Quickstart

This guide walks you through running your first lipid prediction with LipiDetective.

1. Copy the Config Template

$ cp config/config_templates/config_transformer.yaml my_config.yaml

2. Edit the Configuration

Open my_config.yaml and set the file paths for your data:

model: 'transformer'

files:
  predict_input: 'raw/my_spectra.mzML'      # Your input mzML file
  saved_model: 'lipidetective_model.pth'     # Pre-trained model
  output: 'my_first_run'                     # Output directory

workflow:
  predict: True
  load_model: True

See Configuration for all available options.

3. Run the Prediction

$ uv run lipidetective --config my_config.yaml

4. View the Results

Results are written to a timestamped subdirectory inside the output path you specified. The prediction CSV contains identified lipid species with confidence scores:

experiments/my_first_run/LipiDetective_Output_2026_02_08_14_30_00/
├── predictions.csv       # Lipid identifications
└── ...

See Output & Metrics for a detailed explanation of all output files.

Next Steps