Fix/cad validation matlab

[Moritz-Alexander-Kern]

This is a follow up PR to #576 , adding a validation test.

Bug

This was discovered in issue #443 .

Summary: CAD (cell assembly detection) output is not the same as the original MATLAB version provided by the article's author.

The MATLAB implementation by Eleonora Russo can be found here:
https://github.com/DurstewitzLab/Cell-Assembly-Detection .
This implementation was used in:
Eleonora Russo and Daniel Durstewitz. Cell assemblies at multiple time scales with arbitrary lag constellations. Elife, 6:e19428, 2017.

MATLAB

The MATLAB implementation defines alph as the input parameter of the function:
Line 1 in FindAssemblies_recursive.m

function [assembly_output]=FindAssemblies_recursive(binM,maxlag,alph,gg,Dc,No_th,O_th,bytelimit,reference_lag)

In later steps, the original input alph is kept and derived values are stored as a separate variable alpha .
Line 30 in FindAssemblies_recursive.m

alpha=alph*2/(nu*(nu-1)*(2*maxlag+1));      %% bonferroni correction 

Line 106 in FindAssemblies_recursive.m

alpha=alph/(length(w2_to_test)*n_as*(2*maxlag+1));  %% bonferroni correction only for the test that I actually perform

Elephant

The Elephant implementation defines alpha as the input parameter of the function:

elephant/elephant/cell_assembly_detection.py

Lines 90 to 95 in b9d0d54

	def cell_assembly_detection(binned_spiketrain, max_lag, reference_lag=2,
	alpha=0.05, min_occurrences=1, size_chunks=100,
	max_spikes=np.inf, significance_pruning=True,
	subgroup_pruning=True,
	same_configuration_pruning=False,
	bool_times_format=None, verbose=False):

In subsequent steps, the original input alpha is changed:

elephant/elephant/cell_assembly_detection.py

Line 255 in b9d0d54

alpha = alpha * 2 / float(number_test_performed)

elephant/elephant/cell_assembly_detection.py

Line 363 in b9d0d54

alpha = alpha / float(len(w2_to_test) * n_as * (2 * max_lag + 1))

As the value of alpha changes, the results differ from the MATLAB implementation, where the original input is stored as alph and is not changed inside the function.

Fix

Introduced a new variable alph, to store the input value of alpha.

todo

• implement validation test: compare results obtained with the MATLAB implementation against results from Elephant implementation.

[coveralls]

coverage: 86.977% (+0.04%) from 86.937% when pulling 7994542 on INM-6:fix/CAD_validation_MATLAB into 5a56c31 on NeuralEnsemble:master.

[Moritz-Alexander-Kern]

This was covered with #576 , can be reopened at any time.