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
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API Reference

  • dreams package
    • Subpackages
      • dreams.algorithms package
        • Subpackages
        • Module contents
      • dreams.models package
        • Subpackages
        • Module contents
      • dreams.training package
        • Submodules
        • dreams.training.train module
        • dreams.training.train_argparse module
        • Module contents
      • dreams.utils package
        • Submodules
        • dreams.utils.annotation module
        • dreams.utils.data module
        • dreams.utils.dformats module
        • dreams.utils.io module
        • dreams.utils.lcms module
        • dreams.utils.misc module
        • dreams.utils.mols module
        • dreams.utils.plots module
        • dreams.utils.spectra module
        • Module contents
    • Submodules
    • dreams.api module
      • DreaMSAtlas
        • DreaMSAtlas.decode_knn_i()
        • DreaMSAtlas.encode_knn_i()
        • DreaMSAtlas.get_data()
        • DreaMSAtlas.get_lib_idx()
        • DreaMSAtlas.get_lsh_cluster()
        • DreaMSAtlas.get_neighbors()
        • DreaMSAtlas.get_node_cluster()
        • DreaMSAtlas.get_node_repr()
        • DreaMSAtlas.is_library_i()
      • DreaMSSearch
        • DreaMSSearch.query()
      • PreTrainedModel
        • PreTrainedModel.available_models()
        • PreTrainedModel.from_ckpt()
        • PreTrainedModel.from_name()
        • PreTrainedModel.remove_unused_backbone_parameters()
      • dreams_attn_scores()
      • dreams_embeddings()
      • dreams_intermediates()
      • dreams_predictions()
      • predict_fluorine()
    • dreams.cli module
      • serialize()
    • dreams.definitions module
      • export()
    • Module contents
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