| coconad.pdf | (4963 kb) | CoCoNAD result diagrams |
| cocoexp.zip | (63 kb) | scripts and other source files |
| cocoexp.tar.gz | (53 kb) | |
| jitter.pdf | (12397 kb) | frequent item set mining result diagrams |
| jitter.zip | (42 kb) | scripts and other source files |
| jitter.tar.gz | (35 kb) | |
| prefer.pdf | (103 kb) | preference relations for pattern set reduction |
| prefer.zip | (5 kb) | sources for document prefer.pdf |
| prefer.tar.gz | (4 kb) | |
| psf+psr.zip | (78 kb) | Python scripts for Pattern Spectrum Filtering |
| psf+psr.tar.gz | (70 kb) | and Pattern Set Reduction |
The document coconad.pdf contains the result diagrams for
the complete set of experiments with CoCoNAD (Continuous-time Closed
Neuron Assembly Detection) to find inexactly synchronous spiking events
in parallel neural spike trains, that were conducted for a paper that
is currently under review. Only few of these diagrams are contained
in the paper due to a lack of space. For the theory underlying the
methods, please consult the paper and for the different patterns set
reduction methods, the paper [Torre
et al. 2013].
The archives cocoexp.{zip,tar.gz} contain scripts and other
source files, with which the experiments were conducted and the document
with the result diagrams was created.
The document jitter.pdf contains the diagrams for the
complete set of experiments concerning the alternative method based
on time binning and then applying standard frequent item set mining
(FIM), to which CoCoNAD is compared in a paper that is currently under
review. Only few of these diagrams are contained in the paper. For the
theory underlying the methods, please consult the paper and for the
different patterns set reduction methods, the paper
Torre et al. 2013.
The archive jitter.zip contains scripts and other source
files, with which the experiments were conducted and the document
with the result diagrams was created.
The document prefer.pdf contains diagrams that illustrate
the various preference relations used for the pattern set reduction
for signatures close to the detection border. For the theory underlying
these methods, consult the paper Torre
et al. 2013 referenced below. The archive
prefer.zip contains scripts and other source files,
with which these diagrams were created.
The scripts in the archives psf+psr.{zip,tar.gz} implement
the full analysis process of parallel (spike) trains/point processes as
it is described (although for standard frequent item set mining) in
[Picado-Muiño et al.
2013] and [Torre et al.
2013]. A documentation of these scripts can be found
here.
Call the main script ccn+psf+psr.py without any arguments to
obtain a help message that shows the invocation and the available
options.
Note that the scripts etc. were developed on/for a GNU/Linux
system (Ubuntu 12.10 or later) and thus are directly executable on such
a system or a similar one (that is, some other GNU/Linux distribution).
Although at least most of the Python scripts should also be working
on a Windows system (with the possible exception of the parallelization
scripts), most of the other scripts (like the run script,
which is the main control script, and the makefile, which
controls generating the diagrams from the result data) may need
porting to batch files or something similar.
On a GNU/Linux system, the following software needs to be installed to run the experiments:
jitter package will also work without this
extension module, namely by falling back on a pure Python
replacement, which, however, is slower by a factor of about 40
or more),cocoexp
package will also work without this extension module, namely by
falling back on a pure Python replacement, which, however, is
slower by a factor of about 40 or more),pdflatex program,mptopdf command,bash,
awk, tar etc.) and are easy to install
otherwise.On such a system the experiments can be run by simply calling
the main script run (in the directory cocoexp
or jitter, respectively) on the command line, which does
everything. The execution of the experiments exploits 4-fold
parallelization, thus making full use of the quadcore processors
basically all modern computers are equipped with. The progress of
the experiments can be followed on the command line, to which regular
progress messages are written. Once all experiments are completed
(which, even on a modern computer system, can take more than
5 hours for the coconad experiments and more than
10 hours for the jitter experiments, mainly because
of the huge number of individual experimental runs, namely in the
hundreds of thousands), the result diagrams are created and compiled
into the final documents, which are also directly available above.