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run_lupus.sh
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run_lupus.sh
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#!/bin/bash
centers="5 10 15 20 25"
for seed in `seq 25`
do
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/cloudpred_${seed} --cloudpred --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/linear_${seed} --linear --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/generative_${seed} --generative --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/genpat_${seed} --genpat --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/deepset_${seed} --deepset --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_
python3 -m cloudpred data/lupus -t log --logfile log/lupus/cloudpred_${seed} --cloudpred --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_
python3 -m cloudpred data/lupus -t log --logfile log/lupus/linear_${seed} --linear --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_
python3 -m cloudpred data/lupus -t log --logfile log/lupus/generative_${seed} --generative --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_
python3 -m cloudpred data/lupus -t log --logfile log/lupus/genpat_${seed} --genpat --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_
python3 -m cloudpred data/lupus -t log --logfile log/lupus/deepset_${seed} --deepset --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_
python3 -m cloudpred data/mono -t log --logfile log/mono/cloudpred_${seed} --cloudpred --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/mono_${seed}_ --regression
python3 -m cloudpred data/mono -t log --logfile log/mono/linear_${seed} --linear --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/mono_${seed}_ --regression
python3 -m cloudpred data/mono -t log --logfile log/mono/deepset_${seed} --deepset --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/mono_${seed}_ --regression
done
for seed in `seq 10 25`
do
for train in 10 20 30 40 50 60 70
do
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/cloudpred_${seed}_train_${train} --cloudpred --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_train_${train}_ --train_patients ${train}
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/linear_${seed}_train_${train} --linear --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_train_${train}_ --train_patients ${train}
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/generative_${seed}_train_${train} --generative --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_train_${train}_ --train_patients ${train}
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/genpat_${seed}_train_${train} --genpat --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_train_${train}_ --train_patients ${train}
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/deepset_${seed}_train_${train} --deepset --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_train_${train}_ --train_patients ${train}
python3 -m cloudpred data/lupus -t log --logfile log/lupus/cloudpred_${seed}_train_${train} --cloudpred --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_train_${train}_ --train_patients ${train}
python3 -m cloudpred data/lupus -t log --logfile log/lupus/linear_${seed}_train_${train} --linear --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_train_${train}_ --train_patients ${train}
python3 -m cloudpred data/lupus -t log --logfile log/lupus/generative_${seed}_train_${train} --generative --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_train_${train}_ --train_patients ${train}
python3 -m cloudpred data/lupus -t log --logfile log/lupus/genpat_${seed}_train_${train} --genpat --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_train_${train}_ --train_patients ${train}
python3 -m cloudpred data/lupus -t log --logfile log/lupus/deepset_${seed}_train_${train} --deepset --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_train_${train}_ --train_patients ${train}
python3 -m cloudpred data/mono -t log --logfile log/mono/cloudpred_${seed}_train_${train} --cloudpred --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/mono_${seed}_train_${train} --regression --train_patients ${train}
python3 -m cloudpred data/mono -t log --logfile log/mono/linear_${seed}_train_${train} --linear --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/mono_${seed}_train_${train} --regression --train_patients ${train}
python3 -m cloudpred data/mono -t log --logfile log/mono/deepset_${seed}_train_${train} --deepset --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/mono_${seed}_train_${train} --regression --train_patients ${train}
done
for cells in 1 10 50 100 250 500 1000 2000 3000 4000 5000 6000 7000 8000
do
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/cloudpred_${seed}_cells_${cells} --cloudpred --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_cells_${cells}_ --cells ${cells}
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/linear_${seed}_cells_${cells} --linear --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_cells_${cells}_ --cells ${cells}
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/generative_${seed}_cells_${cells} --generative --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_cells_${cells}_ --cells ${cells}
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/genpat_${seed}_cells_${cells} --genpat --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_cells_${cells}_ --cells ${cells}
python3 -m cloudpred data/lupus_pop -t log --logfile log/lupus_pop/deepset_${seed}_cells_${cells} --deepset --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_pop_${seed}_cells_${cells}_ --cells ${cells}
python3 -m cloudpred data/lupus -t log --logfile log/lupus/cloudpred_${seed}_cells_${cells} --cloudpred --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_cells_${cells}_ --cells ${cells}
python3 -m cloudpred data/lupus -t log --logfile log/lupus/linear_${seed}_cells_${cells} --linear --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_cells_${cells}_ --cells ${cells}
python3 -m cloudpred data/lupus -t log --logfile log/lupus/generative_${seed}_cells_${cells} --generative --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_cells_${cells}_ --cells ${cells}
python3 -m cloudpred data/lupus -t log --logfile log/lupus/genpat_${seed}_cells_${cells} --genpat --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_cells_${cells}_ --cells ${cells}
python3 -m cloudpred data/lupus -t log --logfile log/lupus/deepset_${seed}_cells_${cells} --deepset --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/lupus_${seed}_cells_${cells}_ --cells ${cells}
python3 -m cloudpred data/mono -t log --logfile log/mono/cloudpred_${seed}_cells_${cells} --cloudpred --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/mono_${seed}_cells_${cells} --regression --cells ${cells}
python3 -m cloudpred data/mono -t log --logfile log/mono/linear_${seed}_cells_${cells} --linear --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/mono_${seed}_cells_${cells} --regression --cells ${cells}
python3 -m cloudpred data/mono -t log --logfile log/mono/deepset_${seed}_cells_${cells} --deepset --centers ${centers} --dim 100 --seed ${seed} --valid 0.25 --test 0.25 --figroot fig/mono_${seed}_cells_${cells} --regression --cells ${cells}
done
done
for method in Linear Generative Genpat Cloud DeepSet
do
echo ${method}
grep INFO log/lupus_pop_* | grep AUC | grep ${method} | awk '{ total += $6; count++ } END { print total/count }'
done