391 lines
10 KiB
Bash
391 lines
10 KiB
Bash
#!/usr/bin/env bash
|
|
#
|
|
# Run the matched experiments required after the all-future first-onset update.
|
|
#
|
|
# Shared by every experiment:
|
|
# - corrected first-onset likelihood and outcome-specific risk exposure;
|
|
# - patient/interval/time-uniform query sampling in train/valid/test;
|
|
# - timed disease history and smoking/alcohol/BMI extra information.
|
|
#
|
|
# Per seed, the script trains:
|
|
# 1. TrajMixer + relative Weibull + fitted risk baseline (primary model);
|
|
# 2. the primary model without the fitted risk baseline (baseline ablation);
|
|
# 3. TrajMixer + relative exponential (time-distribution control);
|
|
# 4. FFN + relative Weibull (architecture control).
|
|
#
|
|
# After training, AUC and calibration/point-process-NLL evaluation run
|
|
# automatically unless --train-only is supplied.
|
|
|
|
set -uo pipefail
|
|
|
|
SCRIPT_DIR="$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")" && pwd)"
|
|
cd "$SCRIPT_DIR"
|
|
|
|
GPU_CSV=""
|
|
SEED_CSV="42,43,44"
|
|
NUM_WORKERS=4
|
|
PYTHON_BIN="${PYTHON_BIN:-python}"
|
|
CAMPAIGN_NAME="all_future_first_onset_v2_multiseed"
|
|
DRY_RUN=0
|
|
TRAIN_ONLY=0
|
|
|
|
BATCH_SIZE=256
|
|
EXTRA_INFO_TYPES_FILE="$SCRIPT_DIR/extra_info_types_smoking_alcohol_bmi.txt"
|
|
TRAIN_EID_FILE="$SCRIPT_DIR/ukb_train_eid.csv"
|
|
VAL_EID_FILE="$SCRIPT_DIR/ukb_val_eid.csv"
|
|
TEST_EID_FILE="$SCRIPT_DIR/ukb_test_eid.csv"
|
|
|
|
usage() {
|
|
cat <<'EOF'
|
|
Usage:
|
|
bash run_all_future_first_onset_experiments_linux.sh --gpus LIST [options]
|
|
|
|
Required:
|
|
--gpus LIST Comma-separated GPU ids, for example 0 or 0,1,2,3.
|
|
|
|
Options:
|
|
--seeds LIST Comma-separated seeds (default: 42,43,44).
|
|
--num-workers N DataLoader workers per active GPU (default: 4).
|
|
--python PATH Python executable (default: $PYTHON_BIN or python).
|
|
--campaign NAME Output campaign directory name.
|
|
--train-only Skip AUC and calibration/NLL evaluation.
|
|
--dry-run Print commands without running them.
|
|
-h, --help Show this help message.
|
|
|
|
Fixed settings:
|
|
batch_size 256
|
|
extra information smoking + alcohol + BMI
|
|
patient split fixed train/validation/test EID files
|
|
disease history timed
|
|
experiments per seed 4
|
|
|
|
Outputs:
|
|
runs/<campaign>/seed_<seed>/<architecture>/...
|
|
batch_logs/<campaign>/seed_<seed>/<experiment>.log
|
|
EOF
|
|
}
|
|
|
|
while (($# > 0)); do
|
|
case "$1" in
|
|
--gpus)
|
|
[[ $# -ge 2 ]] || {
|
|
echo "ERROR: --gpus requires a value." >&2
|
|
exit 2
|
|
}
|
|
GPU_CSV="$2"
|
|
shift 2
|
|
;;
|
|
--seeds)
|
|
[[ $# -ge 2 ]] || {
|
|
echo "ERROR: --seeds requires a value." >&2
|
|
exit 2
|
|
}
|
|
SEED_CSV="$2"
|
|
shift 2
|
|
;;
|
|
--num-workers)
|
|
[[ $# -ge 2 ]] || {
|
|
echo "ERROR: --num-workers requires a value." >&2
|
|
exit 2
|
|
}
|
|
NUM_WORKERS="$2"
|
|
shift 2
|
|
;;
|
|
--python)
|
|
[[ $# -ge 2 ]] || {
|
|
echo "ERROR: --python requires a value." >&2
|
|
exit 2
|
|
}
|
|
PYTHON_BIN="$2"
|
|
shift 2
|
|
;;
|
|
--campaign)
|
|
[[ $# -ge 2 ]] || {
|
|
echo "ERROR: --campaign requires a value." >&2
|
|
exit 2
|
|
}
|
|
CAMPAIGN_NAME="$2"
|
|
shift 2
|
|
;;
|
|
--train-only)
|
|
TRAIN_ONLY=1
|
|
shift
|
|
;;
|
|
--dry-run)
|
|
DRY_RUN=1
|
|
shift
|
|
;;
|
|
-h|--help)
|
|
usage
|
|
exit 0
|
|
;;
|
|
*)
|
|
echo "ERROR: unknown argument: $1" >&2
|
|
usage >&2
|
|
exit 2
|
|
;;
|
|
esac
|
|
done
|
|
|
|
[[ -n "$GPU_CSV" ]] || {
|
|
echo "ERROR: --gpus is required." >&2
|
|
usage >&2
|
|
exit 2
|
|
}
|
|
[[ -n "$SEED_CSV" ]] || {
|
|
echo "ERROR: --seeds must not be empty." >&2
|
|
exit 2
|
|
}
|
|
[[ "$NUM_WORKERS" =~ ^[0-9]+$ ]] || {
|
|
echo "ERROR: --num-workers must be a non-negative integer." >&2
|
|
exit 2
|
|
}
|
|
[[ "$CAMPAIGN_NAME" =~ ^[A-Za-z0-9._-]+$ ]] || {
|
|
echo "ERROR: --campaign may contain only letters, numbers, ., _, and -." >&2
|
|
exit 2
|
|
}
|
|
|
|
required_files=(
|
|
"$SCRIPT_DIR/train_all_future.py"
|
|
"$SCRIPT_DIR/evaluate_all_runs_linux.sh"
|
|
"$SCRIPT_DIR/evaluate_calibration_all_runs_linux.sh"
|
|
"$EXTRA_INFO_TYPES_FILE"
|
|
"$TRAIN_EID_FILE"
|
|
"$VAL_EID_FILE"
|
|
"$TEST_EID_FILE"
|
|
)
|
|
for required_file in "${required_files[@]}"; do
|
|
[[ -f "$required_file" ]] || {
|
|
echo "ERROR: missing required file: $required_file" >&2
|
|
exit 2
|
|
}
|
|
done
|
|
command -v "$PYTHON_BIN" >/dev/null 2>&1 || {
|
|
echo "ERROR: Python executable not found: $PYTHON_BIN" >&2
|
|
exit 2
|
|
}
|
|
|
|
IFS=',' read -r -a GPU_IDS <<< "$GPU_CSV"
|
|
declare -A SEEN_GPUS=()
|
|
for gpu in "${GPU_IDS[@]}"; do
|
|
[[ -n "$gpu" && "$gpu" =~ ^[A-Za-z0-9._:-]+$ ]] || {
|
|
echo "ERROR: invalid GPU id: $gpu" >&2
|
|
exit 2
|
|
}
|
|
[[ -z "${SEEN_GPUS[$gpu]+x}" ]] || {
|
|
echo "ERROR: duplicate GPU id: $gpu" >&2
|
|
exit 2
|
|
}
|
|
SEEN_GPUS["$gpu"]=1
|
|
done
|
|
|
|
IFS=',' read -r -a SEEDS <<< "$SEED_CSV"
|
|
declare -A SEEN_SEEDS=()
|
|
for seed in "${SEEDS[@]}"; do
|
|
[[ "$seed" =~ ^[0-9]+$ ]] || {
|
|
echo "ERROR: invalid seed: $seed" >&2
|
|
exit 2
|
|
}
|
|
[[ -z "${SEEN_SEEDS[$seed]+x}" ]] || {
|
|
echo "ERROR: duplicate seed: $seed" >&2
|
|
exit 2
|
|
}
|
|
SEEN_SEEDS["$seed"]=1
|
|
done
|
|
|
|
RUNS_ROOT="$SCRIPT_DIR/runs/$CAMPAIGN_NAME"
|
|
LOG_ROOT="$SCRIPT_DIR/batch_logs/$CAMPAIGN_NAME"
|
|
if ((DRY_RUN == 0)); then
|
|
mkdir -p "$RUNS_ROOT" "$LOG_ROOT"
|
|
fi
|
|
|
|
declare -a JOB_NAMES=()
|
|
declare -a JOB_SEEDS=()
|
|
declare -a JOB_ARCHITECTURES=()
|
|
declare -a JOB_DIST_MODES=()
|
|
declare -a JOB_BASELINES=()
|
|
|
|
add_job() {
|
|
JOB_NAMES+=("$1")
|
|
JOB_SEEDS+=("$2")
|
|
JOB_ARCHITECTURES+=("$3")
|
|
JOB_DIST_MODES+=("$4")
|
|
JOB_BASELINES+=("$5")
|
|
}
|
|
|
|
for seed in "${SEEDS[@]}"; do
|
|
add_job \
|
|
"traj_mixer_relative_weibull_first_onset" \
|
|
"$seed" \
|
|
"traj_mixer_v5" \
|
|
"weibull" \
|
|
"on"
|
|
add_job \
|
|
"traj_mixer_relative_weibull_no_rate_baseline" \
|
|
"$seed" \
|
|
"traj_mixer_v5" \
|
|
"weibull" \
|
|
"off"
|
|
add_job \
|
|
"traj_mixer_relative_exponential_first_onset" \
|
|
"$seed" \
|
|
"traj_mixer_v5" \
|
|
"exponential" \
|
|
"on"
|
|
add_job \
|
|
"ffn_relative_weibull_first_onset" \
|
|
"$seed" \
|
|
"transformer_ffn_v1" \
|
|
"weibull" \
|
|
"on"
|
|
done
|
|
|
|
print_command() {
|
|
printf '%q ' "$@"
|
|
printf '\n'
|
|
}
|
|
|
|
run_job() {
|
|
local job_index="$1"
|
|
local gpu="$2"
|
|
local job_name="${JOB_NAMES[$job_index]}"
|
|
local seed="${JOB_SEEDS[$job_index]}"
|
|
local architecture="${JOB_ARCHITECTURES[$job_index]}"
|
|
local dist_mode="${JOB_DIST_MODES[$job_index]}"
|
|
local baseline="${JOB_BASELINES[$job_index]}"
|
|
local seed_runs_root="$RUNS_ROOT/seed_$seed"
|
|
local seed_log_root="$LOG_ROOT/seed_$seed"
|
|
local log_file="$seed_log_root/$job_name.log"
|
|
local -a command=(
|
|
"$PYTHON_BIN"
|
|
-u
|
|
"$SCRIPT_DIR/train_all_future.py"
|
|
--runs_root "$seed_runs_root"
|
|
--seed "$seed"
|
|
--batch_size "$BATCH_SIZE"
|
|
--num_workers "$NUM_WORKERS"
|
|
--device cuda
|
|
--model_architecture "$architecture"
|
|
--time_mode relative
|
|
--dist_mode "$dist_mode"
|
|
--disease_history_mode timed
|
|
--extra_info_types_file "$EXTRA_INFO_TYPES_FILE"
|
|
--train_eid_file "$TRAIN_EID_FILE"
|
|
--val_eid_file "$VAL_EID_FILE"
|
|
--test_eid_file "$TEST_EID_FILE"
|
|
)
|
|
|
|
if [[ "$baseline" == "on" ]]; then
|
|
command+=(--risk_head_bias)
|
|
else
|
|
command+=(--no-risk_head_bias)
|
|
fi
|
|
|
|
if ((DRY_RUN == 0)); then
|
|
mkdir -p "$seed_runs_root" "$seed_log_root"
|
|
fi
|
|
|
|
echo "[$(date '+%F %T')] START seed=$seed job=$job_name gpu=$gpu"
|
|
echo " log=$log_file"
|
|
if ((DRY_RUN)); then
|
|
printf ' CUDA_VISIBLE_DEVICES=%q ' "$gpu"
|
|
print_command "${command[@]}"
|
|
return 0
|
|
fi
|
|
|
|
if CUDA_VISIBLE_DEVICES="$gpu" PYTHONUNBUFFERED=1 \
|
|
"${command[@]}" >"$log_file" 2>&1; then
|
|
echo "[$(date '+%F %T')] DONE seed=$seed job=$job_name gpu=$gpu"
|
|
return 0
|
|
else
|
|
local exit_code=$?
|
|
echo "[$(date '+%F %T')] FAIL seed=$seed job=$job_name gpu=$gpu exit=$exit_code" >&2
|
|
echo " See: $log_file" >&2
|
|
return "$exit_code"
|
|
fi
|
|
}
|
|
|
|
worker() {
|
|
local slot="$1"
|
|
local gpu="${GPU_IDS[$slot]}"
|
|
local job_index
|
|
local failed=0
|
|
|
|
for ((job_index = slot; job_index < ${#JOB_NAMES[@]}; job_index += ${#GPU_IDS[@]})); do
|
|
run_job "$job_index" "$gpu" || failed=1
|
|
done
|
|
return "$failed"
|
|
}
|
|
|
|
echo "Campaign: $CAMPAIGN_NAME"
|
|
echo "Seeds: ${SEEDS[*]}"
|
|
echo "GPUs: ${GPU_IDS[*]}"
|
|
echo "Experiments per seed: 4"
|
|
echo "Total training tasks: ${#JOB_NAMES[@]}"
|
|
echo "Runs root: $RUNS_ROOT"
|
|
echo "Log root: $LOG_ROOT"
|
|
echo
|
|
|
|
declare -a WORKER_PIDS=()
|
|
for ((slot = 0; slot < ${#GPU_IDS[@]}; slot++)); do
|
|
worker "$slot" &
|
|
WORKER_PIDS+=("$!")
|
|
done
|
|
|
|
overall_status=0
|
|
for pid in "${WORKER_PIDS[@]}"; do
|
|
wait "$pid" || overall_status=1
|
|
done
|
|
|
|
if ((overall_status != 0)); then
|
|
echo "One or more training tasks failed. Inspect: $LOG_ROOT" >&2
|
|
exit 1
|
|
fi
|
|
|
|
if ((TRAIN_ONLY == 0)); then
|
|
evaluation_status=0
|
|
auc_command=(
|
|
bash
|
|
"$SCRIPT_DIR/evaluate_all_runs_linux.sh"
|
|
--gpus "$GPU_CSV"
|
|
--runs-root "$RUNS_ROOT"
|
|
--log-root "$LOG_ROOT/evaluate_auc"
|
|
--python "$PYTHON_BIN"
|
|
--num-workers "$NUM_WORKERS"
|
|
--num-workers-auc "$NUM_WORKERS"
|
|
)
|
|
calibration_command=(
|
|
bash
|
|
"$SCRIPT_DIR/evaluate_calibration_all_runs_linux.sh"
|
|
--gpus "$GPU_CSV"
|
|
--runs-root "$RUNS_ROOT"
|
|
--log-root "$LOG_ROOT/evaluate_calibration"
|
|
--python "$PYTHON_BIN"
|
|
--num-workers "$NUM_WORKERS"
|
|
--num-workers-calibration "$NUM_WORKERS"
|
|
)
|
|
|
|
echo ">> AUC evaluation"
|
|
print_command "${auc_command[@]}"
|
|
if ((DRY_RUN == 0)); then
|
|
"${auc_command[@]}" || evaluation_status=1
|
|
fi
|
|
|
|
echo ">> Calibration and point-process NLL evaluation"
|
|
print_command "${calibration_command[@]}"
|
|
if ((DRY_RUN == 0)); then
|
|
"${calibration_command[@]}" || evaluation_status=1
|
|
fi
|
|
|
|
if ((evaluation_status != 0)); then
|
|
echo "One or more evaluation workflows failed. Inspect: $LOG_ROOT" >&2
|
|
exit 1
|
|
fi
|
|
fi
|
|
|
|
if ((DRY_RUN)); then
|
|
echo "Dry run completed successfully."
|
|
else
|
|
echo "All required all-future experiments completed successfully."
|
|
fi
|