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AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.","strmt7\u002Fai_skills_collection_benchmarked","strmt7","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F28989754?v=4","01M71929P914SWKQ7QJV24NBBY","Stratos","01M71929Q9VGKQ7PWYR95VSQQQ",1,"MIT","https:\u002F\u002Fgithub.com\u002Fstrmt7\u002Fai_skills_collection_benchmarked\u002Fblob\u002Fmain\u002Fincluded\u002Fskills\u002Fby-category\u002Fscience-research-data-analysis\u002Flatest-release-community\u002Fpytdc\u002FSKILL.md",[],[5,19,20,21,22,23,24,25,26,27,28,29,30,31],"scaffold","ml","data","discovery","ready","datasets","benchmarks","molecular","drug discovery","for","splits","prediction","toxicity","2026-11-10 10:12:30",false,"---\nname: pytdc\ndescription: Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.\nlicense: MIT license\nmetadata:\n    skill-author: K-Dense Inc.\n---\n\n# PyTDC (Therapeutics Data Commons)\n\n## Overview\n\nPyTDC 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\u002Fprotein properties), multi-instance prediction (drug-target interactions, DDI), and generation (molecule generation, retrosynthesis).\n\n## When to Use This Skill\n\nThis skill should be used when:\n- Working with drug discovery or therapeutic ML datasets\n- Benchmarking machine learning models on standardized pharmaceutical tasks\n- Predicting molecular properties (ADME, toxicity, bioactivity)\n- Predicting drug-target or drug-drug interactions\n- Generating novel molecules with desired properties\n- Accessing curated datasets with proper train\u002Ftest splits (scaffold, cold-split)\n- Using molecular oracles for property optimization\n\n## Installation & Setup\n\nInstall PyTDC using pip:\n\n```bash\nuv pip install PyTDC\n```\n\nTo upgrade to the latest version:\n\n```bash\nuv pip install PyTDC --upgrade\n```\n\nCore dependencies (automatically installed):\n- numpy, pandas, tqdm, seaborn, scikit_learn, fuzzywuzzy\n\nAdditional packages are installed automatically as needed for specific features.\n\n## Quick Start\n\nThe basic pattern for accessing any TDC dataset follows this structure:\n\n```python\nfrom tdc.\u003Cproblem> import \u003CTask>\ndata = \u003CTask>(name='\u003CDataset>')\nsplit = data.get_split(method='scaffold', seed=1, frac=[0.7, 0.1, 0.2])\ndf = data.get_data(format='df')\n```\n\nWhere:\n- `\u003Cproblem>`: One of `single_pred`, `multi_pred`, or `generation`\n- `\u003CTask>`: Specific task category (e.g., ADME, DTI, MolGen)\n- `\u003CDataset>`: Dataset name within that task\n\n**Example - Loading ADME data:**\n\n```python\nfrom tdc.single_pred import ADME\ndata = ADME(name='Caco2_Wang')\nsplit = data.get_split(method='scaffold')\n# Returns dict with 'train', 'valid', 'test' DataFrames\n```\n\n## Single-Instance Prediction Tasks\n\nSingle-instance prediction involves forecasting properties of individual biomedical entities (molecules, proteins, etc.).\n\n### Available Task Categories\n\n#### 1. ADME (Absorption, Distribution, Metabolism, Excretion)\n\nPredict pharmacokinetic properties of drug molecules.\n\n```python\nfrom tdc.single_pred import ADME\ndata = ADME(name='Caco2_Wang')  # Intestinal permeability\n# Other datasets: HIA_Hou, Bioavailability_Ma, Lipophilicity_AstraZeneca, etc.\n```\n\n**Common ADME datasets:**\n- Caco2 - Intestinal permeability\n- HIA - Human intestinal absorption\n- Bioavailability - Oral bioavailability\n- Lipophilicity - Octanol-water partition coefficient\n- Solubility - Aqueous solubility\n- BBB - Blood-brain barrier penetration\n- CYP - Cytochrome P450 metabolism\n\n#### 2. Toxicity (Tox)\n\nPredict toxicity and adverse effects of compounds.\n\n```python\nfrom tdc.single_pred import Tox\ndata = Tox(name='hERG')  # Cardiotoxicity\n# Other datasets: AMES, DILI, Carcinogens_Lagunin, etc.\n```\n\n**Common toxicity datasets:**\n- hERG - Cardiac toxicity\n- AMES - Mutagenicity\n- DILI - Drug-induced liver injury\n- Carcinogens - Carcinogenicity\n- ClinTox - Clinical trial toxicity\n\n#### 3. HTS (High-Throughput Screening)\n\nBioactivity predictions from screening data.\n\n```python\nfrom tdc.single_pred import HTS\ndata = HTS(name='SARSCoV2_Vitro_Touret')\n```\n\n#### 4. QM (Quantum Mechanics)\n\nQuantum mechanical properties of molecules.\n\n```python\nfrom tdc.single_pred import QM\ndata = QM(name='QM7')\n```\n\n#### 5. Other Single Prediction Tasks\n\n- **Yields**: Chemical reaction yield prediction\n- **Epitope**: Epitope prediction for biologics\n- **Develop**: Development-stage predictions\n- **CRISPROutcome**: Gene editing outcome prediction\n\n### Data Format\n\nSingle prediction datasets typically return DataFrames with columns:\n- `Drug_ID` or `Compound_ID`: Unique identifier\n- `Drug` or `X`: SMILES string or molecular representation\n- `Y`: Target label (continuous or binary)\n\n## Multi-Instance Prediction Tasks\n\nMulti-instance prediction involves forecasting properties of interactions between multiple biomedical entities.\n\n### Available Task Categories\n\n#### 1. DTI (Drug-Target Interaction)\n\nPredict binding affinity between drugs and protein targets.\n\n```python\nfrom tdc.multi_pred import DTI\ndata = DTI(name='BindingDB_Kd')\nsplit = data.get_split()\n```\n\n**Available datasets:**\n- BindingDB_Kd - Dissociation constant (52,284 pairs)\n- BindingDB_IC50 - Half-maximal inhibitory concentration (991,486 pairs)\n- BindingDB_Ki - Inhibition constant (375,032 pairs)\n- DAVIS, KIBA - Kinase binding datasets\n\n**Data format:** Drug_ID, Target_ID, Drug (SMILES), Target (sequence), Y (binding affinity)\n\n#### 2. DDI (Drug-Drug Interaction)\n\nPredict interactions between drug pairs.\n\n```python\nfrom tdc.multi_pred import DDI\ndata = DDI(name='DrugBank')\nsplit = data.get_split()\n```\n\nMulti-class classification task predicting interaction types. Dataset contains 191,808 DDI pairs with 1,706 drugs.\n\n#### 3. PPI (Protein-Protein Interaction)\n\nPredict protein-protein interactions.\n\n```python\nfrom tdc.multi_pred import PPI\ndata = PPI(name='HuRI')\n```\n\n#### 4. Other Multi-Prediction Tasks\n\n- **GDA**: Gene-disease associations\n- **DrugRes**: Drug resistance prediction\n- **DrugSyn**: Drug synergy prediction\n- **PeptideMHC**: Peptide-MHC binding\n- **AntibodyAff**: Antibody affinity prediction\n- **MTI**: miRNA-target interactions\n- **Catalyst**: Catalyst prediction\n- **TrialOutcome**: Clinical trial outcome prediction\n\n## Generation Tasks\n\nGeneration tasks involve creating novel biomedical entities with desired properties.\n\n### 1. Molecular Generation (MolGen)\n\nGenerate diverse, novel molecules with desirable chemical properties.\n\n```python\nfrom tdc.generation import MolGen\ndata = MolGen(name='ChEMBL_V29')\nsplit = data.get_split()\n```\n\nUse with oracles to optimize for specific properties:\n\n```python\nfrom tdc import Oracle\noracle = Oracle(name='GSK3B')\nscore = oracle('CC(C)Cc1ccc(cc1)C(C)C(O)=O')  # Evaluate SMILES\n```\n\nSee `references\u002Foracles.md` for all available oracle functions.\n\n### 2. Retrosynthesis (RetroSyn)\n\nPredict reactants needed to synthesize a target molecule.\n\n```python\nfrom tdc.generation import RetroSyn\ndata = RetroSyn(name='USPTO')\nsplit = data.get_split()\n```\n\nDataset contains 1,939,253 reactions from USPTO database.\n\n### 3. Paired Molecule Generation\n\nGenerate molecule pairs (e.g., prodrug-drug pairs).\n\n```python\nfrom tdc.generation import PairMolGen\ndata = PairMolGen(name='Prodrug')\n```\n\nFor detailed oracle documentation and molecular generation workflows, refer to `references\u002Foracles.md` and `scripts\u002Fmolecular_generation.py`.\n\n## Benchmark Groups\n\nBenchmark groups provide curated collections of related datasets for systematic model evaluation.\n\n### ADMET Benchmark Group\n\n```python\nfrom tdc.benchmark_group import admet_group\ngroup = admet_group(path='data\u002F')\n\n# Get benchmark datasets\nbenchmark = group.get('Caco2_Wang')\npredictions = {}\n\nfor seed in [1, 2, 3, 4, 5]:\n    train, valid = benchmark['train'], benchmark['valid']\n    # Train model here\n    predictions[seed] = model.predict(benchmark['test'])\n\n# Evaluate with required 5 seeds\nresults = group.evaluate(predictions)\n```\n\n**ADMET Group includes 22 datasets** covering absorption, distribution, metabolism, excretion, and toxicity.\n\n### Other Benchmark Groups\n\nAvailable benchmark groups include collections for:\n- ADMET properties\n- Drug-target interactions\n- Drug combination prediction\n- And more specialized therapeutic tasks\n\nFor benchmark evaluation workflows, see `scripts\u002Fbenchmark_evaluation.py`.\n\n## Data Functions\n\nTDC provides comprehensive data processing utilities organized into four categories.\n\n### 1. Dataset Splits\n\nRetrieve train\u002Fvalidation\u002Ftest partitions with various strategies:\n\n```python\n# Scaffold split (default for most tasks)\nsplit = data.get_split(method='scaffold', seed=1, frac=[0.7, 0.1, 0.2])\n\n# Random split\nsplit = data.get_split(method='random', seed=42, frac=[0.8, 0.1, 0.1])\n\n# Cold split (for DTI\u002FDDI tasks)\nsplit = data.get_split(method='cold_drug', seed=1)  # Unseen drugs in test\nsplit = data.get_split(method='cold_target', seed=1)  # Unseen targets in test\n```\n\n**Available split strategies:**\n- `random`: Random shuffling\n- `scaffold`: Scaffold-based (for chemical diversity)\n- `cold_drug`, `cold_target`, `cold_drug_target`: For DTI tasks\n- `temporal`: Time-based splits for temporal datasets\n\n### 2. Model Evaluation\n\nUse standardized metrics for evaluation:\n\n```python\nfrom tdc import Evaluator\n\n# For binary classification\nevaluator = Evaluator(name='ROC-AUC')\nscore = evaluator(y_true, y_pred)\n\n# For regression\nevaluator = Evaluator(name='RMSE')\nscore = evaluator(y_true, y_pred)\n```\n\n**Available metrics:** ROC-AUC, PR-AUC, F1, Accuracy, RMSE, MAE, R2, Spearman, Pearson, and more.\n\n### 3. Data Processing\n\nTDC provides 11 key processing utilities:\n\n```python\nfrom tdc.chem_utils import MolConvert\n\n# Molecule format conversion\nconverter = MolConvert(src='SMILES', dst='PyG')\npyg_graph = converter('CC(C)Cc1ccc(cc1)C(C)C(O)=O')\n```\n\n**Processing utilities include:**\n- Molecule format conversion (SMILES, SELFIES, PyG, DGL, ECFP, etc.)\n- Molecule filters (PAINS, drug-likeness)\n- Label binarization and unit conversion\n- Data balancing (over\u002Funder-sampling)\n- Negative sampling for pair data\n- Graph transformation\n- Entity retrieval (CID to SMILES, UniProt to sequence)\n\nFor comprehensive utilities documentation, see `references\u002Futilities.md`.\n\n### 4. Molecule Generation Oracles\n\nTDC provides 17+ oracle functions for molecular optimization:\n\n```python\nfrom tdc import Oracle\n\n# Single oracle\noracle = Oracle(name='DRD2')\nscore = oracle('CC(C)Cc1ccc(cc1)C(C)C(O)=O')\n\n# Multiple oracles\noracle = Oracle(name='JNK3')\nscores = oracle(['SMILES1', 'SMILES2', 'SMILES3'])\n```\n\nFor complete oracle documentation, see `references\u002Foracles.md`.\n\n## Advanced Features\n\n### Retrieve Available Datasets\n\n```python\nfrom tdc.utils import retrieve_dataset_names\n\n# Get all ADME datasets\nadme_datasets = retrieve_dataset_names('ADME')\n\n# Get all DTI datasets\ndti_datasets = retrieve_dataset_names('DTI')\n```\n\n### Label Transformations\n\n```python\n# Get label mapping\nlabel_map = data.get_label_map(name='DrugBank')\n\n# Convert labels\nfrom tdc.chem_utils import label_transform\ntransformed = label_transform(y, from_unit='nM', to_unit='p')\n```\n\n### Database Queries\n\n```python\nfrom tdc.utils import cid2smiles, uniprot2seq\n\n# Convert PubChem CID to SMILES\nsmiles = cid2smiles(2244)\n\n# Convert UniProt ID to amino acid sequence\nsequence = uniprot2seq('P12345')\n```\n\n## Common Workflows\n\n### Workflow 1: Train a Single Prediction Model\n\nSee `scripts\u002Fload_and_split_data.py` for a complete example:\n\n```python\nfrom tdc.single_pred import ADME\nfrom tdc import Evaluator\n\n# Load data\ndata = ADME(name='Caco2_Wang')\nsplit = data.get_split(method='scaffold', seed=42)\n\ntrain, valid, test = split['train'], split['valid'], split['test']\n\n# Train model (user implements)\n# model.fit(train['Drug'], train['Y'])\n\n# Evaluate\nevaluator = Evaluator(name='MAE')\n# score = evaluator(test['Y'], predictions)\n```\n\n### Workflow 2: Benchmark Evaluation\n\nSee `scripts\u002Fbenchmark_evaluation.py` for a complete example with multiple seeds and proper evaluation protocol.\n\n### Workflow 3: Molecular Generation with Oracles\n\nSee `scripts\u002Fmolecular_generation.py` for an example of goal-directed generation using oracle functions.\n\n## Resources\n\nThis skill includes bundled resources for common TDC workflows:\n\n### scripts\u002F\n\n- `load_and_split_data.py`: Template for loading and splitting TDC datasets with various strategies\n- `benchmark_evaluation.py`: Template for running benchmark group evaluations with proper 5-seed protocol\n- `molecular_generation.py`: Template for molecular generation using oracle functions\n\n### references\u002F\n\n- `datasets.md`: Comprehensive catalog of all available datasets organized by task type\n- `oracles.md`: Complete documentation of all 17+ molecule generation oracles\n- `utilities.md`: Detailed guide to data processing, splitting, and evaluation utilities\n\n## Additional Resources\n\n- **Official Website**: https:\u002F\u002Ftdcommons.ai\n- **Documentation**: https:\u002F\u002Ftdc.readthedocs.io\n- **GitHub**: https:\u002F\u002Fgithub.com\u002Fmims-harvard\u002FTDC\n- **Paper**: NeurIPS 2021 - \"Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development\"\n","# PyTDC (Therapeutics Data Commons)\n\n## Overview\n\nPyTDC 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\u002Fprotein properties), multi-instance prediction (drug-target interactions, DDI), and generation (molecule generation, retrosynthesis).\n\n## When to Use This Skill\n\nThis skill should be used when:\n- Working with drug discovery or therapeutic ML datasets\n- Benchmarking machine learning models on standardized pharmaceutical tasks\n- Predicting molecular properties (ADME, toxicity, bioactivity)\n- Predicting drug-target or drug-drug interactions\n- Generating novel molecules with desired properties\n- Accessing curated datasets with proper train\u002Ftest splits (scaffold, cold-split)\n- Using molecular oracles for property optimization\n\n## Installation & Setup\n\nInstall PyTDC using pip:\n\n```bash\nuv pip install PyTDC\n```\n\nTo upgrade to the latest version:\n\n```bash\nuv pip install PyTDC --upgrade\n```\n\nCore dependencies (automatically installed):\n- numpy, pandas, tqdm, seaborn, scikit_learn, fuzzywuzzy\n\nAdditional packages are installed automatically as needed for specific features.\n\n## Quick Start\n\nThe basic pattern for accessing any TDC dataset follows this structure:\n\n```python\nfrom tdc.\u003Cproblem> import \u003CTask>\ndata = \u003CTask>(name='\u003CDataset>')\nsplit = data.get_split(method='scaffold', seed=1, frac=[0.7, 0.1, 0.2])\ndf = data.get_data(format='df')\n```\n\nWhere:\n- `\u003Cproblem>`: One of `single_pred`, `multi_pred`, or `generation`\n- `\u003CTask>`: Specific task category (e.g., ADME, DTI, MolGen)\n- `\u003CDataset>`: Dataset name within that task\n\n**Example - Loading ADME data:**\n\n```python\nfrom tdc.single_pred import ADME\ndata = ADME(name='Caco2_Wang')\nsplit = data.get_split(method='scaffold')\n# Returns dict with 'train', 'valid', 'test' DataFrames\n```\n\n## Single-Instance Prediction Tasks\n\nSingle-instance prediction involves forecasting properties of individual biomedical entities (molecules, proteins, etc.).\n\n### Available Task Categories\n\n#### 1. ADME (Absorption, Distribution, Metabolism, Excretion)\n\nPredict pharmacokinetic properties of drug molecules.\n\n```python\nfrom tdc.single_pred import ADME\ndata = ADME(name='Caco2_Wang')  # Intestinal permeability\n# Other datasets: HIA_Hou, Bioavailability_Ma, Lipophilicity_AstraZeneca, etc.\n```\n\n**Common ADME datasets:**\n- Caco2 - Intestinal permeability\n- HIA - Human intestinal absorption\n- Bioavailability - Oral bioavailability\n- Lipophilicity - Octanol-water partition coefficient\n- Solubility - Aqueous solubility\n- BBB - Blood-brain barrier penetration\n- CYP - Cytochrome P450 metabolism\n\n#### 2. Toxicity (Tox)\n\nPredict toxicity and adverse effects of compounds.\n\n```python\nfrom tdc.single_pred import Tox\ndata = Tox(name='hERG')  # Cardiotoxicity\n# Other datasets: AMES, DILI, Carcinogens_Lagunin, etc.\n```\n\n**Common toxicity datasets:**\n- hERG - Cardiac toxicity\n- AMES - Mutagenicity\n- DILI - Drug-induced liver injury\n- Carcinogens - Carcinogenicity\n- ClinTox - Clinical trial toxicity\n\n#### 3. HTS (High-Throughput Screening)\n\nBioactivity predictions from screening data.\n\n```python\nfrom tdc.single_pred import HTS\ndata = HTS(name='SARSCoV2_Vitro_Touret')\n```\n\n#### 4. QM (Quantum Mechanics)\n\nQuantum mechanical properties of molecules.\n\n```python\nfrom tdc.single_pred import QM\ndata = QM(name='QM7')\n```\n\n#### 5. Other Single Prediction Tasks\n\n- **Yields**: Chemical reaction yield prediction\n- **Epitope**: Epitope prediction for biologics\n- **Develop**: Development-stage predictions\n- **CRISPROutcome**: Gene editing outcome prediction\n\n### Data Format\n\nSingle prediction datasets typically return DataFrames with columns:\n- `Drug_ID` or `Compound_ID`: Unique identifier\n- `Drug` or `X`: SMILES string or molecular representation\n- `Y`: Target label (continuous or binary)\n\n## Multi-Instance Prediction Tasks\n\nMulti-instance prediction involves forecasting properties of interactions between multiple biomedical entities.\n\n### Available Task Categories\n\n#### 1. DTI (Drug-Target Interaction)\n\nPredict binding affinity between drugs and protein targets.\n\n```python\nfrom tdc.multi_pred import DTI\ndata = DTI(name='BindingDB_Kd')\nsplit = data.get_split()\n```\n\n**Available datasets:**\n- BindingDB_Kd - Dissociation constant (52,284 pairs)\n- BindingDB_IC50 - Half-maximal inhibitory concentration (991,486 pairs)\n- BindingDB_Ki - Inhibition constant (375,032 pairs)\n- DAVIS, KIBA - Kinase binding datasets\n\n**Data format:** Drug_ID, Target_ID, Drug (SMILES), Target (sequence), Y (binding affinity)\n\n#### 2. DDI (Drug-Drug Interaction)\n\nPredict interactions between drug pairs.\n\n```python\nfrom tdc.multi_pred import DDI\ndata = DDI(name='DrugBank')\nsplit = data.get_split()\n```\n\nMulti-class classification task predicting interaction types. Dataset contains 191,808 DDI pairs with 1,706 drugs.\n\n#### 3. PPI (Protein-Protein Interaction)\n\nPredict protein-protein interactions.\n\n```python\nfrom tdc.multi_pred import PPI\ndata = PPI(name='HuRI')\n```\n\n#### 4. Other Multi-Prediction Tasks\n\n- **GDA**: Gene-disease associations\n- **DrugRes**: Drug resistance prediction\n- **DrugSyn**: Drug synergy prediction\n- **PeptideMHC**: Peptide-MHC binding\n- **AntibodyAff**: Antibody affinity prediction\n- **MTI**: miRNA-target interactions\n- **Catalyst**: Catalyst prediction\n- **TrialOutcome**: Clinical trial outcome prediction\n\n## Generation Tasks\n\nGeneration tasks involve creating novel biomedical entities with desired properties.\n\n### 1. Molecular Generation (MolGen)\n\nGenerate diverse, novel molecules with desirable chemical properties.\n\n```python\nfrom tdc.generation import MolGen\ndata = MolGen(name='ChEMBL_V29')\nsplit = data.get_split()\n```\n\nUse with oracles to optimize for specific properties:\n\n```python\nfrom tdc import Oracle\noracle = Oracle(name='GSK3B')\nscore = oracle('CC(C)Cc1ccc(cc1)C(C)C(O)=O')  # Evaluate SMILES\n```\n\nSee `references\u002Foracles.md` for all available oracle functions.\n\n### 2. Retrosynthesis (RetroSyn)\n\nPredict reactants needed to synthesize a target molecule.\n\n```python\nfrom tdc.generation import RetroSyn\ndata = RetroSyn(name='USPTO')\nsplit = data.get_split()\n```\n\nDataset contains 1,939,253 reactions from USPTO database.\n\n### 3. Paired Molecule Generation\n\nGenerate molecule pairs (e.g., prodrug-drug pairs).\n\n```python\nfrom tdc.generation import PairMolGen\ndata = PairMolGen(name='Prodrug')\n```\n\nFor detailed oracle documentation and molecular generation workflows, refer to `references\u002Foracles.md` and `scripts\u002Fmolecular_generation.py`.\n\n## Benchmark Groups\n\nBenchmark groups provide curated collections of related datasets for systematic model evaluation.\n\n### ADMET Benchmark Group\n\n```python\nfrom tdc.benchmark_group import admet_group\ngroup = admet_group(path='data\u002F')\n\n# Get benchmark datasets\nbenchmark = group.get('Caco2_Wang')\npredictions = {}\n\nfor seed in [1, 2, 3, 4, 5]:\n    train, valid = benchmark['train'], benchmark['valid']\n    # Train model here\n    predictions[seed] = model.predict(benchmark['test'])\n\n# Evaluate with required 5 seeds\nresults = group.evaluate(predictions)\n```\n\n**ADMET Group includes 22 datasets** covering absorption, distribution, metabolism, excretion, and toxicity.\n\n### Other Benchmark Groups\n\nAvailable benchmark groups include collections for:\n- ADMET properties\n- Drug-target interactions\n- Drug combination prediction\n- And more specialized therapeutic tasks\n\nFor benchmark evaluation workflows, see `scripts\u002Fbenchmark_evaluation.py`.\n\n## Data Functions\n\nTDC provides comprehensive data processing utilities organized into four categories.\n\n### 1. Dataset Splits\n\nRetrieve train\u002Fvalidation\u002Ftest partitions with various strategies:\n\n```python\n# Scaffold split (default for most tasks)\nsplit = data.get_split(method='scaffold', seed=1, frac=[0.7, 0.1, 0.2])\n\n# Random split\nsplit = data.get_split(method='random', seed=42, frac=[0.8, 0.1, 0.1])\n\n# Cold split (for DTI\u002FDDI tasks)\nsplit = data.get_split(method='cold_drug', seed=1)  # Unseen drugs in test\nsplit = data.get_split(method='cold_target', seed=1)  # Unseen targets in test\n```\n\n**Available split strategies:**\n- `random`: Random shuffling\n- `scaffold`: Scaffold-based (for chemical diversity)\n- `cold_drug`, `cold_target`, `cold_drug_target`: For DTI tasks\n- `temporal`: Time-based splits for temporal datasets\n\n### 2. Model Evaluation\n\nUse standardized metrics for evaluation:\n\n```python\nfrom tdc import Evaluator\n\n# For binary classification\nevaluator = Evaluator(name='ROC-AUC')\nscore = evaluator(y_true, y_pred)\n\n# For regression\nevaluator = Evaluator(name='RMSE')\nscore = evaluator(y_true, y_pred)\n```\n\n**Available metrics:** ROC-AUC, PR-AUC, F1, Accuracy, RMSE, MAE, R2, Spearman, Pearson, and more.\n\n### 3. Data Processing\n\nTDC provides 11 key processing utilities:\n\n```python\nfrom tdc.chem_utils import MolConvert\n\n# Molecule format conversion\nconverter = MolConvert(src='SMILES', dst='PyG')\npyg_graph = converter('CC(C)Cc1ccc(cc1)C(C)C(O)=O')\n```\n\n**Processing utilities include:**\n- Molecule format conversion (SMILES, SELFIES, PyG, DGL, ECFP, etc.)\n- Molecule filters (PAINS, drug-likeness)\n- Label binarization and unit conversion\n- Data balancing (over\u002Funder-sampling)\n- Negative sampling for pair data\n- Graph transformation\n- Entity retrieval (CID to SMILES, UniProt to sequence)\n\nFor comprehensive utilities documentation, see `references\u002Futilities.md`.\n\n### 4. Molecule Generation Oracles\n\nTDC provides 17+ oracle functions for molecular optimization:\n\n```python\nfrom tdc import Oracle\n\n# Single oracle\noracle = Oracle(name='DRD2')\nscore = oracle('CC(C)Cc1ccc(cc1)C(C)C(O)=O')\n\n# Multiple oracles\noracle = Oracle(name='JNK3')\nscores = oracle(['SMILES1', 'SMILES2', 'SMILES3'])\n```\n\nFor complete oracle documentation, see `references\u002Foracles.md`.\n\n## Advanced Features\n\n### Retrieve Available Datasets\n\n```python\nfrom tdc.utils import retrieve_dataset_names\n\n# Get all ADME datasets\nadme_datasets = retrieve_dataset_names('ADME')\n\n# Get all DTI datasets\ndti_datasets = retrieve_dataset_names('DTI')\n```\n\n### Label Transformations\n\n```python\n# Get label mapping\nlabel_map = data.get_label_map(name='DrugBank')\n\n# Convert labels\nfrom tdc.chem_utils import label_transform\ntransformed = label_transform(y, from_unit='nM', to_unit='p')\n```\n\n### Database Queries\n\n```python\nfrom tdc.utils import cid2smiles, uniprot2seq\n\n# Convert PubChem CID to SMILES\nsmiles = cid2smiles(2244)\n\n# Convert UniProt ID to amino acid sequence\nsequence = uniprot2seq('P12345')\n```\n\n## Common Workflows\n\n### Workflow 1: Train a Single Prediction Model\n\nSee `scripts\u002Fload_and_split_data.py` for a complete example:\n\n```python\nfrom tdc.single_pred import ADME\nfrom tdc import Evaluator\n\n# Load data\ndata = ADME(name='Caco2_Wang')\nsplit = data.get_split(method='scaffold', seed=42)\n\ntrain, valid, test = split['train'], split['valid'], split['test']\n\n# Train model (user implements)\n# model.fit(train['Drug'], train['Y'])\n\n# Evaluate\nevaluator = Evaluator(name='MAE')\n# score = evaluator(test['Y'], predictions)\n```\n\n### Workflow 2: Benchmark Evaluation\n\nSee `scripts\u002Fbenchmark_evaluation.py` for a complete example with multiple seeds and proper evaluation protocol.\n\n### Workflow 3: Molecular Generation with Oracles\n\nSee `scripts\u002Fmolecular_generation.py` for an example of goal-directed generation using oracle functions.\n\n## Resources\n\nThis skill includes bundled resources for common TDC workflows:\n\n### scripts\u002F\n\n- `load_and_split_data.py`: Template for loading and splitting TDC datasets with various strategies\n- `benchmark_evaluation.py`: Template for running benchmark group evaluations with proper 5-seed protocol\n- `molecular_generation.py`: Template for molecular generation using oracle functions\n\n### references\u002F\n\n- `datasets.md`: Comprehensive catalog of all available datasets organized by task type\n- `oracles.md`: Complete documentation of all 17+ molecule generation oracles\n- `utilities.md`: Detailed guide to data processing, splitting, and evaluation utilities\n\n## Additional Resources\n\n- **Official Website**: https:\u002F\u002Ftdcommons.ai\n- **Documentation**: https:\u002F\u002Ftdc.readthedocs.io\n- **GitHub**: https:\u002F\u002Fgithub.com\u002Fmims-harvard\u002FTDC\n- **Paper**: NeurIPS 2021 - 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