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.
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Keep pressing 0 to reroll objective until the object set with the desired overlap is created.
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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
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Load input files in EMERGENT without headers.
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Change ApplyInputs and EpochTrain inputs to created input.
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Train model by first Initializing and Running until reaching desired error level.
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Test model by placing input in TrialTest, Initialize and Run.
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Export test results found in TrailTestOutput into a .csv file.
Analyzing EMERGENT Outputs
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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.
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In MATLAB run metric.m by typing metric.
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At the prompt type in the EMERGENT output file.
Creating Noise Input for Sleep Simulations
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In MATLAB run big_noise_input.m by typing big_noise_input.
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At the prompt select if you would like to add an odor to the noise input.
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Name the file with the .dat extension.
Simulating Sleep in EMERGENT
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Load sleep input file in EMERGENT without headers.
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Train EMERGENT on previously made object-context pair.
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Test model on 'sleep' noise input.
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Save output with .csv extension.
Turning Spontaneous Memory Replays into Inputs
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Compare replay output with original object-context input using metric.m as described above.
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To create EMERGENT input from replay output run big_metricer.m in MATLAB by typing big_metricer.
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At the prompt type on the output filename.
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At the prompt type in a name for the created input file.
Running Sleep Simulations
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Load input file created using big_metricer into EMERGENT.
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Train the previously trained network on the new input for 3 epochs.