ChemicalX

Data Structures and Loaders

Datasets and utilities.

Classes

BatchGenerator(batch_size, context_features, …)

Generator to create batches of drug pairs efficiently.

ContextFeatureSet(**kwargs)

Context feature set for biological/chemical context feature vectors.

DrugFeatureSet(**kwargs)

Drug feature set for compounds.

DrugPairBatch(identifiers, …)

A data class to store a labeled drug pair batch.

LabeledTriples(data)

Labeled triples for drug pair scoring.

DatasetLoader()

A generic dataset.

RemoteDatasetLoader(dataset_name)

A dataset loader for remote data.

LocalDatasetLoader([directory])

A dataset loader that processes and caches data locally.

DrugbankDDI()

A dataset loader for Drugbank DDI.

TwoSides()

A dataset loader for a sample of TWOSIDES.

DrugComb()

A dataset loader for DrugComb.

DrugCombDB()

A dataset loader for DrugCombDB.

OncoPolyPharmacology([directory])

A large-scale oncology screen of drug-drug synergy from [oneil2016].

Pair Scoring Models

Models for ChemicalX.

Classes

Model()

The base class for ChemicalX models.

UnimplementedModel(x)

The base class for unimplemented ChemicalX models.

CASTER(*, drug_channels[, …])

An implementation of the CASTER model from [huang2020].

DeepDDI(*, drug_channels[, hidden_channels, …])

An implementation of the DeepDDI model from [ryu2018].

DeepDDS(*, context_channels[, …])

An implementation of the DeepDDS model from [wang2021].

DeepDrug(*[, molecule_channels, …])

An implementation of the DeepDrug model from [cao2020].

DeepSynergy(*, context_channels, drug_channels)

An implementation of the DeepSynergy model from [preuer2018].

EPGCNDS(*[, molecule_channels, …])

An implementation of the EPGCN-DS model from [sun2020].

GCNBMP(*[, molecule_channels, …])

An implementation of the GCN-BMP model from [chen2020].

MatchMaker(*, context_channels, drug_channels)

An implementation of the MatchMaker model from [kuru2021].

MHCADDI(*[, atom_feature_channels, …])

An implementation of the MHCADDI model from [deac2019].

MRGNN(*[, molecule_channels, …])

An implementation of the MR-GNN model from [xu2019].

SSIDDI(*[, molecule_channels, …])

An implementation of the SSI-DDI model from [nyamabo2021].