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NeuroSim CartPole model

Adatapted from SMARTAgent on May 24th 2021

A closed-loop neuronal network model that senses dynamic visual information from the AIgame enviroment and learns to produce actions that maximize game reward through spike-timing dependent reinforcement learning.

This project is related to the paper:

Training spiking neuronal networks to perform motor control using reinforcement and evolutionary learning

Hasegan D, Deible M, Earl C, D'Onofrio D, Hazan H, Anwar H, Neymotin SA.

bioRxiv: https://doi.org/10.1101/2021.11.20.469405

Published in: TODO

Project structure

  • config.json the current configuration that we will work with. This gets picked by default

  • requirements.txt the pip packages needed for installation

  • notebooks/ folder with jupyter notebooks that are used for exploration and data analysis before translating into tools

  • results/ default place for storing the resulting trained models

  • neurosim/ the code

    • main.py main extry point to the code (run training, evaluation, contiuation)
    • sim.py the NetPyNE model setup and run
    • critic.py the critic in the actor-critic model for RL (provides reward/punishment)
    • aigame.py wrapper for OpenAI gym
    • game_interface.py simple interface between the game and firing rates or receptive fields
    • conf.py utility for configuration files
    • utils/ folder for helper functions
    • tools/ folder of evaluation tools
    • cells/ folder for defined cells

  • mod/ the NEURON objects that will get compiled by nvrnivmodl

  • x86_64/ the compiled NEURON objects

Install on Mac

install python >3.7 (previous versions might not work)

install ffmpeg

brew install ffmpeg

create a virtual environment

virtualenv -p python3 venv

activate the environment

source ./venv/bin/activate
export PYTHONPATH="`pwd`"

install all dependencies:

pip install -r requirements.txt

Compile mod files

nrnivmodl mod

Install on Ubuntu 18.04

Running this on a VM on gcloud

EMAIL="..."
ssh-keygen -t ed25519 -C $EMAIL
cat .ssh/id_ed25519.pub 
# Copy the pub key here: https://github.com/settings/keys
git clone git@github.com:NathanKlineInstitute/netpyne-STDP.git
cd netpyne-STDP/

then run the whole script below

git config --global alias.co checkout
git config --global alias.br branch
git config --global alias.ci commit
git config --global alias.st status
git config --global user.name "$USER"
git config --global user.email $EMAIL

# install pacakges
sudo apt-get update
yes | sudo apt-get install python3.7 python3.7-distutils cmake build-essential libz-dev ffmpeg

# install pip and create the environment
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python3.7 get-pip.py
python3.7 -m pip install virtualenv
python3.7 -m virtualenv venv

# activate
source ./venv/bin/activate
export PYTHONPATH="`pwd`"
alias py=python3

# install requirements
pip install -r requirements.txt

# compile neuron
nrnivmodl mod

Then run commands with screen to avoid network disconnecting

screen -L -Logfile logfile.log ...

run

python3 neurosim/main.py run

Check notebooks:

jupyter notebook

Run tests:

pytest tests

Run ES

python3 neurosim/train_es.py train

Or continue training model

python3 neurosim/train_es.py continue results/20210907-ES1500it --iterations 500

Tools/Evaluation

Evaluate the model before and after training:

WDIR=results/20210707
py neurosim/main.py eval $WDIR --resume_tidx=0
py neurosim/main.py eval $WDIR --resume_tidx=-1 --duration 250

# To evaluate and use for poster/presentation:
py neurosim/main.py eval $WDIR --resume_tidx=-1 \
    --env-seed 42 \
    --eps-duration 105 \
    --save-data

# To evaluate one specific episode over and over again
# for EPISODE_ID in 74 68 77 55 31 50 32 10 19 59 22
for EPISODE_ID in 74 68 77 55 31 50 32 10 19 59 22
do
    py neurosim/main.py eval $WDIR --resume_tidx=-1 \
        --env-seed 42 \
        --eps-duration 25 \
        --save-data \
        --saveEnvObs \
        --rerun-episode ${EPISODE_ID}
done


# To display the model run
py neurosim/main.py eval $WDIR --resume_tidx=-1 --display --env-seed 42 \
    --eps-duration 105

Optional: Maybe evaluate in depth

py neurosim/main.py eval $WDIR --resume_best_training --env-seed 42 \
    --eps-duration 105

for ((i=8;i>=0;i-=1)); do
    echo "Evaluating at $i"
    py neurosim/main.py eval $WDIR --resume_tidx=$i --env-seed 42 \
        --eps-duration 105 \
        --save-data
done

Evaluate how the model is responding to one neuron firing:

py neurosim/main.py eval $WDIR --resume_tidx=-1 --eps-duration 2 \
    --mock-env

# For a more comprehensive approach to run on all steps

mkdir $WDIR/evalmockAllStates
STEPS=20
for ((i=0;i<$STEPS;i+=1)); do
    echo "Evaluating Step $i / $STEPS"
    py neurosim/main.py eval $WDIR --resume_tidx=-1 --eps-duration 1 \
        --mock-env 2 \
        --duration 1300 \
        --mock_curr_step $i \
        --mock_total_steps $STEPS \
        --outdir $WDIR/evalmockAllStates/step_${i}
done

Run all evaluation:

WDIR=results/20210907
py neurosim/tools/evaluate.py medians $WDIR
py neurosim/tools/evaluate.py rewards $WDIR
py neurosim/tools/evaluate.py rewards-vals $WDIR
py neurosim/tools/evaluate.py eval-motor $WDIR
py neurosim/tools/evaluate.py eval-moves $WDIR --unk_moves
py neurosim/tools/evaluate.py eval-moves $WDIR --abs_move_diff

py neurosim/tools/evaluate.py weights-adj $WDIR
py neurosim/tools/evaluate.py weights-adj $WDIR --index 0
py neurosim/tools/evaluate.py weights-diffs $WDIR
py neurosim/tools/evaluate.py weights-diffs $WDIR --relative
py neurosim/tools/evaluate.py weights-ch $WDIR
py neurosim/tools/evaluate.py weights-ch $WDIR --separate_movement True

py neurosim/tools/evaluate.py frequency $WDIR --timestep 10000
py neurosim/tools/evaluate.py variance $WDIR

py neurosim/tools/evaluate.py boxplot $WDIR
py neurosim/tools/evaluate.py perf $WDIR

Continue training from a already trained model:

WDIR=results/...
py neurosim/main.py continue $WDIR --duration 5000
# note: this script needs more care on how to integrate with different/new params

# more detailed example:
py neurosim/main.py continue results/20210801-1000it-1eps/ \
    --copy-from-config config.json \
    --copy-fields critic,sim,STDP-RL \
    --duration 100 \
    --index=3

Critic evaluation

py neurosim/tools/critic.py eval \
    --best-wdir results/20210801-1000it-1eps/500s-evaluation_10 \
    --critic-config results/20210801-1000it-1eps/backupcfg_sim.json \
    --verbose

py neurosim/tools/critic.py eval \
    --best-wdir results/20210801-1000it-1eps/500s-evaluation_10 \
    --critic-config config.json \
    --verbose

py neurosim/tools/critic.py hpsearch \
    --best-wdir results/20210801-1000it-1eps/500s-evaluation_10 \
    --critic-config config.json

Train the same config on many network configs

WDIR=results/seedrun_m1-2022-01-16
mkdir $WDIR

python3 neurosim/main.py seedrun $WDIR --conn-seed 2542033

for ((i=0;i<20;i+=1)); do
    echo "Running $i th seed"
    python3 neurosim/main.py seedrun $WDIR --fnjson $WDIR/config.json
done

Evaluate seedrun:

python3 neurosim/tools/eval_seedrun.py analyze $WDIR

Continue seedrun:

cp results/hpsearch-2022-01-11/best/1_run_2371/backupcfg_sim.json results/seedrun_m1-2022-01-16/config2.json
py neurosim/main.py cont_seedrun $WDIR/run_seed1139028 $WDIR/config2.json

Run Hyperparameter search

Change hpsearch_config.json to the needed params

WDIR=results/hpsearch-2021-09-13

# Just for setup:
py neurosim/hpsearch.py sample $WDIR --just-init

# run one sample
py neurosim/hpsearch.py sample $WDIR


# run 100 samples
for ((i=0;i<100;i+=1)); do
    echo "Sampling $i th run"
    time py neurosim/hpsearch.py sample $WDIR
done

Alternatively you can run HPSearch with random networks instead:

# run one sample with a random initialization
py neurosim/hpsearch.py sample $WDIR --random_network

# run 100 samples
for ((i=0;i<100;i+=1)); do
    echo "Sampling $i th run"
    time py neurosim/hpsearch.py sample $WDIR --random_network
done

Results are posted in $WDIR/results.tsv, then you can analyze with:

py neurosim/tools/eval_hpsearch.py analyze $WDIR
py neurosim/tools/eval_hpsearch.py combine $WDIR

Evaluation of best models:

STDP model process:

WDIR=results/hpsearch-2021-09-01/run_106756
WDIR=results/hpsearch-2021-09-04/best/1_run_2703
WDIR=results/hpsearch-2021-09-06/best/1_run_168

ES model:

WDIR=results/20210907-ES1500it

To trace the model

Use this on the latest step of the model

py neurosim/tools/eval_multimodel.py trace $WDIR

To generate more results:

Beware: this specific code was used for previous versions. New and updated plot-generation scripts are found in the logs of the individual seedruns: seedrun_m1-2022-01-16 and seedrun_evol-2022-02-20.

BSTDP_WDIR=results/hpsearch-2021-09-06/best/1_run_168
BEVOL_WDIR=results/20210907-ES1500it
BCOMB_WDIR=results/evol-stdp-rl
BEFORE_CONF="Before Training:${BEVOL_WDIR}:0"
BSTDP_CONF="After STDP-RL Training:${BSTDP_WDIR}:-1"
BEVOL_CONF="After EVOL Training:${BEVOL_WDIR}:-1"
BCOMB_CONF="After EVOL+STDP-RL Training:${BCOMB_WDIR}:-1"
OUTDIR=results/final-results-2021-09

py neurosim/tools/eval_multimodel.py boxplot "${BEFORE_CONF},${BSTDP_CONF},${BEVOL_CONF},${BCOMB_CONF}" --outdir=$OUTDIR

py neurosim/tools/evaluate.py frequency ${BSTDP_WDIR}/evaluation_8 --timestep 10000
py neurosim/tools/evaluate.py frequency ${BEVOL_WDIR}/evaluation_15 --timestep 10000
py neurosim/tools/evaluate.py frequency ${BEVOL_WDIR}/evaluation_0 --timestep 10000
py neurosim/tools/evaluate.py variance ${BSTDP_WDIR}/evaluation_8
py neurosim/tools/evaluate.py variance ${BEVOL_WDIR}/evaluation_15
py neurosim/tools/evaluate.py variance ${BEVOL_WDIR}/evaluation_0

py neurosim/tools/eval_multimodel.py spk-freq "${BEFORE_CONF},${BSTDP_CONF},${BEVOL_CONF}" --outdir=$OUTDIR

py neurosim/tools/eval_multimodel.py train-perf $BSTDP_WDIR --wdir-name "STDP-RL Model" --outdir=$OUTDIR
py neurosim/tools/eval_multimodel.py train-perf $BEVOL_WDIR --wdir-name "ES Model" --outdir=$OUTDIR
py neurosim/tools/eval_multimodel.py train-perf $BEVOL_WDIR --wdir-name "ES Model" --outdir=$OUTDIR --merge-es
py neurosim/tools/eval_multimodel.py train-perf-comb "${BSTDP_CONF},${BEVOL_CONF}" --outdir=$OUTDIR

py neurosim/tools/eval_multimodel.py train-unk-moves "${BSTDP_CONF},${BEVOL_CONF}" --outdir=$OUTDIR

py neurosim/tools/eval_multimodel.py select-eps \
        ${BSTDP_WDIR}/evaluation_8,${BEVOL_WDIR}/evaluation_15

py neurosim/tools/eval_multimodel.py eval-selected-eps \
        ${BSTDP_CONF},${BEVOL_CONF},${BCOMB_CONF} \
        --outdir=$OUTDIR \
        --sort-by "68,74,10,19,55,32,31,22,77"
        

# Weights:
py neurosim/tools/eval_multimodel_weights.py changes \
            "${BSTDP_CONF},${BEVOL_CONF}" --outdir=$OUTDIR

# Observation Space Receptive Fields
py neurosim/tools/eval_obsspace.py rf $OUTDIR

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