Commit 7bd486dd authored by Shengpu Tang (tangsp)'s avatar Shengpu Tang (tangsp)
Browse files

run FIDDLE

parent b8eb8f92
#!/bin/bash
set -euxo pipefail
export PYTHONPATH="$PYTHONPATH:../../"
export PYTHONPATH="../../"
DATAPATH=$(python -c "import yaml;print(yaml.full_load(open('../config.yaml'))['data_path']);")
mkdir -p log
OUTCOME=ARF
T=4.0
dt=1.0
python -m FIDDLE.run \
--data_path="$DATAPATH/features/outcome=$OUTCOME,T=$T,dt=$dt/" \
--population="$DATAPATH/population/${OUTCOME}_${T}h.csv" \
--T=$T \
--dt=$dt \
--theta_1=0.001 \
--theta_2=0.001 \
--theta_freq=1 \
--stats_functions 'min' 'max' 'mean' \
> >(tee "log/outcome=$OUTCOME,T=$T,dt=$dt.out") \
2> >(tee "log/outcome=$OUTCOME,T=$T,dt=$dt.err" >&2)
OUTCOME=ARF
T=12.0
dt=1.0
python -m FIDDLE.run \
--data_path="$DATAPATH/features/outcome=$OUTCOME,T=$T,dt=$dt/" \
--population="$DATAPATH/population/${OUTCOME}_${T}h.csv" \
--T=$T \
--dt=$dt \
--theta_1=0.001 \
--theta_2=0.001 \
--theta_freq=1 \
--stats_functions 'min' 'max' 'mean' \
> >(tee "log/outcome=$OUTCOME,T=$T,dt=$dt.out") \
2> >(tee "log/outcome=$OUTCOME,T=$T,dt=$dt.err" >&2)
OUTCOME=Shock
T=4.0
dt=1.0
python -m FIDDLE.run \
--data_path="$DATAPATH/features/outcome=$OUTCOME,T=$T,dt=$dt/" \
--population="$DATAPATH/population/${OUTCOME}_${T}h.csv" \
--T=$T \
--dt=$dt \
--theta_1=0.001 \
--theta_2=0.001 \
--theta_freq=1 \
--stats_functions 'min' 'max' 'mean' \
> >(tee "log/outcome=$OUTCOME,T=$T,dt=$dt.out") \
2> >(tee "log/outcome=$OUTCOME,T=$T,dt=$dt.err" >&2)
OUTCOME=Shock
T=12.0
dt=1.0
python -m FIDDLE.run \
--data_path="$DATAPATH/features/outcome=$OUTCOME,T=$T,dt=$dt/" \
--population="$DATAPATH/population/${OUTCOME}_${T}h.csv" \
--T=$T \
--dt=$dt \
--theta_1=0.001 \
--theta_2=0.001 \
--theta_freq=1 \
--stats_functions 'min' 'max' 'mean' \
> >(tee "log/outcome=$OUTCOME,T=$T,dt=$dt.out") \
2> >(tee "log/outcome=$OUTCOME,T=$T,dt=$dt.err" >&2)
python prepare_input.py --outcome=ARF --T=4 --dt='1.0'
# python prepare_input.py --outcome=ARF --T=12 --dt='1.0'
# python prepare_input.py --outcome=Shock --T=4 --dt='1.0'
# python prepare_input.py --outcome=Shock --T=12 --dt='1.0'
# python make_features.py --outcome=ARF --T=4 --dt='1.0' > 'log/outcome=ARF.T=4.dt=1.0.out' 2> 'log/outcome=ARF.T=4.dt=1.0.err'
# python make_features.py --outcome=ARF --T=12 --dt='1.0' > >(tee 'log/outcome=ARF.T=12.dt=1.0.out') 2> >(tee 'log/outcome=ARF.T=12.dt=1.0.err' >&2)
# python make_features.py --outcome=Shock --T=4 --dt='1.0' > >(tee 'log/outcome=Shock.T=4.dt=1.0.out') 2> >(tee 'log/outcome=Shock.T=4.dt=1.0.err' >&2)
# python make_features.py --outcome=Shock --T=12 --dt='1.0' > >(tee 'log/outcome=Shock.T=12.dt=1.0.out') 2> >(tee 'log/outcome=Shock.T=12.dt=1.0.err' >&2)
# python make_features.py \
# --data_path='/data4/tangsp/mimic3_features/features/outcome=mortality.T=48.dt=1.0/' \
# --population='/data4/tangsp/mimic3_features/population/mortality_48h.csv' \
# --T=48 --dt='1.0' \
# > >(tee 'log/outcome=mortality.T=48.dt=1.0.out') \
# 2> >(tee 'log/outcome=mortality.T=48.dt=1.0.err' >&2)
python make_features.py \
--data_path='/data4/tangsp/mimic3_features/features/outcome=mortality.T=48.dt=1.0/' \
--population='/data4/tangsp/mimic3_features/population/mortality_48h.csv' \
--T=48 --dt='1.0'
python -m FIDDLE.run \
--data_path='./small_test/' \
--population='./small_test/pop.csv' \
--T=4 \
--data_path="$DATAPATH/features/benchmark,outcome=mortality,T=48.0,dt=1.0/" \
--population="$DATAPATH/population/pop.mortality_benchmark.csv" \
--T=48.0 \
--dt=1.0 \
--theta_1=0.001 \
--theta_2=0.001 \
--theta_freq=1 \
--stats_functions 'min' 'max' 'mean' \
> >(tee 'log/outcome=mortality.T=48.dt=1.0.out') \
2> >(tee 'log/outcome=mortality.T=48.dt=1.0.err' >&2)
> >(tee 'log/benchmark,outcome=mortality,T=48.0,dt=1.0.out') \
2> >(tee 'log/benchmark,outcome=mortality,T=48.0,dt=1.0.err' >&2)
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