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#!/usr/bin/env -S bash -i | ||
echo "Creating conda environment" | ||
mamba env create -f environment.yaml | ||
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# get the CycleGAN code and dependencies | ||
git clone https://github.com/funkey/neuromatch_xai | ||
mv neuromatch_xai/cycle_gan . | ||
rm -rf neuromatch_xai | ||
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# Download checkpoints and data | ||
wget 'https://dl-at-mbl-2023-data.s3.us-east-2.amazonaws.com/knowledge_extraction_resources.zip' -O resources.zip | ||
# Unzip the checkpoints and data | ||
unzip -o resources.zip data.zip | ||
unzip -o resources.zip checkpoints.zip | ||
unzip -o checkpoints.zip 'checkpoints/synapses/*' | ||
unzip -o data.zip 'data/raw/synapses/*' | ||
# make sure the order of classes matches the pretrained model | ||
mv data/raw/synapses/gaba data/raw/synapses/0_gaba | ||
mv data/raw/synapses/acetylcholine data/raw/synapses/1_acetylcholine | ||
mv data/raw/synapses/glutamate data/raw/synapses/2_glutamate | ||
mv data/raw/synapses/serotonin data/raw/synapses/3_serotonin | ||
mv data/raw/synapses/octopamine data/raw/synapses/4_octopamine | ||
mv data/raw/synapses/dopamine data/raw/synapses/5_dopamine | ||
mamba create -n 08_knowledge_extraction python=3.11 pytorch torchvision pytorch-cuda-12.1 -c conda-forge -c pytorch -c nvidia | ||
mamba activate 08_knowledge_extraction | ||
pip install -r requirements.txt |