generate_latent_spaces.sh

#!/bin/bash -l

# ----------------------------------------------------------------------------
# generate_latent_spaces.sh
# Author: Antoine Beauchamp
#
# This script generates 500 gene expression latent spaces by repeatedly 
# training the multi-layer perceptron neural network and using the network
# architecture to transform the input space into the latent space.

source activate_venv.sh

datadir=data/
# datadir=data/isocortex/

outdir=data/MLP_outcomes/
# outdir=data/MLP_outcomes_isocortex/

if [ ! -d "$outdir" ]; then
	mkdir -p "$outdir"
fi

niterations=500
nunits=200
L2=0.0
nepochs=150
totalsteps=200
learningrate=1e-05
optimizer=AdamW
confusionmatrix=false
voxeltransform=true
integratedgrads=false

for i in $(seq 1 $niterations);
do
 echo "Iteration $i"

 python3 train_multilayer_perceptron.py \
	 --datadir $datadir \
	 --outdir $outdir \
	 --labels region67 \
	 --mousedata region67 \
	 --humandata region88 \
	 --nunits $nunits \
	 --L2 $L2 \
	 --nepochs $nepochs \
	 --totalsteps $totalsteps \
     --optimizer $optimizer \
	 --learningrate $learningrate \
	 --confusionmatrix $confusionmatrix \
	 --voxeltransform $voxeltransform \
     --integratedgrads $integratedgrads \
	 --seed $i

 mv ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_HumanProb_Region88.csv \
	 ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_HumanProb_Region88_$i.csv

 mv ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_HumanTx_Region88.csv \
	 ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_HumanTx_Region88_$i.csv

 mv ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_MouseProb_Region67.csv \
	 ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_MouseProb_Region67_$i.csv

 mv ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_MouseTx_Region67.csv \
	 ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_MouseTx_Region67_$i.csv
     
 if [ $confusionmatrix = 'true' ];
 then
    mv ${outdir}MLP_ConfusionMatrix_Training_Region67_Layers3_Units${nunits}_L2${L2}.csv \
    ${outdir}MLP_ConfusionMatrix_Training_Region67_Layers3_Units${nunits}_L2${L2}_$i.csv
 fi
     
 if [ $voxeltransform = 'true' ];
 then
    mv ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_MouseVoxelTx.csv \
        ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_MouseVoxelTx_$i.csv

    mv ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_HumanVoxelTx.csv \
        ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_HumanVoxelTx_$i.csv
 fi
 
 if [ $integratedgrads = 'true' ];
 then
     mv ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_IntegratedGradients.csv \
         ${outdir}MLP_Region67_Layers3_Units${nunits}_L2${L2}_IntegratedGradients_$i.csv
 fi

done

deactivate