pytdc

What this skill does

# PyTDC (Therapeutics Data Commons)

## Overview

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).

## When to Use This Skill

This skill should be used when:
- Working with drug discovery or therapeutic ML datasets
- Benchmarking machine learning models on standardized pharmaceutical tasks
- Predicting molecular properties (ADME, toxicity, bioactivity)
- Predicting drug-target or drug-drug interactions
- Generating novel molecules with desired properties
- Accessing curated datasets with proper train/test splits (scaffold, cold-split)
- Using molecular oracles for property optimization

## Installation & Setup

Install PyTDC using pip:

```bash
uv pip install PyTDC
```

To upgrade to the latest version:

```bash
uv pip install PyTDC --upgrade
```

Core dependencies (automatically installed):
- numpy, pandas, tqdm, seaborn, scikit_learn, fuzzywuzzy

Additional packages are installed automatically as needed for specific features.

## Quick Start

The basic pattern for accessing any TDC dataset follows this structure:

```python
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 task

**Example - Loading ADME data:**

```python
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 Tasks

Single-instance prediction involves forecasting properties of individual biomedical entities (molecules, proteins, etc.).

### Available Task Categories

#### 1. ADME (Absorption, Distribution, Metabolism, Excretion)

Predict pharmacokinetic properties of drug molecules.

```python
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:**
- Caco2 - Intestinal permeability
- HIA - Human intestinal absorption
- Bioavailability - Oral bioavailability
- Lipophilicity - Octanol-water partition coefficient
- Solubility - Aqueous solubility
- BBB - Blood-brain barrier penetration
- CYP - Cytochrome P450 metabolism

#### 2. Toxicity (Tox)

Predict toxicity and adverse effects of compounds.

```python
from tdc.single_pred import Tox
data = Tox(name='hERG')  # Cardiotoxicity
# Other datasets: AMES, DILI, Carcinogens_Lagunin, etc.
```

**Common toxicity datasets:**
- hERG - Cardiac toxicity
- AMES - Mutagenicity
- DILI - Drug-induced liver injury
- Carcinogens - Carcinogenicity
- ClinTox - Clinical trial toxicity

#### 3. HTS (High-Throughput Screening)

Bioactivity predictions from screening data.

```python
from tdc.single_pred import HTS
data = HTS(name='SARSCoV2_Vitro_Touret')
```

#### 4. QM (Quantum Mechanics)

Quantum mechanical properties of molecules.

```python
from tdc.single_pred import QM
data = QM(name='QM7')
```

#### 5. Other Single Prediction Tasks

- **Yields**: Chemical reaction yield prediction
- **Epitope**: Epitope prediction for biologics
- **Develop**: Development-stage predictions
- **CRISPROutcome**: Gene editing outcome prediction

### Data Format

Single prediction datasets typically return DataFrames with columns:
- `Drug_ID` or `Compound_ID`: Unique identifier
- `Drug` or `X`: SMILES string or molecular representation
- `Y`: Target label (continuous or binary)

## Multi-Instance Prediction Tasks

Multi-instance prediction involves forecasting properties of interactions between multiple biomedical entities.

### Available Task Categories

#### 1. DTI (Drug-Target Interaction)

Predict binding affinity between drugs and protein targets.

```python
from tdc.multi_pred import DTI
data = DTI(name='BindingDB_Kd')
split = data.get_split()
```

**Available datasets:**
- BindingDB_Kd - Dissociation constant (52,284 pairs)
- BindingDB_IC50 - Half-maximal inhibitory concentration (991,486 pairs)
- BindingDB_Ki - Inhibition constant (375,032 pairs)
- DAVIS, KIBA - Kinase binding datasets

**Data format:** Drug_ID, Target_ID, Drug (SMILES), Target (sequence), Y (binding affinity)

#### 2. DDI (Drug-Drug Interaction)

Predict interactions between drug pairs.

```python
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.

#### 3. PPI (Protein-Protein Interaction)

Predict protein-protein interactions.

```python
from tdc.multi_pred import PPI
data = PPI(name='HuRI')
```

#### 4. Other Multi-Prediction Tasks

- **GDA**: Gene-disease associations
- **DrugRes**: Drug resistance prediction
- **DrugSyn**: Drug synergy prediction
- **PeptideMHC**: Peptide-MHC binding
- **AntibodyAff**: Antibody affinity prediction
- **MTI**: miRNA-target interactions
- **Catalyst**: Catalyst prediction
- **TrialOutcome**: Clinical trial outcome prediction

## Generation Tasks

Generation tasks involve creating novel biomedical entities with desired properties.

### 1. Molecular Generation (MolGen)

Generate diverse, novel molecules with desirable chemical properties.

```python
from tdc.generation import MolGen
data = MolGen(name='ChEMBL_V29')
split = data.get_split()
```

Use with oracles to optimize for specific properties:

```python
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.

### 2. Retrosynthesis (RetroSyn)

Predict reactants needed to synthesize a target molecule.

```python
from tdc.generation import RetroSyn
data = RetroSyn(name='USPTO')
split = data.get_split()
```

Dataset contains 1,939,253 reactions from USPTO database.

### 3. Paired Molecule Generation

Generate molecule pairs (e.g., prodrug-drug pairs).

```python
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

Benchmark groups provide curated collections of related datasets for systematic model evaluation.

### ADMET Benchmark Group

```python
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.

### Other Benchmark Groups

Available benchmark groups include collections for:
- ADMET properties
- Drug-target interactions
- Drug combination prediction
- And more specialized therapeutic tasks

For benchmark evaluation workflows, see `scripts/benchmark_evaluation.py`.

## Data Functions

TDC provides comprehensive data processing utilities organized into four categories.

### 1. Dataset Splits

Retrieve train/validation/test partitions with various strategies:

```python
# 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='r