dsadd4/UltraMS-MoNA-Contrastive

UltraMS MoNA Contrastive

The UltraMS MS/MS encoder with a spectrum-level projection learned through contrastive training on MoNA spectra. encode(...).embedding returns the learned projection of the encoder's CLS embedding. Use cosine similarity to compare spectra in this space.

Output	Value
Embedding dimension	1024
Maximum spectral peaks	100
Python model name	"mona"
Weights SHA-256	3b8ae5bd85ff8f6991f8a78b6d70531aab74f32914878730e7296aaddb79afb0

python -m pip install ultrams

from ultrams import UltraMS

model = UltraMS.from_pretrained("mona")
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 100 most intense spectral peaks when needed. See the input format, model selection, and spectrum search example.

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.