[Problem Set 3 Spike trains] Problem 1: Poisson spike trains

Link of the iPython notebook for the code

AT2 – Neuromodeling: Problem set #3 SPIKE TRAINS

PROBLEM 1: Poisson spike trains

Brain neuron emit spikes seemingly randomly: we will aim to model such spike trains, by relying on the following assumptions:

  1. spike events occur independently of one another
  2. they occur at a constant firing rate $r$
  3. there exists a time bin $Δt$ within which no two spikes can be fired
  4. within each time span $Δt$, the probability of the neuron firing is $rΔt$.

    • In other words: the random variable $X_t$ whose outcome is $1$ (resp. $0$) if there is a (resp. no) spike between $t$ and $t+Δt$ follows a Bernoulli distribution:

      \[X_t \sim ℬ(r Δt)\]

1. Generating spike trains

Let $M ≝ T/Δt$, where $T$ is the length (in seconds) of the spike trains we will consider from now on.

In compliance with what we assumed before, a spike train can be modeled as a $M$-dimensional random vector whose $i$-th coordinate (for $0 ≤ i ≤ M-1$) is the output of $X_{i Δt}$ (the values of which are in $\lbrace 0, 1 \rbrace$). In concrete terms, when implementing such a vector of $\lbrace 0, 1 \rbrace^M$: at each coordinate, it has a constant probability to be equal to $1$ ($0$ otherwise).

Example: For instance, if on average every fourth element in the vector is made to indicate a spike (i.e. is equal to $1$), that is: the previously mentioned constant probability is equal to $1/4$:

Figure a. - Spike train such that there is a spike every fourth time bin on average

To clarify the time units, let us set

  • $Δt ≝ 2 \text{ ms}$
  • $T = 1 \text{ s}$
  • $r = 25 \text{ spikes/sec}$

Then here is an example of a spike train:

Figure b. - Spike train with a $25 \text{ spikes/sec}$ average rate over $1 \text{ sec}$

2. Spike counts & Interspike intervals

Now, informative features can be extracted from each spike train, such as:

  • its total number of spikes (which gives a global information about the spike train, but have us overlook the time step at which each spike occurred)
  • the interspike intervals (which give us local clues on the contrary, but encompass the time-related information we lost with the spike counts only)

A natural question to ask ourselves is: what is their distribution? To this end, let us generate $N ≝ 200$ spike trains with firing rate $r ≝ 25 \text{ Hz}$.

Here is the rastergram of $50$ of them:

Figure c.1. - Rastergram of $50$ spike trains with a $25 \text{ Hz}$ firing rate

Spike counts

Here is the spike count histogram of all of these $200$ spike trains:

Figure c.2. - Histogram of spike counts for the $N ≝ 200$ spike trains with firing rate $r ≝ 25 \text{ Hz}$

We claim that spike counts are following a Poisson distribution of mean $rT ≝ 25$ (spikes), which may not seem obvious at first sight with so few spike trains:

Figure c.3. - Comparison of the empirical distribution of $N ≝ 200$ spike counts (with firing rate $r ≝ 25 \text{ Hz}$) and the Poisson distribution of mean $rT ≝ 25 \text{ spikes}$

However, it becomes more apparent when the number $N$ of spike trains is increased. For $N ≝ 100000$ for instance:

Figure c.4. - Histogram of spike counts for the $N ≝ 100000$ spike trains with firing rate $r ≝ 25 \text{ Hz}$

the spike counts distribution matches very well the Poisson one:

Figure c.5. - Comparison of the empirical distribution of $N ≝ 100000$ spike counts (with firing rate $r ≝ 25 \text{ Hz}$) and the Poisson distribution of mean $rT ≝ 25 \text{ spikes}$

This can be explained theoretically: the assumptions stated in the introduction make the Poisson distribution perfectly suited to model the spike counts distribution. More precisely: by definition, the random variable $X$ counting the number of spikes is binomial:

\[X ≝ \sum\limits_{ n=0 }^{M-1} \underbrace{X_{nΔt}}_{\; \sim \; ℬ(rΔt)} \; \sim \; ℬ(M, rΔt)\]

as the $X_t$ are independent (by hypothesis) and identically distributed ($∀t, X_t \sim \; ℬ(rΔt)$).

But it is well known that the Poisson distribution $𝒫(\underbrace{M × rΔt}_{= \, rT})$ successfully approximates such a binomial distribution provided that $M$ is large enough and $rΔt$ is small enough. Here:

  • $M ≝ T/Δt = \frac{1000}{2} = 500$
  • $rΔt = 25 × 2 \cdot 10^{-3} = 0.05$

which makes the Poisson distribution $𝒫(rT)$, i.e. $𝒫(25)$, perfectly suited to approximate the binomial distribution $ℬ(M, rΔt)$!

Interspike intervals

Here is the interspike interval histogram of $200$ spike trains with firing rate $r ≝ 25 \text{ Hz}$:

Figure d. - Interspike interval histogram of the $N ≝ 200$ spike trains with firing rate $r ≝ 25 \text{ Hz}$

From a theoretical standpoint: if we denote by $Y$ the random variable whose outcome is the length of an interspike interval, in compliance with the assumptions in the introduction, it comes that:

\[\begin{cases} ∀t ≤ 0, \quad P(Y > t) = 1 \\ ∀t > 0, \quad P(Y > t) = (1 - rΔt)^{t/Δt} = \exp\left(\frac{t}{Δt} \ln(1 - rΔt)\right) = \exp\left(- t \, \frac{\ln\left(\frac{1}{1 - rΔt}\right)}{Δt}\right) \end{cases}\]


\[\begin{cases} ∀t ≤ 0, \quad P(Y ≤ t) = 0 \\ ∀t > 0, \quad P(Y ≤ t) = 1 - \exp\left(- t \, \ln\left(\frac{1}{1 - rΔt}\right)/Δt\right) \end{cases}\]

Therefore, by definition of its cumulative distribution function, the interspike interval variable $Y$ follows an exponential distribution of rate $\ln\left(\frac{1}{1 - rΔt}\right)/Δt$

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