| --- |
| license: apache-2.0 |
| tags: |
| - mass-spectrometry |
| - metabolomics |
| - spectrum-embedding |
| --- |
| |
| # UltraMS Unsupervised |
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| The general UltraMS MS/MS encoder, released from the completed retention-time-only epoch 11 (`rtonly11`) training checkpoint. UltraMS learned from UltraMSdata through masked peak reconstruction (MPR), followed by retention-time training. This model returns the encoder's normalized spectrum-level CLS embedding. |
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| | Output | Value | |
| | --- | --- | |
| | Embedding dimension | 1024 | |
| | Maximum spectral peaks | 150 | |
| | Python model name | `"unsupervised"` | |
| | Weights SHA-256 | `6a4c6660999848c409303119f6caa54fbae9444d0b75c7fcd8bafd303cde9830` | |
|
|
| ```bash |
| python -m pip install ultrams |
| ``` |
|
|
| ```python |
| from ultrams import UltraMS |
| |
| model = UltraMS.from_pretrained("unsupervised") |
| embedding = model.encode( |
| mz=[100.1, 121.1, 150.0], intensity=[20, 100, 35], precursor_mz=301.2 |
| ).embedding |
| print(embedding.shape) # (1024,) |
| ``` |
|
|
| Supply measured spectral peak `m/z` and intensity arrays plus precursor-ion `m/z`. UltraMS requires at least three spectral peaks with positive `m/z`, normalizes intensities by their maximum when positive, and retains the 150 most intense spectral peaks when needed. See the [input format](https://github.com/Dsadd4/UltraMS/blob/main/docs/data-format.md), [model selection](https://github.com/Dsadd4/UltraMS/blob/main/docs/model-selection.md), and [PyTorch fine-tuning example](https://github.com/Dsadd4/UltraMS/blob/main/examples/pytorch_finetune.py). |
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| Use `return_peaks=True` in `model.encode(...)` to obtain final encoder embeddings aligned with the retained spectral peaks. The three released checkpoints are in the [UltraMS model family](https://huggingface.co/collections/dsadd4/ultrams-6ab4cfaa860cbbd1f9a6b9b6). |
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