Document UltraMS 0.3.0 peak embeddings

README.md

@@ -15,6 +15,7 @@ The general UltraMS MS/MS encoder, released from the completed retention-time-on
 | Embedding dimension | 1024 |
 | Maximum spectral peaks | 150 |
 | Python model name | `"unsupervised"` |
+| Weights SHA-256 | `6a4c6660999848c409303119f6caa54fbae9444d0b75c7fcd8bafd303cde9830` |
 
 ```bash
 python -m pip install ultrams
@@ -31,3 +32,5 @@ 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).
+
+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).