Neural coding

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Neural coding is a neuroscience-related field concerned with characterizing the relationship between the stimulus and the individual or ensemble neuronal responses and the relationship among the electrical activity of the neurons in the ensemble.[1] Based on the theory that sensory and other information is represented in the brain by networks of neurons, it is thought that neurons can encode both digital and analog information[2] (see Neural networks).

Overview

Neurons are remarkable among the cells of the body in their ability to propagate signals rapidly over large distances. They do this by generating characteristic electrical pulses called action potentials: voltage spikes that can travel down nerve fibers. Sensory neurons change their activities by firing sequences of action potentials in various temporal patterns, with the presence of external sensory stimuli, such as light, sound, taste, smell and touch. It is known that information about the stimulus is encoded in this pattern of action potentials and transmitted into and around the brain.

Although action potentials can vary somewhat in duration, amplitude and shape, they are typically treated as identical stereotyped events in neural coding studies. If the brief duration of an action potential (about 1ms) is ignored, an action potential sequence, or spike train, can be characterized simply by a series of all-or-none point events in time.[3] The lengths of interspike intervals (ISIs) between two successive spikes in a spike train often vary, apparently randomly.[4] The study of neural coding involves measuring and characterizing how stimulus attributes, such as light or sound intensity, or motor actions, such as the direction of an arm movement, are represented by neuron action potentials or spikes. In order to describe and analyze neuronal firing, statistical methods and methods of probability theory and stochastic point processes have been widely applied.

Encoding and decoding

The link between stimulus and response can be studied from two opposite points of view. Neural encoding refers to the map from stimulus to response. The main focus is to understand how neurons respond to a wide variety of stimuli, and to construct models that attempt to predict responses to other stimuli. Neural decoding refers to the reverse map, from response to stimulus, and the challenge is to reconstruct a stimulus, or certain aspects of that stimulus, from the spike sequences it evokes.

Coding schemes

A sequence, or 'train', of spikes may contain information based on different coding schemes. In motor neurons, for example, the strength at which an innervated muscle is flexed depends solely on the 'firing rate', the average number of spikes per unit time (a 'rate code'). At the other end, a complex 'temporal code' is based on the precise timing of single spikes. They may be locked to an external stimulus such as in the auditory system or be generated intrinsically by the neural circuitry.[5]

Whether neurons use rate coding or temporal coding is a topic of intense debate within the neuroscience community, even though there is no clear definition of what these terms mean.

Rate coding

The rate coding model of neuronal firing communication states that as the intensity of a stimulus increases, the frequency or rate of action potentials, or "spike firing", increases. Rate coding is sometimes called frequency coding.

Rate coding is a traditional coding scheme, assuming that most, if not all, information about the stimulus is contained in the firing rate of the neuron. Because the sequence of action potentials generated by a given stimulus varies from trial to trial, neuronal responses are typically treated statistically or probabilistically. They may be characterized by firing rates, rather than as specific spike sequences. In most sensory systems, the firing rate increases, generally non-linearly, with increasing stimulus intensity.[6] Any information possibly encoded in the temporal structure of the spike train is ignored. Consequently, rate coding is inefficient but highly robust with respect to the ISI 'noise'.[4]

During rate coding, precisely calculating firing rate is very important. In fact, the term "firing rate" has a few different definitions, which refer to different averaging procedures, such as an average over time or an average over several repetitions of experiment.

In rate coding, learning is based on activity-dependent synaptic weight modifications.

Rate coding was originally shown by ED Adrian and Y Zotterman in 1926.[7] In this simple experiment different weights were hung from a muscle. As the weight of the stimulus increased, the number of spikes recorded from sensory nerves innervating the muscle also increased. From these original experiments, Adrian and Zotterman concluded that action potentials were unitary events, and that the frequency of events, and not individual event magnitude, was the basis for most inter-neuronal communication.

In the following decades, measurement of firing rates became a standard tool for describing the properties of all types of sensory or cortical neurons, partly due to the relative ease of measuring rates experimentally. However, this approach neglects all the information possibly contained in the exact timing of the spikes. During recent years, more and more experimental evidence has suggested that a straightforward firing rate concept based on temporal averaging may be too simplistic to describe brain activity.[4]

Spike-count rate

The Spike-count rate, also referred to as temporal average, is obtained by counting the number of spikes that appear during a trial and dividing by the duration of trial. The length T of the time window is set by experimenter and depends on the type of neuron recorded from and the stimulus. In practice, to get sensible averages, several spikes should occur within the time window. Typical values are T = 100 ms or T = 500 ms, but the duration may also be longer or shorter.

The spike-count rate can be determined from a single trial, but at the expense of losing all temporal resolution about variations in neural response during the course of the trial. Temporal averaging can work well in cases where the stimulus is constant or slowly varying and does not require a fast reaction of the organism — and this is the situation usually encountered in experimental protocols. Real-world input, however, is hardly stationary, but often changing on a fast time scale. For example, even when viewing a static image, humans perform saccades, rapid changes of the direction of gaze. The image projected onto the retinal photoreceptors changes therefore every few hundred milliseconds.

Despite its shortcomings, the concept of a spike-count rate code is widely used not only in experiments, but also in models of neural networks. It has led to the idea that a neuron transforms information about a single input variable (the stimulus strength) into a single continuous output variable (the firing rate).

Time-dependent firing rate

The time-dependent firing rate is defined as the average number of spikes (averaged over trials) appearing during a short interval between times t and t+Δt, divided by the duration of the interval. It works for stationary as well as for time-dependent stimuli. To experimentally measure the time-dependent firing rate, the experimenter records from a neuron while stimulating with some input sequence. The same stimulation sequence is repeated several times and the neuronal response is reported in a Peri-Stimulus-Time Histogram (PSTH). The time t is measured with respect to the start of the stimulation sequence. The Δt must be large enough (typically in the range of one or a few milliseconds) so there are sufficient number of spikes within the interval to obtain a reliable estimate of the average. The number of occurrences of spikes nK(t;t+Δt) summed over all repetitions of the experiment divided by the number K of repetitions is a measure of the typical activity of the neuron between time t and t+Δt. A further division by the interval length Δt yields time-dependent firing rate r(t) of the neuron, which is equivalent to the spike density of PSTH.

For sufficiently small Δt, r(t)Δt is the average number of spikes occurring between times t and t+Δt over multiple trials. If Δt is small, there will never be more than one spike within the interval between t and t+Δt on any given trial. This means that r(t)Δt is also the fraction of trials on which a spike occurred between those times. Equivalently, r(t)Δt is the probability that a spike occurs during this time interval.

As an experimental procedure, the time-dependent firing rate measure is a useful method to evaluate neuronal activity, in particular in the case of time-dependent stimuli. The obvious problem with this approach is that it can not be the coding scheme used by neurons in the brain. Neurons can not wait for the stimuli to repeatedly present in an exactly same manner before generating response.

Nevertheless, the experimental time-dependent firing rate measure can make sense, if there are large populations of independent neurons that receive the same stimulus. Instead of recording from a population of N neurons in a single run, it is experimentally easier to record from a single neuron and average over N repeated runs. Thus, the time-dependent firing rate coding relies on the implicit assumption that there are always populations of neurons.

Temporal coding


When precise spike timing or high-frequency firing-rate fluctuations are found to carry information, the neural code is often identified as a temporal code.[8] A number of studies have found that the temporal resolution of the neural code is on a millisecond time scale, indicating that precise spike timing is a significant element in neural coding.[2][9]

Temporal codes employ those features of the spiking activity that cannot be described by the firing rate. For example, time to first spike after the stimulus onset, characteristics based on the second and higher statistical moments of the ISI probability distribution, spike randomness, or precisely timed groups of spikes (temporal patterns) are candidates for temporal codes.[10] As there is no absolute time reference in the nervous system, the information is carried either in terms of the relative timing of spikes in a population of neurons or with respect to an ongoing brain oscillation.[2][4]

The temporal structure of a spike train or firing rate evoked by a stimulus is determined both by the dynamics of the stimulus and by the nature of the neural encoding process. Stimuli that change rapidly tend to generate precisely timed spikes and rapidly changing firing rates no matter what neural coding strategy is being used. Temporal coding refers to temporal precision in the response that does not arise solely from the dynamics of the stimulus, but that nevertheless relates to properties of the stimulus. The interplay between stimulus and encoding dynamics makes the identification of a temporal code difficult.

The issue of temporal coding is distinct and independent from the issue of independent-spike coding. If each spike is independent of all the other spikes in the train, the temporal character of the neural code is determined by the behavior of time-dependent firing rate r(t). If r(t) varies slowly with time, the code is typically called a rate code, and if it varies rapidly, the code is called temporal.

To account for the fast encoding of visual stimuli, it has been suggested that neurons of the retina encode visual information in the latency time between stimulus onset and first action potential, also called latency to first spike.[11] This type of temporal coding has been shown also in the auditory and somato-sensory system. The main drawback of such a coding scheme is its sensitivity to intrinsic neuronal fluctuations.[12]

In temporal coding, learning can be explained by activity-dependent synaptic delay modifications.[13] The modifications can themselves depend not only on spike rates (rate coding) but also on spike timing patterns (temporal coding), i.e., can be a special case of spike-timing-dependent plasticity.

Phase-of-firing code

Phase-of-firing code is a neural coding scheme that combines the spike count code with a time reference based on oscillations. This type of code takes into account a time label for each spike according to a time reference based on phase of local ongoing oscillations at low[14] or high frequencies.[15] A feature of this code is that neurons adhere to a preferred order of spiking, resulting in firing sequence.[16]

It has been shown that neurons in some cortical sensory areas encode rich naturalistic stimuli in terms of their spike times relative to the phase of ongoing network fluctuations, rather than only in terms of their spike count.[17][14] Oscillations reflect local field potential signals. It is often categorized as a temporal code although the time label used for spikes is coarse grained. That is, four discrete values for phase are enough to represent all the information content in this kind of code with respect to the phase of oscillations in low frequencies. Phase-of-firing code is loosely based on the phase precession phenomena observed in place cells of the hippocampus.

Phase code has been shown in visual cortex to involve also high-frequency oscillations.[16] Within a cycle of gamma oscillation, each neuron has it own preferred relative firing time. As a result, an entire population of neurons generates a firing sequence that has a duration of up to about 15 ms.[16]

Population coding

Population coding is a method to represent stimuli by using the joint activities of a number of neurons. In population coding, each neuron has a distribution of responses over some set of inputs, and the responses of many neurons may be combined to determine some value about the inputs.

From the theoretical point of view, population coding is one of a few mathematically well-formulated problems in neuroscience. It grasps the essential features of neural coding and yet, is simple enough for theoretic analysis.[18] Experimental studies have revealed that this coding paradigm is widely used in the sensor and motor areas of the brain. For example, in the visual area medial temporal (MT), neurons are tuned to the moving direction.[19] In response to an object moving in a particular direction, many neurons in MT fire, with a noise-corrupted and bell-shaped activity pattern across the population. The moving direction of the object is retrieved from the population activity, to be immune from the fluctuation existing in a single neuron’s signal. In one classic example in the primary motor cortex, Apostolos Georgopoulos and colleagues trained monkeys to move a joystick towards a lit target.[20][21] They found that a single neuron would fire for multiple target directions. However it would fire fastest for one direction and more slowly depending on how close the target was to the neuron's 'preferred' direction.

Kenneth Johnson originally derived that if each neuron represents movement in its preferred direction, and the vector sum of all neurons is calculated (each neuron has a firing rate and a preferred direction), the sum points in the direction of motion. In this manner, the population of neurons codes the signal for the motion. This particular population code is referred to as population vector coding. This particular study divided the field of motor physiologists between Evarts' "upper motor neuron" group, which followed the hypothesis that motor cortex neurons contributed to control of single muscles, and the Georgopoulos group studying the representation of movement directions in cortex. [citation needed]

Population coding has a number of advantages, including reduction of uncertainty due to neuronal variability and the ability to represent a number of different stimulus attributes simultaneously. Population coding is also much faster than rate coding and can reflect changes in the stimulus conditions nearly instantaneously.[22] Individual neurons in such a population typically have different but overlapping selectivities, so that many neurons, but not necessarily all, respond to a given stimulus.

Typically an encoding function has a peak value such that activity of the neuron is greatest if the perceptual value is close to the peak value, and becomes reduced accordingly for values less close to the peak value. [citation needed]

It follows that the actual perceived value can be reconstructed from the overall pattern of activity in the set of neurons. The Johnson/Georgopoulos vector coding is an example of simple averaging. A more sophisticated mathematical technique for performing such a reconstruction is the method of maximum likelihood based on a multivariate distribution of the neuronal responses. These models can assume independence, second order correlations ,[23] or even more detailed dependencies such as higher order maximum entropy models[24] or copulas.[25]

Correlation coding

The correlation coding model of neuronal firing claims that correlations between action potentials, or "spikes", within a spike train may carry additional information above and beyond the simple timing of the spikes. It has been theoretically demonstrated that correlation between spike trains can only reduce, and never increase, the total mutual information present in the two spike trains about a stimulus feature. [26] Any degree of correlation reduces the total entropy; thus, by Fisher's Information Theorem, correlations can only reduce information.

However, this does not prevent correlations from carrying information not present in the average firing rate of two pairs of neurons. A good example of this exists in the pentobarbital-anesthetized marmoset auditory cortex, in which a pure tone causes an increase in the number of correlated spikes, but not an increase in the mean firing rate, of pairs of neurons. [27]

Independent-spike coding

The independent-spike coding model of neuronal firing claims that each individual action potential, or "spike", is independent of each other spike within the spike train.[28][29]

Position coding

A typical population code involves neurons with a Gaussian tuning curve whose means vary linearly with the stimulus intensity, meaning that the neuron responds most strongly (in terms of spikes per second) to a stimulus near the mean. The actual intensity could be recovered as the stimulus level corresponding to the mean of the neuron with the greatest response. However, the noise inherent in neural responses means that a maximum likelihood estimation function is more accurate.

This type of code is used to encode continuous variables such as joint position, eye position, color, or sound frequency. Any individual neuron is too noisy to faithfully encode the variable using rate coding, but an entire population ensures greater fidelity and precision. For a population of unimodal tuning curves, i.e. with a single peak, the precision typically scales linearly with the number of neurons. Hence, for half the precision, half as many neurons are required. In contrast, when the tuning curves have multiple peaks, as in grid cells that represent space, the precision of the population can scale exponentially with the number of neurons. This greatly reduces the number of neurons required for the same precision.[30]

  • Plot of typical position coding.

  • Neural responses are noisy and unreliable.

See also

References

  1. ↑ Brown EN, Kass RE, Mitra PP (May 2004). "Multiple neural spike train data analysis: state-of-the-art and future challenges". Nat. Neurosci. 7 (5): 456–61. doi:10.1038/nn1228. PMID 15114358. 
  2. ↑ 2.0 2.1 2.2 Thorpe, S.J. (1990). "Spike arrival times: A highly efficient coding scheme for neural networks". In Eckmiller, R.; Hartmann, G.; Hauske, G. Parallel processing in neural systems and computers (PDF). North-Holland. pp. 91–94. ISBN 978-0-444-88390-2. 
  3. ↑ Gerstner, Wulfram; Kistler, Werner M. (2002). Spiking Neuron Models: Single Neurons, Populations, Plasticity. Cambridge University Press. ISBN 978-0-521-89079-3. 
  4. ↑ 4.0 4.1 4.2 4.3 Stein RB, Gossen ER, Jones KE (May 2005). "Neuronal variability: noise or part of the signal?". Nat. Rev. Neurosci. 6 (5): 389–97. doi:10.1038/nrn1668. PMID 15861181. 
  5. ↑ Gerstner W, Kreiter AK, Markram H, Herz AV; Kreiter; Markram; Herz (November 1997). "Neural codes: firing rates and beyond". Proc. Natl. Acad. Sci. U.S.A. 94 (24): 12740–1. Bibcode:1997PNAS...9412740G. doi:10.1073/pnas.94.24.12740. PMC 34168. PMID 9398065. 
  6. ↑ Kandel, E.; Schwartz, J.; Jessel, T.M. (1991). Principles of Neural Science (3rd ed.). Elsevier. ISBN 0444015620. 
  7. ↑ Adrian ED & Zotterman Y. (1926). "The impulses produced by sensory nerve endings: Part II: The response of a single end organ.". J Physiol (Lond.) 61: 151–171. 
  8. ↑ Dayan, Peter; Abbott, L. F. (2001). Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems. Massachusetts Institute of Technology Press. ISBN 978-0-262-04199-7. 
  9. ↑ Butts DA, Weng C, Jin J, et al. (September 2007). "Temporal precision in the neural code and the timescales of natural vision". Nature 449 (7158): 92–5. Bibcode:2007Natur.449...92B. doi:10.1038/nature06105. PMID 17805296. 
  10. ↑ Kostal L, Lansky P, Rospars JP (November 2007). "Neuronal coding and spiking randomness". Eur. J. Neurosci. 26 (10): 2693–701. doi:10.1111/j.1460-9568.2007.05880.x. PMID 18001270. 
  11. ↑ Gollisch, T.; Meister, M. (22 February 2008). "Rapid Neural Coding in the Retina with Relative Spike Latencies". Science 319 (5866): 1108–1111. doi:10.1126/science.1149639. 
  12. ↑ Wainrib, Gilles; Michèle, Thieullen; Khashayar, Pakdaman (7 April 2010). "Intrinsic variability of latency to first-spike". Biological Cybernetics 103 (1): 43–56. doi:10.1007/s00422-010-0384-8. 
  13. ↑ Geoffrois, E.; Edeline, J.M.; Vibert, J.F. (1994). "Learning by Delay Modifications". In Eeckman, Frank H. Computation in Neurons and Neural Systems. Springer. pp. 133–8. ISBN 978-0-7923-9465-5. 
  14. ↑ 14.0 14.1 Montemurro MA, Rasch MJ, Murayama Y, Logothetis NK, Panzeri S (March 2008). "Phase-of-firing coding of natural visual stimuli in primary visual cortex". Curr. Biol. 18 (5): 375–80. doi:10.1016/j.cub.2008.02.023. PMID 18328702. 
  15. ↑ Fries P, Nikolić D, Singer W (July 2007). "The gamma cycle". Trends Neurosci. 30 (7): 309–16. doi:10.1016/j.tins.2007.05.005. PMID 17555828. 
  16. ↑ 16.0 16.1 16.2 Havenith MN, Yu S, Biederlack J, Chen NH, Singer W, Nikolić D (June 2011). "Synchrony makes neurons fire in sequence, and stimulus properties determine who is ahead". J. Neurosci. 31 (23): 8570–84. doi:10.1523/JNEUROSCI.2817-10.2011. PMID 21653861. 
  17. ↑ Spike arrival times: A highly efficient coding scheme for neural networks, SJ Thorpe - Parallel processing in neural systems, 1990
  18. ↑ Wu S, Amari S, Nakahara H (May 2002). "Population coding and decoding in a neural field: a computational study". Neural Comput 14 (5): 999–1026. doi:10.1162/089976602753633367. PMID 11972905. 
  19. ↑ Maunsell JH, Van Essen DC (May 1983). "Functional properties of neurons in middle temporal visual area of the macaque monkey. I. Selectivity for stimulus direction, speed, and orientation". J. Neurophysiol. 49 (5): 1127–47. PMID 6864242. 
  20. ↑ Intro to Sensory Motor Systems Ch. 38 page 766
  21. ↑ Science. 1986 Sep 26;233(4771):1416-9
  22. ↑ Hubel DH, Wiesel TN (October 1959). "Receptive fields of single neurones in the cat's striate cortex". J. Physiol. (Lond.) 148 (3): 574–91. PMC 1363130. PMID 14403679. 
  23. ↑ Schneidman, E, Berry, MJ, Segev, R, Bialek, W (2006), Weak Pairwise Correlations Imply Strongly Correlated Network States in a Neural Population, Nature 440, 1007-1012 
  24. ↑ Amari, SL (2001), Information Geometry on Hierarchy of Probability Distributions, IEEE Transactions on Information Theory 47, 1701-1711, CiteSeerX: 10.1.1.46.5226 
  25. ↑ Onken, A, Grünewälder, S, Munk, MHJ, Obermayer, K (2009), Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation, PLoS Comput Biol 5(11): e1000577 
  26. ↑ KO Johnson, J Neurophysiol. 1980 Jun;43(6):1793-815.
  27. ↑ Nature. 1996 Jun 13;381(6583):610-3
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  29. ↑ Rieke F, Warland D, de Ruyter van Steveninck R, Bialek W. Spikes: Exploring the Neural Code. Cambridge, Massachusetts: The MIT Press; 1999. ISBN 0-262-68108-0
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