There are several math-heavy papers that describe the Bayesian Lasso, but I want tested, correct JAGS code that I can use.
Could someone post sample BUGS / JAGS code that implements regularized logistic regression? Any scheme (L1, L2, Elasticnet) would be great, but Lasso is preferred. I also wonder if there are interesting alternative implementation strategies.
Since L1 regularization is equivalent to a Laplace (double exponential) prior on the relevant coefficients, you can do it as follows. Here I have three independent variables x1, x2, and x3, and y is the binary target variable. Selection of the regularization parameter $\lambda$ is done here by putting a hyperprior on it, in this case just uniform over a good-sized range.
model {
# Likelihood
for (i in 1:N) {
y[i] ~ dbern(p[i])
logit(p[i]) <- b0 + b[1]*x1[i] + b[2]*x2[i] + b[3]*x3[i]
}
# Prior on constant term
b0 ~ dnorm(0,0.1)
# L1 regularization == a Laplace (double exponential) prior
for (j in 1:3) {
b[j] ~ ddexp(0, lambda)
}
lambda ~ dunif(0.001,10)
# Alternatively, specify lambda via lambda <- 1 or some such
}
Let's try it out using the dclone package in R!
library(dclone)
x1 <- rnorm(100)
x2 <- rnorm(100)
x3 <- rnorm(100)
prob <- exp(x1+x2+x3) / (1+exp(x1+x2+x3))
y <- rbinom(100, 1, prob)
data.list <- list(
y = y,
x1 = x1, x2 = x2, x3 = x3,
N = length(y)
)
params = c("b0", "b", "lambda")
temp <- jags.fit(data.list,
params=params,
model="modela.jags",
n.chains=3,
n.adapt=1000,
n.update=1000,
thin=10,
n.iter=10000)
And here are the results, compared to an unregularized logistic regression:
> summary(temp)
<< blah, blah, blah >>
1. Empirical mean and standard deviation for each variable,
plus standard error of the mean:
Mean SD Naive SE Time-series SE
b[1] 1.21064 0.3279 0.005987 0.005641
b[2] 0.64730 0.3192 0.005827 0.006014
b[3] 1.25340 0.3217 0.005873 0.006357
b0 0.03313 0.2497 0.004558 0.005580
lambda 1.34334 0.7851 0.014333 0.014999
2. Quantiles for each variable: << deleted to save space >>
> summary(glm(y~x1+x2+x3, family="binomial"))
<< blah, blah, blah >>
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.02784 0.25832 0.108 0.9142
x1 1.34955 0.32845 4.109 3.98e-05 ***
x2 0.78031 0.32191 2.424 0.0154 *
x3 1.39065 0.32863 4.232 2.32e-05 ***
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
<< more stuff deleted to save space >>
And we can see that the three b parameters have indeed been shrunk towards zero.
I don't know much about priors for the hyperparameter of the Laplace distribution / the regularization parameter, I'm sorry to say. I tend to use uniform distributions and look at the posterior to see if it looks reasonably well-behaved, e.g., not piled up near an endpoint and pretty much peaked in the middle w/o horrible skewness problems. So far, that's typically been the case. Treating it as a variance parameter and using the recommendation(s) by Gelman Prior distributions for variance parameters in hierarchical models works for me, too.
