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Add tutorials and usage examples #119

@j-adamczyk

Description

@j-adamczyk

We should add example usage of molecular fingerprints, in particular:

  1. Molecular property prediction (classification, regression, multioutput classification), with MoleculeNet and TDC benchmarks
  2. Visualization and clustering
  3. Virtual screening, e.g. with https://github.com/rdkit/benchmarking_platform

Those should also include computing fingerprints, tuning, and using parallelization. We should cover hashed fingerprints, descriptors, 3D variants with conformations etc.

Proposed tutorials list:

  • introduction
  • comparing different fingerprints (e.g. types, outputs, computation time)
  • scikit-learn pipelines (e.g. concatenating fingerprints, normalizing, preprocessing)
  • conformers and 3D fingerprints
  • hyperparameter tuning
  • different dataset splits
  • loading built-in datasets, benchmarking
  • distances and similarities, kNN, bulk functions
  • custom fingerprints
  • fingerprints for peptides, custom fingerprints using FASTA
  • molecular filters, custom filters
  • introduction to fingerprints and scikit-fingerprints for different backgrounds, e.g. chemists, chemoinformaticians, GNN researchers, ML scientists
  • virtual screening, similarity searching, classification
  • applicability domain checkers

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