cnn-inference-on-spectral-data - Generate molecular embeddings from MS/MS spectra with CNN
Passes preprocessed MS/MS spectra through a trained CNN model to extract multidimensional molecular embedding vectors for downstream metabolite matching.
Tags
Updated: 2026-09-19Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Load preprocessed MS/MS spectral data
- Initialize trained CNN model checkpoint
- Extract molecular embedding vectors
- Save embedding feature matrix
Inputs
- Preprocessed MS/MS spectral data
- Trained CNN model checkpoint file
- MSP format spectra file
- YAML configuration file
Outputs
- Multidimensional molecular embedding vectors
- Embedding feature matrix in CSV or NumPy format
Requirements
- PyTorch framework
- ChemEmbed cnn_train module
- Pre-trained CNN model checkpoint