For spiking neurons, the entropy rate places an upper bound on the rate at which the spike train can convey stimulus information, and a large literature has focused on the problem of estimating entropy rate from spike train data. Our estimator leverages the fact that the entropy rate of an ergodic Markov Chain with known transition probabilities can be calculated analytically, and many stochastic processes that are non-Markovian can still be well approximated by Markov processes of sufficient depth. Choosing an appropriate depth of Markov model presents challenges due to possibly long time dependencies and short data sequences: a deeper model can better account for long time-dependencies, but is more difficult to infer from limited data. Our approach mitigates this difficulty by using a hierarchical prior to share statistical power across Markov chains of different depths. We present both a fully Bayesian and empirical Bayes entropy rate estimator based on this model, and demonstrate their performance on simulated and real neural spike train data.

For spiking neurons, the entropy rate places an upper bound on the rate at which the spike train can convey stimulus information, and a large literature has focused on the problem of estimating entropy rate from spike train data.

For spiking neurons, the entropy rate places an upper bound on the rate at which the spike train can convey stimulus information, and a large literature has focused on the problem of estimating entropy rate from spike train data. Our estimator leverages the fact that the entropy rate of an ergodic Markov Chain with known transition probabilities can be calculated analytically, and many stochastic processes that are non-Markovian can still be well approximated by Markov processes of sufficient depth. Choosing an appropriate depth of Markov model presents challenges due to possibly long time dependencies and short data sequences: a deeper model can better account for long time-dependencies, but is more difficult to infer from limited data. Our approach mitigates this difficulty by using a hierarchical prior to share statistical power across Markov chains of different depths. We present both a fully Bayesian and empirical Bayes entropy rate estimator based on this model, and demonstrate their performance on simulated and real neural spike train data.

For spiking neurons, the entropy rate places an upper bound on the rate at which the spike train can convey stimulus information, and a large literature has focused on the problem of estimating entropy rate from spike train data. Our estimator leverages the fact that the entropy rate of an ergodic Markov Chain with known transition probabilities can be calculated analytically, and many stochastic processes that are non-Markovian can still be well approximated by Markov processes of sufficient depth. Choosing an appropriate depth of Markov model presents challenges due to possibly long time dependencies and short data sequences: a deeper model can better account for long time-dependencies, but is more difficult to infer from limited data. Our approach mitigates this difficulty by using a hierarchical prior to share statistical power across Markov chains of different depths. We present both a fully Bayesian and empirical Bayes entropy rate estimator based on this model, and demonstrate their performance on simulated and real neural spike train data.

Estimating the entropy based on data is one of the prototypical problems in distribution property testing and estimation. For estimating the Shannon entropy of a distribution on $S$ elements with independent samples, [Paninski2004] showed that the sample complexity is sublinear in $S$, and [Valiant--Valiant2011] showed that consistent estimation of Shannon entropy is possible if and only if the sample size $n$ far exceeds $\frac{S}{\log S}$. In this paper we consider the problem of estimating the entropy rate of a stationary reversible Markov chain with $S$ states from a sample path of $n$ observations. We show that: (1) As long as the Markov chain mixes not too slowly, i.e., the relaxation time is at most $O(\frac{S}{\ln^3 S})$, consistent estimation is achievable when $n \gg \frac{S^2}{\log S}$. (2) As long as the Markov chain has some slight dependency, i.e., the relaxation time is at least $1+\Omega(\frac{\ln^2 S}{\sqrt{S}})$, consistent estimation is impossible when $n \lesssim \frac{S^2}{\log S}$. Under both assumptions, the optimal estimation accuracy is shown to be $\Theta(\frac{S^2}{n \log S})$. In comparison, the empirical entropy rate requires at least $\Omega(S^2)$ samples to be consistent, even when the Markov chain is memoryless. In addition to synthetic experiments, we also apply the estimators that achieve the optimal sample complexity to estimate the entropy rate of the English language in the Penn Treebank and the Google One Billion Words corpora, which provides a natural benchmark for language modeling and relates it directly to the widely used perplexity measure.

Entropy rate quantifies the amount of disorder in a stochastic process. For spiking neurons, the entropy rate places an upper bound on the rate at which the spike train can convey stimulus information, and a large literature has focused on the problem of estimating entropy rate from spike train data. Here we present Bayes Least Squares and Empirical Bayesian entropy rate estimators for binary spike trains using Hierarchical Dirichlet Process (HDP) priors. Our estimator leverages the fact that the entropy rate of an ergodic Markov Chain with known transition probabilities can be calculated analytically, and many stochastic processes that are non-Markovian can still be well approximated by Markov processes of sufficient depth. Choosing an appropriate depth of Markov model presents challenges due to possibly long time dependencies and short data sequences: a deeper model can better account for long time-dependencies, but is more difficult to infer from limited data. Our approach mitigates this difficulty by using a hierarchical prior to share statistical power across Markov chains of different depths. We present both a fully Bayesian and empirical Bayes entropy rate estimator based on this model, and demonstrate their performance on simulated and real neural spike train data.