Assume $(E,\mathcal E,\lambda)$ is a $\sigma$-finite measure space and $\nu$ is a probability measure on $(E,\mathcal E)$ with $\nu\ll\lambda$. Furthermore, assume that $\mu=\sum_{i=0}^{n-1}\delta_{X_i}$, where $(X_n)_{n\in\mathbb N_0}$ is a Markov chain on $(E,\mathcal E)$ with invariant distribution $\nu$. Can we give a nice expression for the KL divergence $$H(\mu,\nu):=\begin{cases}\displaystyle\int\ln\frac{{\rm d}\mu}{{\rm d}\nu}\;{\rm d}\mu=\int\frac{{\rm d}\mu}{{\rm d}\nu}\ln\frac{{\rm d}\mu}{{\rm d}\nu}\;{\rm d}\nu&\text{, if }\mu\ll\nu;\\\infty&\text{, otherwise}\end{cases}$$ between $\mu$ and $\nu$? The idea is that I want to compute the KL divergence between samples $x_0,\ldots,x_{n-1}$ of a MCMC method, which correspond to realizations of $X_0,\ldots,X_{n-1}$, and the target distribution $\nu$. If necessarily, you can assume that $\lambda$ is the $d$-dimensional Lebesgue measure. In light of the ergodic theorem, we should be able to get an estimator for $H(\mu,\nu)$. But I struggle to see why we should have $\mu\ll\nu$ at all ...
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1$\begingroup$ You present an impossibility, because $\mu$ is singular. Your $H$ is always $\infty$ by definition. $\endgroup$– whuber ♦Commented Nov 7 at 17:15
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1$\begingroup$ You need to use an a.c. approximation to the distribution of the sample,eg a kernel based non-parametric estimate, $\hat p$, and then consider$$\frac1n\sum_0^{n-1} \ln \frac{\hat p(x_i)}{p(x_i)}$$where $p$ is the density of the target (normalising constant included). See this survey by V. Roy. $\endgroup$– Xi'anCommented Nov 8 at 4:58
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$\begingroup$ I see. Any reason why not $\frac1n\sum_0^{n-1}\frac{\hat p(x_i)}{p(x_i)} \ln \frac{\hat p(x_i)}{p(x_i)}$ instead? $\endgroup$– 0xbadf00dCommented Nov 8 at 10:07
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1$\begingroup$ @0xbadf00d: I reasoned that the sample is distributed from $\hat p$ rather than from $p$, since we are unsure of convergence. $\endgroup$– Xi'anCommented Nov 8 at 12:09
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As you note, there's no reason $\mu\ll \nu$ (or $\nu\ll \mu$) so the KL-divergence will typically not be finite/not exist.
You might need to look at other metrics such as total variation or Wasserstein distance