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Fig.
1. Neuron and myelinated axon, with signal flow from inputs at
dendrites to outputs at axon terminals. The signal is a short electrical
pulse called action potential or 'spike'.
Fig
2. Time course of neuronal action potential ("spike"). Note that the
amplitude and the exact shape of the action potential can vary according
to the exact experimental technique used for acquiring the signal.
Biological neuron models, also known as a spiking neuron models,
are mathematical descriptions of the properties of certain cells in
the nervous system that generate sharp electrical potentials across their cell membrane, roughly one millisecond in duration, called action potentials or spikes (Fig. 2). Since spikes are transmitted along the axon and synapses from the sending neuron to many other neurons, spiking neurons are considered to be a major information processing unit of the nervous system.
Spiking neuron models can be divided into different categories: the
most detailed mathematical models are biophysical neuron models (also
called Hodgkin-Huxley models) that describe the membrane voltage as a
function of the input current and the activation of ion channels.
Mathematically simpler are integrate-and-fire models that describe the
membrane voltage as a function of the input current and predict the
spike times without a description of the biophysical processes that
shape the time course of an action potential. Even more abstract models
only predict output spikes (but not membrane voltage) as a function of
the stimulation where the stimulation can occur through sensory input or
pharmacologically. This article provides a short overview of different
spiking neuron models and links, whenever possible to experimental
phenomena. It includes deterministic and probabilistic models.
Introduction: Biological background, classification and aims of neuron models
Non-spiking cells, spiking cells, and their measurement
Not all the cells of the nervous system produce the type of spike
that define the scope of the spiking neuron models. For example, cochlear hair cells, retinal receptor cells, and retinal bipolar cells do not spike. Furthermore, many cells in the nervous system are not classified as neurons but instead are classified as glia.
Neuronal activity can be measured with different experimental
techniques, such as the "Whole cell" measurement technique, which
captures the spiking activity of a single neuron and produces full
amplitude action potentials.
With extracellular measurement techniques an electrode (or array
of several electrodes) is located in the extracellular space. Spikes,
often from several spiking sources, depending on the size of the
electrode and its proximity to the sources, can be identified with
signal processing techniques. Extracellular measurement has several
advantages: 1) Is easier to obtain experimentally; 2) Is robust and
lasts for a longer time; 3) Can reflect the dominant effect, especially
when conducted in an anatomical region with many similar cells.
Overview of neuron models
Neuron models can be divided into two categories according to the
physical units of the interface of the model. Each category could be
further divided according to the abstraction/detail level:
- Electrical input–output membrane voltage models
– These models produce a prediction for membrane output voltage as a
function of electrical stimulation given as current or voltage input.
The various models in this category differ in the exact functional
relationship between the input current and the output voltage and in the
level of details. Some models in this category predict only the moment
of occurrence of output spike (also known as "action potential"); other
models are more detailed and account for sub-cellular processes. The
models in this category can be either deterministic or probabilistic.
- Natural stimulus or pharmacological input neuron models
– The models in this category connect between the input stimulus which
can be either pharmacological or natural, to the probability of a spike
event. The input stage of these models is not electrical, but rather has
either pharmacological (chemical) concentration units, or physical
units that characterize an external stimulus such as light, sound or
other forms of physical pressure. Furthermore, the output stage
represents the probability of a spike event and not an electrical
voltage.
Although it is not unusual in science and engineering to have several
descriptive models for different abstraction/detail levels, the number
of different, sometimes contradicting, biological neuron models is
exceptionally high. This situation is partly the result of the many
different experimental settings, and the difficulty to separate the
intrinsic properties of a single neuron from measurements effects and
interactions of many cells (network
effects). To accelerate the convergence to a unified theory, we list
several models in each category, and where applicable, also references
to supporting experiments.
Aims of neuron models
Ultimately, biological neuron models aim to explain the
mechanisms underlying the operation of the nervous system. However
several approaches can be distinguished from more realistic models
(e.g., mechanistic models) to more pragmatic models (e.g.,
phenomenological models).
Modeling helps to analyze experimental data and address questions such
as: How are the spikes of a neuron related to sensory stimulation or
motor activity such as arm movements? What is the neural code used by
the nervous system? Models are also important in the context of
restoring lost brain functionality through neuroprosthetic devices.
Electrical input–output membrane voltage models
The
models in this category describe the relationship between neuronal
membrane currents at the input stage, and membrane voltage at the output
stage. This category includes (generalized) integrate-and-fire models
and biophysical models inspired by the work of Hodgkin–Huxley in the
early 1950s using an experimental setup that punctured the cell membrane
and allowed to force a specific membrane voltage/current.
Most modern electrical neural interfaces
apply extra-cellular electrical stimulation to avoid membrane
puncturing which can lead to cell death and tissue damage. Hence, it is
not clear to what extent the electrical neuron models hold for
extra-cellular stimulation.
Hodgkin–Huxley
The Hodgkin–Huxley model (H&H model)
is a model of the relationship between the flow of ionic currents across
the neuronal cell membrane and the membrane voltage of the cell. It consists of a set of nonlinear differential equations describing the behaviour of ion channels that permeate the cell membrane of the squid giant axon. Hodgkin and Huxley were awarded the 1963 Nobel Prize in Physiology or Medicine for this work.
We note the voltage-current relationship, with multiple voltage-dependent currents charging the cell membrane of capacity Cm
The above equation is the time derivative of the law of capacitance, Q = CV where the change of the total charge must be explained as the sum over the currents. Each current is given by
where g(t,V) is the conductance, or inverse resistance, which can be expanded in terms of its maximal conductance ḡ and the activation and inactivation fractions m and h, respectively, that determine how many ions can flow through available membrane channels. This expansion is given by
and our fractions follow the first-order kinetics
with similar dynamics for h, where we can use either τ and m∞ or α and β to define our gate fractions.
The Hodgkin–Huxley model may be extended to include additional ionic currents. Typically, these include inward Ca2+ and Na+ input currents, as well as several varieties of K+ outward currents, including a "leak" current.
The end result can be at the small end 20 parameters which one
must estimate or measure for an accurate model. In a model of a complex
systems of neurons, numerical integration of the equations are computationally expensive. Careful simplifications of the Hodgkin–Huxley model are therefore needed.
The model can be reduced to two dimensions thanks to the dynamic
relations which can be established between the gating variables.
it is also possible to extend it to take into account the evolution of
the concentrations (considered fixed in the original model).
Perfect Integrate-and-fire
One
of the earliest models of a neuron is the perfect integrate-and-fire
model (also called non-leaky integrate-and-fire), first investigated in
1907 by Louis Lapicque. A neuron is represented by its membrane voltage V which evolves in time during stimulation with an input current I(t) according
which is just the time derivative of the law of capacitance, Q = CV. When an input current is applied, the membrane voltage increases with time until it reaches a constant threshold Vth, at which point a delta function spike occurs and the voltage is reset to its resting potential, after which the model continues to run. The firing frequency of the model thus increases linearly without bound as input current increases.
The model can be made more accurate by introducing a refractory period tref that limits the firing frequency of a neuron by preventing it from firing during that period. For constant input I(t)=I the threshold voltage is reached after an integration time tint=CVthr/I
after start from zero. After a reset, the refractory period introduces a
dead time so that the total time until the next firing is tref+tint
. The firing frequency is the inverse of the total inter-spike interval
(including dead time). The firing frequency as a function of a constant
input current is therefore
A shortcoming of this model is that it describes neither adaptation
nor leakage. If the model receives a below-threshold short current
pulse at some time, it will retain that voltage boost forever - until
another input later makes it fire. This characteristic is clearly not in
line with observed neuronal behavior. The following extensions make the
integrate-and-fire model more plausible from a biological point of
view.
Leaky integrate-and-fire
The leaky integrate-and-fire model which can be traced back to Louis Lapicque,
contains, compared to the non-leaky integrate-and-fire model a "leak"
term in the membrane potential equation, reflecting the diffusion of
ions through the membrane. The model equation looks like
A
neuron is represented by an RC circuit with a threshold. Each input
pulse (e.g. caused by a spike from a different neuron) causes a short
current pulse. Voltage decays exponentially. If the threshold is reached
an output spike is generated and the voltage is reset.
where Vm is the voltage across the cell membrane and Rm is the membrane resistance. (The non-leaky integrate-and-fire model is retrieved in the limit Rm
to infinity, i.e. if the membrane is a perfect insulator). The model
equation is valid for arbitrary time-dependent input until a threshold Vth is reached; thereafter the membrane potential is reset.
For constant input, the minimum input to reach the threshold is Ith = Vth / Rm. Assuming a reset to zero, the firing frequency thus looks like
which converges for large input currents to the previous leak-free model with refractory period. The model can also be used for inhibitory neurons.
The biggest disadvantage of the Leaky integrate-and-fire neuron
is that it does not contain neuronal adaptation so that it cannot
describe an experimentally measured spike train in response to constant
input current.
This disadvantage is removed in generalized integrate-and-fire models
that also contain one or several adaptation-variables and are able to
predict spike times of cortical neurons under current injection to a
high degree of accuracy.
Adaptive integrate-and-fire
Neuronal adaptation refers to the fact that even in the presence of a
constant current injection into the soma, the intervals between output
spikes increase. An adaptive integrate-and-fire neuron model combines
the leaky integration of voltage V with one or several adaptation variables wk
where is the membrane time constant , wk is the adaptation current number, with index k, is the time constant of adaptation current wk, Em is the resting potential and tf
is the firing time of the neuron and the Greek delta denotes the Dirac
delta function. Whenever the voltage reaches the firing threshold the
voltage is reset to a value Vr
below the firing threshold. The reset value is one of the important
parameters of the model. The simplest model of adaptation has only a
single adaptation variable w and the sum over k is removed.
Spike
times and subthreshold voltage of cortical neuron models can be
predicted by generalized integrate-and-fire models such as the adaptive
integrate-and-fire model, the adaptive exponential integrate-and-fire
model, or the spike response model. In the example here, adaptation is
implemented by a dynamic threshold which increases after each spike.
Integrate-and-fire neurons with one or several adaptation variables
can account for a variety of neuronal firing patterns in response to
constant stimulation, including adaptation, bursting and initial
bursting.
Moreover, adaptive integrate-and-fire neurons with several adaptation
variables are able to predict spike times of cortical neurons under
time-dependent current injection into the soma.
Fractional-order leaky integrate-and-fire
Recent
advances in computational and theoretical fractional calculus lead to a
new form of model, called Fractional-order leaky integrate-and-fire. An advantage of this model is that it can capture adaptation effects with a single variable. The model has the following form
Once the voltage hits the threshold it is reset. Fractional
integration has been used to account for neuronal adaptation in
experimental data.
'Exponential integrate-and-fire' and 'adaptive exponential integrate-and-fire'
In the exponential integrate-and-fire model, spike generation is exponential, following the equation:
where is the membrane potential, is the intrinsic membrane potential threshold, is the membrane time constant, is the resting potential, and is the sharpness of action potential initiation, usually around 1 mV for cortical pyramidal neurons. Once the membrane potential crosses , it diverges to infinity in finite time. In numerical simulation the integration is stopped if the membrane potential hits an arbitrary threshold (much larger than ) at which the membrane potential is reset to a value Vr . The voltage reset value Vr
is one of the important parameters of the model. Importantly, the
right-hand side of the above equation contains a nonlinearity that can
be directly extracted from experimental data. In this sense the exponential nonlinearity is strongly supported by experimental evidence.
In the adaptive exponential integrate-and-fire neuron the above exponential nonlinearity of the voltage equation is combined with an adaptation variabe w
Firing
pattern of initial bursting in response to a step current input
generated with the Adaptive exponential integrate-and-fire model. Other
Firing patterns can also be generated.
where w denotes the adaptation current with time scale . Important model parameters are the voltage reset value Vr, the intrinsic threshold , the time constants and as well as the coupling parameters a and b. The adaptive exponential integrate-and-fire model inherits the experimentally derived voltage nonlinearity of the exponential integrate-and-fire model. But going beyond this
model, it can also account for a variety of neuronal firing patterns in
response to constant stimulation, including adaptation, bursting and
initial bursting.
However, since the adaptation is in the form of a current, aberrant
hyperpolarization may appear. This problem was solved by expressing it
as a conductance.
Stochastic models of membrane voltage and spike timing
The
models in this category are generalized integrate-and-fire models that
include a certain level of stochasticity. Cortical neurons in
experiments are found to respond reliably to time-dependent input,
albeit with a small degree of variations between one trial and the next
if the same stimulus is repeated. Stochasticity in neurons has two important sources. First, even in a
very controlled experiment where input current is injected directly into
the soma, ion channels open and close stochastically
and this channel noise leads to a small amount of variability in the
exact value of the membrane potential and the exact timing of output
spikes. Second, for a neuron embedded in a cortical network, it is hard
to control the exact input because most inputs come from unobserved
neurons somewhere else in the brain.
Stochasticity has been introduces into spiking neuron models in two fundamentally different forms: either (i) a noisy input current is added to the differential equation of the neuron model; or (ii) the process of spike generation is noisy.
In both cases, the mathematical theory can be developed for continuous
time, which is then, if desired for the use in computer simulations,
transformed into a discrete-time model.
The relation of noise in neuron models to variability of spike trains and neural codes is discussed in Neural Coding and in Chapter 7 of the textbook Neuronal Dynamics.
Noisy input model (diffusive noise)
A
neuron embedded in a network receives spike input from other neurons.
Since the spike arrival times are not controlled by an experimentalist
they can be considered as stochastic. Thus a (potentially nonlinear)
integrate-and-fire model with nonlinearity f(v) receives two inputs: an
input controlled by the experimentalists and a noisy input current that describes the uncontrolled background input.
Stein's model is the special case of a leaky integrate-and-fire neuron and a stationary white noise current with mean zero and unit variance. In the subthreshold regime, these assumptions yield the equation of the Ornstein–Uhlenbeck process
However, in contrast to the standard Ornstein–Uhlenbeck process, the membrane voltage is reset whenever V hits the firing threshold Vth . Calculating the interval distribution of the Ornstein–Uhlenbeck model for constant input with threshold leads to a first-passage time problem.
Stein's neuron model and variants thereof have been used to fit
interspike interval distributions of spike trains from real neurons
under constant input current.
In the mathematical literature, the above equation of the Ornstein–Uhlenbeck process is written in the form
where is the amplitude of the noise input and dW are increments of a Wiener process. For discrete-time implementations with time step dt the voltage updates are
where y is drawn from a Gaussian distribution with zero mean unit
variance. The voltage is reset when it hits the firing threshold Vth .
The noisy input model can also be used in generalized
integrate-and-fire models. For example, the exponential
integrate-and-fire model with noisy input reads
For constant deterministic input it is possible to calculate the mean firing rate as a function of .
This is important because the frequency-current relation (f-I-curve) is
often used by experimentalists to characterize a neuron. It is also the
transfer function in
The leaky integrate-and-fire with noisy input has been widely used in the analysis of networks of spiking neurons.
Noisy input is also called 'diffusive noise' because it leads to a
diffusion of the subthreshold membrane potential around the noise-free
trajectory (Johannesma, The theory of spiking neurons with noisy input is reviewed in Chapter 8.2 of the textbook Neuronal Dynamics.
Noisy output model (escape noise)
In deterministic integrate-and-fire models, a spike is generated if the membrane potential V(t) hits the threshold .
In noisy output models the strict threshold is replaced by a noisy one
as follows. At each moment in time t, a spike is generated
stochastically with instantaneous stochastic intensity or 'escape rate'
that depends on the momentary difference between the membrane voltage V(t) and the threshold . A common choice for the 'escape rate' (that is consistent with biological data) is
Stochastic
spike generation (noisy output) depends on the momentary difference
between the membrane potential V(t) and the threshold. The membrane
potential V of the spike response model (SRM) has two contributions.
First, input current I is filtered by a first filter k. Second the
sequence of output spikes S(t) is filtered by a second filter η and fed
back. The resulting membrane V(t) potential is used to generate output
spikes by a stochastic process ρ(t) with an intensity that depends on
the distance between membrane potential and threshold. The spike
response model (SRM) is closely related to the Generalized Linear Model
(GLM).
where is a time constant that describes how quickly a spike is fired once the membrane potential reaches the threshold and is a sharpness parameter. For
the threshold becomes sharp and spike firing occurs deterministically
at the moment when the membrane potential hits the threshold from below.
The sharpness value found in experiments is
which means that neuronal firing becomes non-negligible as soon the
membrane potential is a few mV below the formal firing threshold.
The escape rate process via a soft threshold is reviewed in Chapter 9 of the textbook Neuronal Dynamics.
For models in discrete time, a spike is generated with probability
that depends on the momentary difference between the membrane voltage V at time and the threshold . The function F is often taken as a standard sigmoidal with steepness parameter ,
similar to the update dynamics in artificial neural networks. But the
functional form of F can also be derived from the stochastic intensity in continuous time introduced above as where is the distance to threshold.
Integrate-and-fire models with output noise can be used to
predict the PSTH of real neurons under arbitrary time-dependent input.
For non-adaptive integrate-and-fire neurons, the interval distribution
under constant stimulation can be calculated from stationary renewal theory.
Spike response model (SRM)
main article: Spike response model
The spike response model (SRM) is a general linear model for the
subthreshold membrane voltage combined with a nonlinear output noise
process for spike generation. The membrane voltage V(t) at time t is
where tf is the firing time of spike number f of the neuron, Vrest is the resting voltage in the absence of input, I(t-s) is the input current at time t-s and
is a linear filter (also called kernel) that describes the contribution
of an input current pulse at time t-s to the voltage at time t. The
contributions to the voltage caused by a spike at time are described by the refractory kernel . In particular,
describes the reset after the spike and the time course of the
spike-afterpotential following a spike. It therefore expresses the
consequences of refractoriness and adaptation.
The voltage V(t) can be interpreted as the result of an integration of
the differential equation of a leaky integrate-and-fire model coupled to
an arbitrary number of spike-triggered adaptation variables.
Spike firing is stochastic and happens with a time-dependent stochastic intensity (instantaneous rate)
with parameters and and a dynamic threshold given by
Here is the firing threshold of an inactive neuron and describes the increase of the threshold after a spike at time . In case of a fixed threshold, one sets =0. For the threshold process is deterministic.
The time course of the filters that characterize the spike response model can be directly extracted from experimental data.
With optimized parameters the SRM describes the time course of the
subthreshold membrane voltage for time-dependent input with a precision
of 2mV and can predict the timing of most output spikes with a
precision of 4ms. The SRM is closely related to linear-nonlinear-Poisson cascade models (also called Generalized Linear Model).
The estimation of parameters of probabilistic neuron models such as the
SRM using methods developed for Generalized Linear Models is discussed in Chapter 10 of the textbook Neuronal Dynamics.
Spike
arrival causes postsynaptic potentials (red lines) which are summed. If
the total voltage V reaches a threshold (dashed blue line) a spike is
initiated (green) which also includes a spike-afterpotential. The
threshold increases after each spike. Postsynaptic potentials are the
response to incoming spikes while the spike-afterpotential is the
response to outgoing spikes.
The name spike response model arises because in a network, the
input current for neuron i is generated by the spikes of other neurons
so that in the case of a network the voltage equation becomes
where are the firing times of neuron j (i.e., its spike train) , and describes the time course of the spike and the spike after-potential for neuron i, and describe the amplitude and time course of an excitatory or inhibitory postsynaptic potential (PSP) caused by the spike of the presynaptic neuron j. The time course of the PSP results from the convolution of the postsynaptic current caused by the arrival of a presynaptic spike from neuron j with the membrane filter .
SRM0
The SRM0 is a stochastic neuron model related to time-dependent nonlinear renewal theory
and a simplification of the Spike Renose Model (SRM). The main
difference to the voltage equation of the SRM introduced above is that
in the term containing the refractory kernel there is no summation sign over past spikes: only the most recent spike (denoted as the time )
matters. Another difference is that the threshold is constant. The
model SRM0 can be formulated in discrete or continuous time. For
example, in continuous time, the single-neuron equation is
and the network equations of the SRM0 are
where is the last firing time neuron i. Note that the time course of the postsynaptic potential
is also allowed to depend on the time since the last spike of neuron i
so as to describe a change in membrane conductance during
refractoriness. The instantaneous firing rate (stochastic intensity) is
where
is a fixed firing threshold. Thus spike firing of neuron i depends
only on its input and the time since neuron i has fired its last spike.
With the SRM0, the interspike-interval distribution for constant input can be mathematically linked to the shape of the refractory kernel .
Moreover the stationary frequency-current relation can be calculated
from the escape rate in combination with the refractory kernel . With an appropriate choice of the kernels, the SRM0 approximates the dynamics of the Hodgkin-Huxley model to a high degree of accuracy. Moreover, the PSTH response to arbitrary time-dependent input can be predicted.
Galves–Löcherbach model
3D
visualization of the Galves–Löcherbach model for biological neural
nets. This visualization is set for 4,000 neurons (4 layers with one
population of inhibitory neurons and one population of excitatory
neurons each) at 180 intervals of time.
The Galves–Löcherbach model is a stochastic neuron model closely related to the spike response model SRM0 and to the leaky integrate-and-fire model. It is inherently stochastic and, just like the SRM0 linked to time-dependent nonlinear renewal theory. Given the model specifications, the probability that a given neuron spikes in a time period may be described by
where is a synaptic weight, describing the influence of neuron on neuron , expresses the leak, and provides the spiking history of neuron before , according to
Importantly, the spike probability of neuron i depends only on its spike input (filtered with a kernel and weighted with a factor ) and the timing of its most recent output spike (summarized by ).
Didactic toy models of membrane voltage
The
models in this category are highly simplified toy models that
qualitatively describe the membrane voltage as a function of input. They
are mainly used for didactic reasons in teaching but are not considered
valid neuron models for large-scale simulations or data fitting.
FitzHugh–Nagumo
Sweeping simplifications to Hodgkin–Huxley were introduced by
FitzHugh and Nagumo in 1961 and 1962. Seeking to describe "regenerative
self-excitation" by a nonlinear positive-feedback membrane voltage and
recovery by a linear negative-feedback gate voltage, they developed the
model described by
where we again have a membrane-like voltage and input current with a slower general gate voltage w and experimentally-determined parameters a = -0.7, b = 0.8, τ = 1/0.08.
Although not clearly derivable from biology, the model allows for a
simplified, immediately available dynamic, without being a trivial
simplification. The experimental support is weak, but the model is useful as a didactic tool to introduce dynamics of spike generation through phase plane analysis. See Chapter 7 in the textbook Methods of Neuronal Modeling.
Morris–Lecar
In 1981 Morris and Lecar combined the Hodgkin–Huxley and
FitzHugh–Nagumo models into a voltage-gated calcium channel model with a
delayed-rectifier potassium channel, represented by
where .
The experimental support of the model is weak, but the model is useful
as a didactic tool to introduce dynamics of spike generation through phase plane analysis. See Chapter 7 in the textbook Methods of Neuronal Modeling.
A two-dimensional neuron model very similar to the Morris-Lecar
model can be derived step-by-step starting from the Hodgkin-Huxley
model. See Chapter 4.2 in the textbook Neuronal Dynamics.
Hindmarsh–Rose
Building upon the FitzHugh–Nagumo model, Hindmarsh and Rose proposed in 1984 a model of neuronal activity described by three coupled first-order differential equations:
with r2 = x2 + y2 + z2, and r ≈ 10−2 so that the z
variable only changes very slowly. This extra mathematical complexity
allows a great variety of dynamic behaviors for the membrane potential,
described by the x variable of the
model, which include chaotic dynamics. This makes the Hindmarsh–Rose
neuron model very useful, because being still simple, allows a good
qualitative description of the many different firing patterns of the
action potential, in particular bursting, observed in experiments.
Nevertheless, it remains a toy model and has not been fitted to
experimental data. It is widely used as a reference model for bursting
dynamics.
Theta model and quadratic integrate-and-fire.
The theta model, or Ermentrout–Kopell canonical
Type I model, is mathematically equivalent to the quadratic
integrate-and-fire model which in turn is an approximation to the
exponential integrate-and-fire model and the Hodgkin-Huxley model. It is
called a canonical model because it is one of the generic models for
constant input close to the bifurcation point, which means close to the
transition from silent to repetitive firing.
The standard formulation of the theta model is
The equation for the quadratic integrate-and-fire model is (see Chapter 5.3 in the textbook Neuronal Dynamics)
The equivalence of theta model and quadratic integrate-and-fire is
for example reviewed in Chapter 4.1.2.2 of spiking neuron models.
For input I(t) that changes over time or is far away from the
bifurcation point, it is preferable to work with the exponential
integrate-and-fire model (if one wants the stay in the class of
one-dimensional neuron models), because real neurons exhibit the
nonlinearity of the exponential integrate-and-fire model.
Sensory input-stimulus encoding neuron models
The
models in this category were derived following experiments involving
natural stimulation such as light, sound, touch, or odor. In these
experiments, the spike pattern resulting from each stimulus presentation
varies from trial to trial, but the averaged response from several
trials often converges to a clear pattern. Consequently, the models in
this category generate a probabilistic relationship between the input
stimulus to spike occurrences. Importantly, the recorded neurons are
often located several processing steps after the sensory neurons, so
that these models summarize the effects of the sequence of processing
steps in a compact form
The non-homogeneous Poisson process model (Siebert)
Siebert modeled the neuron spike firing pattern using a non-homogeneous Poisson process model, following experiments involving the auditory system. According to Siebert, the probability of a spiking event at the time interval is proportional to a non negative function , where is the raw stimulus.:
Siebert considered several functions as , including for low stimulus intensities.
The main advantage of Siebert's model is its simplicity. The
shortcomings of the model is its inability to reflect properly the
following phenomena:
- The transient enhancement of the neuronal firing activity in response to a step stimulus.
- The saturation of the firing rate.
- The values of inter-spike-interval-histogram at short intervals values (close to zero).
These shortcoming are addressed by the age-dependent point process model and the two-state Markov Model.
Refractoriness and age-dependent point process model
Berry and Meister
studied neuronal refractoriness using a stochastic model that predicts
spikes as a product of two terms, a function f(s(t)) that depends on
the time-dependent stimulus s(t) and one a recovery function that depends on the time since the last spike
The model is also called an inhomogeneous Markov interval (IMI) process. Similar models have been used for many years in auditory neuroscience. Since the model keeps memory of the last spike time it is non-Poisson and falls in the class of time-dependent renewal models. It is closely related to the model SRM0 with exponential escape rate.
Importantly, it is possible to fit parameters of the age-dependent
point process model so as to describe not just the PSTH response, but
also the interspike-interval statistics.
Linear-nonlinear Poisson cascade model and GLM
The linear-nonlinear-Poisson cascade model is a cascade of a linear filtering process followed by a nonlinear spike generation step.
In the case that output spikes feed back, via a linear filtering
process, we arrive at a model that is known in the neurosciences as
Generalized Linear Model (GLM). The GLM is mathematically equivalent to the spike response model SRM)
with escape noise; but whereas in the SRM the internal variables are
interpreted as the membrane potential and the firing threshold, in the
GLM the internal variables are abstract quantities that summarizes the
net effect of input (and recent output spikes) before spikes are
generated in the final step.
The two-state Markov model (Nossenson & Messer)
The spiking neuron model by Nossenson & Messer produces the probability of the neuron to fire a spike as a function of either an external or pharmacological stimulus.
The model consists of a cascade of a receptor layer model and a spiking
neuron model, as shown in Fig 4. The connection between the external
stimulus to the spiking probability is made in two steps: First, a
receptor cell model translates the raw external stimulus to
neurotransmitter concentration, then, a spiking neuron model connects
between neurotransmitter concentration to the firing rate (spiking
probability). Thus, the spiking neuron model by itself depends on
neurotransmitter concentration at the input stage.
Fig 4: High level block diagram of the receptor layer and neuron model by Nossenson & Messer.
Fig 5. The prediction for the firing rate in response to a pulse stimulus as given by the model by Nossenson & Messer.
An important feature of this model is the prediction for neurons
firing rate pattern which captures, using a low number of free
parameters, the characteristic edge emphasized response of neurons to a
stimulus pulse, as shown in Fig. 5. The firing rate is identified both
as a normalized probability for neural spike firing, and as a quantity
proportional to the current of neurotransmitters released by the cell.
The expression for the firing rate takes the following form:
where,
- P0 is the probability of the neuron to be "armed" and ready to fire. It is given by the following differential equation:
P0 could be generally calculated recursively using Euler method, but
in the case of a pulse of stimulus it yields a simple closed form
expression.
- y(t) is the input of the model and is interpreted
as the neurotransmitter concentration on the cell surrounding (in most
cases glutamate). For an external stimulus it can be estimated through
the receptor layer model:
with being short temporal average of stimulus power (given in Watt or other energy per time unit).
- R0 corresponds to the intrinsic spontaneous firing rate of the neuron.
- R1 is the recovery rate of the neuron from the refractory state.
Other predictions by this model include:
1) The averaged evoked response potential (ERP) due to the
population of many neurons in unfiltered measurements resembles the
firing rate.
2) The voltage variance of activity due to multiple neuron
activity resembles the firing rate (also known as Multi-Unit-Activity
power or MUA).
3) The inter-spike-interval probability distribution takes the form a gamma-distribution like function.
Experimental evidence supporting the model by Nossenson & Messer
The shape of the firing rate in response to an auditory stimulus pulse
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The Firing Rate has the same shape of Fig 5.
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The shape of the firing rate in response to a visual stimulus pulse
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The Firing Rate has the same shape of Fig 5.
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The shape of the firing rate in response to an olfactory stimulus pulse
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The Firing Rate has the same shape of Fig 5.
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The shape of the firing rate in response to a somato-sensory stimulus
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The Firing Rate has the same shape of Fig 5.
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The change in firing rate in response to neurotransmitter application (mostly glutamate)
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Firing Rate change in response to neurotransmitter application (Glutamate)
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Square dependence between an auditory stimulus pressure and the firing rate
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Square Dependence between Auditory Stimulus pressure and the Firing Rate (- Linear dependence in pressure square (power)).
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Square dependence between visual stimulus electric field (volts) and the firing rate
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Square dependence between visual stimulus electric field (volts) - Linear Dependence between Visual Stimulus Power and the Firing Rate.
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The shape of the Inter-Spike-Interval Statistics (ISI)
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ISI shape resembles the gamma-function-like
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The ERP resembles the firing rate in unfiltered measurements
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The shape of the averaged evoked response potential in response to stimulus resembles the firing rate (Fig. 5).
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MUA power resembles the firing rate
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The shape of the empirical variance of extra-cellular measurements
in response to stimulus pulse resembles the firing rate (Fig. 5).
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Pharmacological input stimulus neuron models
The models in this category produce predictions for experiments involving pharmacological stimulation.
Synaptic transmission (Koch & Segev)
According to the model by Koch and Segev,
the response of a neuron to individual neurotransmitters can be modeled
as an extension of the classical Hodgkin–Huxley model with both
standard and nonstandard kinetic currents. Four neurotransmitters
primarily have influence in the CNS. AMPA/kainate receptors are fast excitatory mediators while NMDA receptors mediate considerably slower currents. Fast inhibitory currents go through GABAA receptors, while GABAB receptors mediate by secondary G-protein-activated potassium channels. This range of mediation produces the following current dynamics:
where ḡ is the maximal conductance (around 1S) and E is the equilibrium potential of the given ion or transmitter (AMDA, NMDA, Cl, or K), while [O] describes the fraction of receptors that are open. For NMDA, there is a significant effect of magnesium block that depends sigmoidally on the concentration of intracellular magnesium by B(V). For GABAB, [G] is the concentration of the G-protein, and Kd describes the dissociation of G in binding to the potassium gates.
The dynamics of this more complicated model have been
well-studied experimentally and produce important results in terms of
very quick synaptic potentiation and depression, that is, fast, short-term learning.
The stochastic model by Nossenson and Messer translates
neurotransmitter concentration at the input stage to the probability of
releasing neurotransmitter at the output stage. For a more detailed description of this model, see the Two state Markov model section above.
HTM neuron model
The HTM neuron model was developed by Jeff Hawkins and researchers at Numenta and is based on a theory called Hierarchical Temporal Memory, originally described in the book On Intelligence. It is based on neuroscience and the physiology and interaction of pyramidal neurons in the neocortex of the human brain.
Artificial Neural Network (ANN)
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Neocortical Pyramidal Neuron (Biological Neuron)
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HTM Model Neuron
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- Few synapses
- No dendrites
- Sum input x weights
- Learns by modifying weights of synapses
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- Thousands of synapses on the dendrites
- Active dendrites: cell recognizes hundreds of unique patterns
- Co-activation of a set of synapses on a dendritic segment causes an NMDA spike and depolarization at the soma
- Sources of input to the cell:
- Feedforward inputs which form synapses proximal to the soma and directly lead to action potentials
- NMDA spikes generated in the more distal basal
- Apical dendrites that depolarize the soma (usually not sufficient enough to generate a somatic action potential)
- Learns by growing new synapses
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- Inspired by the pyramidal cells in neocortex layers 2/3 and 5
- Thousands of synapses
- Active dendrites: cell recognizes hundreds of unique patterns
- Models dendrites and NMDA spikes with each array of coincident detectors having a set of synapses
- Learns by modeling growth of new synapses
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Applications
Spiking Neuron Models are used in a variety of applications that need
encoding into or decoding from neuronal spike trains in the context of
neuroprosthesis and brain-computer interfaces such as retinal prosthesis: or artificial limb control and sensation. Applications are not part of this article; for more information on this topic please refer to the main article.
Relation between artificial and biological neuron models
The most basic model of a neuron consists of an input with some synaptic weight vector and an activation function or transfer function inside the neuron determining output. This is the basic structure used for artificial neurons, which in a neural network often looks like
where yi is the output of the i th neuron, xj is the jth input neuron signal, wij is the synaptic weight (or strength of connection) between the neurons i and j, and φ is the activation function.
While this model has seen success in machine-learning applications, it
is a poor model for real (biological) neurons, because it lacks
time-dependence in input and output.
When an input is switched on at a time t and kept constant
thereafter, biological neurons emit a spike train. Importantly this
spike train is not regular but exhibits a temporal structure
characterized by adaptation, bursting, or initial bursting followed by
regular spiking. Generalized integrate-and-fire model such as the
Adaptive Exponential Integrate-and-Fire model, the spike response model,
or the (linear) adaptive integrate-and-fire model are able to capture
these neuronal firing patterns.
Moreover, neuronal input in the brain is time-dependent.
Time-dependent input is transformed by complex linear and nonlinear
filters into a spike train in the output. Again, the spike response
model or the adaptive integrate-and-fire model enable to predict the
spike train in the output for arbitrary time-dependent input, whereas an artificial neuron or a simple leaky integrate-and-fire does not.
If we take the Hodkgin-Huxley model as a starting point,
generalized integrate-and-fire models can be derived systematically in a
step-by-step simplification procedure. This has been shown explicitly
for the exponential integrate-and-fire model and the spike response model.
In the case of modelling a biological neuron, physical analogues
are used in place of abstractions such as "weight" and "transfer
function". A neuron is filled and surrounded with water containing ions,
which carry electric charge. The neuron is bound by an insulating cell
membrane and can maintain a concentration of charged ions on either side
that determines a capacitance Cm. The firing of a neuron involves the movement of ions into the cell that occurs when neurotransmitters cause ion channels on the cell membrane to open. We describe this by a physical time-dependent current I(t). With this comes a change in voltage,
or the electrical potential energy difference between the cell and its
surroundings, which is observed to sometimes result in a voltage spike called an action potential
which travels the length of the cell and triggers the release of
further neurotransmitters. The voltage, then, is the quantity of
interest and is given by Vm(t).
If the input current is constant, most neurons emit after some
time of adaptation or initial bursting a regular spike train. The
frequency of regular firing in response to a constant current I is described by the frequency-current relation which corresponds to the transfer function of artificial neural networks. Similarly, for all spiking neuron models the transfer function can be calculated numerically (or analytically).
Cable theory and compartmental models
All of the above deterministic models are point-neuron models because
they do not consider the spatial structure of a neuron. However, the
dendrite contributes to transforming input into output.
Point neuron models are valid description in three cases. (i) If input
current is directly injected into the soma. (ii) If synaptic input
arrives predominantly at or close to the soma (closeness is defined by a
length scale
introduced below. (iii) If synapse arrive anywhere on the dendrite,
but the dendrite is completely linear. In the last case the cable acts
as a linear filter; these linear filter properties can be included in
the formulation of generalized integrate-and-fire models such as the spike response model.
The filter properties can be calculate from a cable equation.
Let us consider a cell membrane in the form a cylindrical cable. The
position on the cable is denoted by x and the voltage across the cell
membrane by V. The cable is characterized by a longitudinal resistance per unit length and a membrane resistance . If everything is linear, the voltage changes as a function of time
-
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(19)
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We introduce a length scale on the left side and time constant on the right side. The cable equation can now be written in its perhaps best known form:
-
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(20)
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The above cable equation is valid for a single cylindrical cable.
Linear cable theory describes the dendritic arbor of a neuron as a cylindrical structure undergoing a regular pattern of bifurcation,
like branches in a tree. For a single cylinder or an entire tree, the
static input conductance at the base (where the tree meets the cell
body, or any such boundary) is defined as
- ,
where L is the electrotonic
length of the cylinder which depends on its length, diameter, and
resistance. A simple recursive algorithm scales linearly with the number
of branches and can be used to calculate the effective conductance of
the tree. This is given by
where AD = πld is the total surface area of the tree of total length l, and LD is its total electrotonic length. For an entire neuron in which the cell body conductance is GS and the membrane conductance per unit area is Gmd = Gm / A, we find the total neuron conductance GN for n dendrite trees by adding up all tree and soma conductances, given by
where we can find the general correction factor Fdga experimentally by noting GD = GmdADFdga.
The linear cable model makes a number of simplifications to give
closed analytic results, namely that the dendritic arbor must branch in
diminishing pairs in a fixed pattern and that dendrites are linear. A
compartmental model
allows for any desired tree topology with arbitrary branches and
lengths, as well as arbitrary nonlinearities. It is essentially a
discretized computational implementation of nonlinear dendrites.
Each individual piece, or compartment, of a dendrite is modeled by a straight cylinder of arbitrary length l and diameter d which connects with fixed resistance to any number of branching cylinders. We define the conductance ratio of the ith cylinder as Bi = Gi / G∞, where and Ri
is the resistance between the current compartment and the next. We
obtain a series of equations for conductance ratios in and out of a
compartment by making corrections to the normal dynamic Bout,i = Bin,i+1, as
where the last equation deals with parents and daughters at branches, and .
We can iterate these equations through the tree until we get the point
where the dendrites connect to the cell body (soma), where the
conductance ratio is Bin,stem. Then our total neuron conductance for static input is given by
Importantly, static input is a very special case. In biology inputs
are time dependent. Moreover, dendrites are not always linear.
Compartmental models enable to include nonlinearities via ion channels positioned at arbitrary locations along the dendrites.
For static inputs, it is sometimes possible to reduce the number of
compartments (increase the computational speed) and yet retain the
salient electrical characteristics.
Conjectures regarding the role of the neuron in the wider context of the brain principle of operation
The neurotransmitter-based energy detection scheme
The neurotransmitter-based energy detection scheme suggests that the neural tissue chemically executes a Radar-like detection procedure.
Fig. 6 The biological neural detection scheme as suggested by Nossenson et al.
As shown in Fig. 6, the key idea of the conjecture is to account
neurotransmitter concentration, neurotransmitter generation and
neurotransmitter removal rates as the important quantities in executing
the detection task, while referring to the measured electrical
potentials as a side effect that only in certain conditions coincide
with the functional purpose of each step. The detection scheme is
similar to a radar-like "energy detection" because it includes signal
squaring, temporal summation and a threshold switch mechanism, just like
the energy detector, but it also includes a unit that emphasizes
stimulus edges and a variable memory length (variable memory). According
to this conjecture, the physiological equivalent of the energy test
statistics is neurotransmitter concentration, and the firing rate
corresponds to neurotransmitter current. The advantage of this
interpretation is that it leads to a unit consistent explanation which
allows to bridge between electrophysiological measurements, biochemical
measurements and psychophysical results.
The evidence reviewed in suggest the following association between functionality to histological classification:
- Stimulus squaring is likely to be performed by receptor cells.
- Stimulus edge emphasizing and signal transduction is performed by neurons.
- Temporal accumulation of neurotransmitters is performed by glial
cells. Short term neurotransmitter accumulation is likely to occur also
in some types of neurons.
- Logical switching is executed by glial cells, and it results from
exceeding a threshold level of neurotransmitter concentration. This
threshold crossing is also accompanied by a change in neurotransmitter
leak rate.
- Physical all-or-non movement switching is due to muscle cells and
results from exceeding a certain neurotransmitter concentration
threshold on muscle surroundings.
Note that although the electrophysiological signals in Fig.6 are
often similar to the functional signal (signal power / neurotransmitter
concentration / muscle force), there are some stages in which the
electrical observation is different from the functional purpose of the
corresponding step. In particular, Nossenson et al. suggested that glia
threshold crossing has a completely different functional operation
compared to the radiated electrophysiological signal, and that the
latter might only be a side effect of glia break.
General comments regarding the modern perspective of scientific and engineering models
- The
models above are still idealizations. Corrections must be made for the
increased membrane surface area given by numerous dendritic spines,
temperatures significantly hotter than room-temperature experimental
data, and nonuniformity in the cell's internal structure.
Certain observed effects do not fit into some of these models. For
instance, the temperature cycling (with minimal net temperature
increase) of the cell membrane during action potential propagation not
compatible with models which rely on modeling the membrane as a
resistance which must dissipate energy when current flows through it.
The transient thickening of the cell membrane during action potential
propagation is also not predicted by these models, nor is the changing
capacitance and voltage spike that results from this thickening
incorporated into these models. The action of some anesthetics such as
inert gases is problematic for these models as well. New models, such as
the soliton model attempt to explain these phenomena, but are less developed than older models and have yet to be widely applied.
- Modern views regarding of the role of the scientific model suggest
that "All models are wrong but some are useful" (Box and Draper, 1987,
Gribbin, 2009; Paninski et al., 2009).
- Recent conjecture suggests that each neuron might function as a
collection of independent threshold units. It is suggested that a neuron
could be anisotropically activated following the origin of its arriving
signals to the membrane, via its dendritic trees. The spike waveform
was also proposed to be dependent on the origin of the stimulus.