Upload run_finetune.sh with huggingface_hub

run_finetune.sh

@@ -0,0 +1,71 @@
+#!/bin/bash
+# ============================================================================
+# Downstream fine-tuning script for ModernProteinLM
+# 
+# Usage:
+#   bash run_finetune.sh --task fluorescence
+#   bash run_finetune.sh --task solubility,fluorescence,stability
+# ============================================================================
+
+set -e
+
+# ----------------------------------------------------------------------------
+# CONFIGURATION
+# ----------------------------------------------------------------------------
+
+# Pretrained checkpoint
+PRETRAIN_DIR="${PRETRAIN_DIR:-./outputs/pretrain/final}"
+TASKS="${TASKS:-fluorescence,solubility}"
+
+# Fine-tuning
+EPOCHS="${EPOCHS:-20}"
+BATCH_SIZE="${BATCH_SIZE:-16}"
+LR="${LR:-1e-4}"
+WARMUP_RATIO="${WARMUP_RATIO:-0.1}"
+WEIGHT_DECAY="${WEIGHT_DECAY:-0.01}"
+
+# System
+OUTPUT_DIR="${OUTPUT_DIR:-./outputs/finetune}"
+NUM_WORKERS="${NUM_WORKERS:-4}"
+NUM_GPUS="${NUM_GPUS:-1}"
+
+# Precision
+USE_AMP="${USE_AMP:-1}"
+
+# Tracking
+USE_TRACKIO="${USE_TRACKIO:-0}"
+TRACKIO_PROJECT="${TRACKIO_PROJECT:-modern-protein-lm}"
+
+# ----------------------------------------------------------------------------
+# LAUNCH
+# ----------------------------------------------------------------------------
+
+PYTHON_ARGS=(
+    train_finetune.py
+    --pretrain_dir "$PRETRAIN_DIR"
+    --tasks "$TASKS"
+    --epochs "$EPOCHS"
+    --batch_size "$BATCH_SIZE"
+    --lr "$LR"
+    --warmup_ratio "$WARMUP_RATIO"
+    --weight_decay "$WEIGHT_DECAY"
+    --output_dir "$OUTPUT_DIR"
+    --num_workers "$NUM_WORKERS"
+)
+
+if [[ "$USE_AMP" == "1" ]]; then
+    PYTHON_ARGS+=(--use_amp)
+fi
+
+if [[ "$USE_TRACKIO" == "1" ]]; then
+    PYTHON_ARGS+=(--use_trackio --trackio_project "$TRACKIO_PROJECT")
+fi
+
+if command -v torchrun &> /dev/null && [[ "$NUM_GPUS" -gt 1 ]]; then
+    echo "Launching with torchrun on $NUM_GPUS GPUs..."
+    torchrun --standalone --nnodes=1 --nproc_per_node="$NUM_GPUS" "${PYTHON_ARGS[@]}"
+else
+    python "${PYTHON_ARGS[@]}"
+fi
+
+echo "Fine-tuning complete. Results in $OUTPUT_DIR"