Code for

DorsoVentral and ProximoDistal Hippocampal Processing Account for the Influences of Sleep and Context on Memory (Re)consolidation: A Connectionist Model

PubMed - PDF file
Justin Lines, Kelsey Nation, and Jean-Marc Fellous.
Computational Intelligence and Neuroscience, 2017:8091780. doi: 10.1155/2017/8091780. Epub 2017 Jul 3


In order to run our code, you will need MATLAB and EMERGENT. You will need to download Matlab Files and the Emergent Simulation File (EMERGENT 6.3.2).

Note: If you are using emergent 8.X, you need to download the LTS Emergent 7 comatibility package emergent-7.1.0-11076-win64.zip or HERE. Copy those two files in the .../Emergent/bin forlder and run emergent7.exe.

This is a quick walk through to create EMERGENT input files and analyzing EMERGENT outputs using custom MATLAB files. More information are found HERE (pptx) or HERE(pdf)

Creating Object-Context Inputs
- In MATLAB run objective.m by typing objective.
- At the prompt type in the desired overlap percent in the input files you are creating.
- Keep pressing 0 to reroll objective until the object set with the desired overlap is created.
- Once the object input is made, type in 1 and follow prompts to name inputs of sets 1 and 2 and intermediate sets. Inputs must be named with a .dat extension.

Training and Testing in EMERGENT
- Load input files in EMERGENT without headers.
- Change ApplyInputs and EpochTrain inputs to created input.
- Train model by first Initializing and Running until reaching desired error level.
- Test model by placing input in TrialTest, Initialize and Run.
- Export test results found in TrailTestOutput into a .csv file.

Analyzing EMERGENT Outputs
- In MATLAB open metric.m and place the input file(s) you wish to compare outputs to in lines 6-8 for the variable names file1, file2, and file3.
- In MATLAB run metric.m by typing metric.
- At the prompt type in the EMERGENT output file.

Creating Noise Input for Sleep Simulations
- In MATLAB run big_noise_input.m by typing big_noise_input.
- At the prompt select if you would like to add an odor to the noise input.
- Name the file with the .dat extension.

Simulating Sleep in EMERGENT
- Load sleep input file in EMERGENT without headers.
- Train EMERGENT on previously made object-context pair.
- Test model on 'sleep' noise input.
- Save output with .csv extension.

Turning Spontaneous Memory Replays into Inputs
- Compare replay output with original object-context input using metric.m as described above.
- To create EMERGENT input from replay output run big_metricer.m in MATLAB by typing big_metricer.
- At the prompt type on the output filename.
- At the prompt type in a name for the created input file.

Running Sleep Simulations
- Load input file created using big_metricer into EMERGENT.
- Train the previously trained network on the new input for 3 epochs.


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