pymaid.sparseness¶

pymaid.sparseness(x, which='LTS')[source]¶

Calculate sparseness.

Sparseness comes in two flavors:

Lifetime kurtosis (LTK) quantifies the widths of tuning curves (according to Muench & Galizia, 2016):

$S = \Bigg\{ \frac{1}{N} \sum^N_{i=1} \Big[ \frac{r_i - \overline{r}}{\sigma_r} \Big] ^4 \Bigg\} - 3$

where $N$ is the number of observations, $r_i$ the value of observation $i$ , and $\overline{r}$ and $\sigma_r$ the mean and the standard deviation of the observations’ values, respectively. LTK is assuming a normal, or at least symmetric distribution.

Lifetime sparseness (LTS) quantifies selectivity (Bhandawat et al., 2007):

$S = \frac{1}{1-1/N} \Bigg[1- \frac{\big(\sum^N_{j=1} r_j / N\big)^2}{\sum^N_{j=1} r_j^2 / N} \Bigg]$

where $N$ is the number of observations, and $r_j$ is the value of an observation.

Notes

NaN values will be ignored. You can use that to e.g. ignore zero values in a large connectivity matrix by changing these values to NaN before passing it to pymaid.sparseness.

Parameters:

x (DataFrame | array-like) – (N, M) dataset with N (rows) observations for M (columns) neurons. One-dimensional data will be converted to two dimensions (N rows, 1 column).
which ("LTS" | "LTK") – Determines whether lifetime sparseness (LTS) or lifetime kurtosis (LTK) is returned.

Returns:

pandas.Series if input was pandas DataFrame, else numpy.array.

Return type:

sparseness

Examples

Calculate sparseness of olfactory inputs to group of neurons:

>>> import numpy as np
>>> import matplotlib.pyplot as plt
>>> # Generate adjacency matrix
>>> adj = pymaid.adjacency_matrix(s='annotation:WTPN2017_excitatory_uPN_right',
...                               t='annotation:ASB LHN')
>>> # Calculate lifetime sparseness
>>> S = pymaid.sparseness(adj, which='LTS')
>>> # Plot distribution
>>> ax = S.plot.hist(bins=np.arange(0, 1, .1))
>>> ax.set_xlabel('LTS')
>>> plt.show()