 0.0243 141584 0.0233 141584
8 0.0184 76048 0.0172 76048
9 0.0169 10576 0.0139 10640
10 0.0149 10640 0.0132 10576
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Real Data
Crime rates in 47 US states, 15 potential regressors (Raftery, Painter, and Volinsky
2005).
GA-RJMCMC Time difference of 3.2 mins
612 models visited out of 32768 candidates
10 most visited models in descending order
M So Ed Po1 Po2 LF M.F Pop NW U1 U2 GDP Ineq Prob Time
0.209 1 0 1 1 0 0 0 0 1 0 1 0 1 1 1
0.123 1 0 1 1 0 0 0 0 1 0 1 0 1 1 0
0.060 1 0 1 1 0 0 0 0 1 0 1 1 1 1 1
0.055 1 0 1 1 0 0 0 1 1 0 1 0 1 1 0
0.053 1 0 1 0 1 0 0 0 1 0 1 0 1 1 0
0.036 1 0 1 0 1 0 0 0 1 0 1 0 1 1 1
0.026 1 0 1 1 0 0 0 0 1 0 0 0 1 1 1
0.025 1 0 1 1 0 0 0 0 1 1 1 0 1 1 1
0.023 1 0 1 1 0 0 0 0 0 0 1 0 1 1 0
0.022 1 0 1 0 1 0 0 0 1 0 1 1 1 1 1
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regressor prob.inc
1 M 0.9890
2 So 0.0549
3 Ed 1.0000
4 Po1 0.7714
5 Po2 0.2459
6 LF 0.0290
7 M.F 0.0347
8 Pop 0.2049
9 NW 0.9227
10 U1 0.0889
11 U2 0.8891
12 GDP 0.2414
13 Ineq 1.0000
14 Prob 0.9956
15 Time 0.4963
births deaths mutations crossovers
proposed 50101 49899 100000 37299
accepted 6792 6793 13585 14678
Ricardo Ehlers Model Uncertainty via MCMC 34
8th Brazilian Meeting on Bayesian Statistics March 26-29, 2006
Models visited by GA−MCMC
Model1 2 3 4 5 7 12 21 54
Time
Prob
Ineq
GDP
U2
U1
NW
Pop
M.F
LF
Po2
Po1
Ed
So
M
Figure 4:
Ricardo Ehlers Model Uncertainty via MCMC 35
8th Brazilian Meeting on Bayesian Statistics March 26-29, 2006REFERENCES
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Ricardo Ehlers Model Uncertainty via MCMC 37