scripts/run_stage2.sh

#!/bin/bash
set -e

SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
PROJECT_ROOT="$(cd "${SCRIPT_DIR}/.." && pwd)"
cd "${PROJECT_ROOT}"

FEATURES="data/areds1_deepseenet_features.npz"

LATE_JSON="data/AREDS1_all_survival_small_Status_late_amd_20190601.json"
GA_JSON="data/AREDS1_all_survival_small_Status_anyga_20190601.json"
NV_JSON="data/AREDS1_all_survival_small_Status_nv_20190601.json"

mkdir -p runs

echo "=============================="
echo "Stage 2: DeepSeeNet Cox models"
echo "=============================="


# ============================================================
# Late AMD
# ============================================================

echo ""
echo ">>> Late AMD: global top16"
python survival/train_cox.py \
  --json "$LATE_JSON" \
  --features "$FEATURES" \
  --endpoint late_amd \
  --feature-set deep_clinical \
  --top-k 16 \
  --penalizer 0.01 \
  --output-dir runs/stage2_late_amd_deep_clinical_top16_p001

echo ""
echo ">>> Late AMD: block2"
python survival/train_cox.py \
  --json "$LATE_JSON" \
  --features "$FEATURES" \
  --endpoint late_amd \
  --feature-set deep_clinical \
  --top-k-per-block 2 \
  --penalizer 0.01 \
  --output-dir runs/stage2_late_amd_deep_clinical_block2_p001

echo ""
echo ">>> Late AMD: block4"
python survival/train_cox.py \
  --json "$LATE_JSON" \
  --features "$FEATURES" \
  --endpoint late_amd \
  --feature-set deep_clinical \
  --top-k-per-block 4 \
  --penalizer 0.01 \
  --output-dir runs/stage2_late_amd_deep_clinical_block4_p001

echo ""
echo ">>> Late AMD: block8"
python survival/train_cox.py \
  --json "$LATE_JSON" \
  --features "$FEATURES" \
  --endpoint late_amd \
  --feature-set deep_clinical \
  --top-k-per-block 8 \
  --penalizer 0.01 \
  --output-dir runs/stage2_late_amd_deep_clinical_block8_p001


# ============================================================
# Any GA
# ============================================================

echo ""
echo ">>> Any GA: global top16"
python survival/train_cox.py \
  --json "$GA_JSON" \
  --features "$FEATURES" \
  --endpoint anyga \
  --feature-set deep_clinical \
  --top-k 16 \
  --penalizer 0.01 \
  --output-dir runs/stage2_anyga_deep_clinical_top16_p001

echo ""
echo ">>> Any GA: block2"
python survival/train_cox.py \
  --json "$GA_JSON" \
  --features "$FEATURES" \
  --endpoint anyga \
  --feature-set deep_clinical \
  --top-k-per-block 2 \
  --penalizer 0.01 \
  --output-dir runs/stage2_anyga_deep_clinical_block2_p001

echo ""
echo ">>> Any GA: block4"
python survival/train_cox.py \
  --json "$GA_JSON" \
  --features "$FEATURES" \
  --endpoint anyga \
  --feature-set deep_clinical \
  --top-k-per-block 4 \
  --penalizer 0.01 \
  --output-dir runs/stage2_anyga_deep_clinical_block4_p001

echo ""
echo ">>> Any GA: block8"
python survival/train_cox.py \
  --json "$GA_JSON" \
  --features "$FEATURES" \
  --endpoint anyga \
  --feature-set deep_clinical \
  --top-k-per-block 8 \
  --penalizer 0.01 \
  --output-dir runs/stage2_anyga_deep_clinical_block8_p001


# ============================================================
# NV
# ============================================================

echo ""
echo ">>> NV: global top8"
python survival/train_cox.py \
  --json "$NV_JSON" \
  --features "$FEATURES" \
  --endpoint nv \
  --feature-set deep_clinical \
  --top-k 8 \
  --penalizer 0.01 \
  --output-dir runs/stage2_nv_deep_clinical_top8_p001

echo ""
echo ">>> NV: global top16"
python survival/train_cox.py \
  --json "$NV_JSON" \
  --features "$FEATURES" \
  --endpoint nv \
  --feature-set deep_clinical \
  --top-k 16 \
  --penalizer 0.01 \
  --output-dir runs/stage2_nv_deep_clinical_top16_p001

echo ""
echo ">>> NV: block2"
python survival/train_cox.py \
  --json "$NV_JSON" \
  --features "$FEATURES" \
  --endpoint nv \
  --feature-set deep_clinical \
  --top-k-per-block 2 \
  --penalizer 0.01 \
  --output-dir runs/stage2_nv_deep_clinical_block2_p001

echo ""
echo ">>> NV: block4"
python survival/train_cox.py \
  --json "$NV_JSON" \
  --features "$FEATURES" \
  --endpoint nv \
  --feature-set deep_clinical \
  --top-k-per-block 4 \
  --penalizer 0.01 \
  --output-dir runs/stage2_nv_deep_clinical_block4_p001

echo ""
echo ">>> NV: block8"
python survival/train_cox.py \
  --json "$NV_JSON" \
  --features "$FEATURES" \
  --endpoint nv \
  --feature-set deep_clinical \
  --top-k-per-block 8 \
  --penalizer 0.01 \
  --output-dir runs/stage2_nv_deep_clinical_block8_p001


echo ""
echo "Stage 2 complete."