MS-ML/SpecTUS_pretrained_only

The SpecTUS model pretrained on synth1_2x4.7 and synth2_2x4.8M combined for 448k steps.

The model is a Transformer-based neural network trained to elucidate molecular structures from GC-EI-MS spectra. The model was pretrained on a large dataset of 17.2M synthetic training spectra generated from two identical sets of 8.6M compounds using the NEIMS and RASSP models.

We mainly aimed to give the model an understanding of the chemical space of small molecules. The training was conducted with a batch size of 128 for 448,000 steps, allowing the model to process each of the 17.2 million spectra approximately three times. The entire pretraining process, including control evaluations every 16,000 steps, took 58 hours on a single Nvidia H100 GPU.

During pretraining, the percentage of correctly reconstructed structures increased steadily but it remained relatively low at the end of the stage: 38% for RASSP-generated spectra, 29% for NEIMS-generated spectra, and 3% for NIST spectra. However, 96% of the generated SMILES strings (RASSP, NEIMS) were valid canonical molecules, with 91% (RASSP), 78% (NEIMS), and 14% (NIST) having correct molecular formulas, though possibly incorrect structures. These results suggest that during the pretraining phase, the model successfully learned molecular structure rules and the relationship between atomic weight and m/z values, forming a good foundation for subsequent finetuning.

We suggest to finetune the model further on experimental data (NIST, Wiley) to reach the performance reported in our preprint. Though we can not make the final model available, since it was finetuned on a proprietary dataset (NIST). If youhave purchased the NIST GC-EI-MS license, you can either fine-tune the model yourself using the code in our GitHub repository or contact us with a proof of the license and we will share the final model with you. The code we used for the data processing, finetuning, evaluation, model comparison and more can also be found in our GitHub repository.

Our preprint provides more information about the task background, the final finetuned model, and the experiments.

How to cite:

@misc{hájek2025spectusspectraltranslatorunknown,
      title={SpecTUS: Spectral Translator for Unknown Structures annotation from EI-MS spectra}, 
      author={Adam Hájek and Helge Hecht and Elliott J. Price and Aleš Křenek},
      year={2025},
      eprint={2502.05114},
      archivePrefix={arXiv},
      primaryClass={cs.LG},
      url={https://arxiv.org/abs/2502.05114}, 
}