From scientific-skills
Loads PyTDC datasets and benchmarks for drug discovery ML: ADME, toxicity, DTI tasks with scaffold splits and molecular oracles.
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PyTDC is an open-science platform providing AI-ready datasets and benchmarks for drug discovery and development. Access curated datasets spanning the entire therapeutics pipeline with standardized evaluation metrics and meaningful data splits, organized into three categories: single-instance prediction (molecular/protein properties), multi-instance prediction (drug-target interactions, DDI), an...
Loads PyTDC datasets and benchmarks for drug discovery ML: ADME, toxicity, DTI tasks with scaffold splits and molecular oracles.
Provides AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, and molecular oracles for therapeutic ML and pharmacological predictions.
Loads PyTDC Therapeutics Data Commons datasets for drug discovery ML including ADME, toxicity, DTI, DDI with scaffold splits, benchmarks, metrics, and molecular oracles.
Share bugs, ideas, or general feedback.
PyTDC is an open-science platform providing AI-ready datasets and benchmarks for drug discovery and development. Access curated datasets spanning the entire therapeutics pipeline with standardized evaluation metrics and meaningful data splits, organized into three categories: single-instance prediction (molecular/protein properties), multi-instance prediction (drug-target interactions, DDI), and generation (molecule generation, retrosynthesis).
This skill should be used when:
Install PyTDC using pip:
uv pip install PyTDC
To upgrade to the latest version:
uv pip install PyTDC --upgrade
Core dependencies (automatically installed):
Additional packages are installed automatically as needed for specific features.
The basic pattern for accessing any TDC dataset follows this structure:
from tdc.<problem> import <Task>
data = <Task>(name='<Dataset>')
split = data.get_split(method='scaffold', seed=1, frac=[0.7, 0.1, 0.2])
df = data.get_data(format='df')
Where:
<problem>: One of single_pred, multi_pred, or generation<Task>: Specific task category (e.g., ADME, DTI, MolGen)<Dataset>: Dataset name within that taskExample - Loading ADME data:
from tdc.single_pred import ADME
data = ADME(name='Caco2_Wang')
split = data.get_split(method='scaffold')
# Returns dict with 'train', 'valid', 'test' DataFrames
Single-instance prediction involves forecasting properties of individual biomedical entities (molecules, proteins, etc.).
Predict pharmacokinetic properties of drug molecules.
from tdc.single_pred import ADME
data = ADME(name='Caco2_Wang') # Intestinal permeability
# Other datasets: HIA_Hou, Bioavailability_Ma, Lipophilicity_AstraZeneca, etc.
Common ADME datasets:
Predict toxicity and adverse effects of compounds.
from tdc.single_pred import Tox
data = Tox(name='hERG') # Cardiotoxicity
# Other datasets: AMES, DILI, Carcinogens_Lagunin, etc.
Common toxicity datasets:
Bioactivity predictions from screening data.
from tdc.single_pred import HTS
data = HTS(name='SARSCoV2_Vitro_Touret')
Quantum mechanical properties of molecules.
from tdc.single_pred import QM
data = QM(name='QM7')
Single prediction datasets typically return DataFrames with columns:
Drug_ID or Compound_ID: Unique identifierDrug or X: SMILES string or molecular representationY: Target label (continuous or binary)Multi-instance prediction involves forecasting properties of interactions between multiple biomedical entities.
Predict binding affinity between drugs and protein targets.
from tdc.multi_pred import DTI
data = DTI(name='BindingDB_Kd')
split = data.get_split()
Available datasets:
Data format: Drug_ID, Target_ID, Drug (SMILES), Target (sequence), Y (binding affinity)
Predict interactions between drug pairs.
from tdc.multi_pred import DDI
data = DDI(name='DrugBank')
split = data.get_split()
Multi-class classification task predicting interaction types. Dataset contains 191,808 DDI pairs with 1,706 drugs.
Predict protein-protein interactions.
from tdc.multi_pred import PPI
data = PPI(name='HuRI')
Generation tasks involve creating novel biomedical entities with desired properties.
Generate diverse, novel molecules with desirable chemical properties.
from tdc.generation import MolGen
data = MolGen(name='ChEMBL_V29')
split = data.get_split()
Use with oracles to optimize for specific properties:
from tdc import Oracle
oracle = Oracle(name='GSK3B')
score = oracle('CC(C)Cc1ccc(cc1)C(C)C(O)=O') # Evaluate SMILES
See references/oracles.md for all available oracle functions.
Predict reactants needed to synthesize a target molecule.
from tdc.generation import RetroSyn
data = RetroSyn(name='USPTO')
split = data.get_split()
Dataset contains 1,939,253 reactions from USPTO database.
Generate molecule pairs (e.g., prodrug-drug pairs).
from tdc.generation import PairMolGen
data = PairMolGen(name='Prodrug')
For detailed oracle documentation and molecular generation workflows, refer to references/oracles.md and scripts/molecular_generation.py.
Benchmark groups provide curated collections of related datasets for systematic model evaluation.
from tdc.benchmark_group import admet_group
group = admet_group(path='data/')
# Get benchmark datasets
benchmark = group.get('Caco2_Wang')
predictions = {}
for seed in [1, 2, 3, 4, 5]:
train, valid = benchmark['train'], benchmark['valid']
# Train model here
predictions[seed] = model.predict(benchmark['test'])
# Evaluate with required 5 seeds
results = group.evaluate(predictions)
ADMET Group includes 22 datasets covering absorption, distribution, metabolism, excretion, and toxicity.
Available benchmark groups include collections for:
For benchmark evaluation workflows, see scripts/benchmark_evaluation.py.
TDC provides comprehensive data processing utilities organized into four categories.
Retrieve train/validation/test partitions with various strategies:
# Scaffold split (default for most tasks)
split = data.get_split(method='scaffold', seed=1, frac=[0.7, 0.1, 0.2])
# Random split
split = data.get_split(method='random', seed=42, frac=[0.8, 0.1, 0.1])
# Cold split (for DTI/DDI tasks)
split = data.get_split(method='cold_drug', seed=1) # Unseen drugs in test
split = data.get_split(method='cold_target', seed=1) # Unseen targets in test
Available split strategies:
random: Random shufflingscaffold: Scaffold-based (for chemical diversity)cold_drug, cold_target, cold_drug_target: For DTI taskstemporal: Time-based splits for temporal datasetsUse standardized metrics for evaluation:
from tdc import Evaluator
# For binary classification
evaluator = Evaluator(name='ROC-AUC')
score = evaluator(y_true, y_pred)
# For regression
evaluator = Evaluator(name='RMSE')
score = evaluator(y_true, y_pred)
Available metrics: ROC-AUC, PR-AUC, F1, Accuracy, RMSE, MAE, R2, Spearman, Pearson, and more.
TDC provides 11 key processing utilities:
from tdc.chem_utils import MolConvert
# Molecule format conversion
converter = MolConvert(src='SMILES', dst='PyG')
pyg_graph = converter('CC(C)Cc1ccc(cc1)C(C)C(O)=O')
Processing utilities include:
For comprehensive utilities documentation, see references/utilities.md.
TDC provides 17+ oracle functions for molecular optimization:
from tdc import Oracle
# Single oracle
oracle = Oracle(name='DRD2')
score = oracle('CC(C)Cc1ccc(cc1)C(C)C(O)=O')
# Multiple oracles
oracle = Oracle(name='JNK3')
scores = oracle(['SMILES1', 'SMILES2', 'SMILES3'])
For complete oracle documentation, see references/oracles.md.
from tdc.utils import retrieve_dataset_names
# Get all ADME datasets
adme_datasets = retrieve_dataset_names('ADME')
# Get all DTI datasets
dti_datasets = retrieve_dataset_names('DTI')
# Get label mapping
label_map = data.get_label_map(name='DrugBank')
# Convert labels
from tdc.chem_utils import label_transform
transformed = label_transform(y, from_unit='nM', to_unit='p')
from tdc.utils import cid2smiles, uniprot2seq
# Convert PubChem CID to SMILES
smiles = cid2smiles(2244)
# Convert UniProt ID to amino acid sequence
sequence = uniprot2seq('P12345')
See scripts/load_and_split_data.py for a complete example:
from tdc.single_pred import ADME
from tdc import Evaluator
# Load data
data = ADME(name='Caco2_Wang')
split = data.get_split(method='scaffold', seed=42)
train, valid, test = split['train'], split['valid'], split['test']
# Train model (user implements)
# model.fit(train['Drug'], train['Y'])
# Evaluate
evaluator = Evaluator(name='MAE')
# score = evaluator(test['Y'], predictions)
See scripts/benchmark_evaluation.py for a complete example with multiple seeds and proper evaluation protocol.
See scripts/molecular_generation.py for an example of goal-directed generation using oracle functions.
This skill includes bundled resources for common TDC workflows:
load_and_split_data.py: Template for loading and splitting TDC datasets with various strategiesbenchmark_evaluation.py: Template for running benchmark group evaluations with proper 5-seed protocolmolecular_generation.py: Template for molecular generation using oracle functionsdatasets.md: Comprehensive catalog of all available datasets organized by task typeoracles.md: Complete documentation of all 17+ molecule generation oraclesutilities.md: Detailed guide to data processing, splitting, and evaluation utilities