attention ablation scripts

Author: mikageorges

analysis/post_training_pipeline/01b_evaluate_ablations.sh

@@ -0,0 +1,98 @@
+#!/bin/bash
+# evaluate_ablations.sh
+# Discovers and evaluates all ablation variants under an ablations/ directory.
+# Reads shared config (fasta paths, biotype CSV) from the parent experiment config.
+#
+# Usage:
+#   bash 01b_evaluate_ablations.sh \
+#       --ablations_dir <path/to/ablations> \
+#       --eval_script   <path/to/01_evaluate_cv_folds.sh> \
+#       --biotype_csv   <path/to/biotype.csv> \
+#       --gencode_version v47|v49 \
+#       [--n_folds 5] \
+#       [--device cuda:0]
+
+set -euo pipefail
+
+ABLATIONS_DIR=""
+EVAL_SCRIPT=""
+BIOTYPE_CSV=""
+GENCODE_VERSION=""
+N_FOLDS=5
+DEVICE="cuda:0"
+
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        --ablations_dir)    ABLATIONS_DIR="$2";    shift 2 ;;
+        --eval_script)      EVAL_SCRIPT="$2";      shift 2 ;;
+        --biotype_csv)      BIOTYPE_CSV="$2";      shift 2 ;;
+        --gencode_version)  GENCODE_VERSION="$2";  shift 2 ;;
+        --n_folds)          N_FOLDS="$2";          shift 2 ;;
+        --device)           DEVICE="$2";           shift 2 ;;
+        *) echo "Unknown argument: $1"; exit 1 ;;
+    esac
+done
+
+# Validate required args
+for var in ABLATIONS_DIR EVAL_SCRIPT BIOTYPE_CSV GENCODE_VERSION; do
+    [[ -z "${!var}" ]] && { echo "ERROR: --${var,,} required"; exit 1; }
+done
+[[ -d "$ABLATIONS_DIR" ]] || { echo "ERROR: $ABLATIONS_DIR not found"; exit 1; }
+[[ -f "$EVAL_SCRIPT"   ]] || { echo "ERROR: $EVAL_SCRIPT not found";   exit 1; }
+
+# Read fasta paths from parent experiment config (one level above ablations/)
+PARENT_CONFIG="$(dirname "$ABLATIONS_DIR")/config.json"
+[[ -f "$PARENT_CONFIG" ]] || { echo "ERROR: parent config not found at $PARENT_CONFIG"; exit 1; }
+
+LNC_TEST_FASTA=$(python3 -c "import json,sys; c=json.load(open('$PARENT_CONFIG')); print(c['data']['lnc_test_fasta'])")
+PC_TEST_FASTA=$(python3  -c "import json,sys; c=json.load(open('$PARENT_CONFIG')); print(c['data']['pc_test_fasta'])")
+
+echo "=== Ablation evaluation ==="
+echo "  Ablations dir  : $ABLATIONS_DIR"
+echo "  Eval script    : $EVAL_SCRIPT"
+echo "  GENCODE version: $GENCODE_VERSION"
+echo "  lnc test fasta : $LNC_TEST_FASTA"
+echo "  pc  test fasta : $PC_TEST_FASTA"
+echo "  Biotype CSV    : $BIOTYPE_CSV"
+echo "  Device         : $DEVICE"
+echo "==========================="
+
+n_total=0; n_skipped=0; n_done=0; n_failed=0
+
+for variant_dir in "$ABLATIONS_DIR"/*/; do
+    [[ -d "$variant_dir" ]] || continue
+    variant=$(basename "$variant_dir")
+
+    if [[ ! -f "$variant_dir/fold_results.json" ]]; then
+        echo "  [SKIP] $variant — training incomplete"
+        ((n_skipped++)); ((n_total++)); continue
+    fi
+
+    if [[ -f "$variant_dir/evaluation_csv/test_predictions.csv" ]]; then
+        echo "  [SKIP] $variant — already evaluated"
+        ((n_skipped++)); ((n_total++)); continue
+    fi
+
+    echo "  [RUN]  $variant"
+    if bash "$EVAL_SCRIPT" \
+        --experiment_dir    "$variant_dir" \
+        --config            "$variant_dir/config.json" \
+        --biotype_csv       "$BIOTYPE_CSV" \
+        --lnc_test_fasta    "$LNC_TEST_FASTA" \
+        --pc_test_fasta     "$PC_TEST_FASTA" \
+        --n_folds           "$N_FOLDS" \
+        --device            "$DEVICE" \
+        --model_label       "$variant" \
+        --gencode_version   "$GENCODE_VERSION" \
+        >> "$variant_dir/eval.log" 2>&1; then
+        echo "  [OK]   $variant"
+        ((n_done++))
+    else
+        echo "  [FAIL] $variant — see $variant_dir/eval.log"
+        ((n_failed++))
+    fi
+    ((n_total++))
+done
+
+echo ""
+echo "=== Summary: $n_total variants | $n_done evaluated | $n_skipped skipped | $n_failed failed ==="

scripts/train_beta_vae_features_ablation.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+#SBATCH --job-name=train_bvae_g47_features_attn_ablation_seqonly    # Job name
+#SBATCH --output=logs/train_bvae_g47_features_attn_ablation_seqonly.out # Standard output log
+#SBATCH --error=logs/train_bvae_g47_features_attn_ablation_seqonly.err  # Standard error log
+#SBATCH --gres=gpu:nvidia_h100_nvl             # Request 1 GPU
+#SBATCH --partition=gpu              # Partition to submit to (e.g., GPU queue)
+#SBATCH --time=64:00:00    # Time limit day:hrs:min:sec
+#SBATCH --mem=64G
+
+# Load modules (if necessary)
+module load nvidia/cuda/12.1                # Load CUDA module (adjust version as needed)
+eval "$(conda shell.bash hook)"
+conda activate beta_lncrna
+
+cd /mnt/cbib/LNClassifier/DL_benchmark
+
+# Run from project root
+python -m experiments.train.main_features_attn_ablation --base_config configs/beta_vae_features_attn_g47.json --variants seq_only seq_te seq_nonb --device cuda:0 --n_folds 5
+#python -m experiments.train.main_features_attn_ablation --base_config configs/beta_vae_features_attn_g49.json --variants seq_only seq_te seq_nonb --device cuda:0 --n_folds 5
+
+
+echo "Training complete at $(date)"
+echo "Job ID: $SLURM_JOB_ID"