Welcome to deepmol’s documentation!

Contents:

• Introduction
• Installation
  • Pip
  • Manually
• Datasets
  • Using CSVLoader
  • Using SDFLoader
  • Directly from numpy arrays / lists
  • Access the data stored in the datasets
• Compound Standardization
  • Let’s see how our molecules look like using RDKit
  • BasicStandardizer
  • CustomStandardizer
  • ChEMBLStandardizer
• Compound Featurization
  • Introduction
  • 1D features: fingerprints and structural keys
  • 0D, 1D and 2D Descriptors
  • 3D descriptors
  • Mix features
  • DeepChem Featurization
  • One hot encoding
• Data Scaling
  • StandardScaler
  • MinMaxScaler
  • MaxAbsScaler
  • RobustScaler
  • Normalizer scaler
  • Binarizer scaler
  • QuantileTransformer
  • PowerTransformer
• Feature Selection
  • LowVarianceFS
  • KbestFS
  • PercentilFS
  • RFECVFS
  • SelectFromModelFS
  • BorutaAlgorithm
• Unsupervised Learning
  • PCA
  • t-SNE
  • KMeans
  • UMAP
  • Do your own analysis
• Data Split
  • SingletaskStratifiedSplitter
  • RandomSplitter
  • MultiTaskSplitter
  • Similarity Splitter
  • Scaffold Splitter
  • Butina splitter
• Unbalanced Datasets
  • Let’s create a dataset with imbalanced labels
  • Over Sampling Methods
  • RandomOverSampler
  • SMOTE
  • Under Sampling Methods
  • RandomUnderSampler
  • ClusterCentroids
  • Combination of Under and Over Sampling
  • SMOTEENN
  • SMOTETomek
• Supervised Learning
  • Scikit-learn models
  • Keras models
  • DeepChem models
• Hyperparameter Optimization
  • Hyperparameter tuning with scikit-learn
  • Hyperparameter tuning with keras
  • Hyperparameter tuning with DeepChem models
• Pipelines
  • Pipeline for supervised learning
  • Pipeline just to visualize the chemical space
  • Optimize model hyperparameters in the pipeline
• Pipeline Optimization
  • Example using a custom objective function
  • Example using a preset
• Feature Importance
  • Compute SHAP values
  • Draw relevant features
• About Us
  • Contributors
• Related Publications
• src
  • deepmol package

Indices and tables

• Module Index

• Search Page