| --- |
| license: other |
| license_name: mixed |
| license_link: https://github.com/harrylaucngd/msms-models/blob/main/THIRD_PARTY_NOTICES.md |
| tags: |
| - mass-spectrometry |
| - massspecgym |
| - molecule-retrieval |
| - de-novo-generation |
| --- |
| |
| # msms-models: weights and frozen inputs for *MassSpecGym in the Wild* |
|
|
| Model weights and frozen inputs for the implemented entries of *MassSpecGym in the Wild: |
| Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery*. The code, |
| configurations and per-entry instructions are in |
| [github.com/harrylaucngd/msms-models](https://github.com/harrylaucngd/msms-models). |
|
|
| Download into the root of a checkout; the paper configurations expect this layout: |
|
|
| ```bash |
| bash environments/install.sh && source .venv/bin/activate |
| bash paper/prepare_data.sh |
| hf download harrylau/msms-models --local-dir . --include 'checkpoints/*' 'data/*' |
| bash paper/table3/mist_4m_aug/run.sh |
| ``` |
|
|
| | Path | Contents | |
| |---|---| |
| | `data/paper/posteriors/` | MIST fingerprint posteriors: the Table 1 encoders, MIST *4M-aug* with MIST-CF or ground-truth formulas (Table 2), and MIST *4M-aug* for Tables 3–5 and Figure 2 | |
| | `data/paper/table2/` | MIST-CF top-1 formulas behind the Table 2 posteriors | |
| | `data/paper/table3/` | Table 3 test queries with imputed collision energies, the forward-model candidate pool, and the MIST vMassSpecGym subformula trees | |
| | `data/paper/table5/mist_vdiffms/` | DiffMS subformula trees | |
| | `checkpoints/mist_msg_aug.ckpt` | MIST *4M-aug* (MassSpecGym training set + GLACIER synthetic spectra) | |
| | `checkpoints/mist_vmassspecgym/` | MIST vMassSpecGym ([Zenodo 11580401](https://zenodo.org/records/11580401)) | |
| | `checkpoints/mist_vdiffms/` | MIST released with DiffMS ([Zenodo 15122968](https://zenodo.org/records/15122968)) | |
| | `checkpoints/molforge/` | MolForge decoder and SentencePiece models (**CC BY-NC-SA 4.0**) | |
| | `checkpoints/frigid/` | FRIGID DLM ([Zenodo 19685145](https://zenodo.org/records/19685145)), SAFE tokenizer and NGBoost length predictor | |
| | `checkpoints/iceberg/`, `checkpoints/glacier/` | ICEBERG pair for FRIGID refinement and FOAM; ICEBERG pair and GLACIER trained on the energy-completed split for Table 3 | |
| | `checkpoints/chemformer/`, `checkpoints/chemformer_two_stage/` | Chemformer two-stage retrieval (inflated and corrected) | |
| | `checkpoints/dreams_chemberta/` | DreaMS + ChemBERTa alignment (inflated and corrected) | |
|
|
| The decoder pretraining sets of the paper's Figure 2 are in |
| [harrylau/ms-gpt-18](https://huggingface.co/datasets/harrylau/ms-gpt-18). |
|
|
| Each component keeps the license of its original method; see the code repository's |
| third-party notices. The inflated checkpoints are the paper's shortcut-learning |
| examples, not valid benchmark models. |
|
|
