Computing loss of efficiency in optimal Bayesian decoders given noisy or incomplete spike trains

Abstract

We investigate Bayesian methods for optimal decoding of noisy or incompletely-observed spike trains. Information about neural identity or temporal resolution may be lost during spike detection and sorting, or spike times measured near the soma may be corrupted with noise due to stochastic membrane channel effects in the axon. We focus on neural encoding models in which the (discrete) neural state evolves according to stimulus-dependent Markovian dynamics. Such models are sufficiently flexible that we may incorporate realistic stimulus encoding and spiking dynamics, but nonetheless permit exact computation via efficient hidden Markov model forward-backward methods. We analyze two types of signal degradation. First, we quantify the information lost due to jitter or downsampling in the spike-times. Second, we quantify the information lost when knowledge of the identities of different spiking neurons is corrupted. In each case the methods introduced here make it possible to quantify the dependence of the information loss on biophysical parameters such as firing rate, spike jitter amplitude, spike observation noise, etc. In particular, decoders that model the probability distribution of spike-neuron assignments significantly outperform decoders that use only the most likely spike assignments, and are ignorant of the posterior spike assignment uncertainty.

• spike train decoding
• population coding
• single neuron computation
• network models

Notes

Notes

[1] Note that the refractory period here is relative. Markov models that impose an absolute refractory period are easy to imagine. Indeed, similar models have been considered that include an absolute refractory period via some number of additional refractory states that the neuron passes through deterministically (e.g., (Herbst et al. 2008; Haslinger et al. 2010)). Our methods apply to such models as well.