alterlab-deepchem

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Runs molecular machine learning with DeepChem — diverse featurizers, pre-built MoleculeNet datasets, and pre-trained models for property prediction (ADMET, toxicity) via traditional ML or GNNs. Use when running quick molecular ML experiments needing extensive featurization options, MoleculeNet benchmarks, or pre-trained models; for graph-first PyTorch workflows use torchdrug, for benchmark datasets use pytdc. Part of the AlterLab Academic Skills suite.

AI & Automation 27 stars 4 forks Updated today MIT

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Skill Content

# DeepChem ## Overview DeepChem is a comprehensive Python library for applying machine learning to chemistry, materials science, and biology. Enable molecular property prediction, drug discovery, materials design, and biomolecule analysis through specialized neural networks, molecular featurization methods, and pretrained models. ## When to Use This Skill This skill should be used when: - Loading and processing molecular data (SMILES strings, SDF files, protein sequences) - Predicting molecular properties (solubility, toxicity, binding affinity, ADMET properties) - Training models on chemical/biological datasets - Using MoleculeNet benchmark datasets (Tox21, BBBP, Delaney, etc.) - Converting molecules to ML-ready features (fingerprints, graph representations, descriptors) - Implementing graph neural networks for molecules (GCN, GAT, MPNN, AttentiveFP) - Applying transfer learning with pretrained models (ChemBERTa, GROVER, MolFormer) - Predicting crystal/materials properties (bandgap, formation energy) - Analyzing protein or DNA sequences ## Core Capabilities ### 1. Molecular Data Loading and Processing DeepChem provides specialized loaders for various chemical data formats: ```python import deepchem as dc # Load CSV with SMILES featurizer = dc.feat.CircularFingerprint(radius=2, size=2048) loader = dc.data.CSVLoader( tasks=['solubility', 'toxicity'], feature_field='smiles', featurizer=featurizer ) dataset = loader.create_dataset('molecules.csv') # Load SD...

Details

Author
AlterLab-IEU
Repository
AlterLab-IEU/AlterLab-Academic-Skills
Created
2 months ago
Last Updated
today
Language
Python
License
MIT

Integrates with

Anthropic · AI

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