.DS_Store
.idea
.vscode
.history
.claude
.cursor
/.pytest_cache/

/data/
/local/
/cache
/model/
/processed/
/prepare_results/
/wandb/
/log/
/logs/
/backup_log/
/backup/
/archive/
# /foreign_dataset_files_to_convert/

__pycache__/
*.pt
*.pkl
# keep notebooks and markdown even if large
/comparison_results/**/*.json
/comparison_results/**/*.md
# 三级里面的是子方法，删除
/comparison_results/*/*/* 

*.out*
nohup.out
*.log*
*.tar.gz

*.tex
/agg/

/tests/
/sbatch_scripts/
*.safetensors
analysis_results/molhiv_comparison.png
analysis_results/peptides_func_comparison.png
analysis_results/zinc_comparison.png
detailed_analysis/aug_vs_noaug_analysis.png
detailed_analysis/comprehensive_heatmaps.png
detailed_analysis/cross_dataset_consistency.png
detailed_analysis/gte_keep_vs_reset_analysis.png
analyze_gte_exploration_results.py
consistency_analysis_summary.png
create_summary_visualization.py
detailed_visualization_analysis.py
gte_exploration_results.csv
key_findings_summary.png
hyperopt/journal/large_batch.db
hyperopt/journal/test_large_batch.db
hyperopt/journal/finetune_with_options.db
comparison_results/
analysis_results
