Neuron Assembly Participation: Experiments

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Description

The document napa.pdf contains the result diagrams for the complete set of experiments with NAPa (Neuron Assembly Participation) to find neurons that likely participate in assembly activity, that were conducted for the paper [Picado-Muiño and Borgelt 2015]. Only few of these diagrams are contained in the paper due to a lack of space.

The archives napaexp.{zip,tar.gz} contain scripts and other source files, with which the experiments were conducted and the document with the result diagrams was created.

Note that the scripts etc. were developed on/for a GNU/Linux system (Ubuntu 14.04 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:

• Python, preferably version 3.10 or later,
• the NAPa program, which is also made available above for download. Simply place the executable for your system (Windows/Linux, 32/64 bit) into the directory that resulted from unpacking the archive napaexp.zip.
• a LaTeX system, preferably TeX Live (which is the standard LaTeX system for Ubuntu and many other Debian based GNU/Linux systems and may be installed directly through the package manager), in particular the pdflatex program,
• the MetaPost program for the LaTeX system (which is usually already contained in standard LaTeX installations, but on some systems may require separate installation), in particular the mptopdf command,
• some standard Unix tools, which are usually available on all Unix systems even with a very basic installation (like 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 napaexp) 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 several days, 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.

References

• Test Statistics for the Identification of Assembly Neurons in Parallel Spike Trains
  David Picado-Muiño and Christian Borgelt
  Computational Intelligence and Neuroscience 2015, Article ID 427829.
  Hindawi Publishing Corporation, Cairo, Egypt, and New York, NY, USA 2015
  doi:10.1155/2015/427829 hindawi.com
  jcin_15.pdf (2273 kb) jcin_15.ps.gz (8414 kb) (12 pages)
• Identification of Neurons Participating in Cell Assemblies
  Sonja Grün, Denise Berger, and Christian Borgelt
  Proc. IEEE Int. Conf. on Acoustics, Speech and Signal Processing, 3493-3496
  IEEE Press, Piscataway, NJ, USA 2009
  doi:10.1109/ICASSP.2009.4960378 ieeexplore.ieee.org
  icassp_09.pdf (202 kb) icassp_09.ps.gz (134 kb) (4 pages)
• Efficient Identification of Assembly Neurons within Massively Parallel Spike Trains
  Denise Berger, Christian Borgelt, Sebastien Louis, Abigail Morrison, and Sonja Grün
  Computational Intelligence and Neuroscience, 2010, Article ID 439648
  Hindawi Publishing Corporation, New York, NY, USA 2009/2010
  doi:10.1155/2010/439648 www.hindawi.com
  jcin_09.pdf (5580 kb) jcin_09.ps.gz (4686 kb) (16 pages)