DreaMS
  • DreaMS documentation

Tutorials

  • Working with MS/MS data using HDF5
    • Opening files and converting them to .hdf5
    • Accessing individual spectra and their metadata
    • Handling all MS/MS spectra
    • Handling all metadata
    • Working with huge files
  • DreaMS embeddings
    • Computing embeddings
    • Visualizing embeddings with UMAP
  • Libray matching with DreaMS
    • Introduction
    • Load data
    • Perform library matching
    • Library matching results
    • Even faster search via approximate nearest neighbors
  • DreaMS molecular networking
    • Introduction
    • Construct molecular network
    • Populate the network with node and edge metadata
    • Export to Cytoscape
    • Tips and tricks
  • Clustering MS/MS spectra with LSH
    • Computing LSH hashes
    • Understanding LSH hashes and clusters
    • Clustering spectra from a collection of .mzML files
  • Assessing spectral quality
  • DreaMS Atlas
    • Initialization
    • Accesing data from the Atlas
    • Exploring local structure of the Atlas
    • Exploring global structure of the Atlas
  • Using pre-trained DreaMS in a custom model
  • DreaMS-Fluorine
    • 1. Obtain model weights
    • 2. Run DreaMS-Fluorine
    • 3. Examine the predictions

Advanced tutorials

  • Constructing GeMS dataset
    • 1. Determine GNPS Files to Download
    • 2. Download and Process Files
    • 3. Merge and filter files to GeMS-X
    • 4. Subset GeMS-X with LSH to get GeMS-XY
    • Accessing GeMS data
  • Murcko histogram split
    • Introduction
    • Load the MassSpecGym dataset
    • 1. Compute Murcko histograms
    • 2. Split the dataset into training and validation sets based on Murcko histograms
    • 3. Evaluate data leakage
    • 4. Store the dataset with a new fold column
  • Self-supervsied pre-training
  • Fine-tuning for downstream tasks

API Reference

  • API Reference
    • dreams package
      • Subpackages
        • dreams.algorithms package
        • dreams.models package
        • dreams.training package
        • dreams.utils package
      • Submodules
      • dreams.api module
        • DreaMSAtlas
        • DreaMSSearch
        • PreTrainedModel
        • dreams_attn_scores()
        • dreams_embeddings()
        • dreams_intermediates()
        • dreams_predictions()
        • predict_fluorine()
      • dreams.cli module
        • serialize()
      • dreams.definitions module
        • export()
      • Module contents
DreaMS
  • API Reference
  • dreams package
  • dreams.algorithms package
  • View page source
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dreams.algorithms package

Subpackages

  • dreams.algorithms.lsh package
    • Submodules
    • dreams.algorithms.lsh.lsh module
      • BatchedPeakListRandomProjection
        • BatchedPeakListRandomProjection.compute()
      • PeakListRandomProjection
        • PeakListRandomProjection.compute()
      • RandomProjection
        • RandomProjection.compute()
    • Module contents
      • BatchedPeakListRandomProjection
        • BatchedPeakListRandomProjection.compute()
      • PeakListRandomProjection
        • PeakListRandomProjection.compute()
  • dreams.algorithms.murcko_hist package
    • Submodules
    • dreams.algorithms.murcko_hist.murcko_hist module
      • are_sub_hists()
      • break_rings()
      • multirings()
      • murcko_hist()
      • murcko_hists_dist()
    • Module contents
      • are_sub_hists()
      • murcko_hist()
      • murcko_hists_dist()

Module contents

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