What does the Deepchem AI skill do?

Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

Why use Deepchem on TypingMind?

Because you install it once and use it with any model. Deepchem is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Deepchem in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/jimmc414/Kosmos/tree/master/kosmos-claude-scientific-skills/scientific-skills/deepchem. TypingMind reads its SKILL.md and bundles its files and installs it as a skill you can enable per chat.

Which AI models can use Deepchem?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Deepchem?

As many as you like. As long as a model supports skills, you can use Deepchem with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Deepchem AI skill free?

It is published on GitHub by jimmc414. Check the repository for licensing terms. You only pay your own AI provider for the tokens you use.

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

Deepchem by jimmc414 — AI Skill for Any LLM

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 SDF files
loader = dc.data.SDFLoader(tasks=['activity'], featurizer=featurizer)
dataset = loader.create_dataset('compounds.sdf')

# Load protein sequences
loader = dc.data.FASTALoader()
dataset = loader.create_dataset('proteins.fasta')

Key Loaders:

CSVLoader: Tabular data with molecular identifiers
SDFLoader: Molecular structure files
FASTALoader: Protein/DNA sequences
ImageLoader: Molecular images
JsonLoader: JSON-formatted datasets

2. Molecular Featurization

Convert molecules into numerical representations for ML models.

Decision Tree for Featurizer Selection


Is the model a graph neural network?
├─ YES → Use graph featurizers
│   ├─ Standard GNN → MolGraphConvFeaturizer
│   ├─ Message passing → DMPNNFeaturizer
│   └─ Pretrained → GroverFeaturizer
│
└─ NO → What type of model?
    ├─ Traditional ML (RF, XGBoost, SVM)
    │   ├─ Fast baseline → CircularFingerprint (ECFP)
    │   ├─ Interpretable → RDKitDescriptors
    │   └─ Maximum coverage → MordredDescriptors
    │
    ├─ Deep learning (non-graph)
    │   ├─ Dense networks → CircularFingerprint
    │   └─ CNN → SmilesToImage
    │
    ├─ Sequence models (LSTM, Transformer)
    │   └─ SmilesToSeq
    │
    └─ 3D structure analysis
        └─ CoulombMatrix

Example Featurization

python
# Fingerprints (for traditional ML)
fp = dc.feat.CircularFingerprint(radius=2, size=2048)

# Descriptors (for interpretable models)
desc = dc.feat.RDKitDescriptors()

# Graph features (for GNNs)
graph_feat = dc.feat.MolGraphConvFeaturizer()

# Apply featurization
features = fp.featurize(['CCO', 'c1ccccc1'])

Selection Guide:

Small datasets (<1K): CircularFingerprint or RDKitDescriptors
Medium datasets (1K-100K): CircularFingerprint or graph featurizers
Large datasets (>100K): Graph featurizers (MolGraphConvFeaturizer, DMPNNFeaturizer)
Transfer learning: Pretrained model featurizers (GroverFeaturizer)

See references/api_reference.md for complete featurizer documentation.

3. Data Splitting

Critical: For drug discovery tasks, use ScaffoldSplitter to prevent data leakage from similar molecular structures appearing in both training and test sets.

python
# Scaffold splitting (recommended for molecules)
splitter = dc.splits.ScaffoldSplitter()
train, valid, test = splitter.train_valid_test_split(
    dataset,
    frac_train=0.8,
    frac_valid=0.1,
    frac_test=0.1
)

# Random splitting (for non-molecular data)
splitter = dc.splits.RandomSplitter()
train, test = splitter.train_test_split(dataset)

# Stratified splitting (for imbalanced classification)
splitter = dc.splits.RandomStratifiedSplitter()
train, test = splitter.train_test_split(dataset)

Available Splitters:

ScaffoldSplitter: Split by molecular scaffolds (prevents leakage)
ButinaSplitter: Clustering-based molecular splitting
MaxMinSplitter: Maximize diversity between sets
RandomSplitter: Random splitting
RandomStratifiedSplitter: Preserves class distributions

4. Model Selection and Training

Quick Model Selection Guide

Dataset Size	Task	Recommended Model	Featurizer
< 1K samples	Any	SklearnModel (RandomForest)	CircularFingerprint
1K-100K	Classification/Regression	GBDTModel or MultitaskRegressor	CircularFingerprint
> 100K	Molecular properties	GCNModel, AttentiveFPModel, DMPNNModel	MolGraphConvFeaturizer
Any (small preferred)	Transfer learning	ChemBERTa, GROVER, MolFormer	Model-specific
Crystal structures	Materials properties	CGCNNModel, MEGNetModel	Structure-based
Protein sequences	Protein properties	ProtBERT	Sequence-based

Example: Traditional ML

python
from sklearn.ensemble import RandomForestRegressor

# Wrap scikit-learn model
sklearn_model = RandomForestRegressor(n_estimators=100)
model = dc.models.SklearnModel(model=sklearn_model)
model.fit(train)

Example: Deep Learning

python
# Multitask regressor (for fingerprints)
model = dc.models.MultitaskRegressor(
    n_tasks=2,
    n_features=2048,
    layer_sizes=[1000, 500],
    dropouts=0.25,
    learning_rate=0.001
)
model.fit(train, nb_epoch=50)

Example: Graph Neural Networks

python
# Graph Convolutional Network
model = dc.models.GCNModel(
    n_tasks=1,
    mode='regression',
    batch_size=128,
    learning_rate=0.001
)
model.fit(train, nb_epoch=50)

# Graph Attention Network
model = dc.models.GATModel(n_tasks=1, mode='classification')
model.fit(train, nb_epoch=50)

# Attentive Fingerprint
model = dc.models.AttentiveFPModel(n_tasks=1, mode='regression')
model.fit(train, nb_epoch=50)

5. MoleculeNet Benchmarks

Quick access to 30+ curated benchmark datasets with standardized train/valid/test splits:

python
# Load benchmark dataset
tasks, datasets, transformers = dc.molnet.load_tox21(
    featurizer='GraphConv',  # or 'ECFP', 'Weave', 'Raw'
    splitter='scaffold',     # or 'random', 'stratified'
    reload=False
)
train, valid, test = datasets

# Train and evaluate
model = dc.models.GCNModel(n_tasks=len(tasks), mode='classification')
model.fit(train, nb_epoch=50)

metric = dc.metrics.Metric(dc.metrics.roc_auc_score)
test_score = model.evaluate(test, [metric])

Common Datasets:

Classification: load_tox21(), load_bbbp(), load_hiv(), load_clintox()
Regression: load_delaney(), load_freesolv(), load_lipo()
Quantum properties: load_qm7(), load_qm8(), load_qm9()
Materials: load_perovskite(), load_bandgap(), load_mp_formation_energy()

See references/api_reference.md for complete dataset list.

6. Transfer Learning

Leverage pretrained models for improved performance, especially on small datasets:

python
# ChemBERTa (BERT pretrained on 77M molecules)
model = dc.models.HuggingFaceModel(
    model='seyonec/ChemBERTa-zinc-base-v1',
    task='classification',
    n_tasks=1,
    learning_rate=2e-5  # Lower LR for fine-tuning
)
model.fit(train, nb_epoch=10)

# GROVER (graph transformer pretrained on 10M molecules)
model = dc.models.GroverModel(
    task='regression',
    n_tasks=1
)
model.fit(train, nb_epoch=20)

When to use transfer learning:

Small datasets (< 1000 samples)
Novel molecular scaffolds
Limited computational resources
Need for rapid prototyping

Use the scripts/transfer_learning.py script for guided transfer learning workflows.

7. Model Evaluation

python
# Define metrics
classification_metrics = [
    dc.metrics.Metric(dc.metrics.roc_auc_score, name='ROC-AUC'),
    dc.metrics.Metric(dc.metrics.accuracy_score, name='Accuracy'),
    dc.metrics.Metric(dc.metrics.f1_score, name='F1')
]

regression_metrics = [
    dc.metrics.Metric(dc.metrics.r2_score, name='R²'),
    dc.metrics.Metric(dc.metrics.mean_absolute_error, name='MAE'),
    dc.metrics.Metric(dc.metrics.root_mean_squared_error, name='RMSE')
]

# Evaluate
train_scores = model.evaluate(train, classification_metrics)
test_scores = model.evaluate(test, classification_metrics)

8. Making Predictions

python
# Predict on test set
predictions = model.predict(test)

# Predict on new molecules
new_smiles = ['CCO', 'c1ccccc1', 'CC(C)O']
new_features = featurizer.featurize(new_smiles)
new_dataset = dc.data.NumpyDataset(X=new_features)

# Apply same transformations as training
for transformer in transformers:
    new_dataset = transformer.transform(new_dataset)

predictions = model.predict(new_dataset)

Typical Workflows

Workflow A: Quick Benchmark Evaluation

For evaluating a model on standard benchmarks:

python
import deepchem as dc

# 1. Load benchmark
tasks, datasets, _ = dc.molnet.load_bbbp(
    featurizer='GraphConv',
    splitter='scaffold'
)
train, valid, test = datasets

# 2. Train model
model = dc.models.GCNModel(n_tasks=len(tasks), mode='classification')
model.fit(train, nb_epoch=50)

# 3. Evaluate
metric = dc.metrics.Metric(dc.metrics.roc_auc_score)
test_score = model.evaluate(test, [metric])
print(f"Test ROC-AUC: {test_score}")

Workflow B: Custom Data Prediction

For training on custom molecular datasets:

python
import deepchem as dc

# 1. Load and featurize data
featurizer = dc.feat.CircularFingerprint(radius=2, size=2048)
loader = dc.data.CSVLoader(
    tasks=['activity'],
    feature_field='smiles',
    featurizer=featurizer
)
dataset = loader.create_dataset('my_molecules.csv')

# 2. Split data (use ScaffoldSplitter for molecules!)
splitter = dc.splits.ScaffoldSplitter()
train, valid, test = splitter.train_valid_test_split(dataset)

# 3. Normalize (optional but recommended)
transformers = [dc.trans.NormalizationTransformer(
    transform_y=True, dataset=train
)]
for transformer in transformers:
    train = transformer.transform(train)
    valid = transformer.transform(valid)
    test = transformer.transform(test)

# 4. Train model
model = dc.models.MultitaskRegressor(
    n_tasks=1,
    n_features=2048,
    layer_sizes=[1000, 500],
    dropouts=0.25
)
model.fit(train, nb_epoch=50)

# 5. Evaluate
metric = dc.metrics.Metric(dc.metrics.r2_score)
test_score = model.evaluate(test, [metric])

Workflow C: Transfer Learning on Small Dataset

For leveraging pretrained models:

python
import deepchem as dc

# 1. Load data (pretrained models often need raw SMILES)
loader = dc.data.CSVLoader(
    tasks=['activity'],
    feature_field='smiles',
    featurizer=dc.feat.DummyFeaturizer()  # Model handles featurization
)
dataset = loader.create_dataset('small_dataset.csv')

# 2. Split data
splitter = dc.splits.ScaffoldSplitter()
train, test = splitter.train_test_split(dataset)

# 3. Load pretrained model
model = dc.models.HuggingFaceModel(
    model='seyonec/ChemBERTa-zinc-base-v1',
    task='classification',
    n_tasks=1,
    learning_rate=2e-5
)

# 4. Fine-tune
model.fit(train, nb_epoch=10)

# 5. Evaluate
predictions = model.predict(test)

See references/workflows.md for 8 detailed workflow examples covering molecular generation, materials science, protein analysis, and more.

Example Scripts

This skill includes three production-ready scripts in the scripts/ directory:

1. `predict_solubility.py`

Train and evaluate solubility prediction models. Works with Delaney benchmark or custom CSV data.

bash
# Use Delaney benchmark
python scripts/predict_solubility.py

# Use custom data
python scripts/predict_solubility.py \
    --data my_data.csv \
    --smiles-col smiles \
    --target-col solubility \
    --predict "CCO" "c1ccccc1"

2. `graph_neural_network.py`

Train various graph neural network architectures on molecular data.

bash
# Train GCN on Tox21
python scripts/graph_neural_network.py --model gcn --dataset tox21

# Train AttentiveFP on custom data
python scripts/graph_neural_network.py \
    --model attentivefp \
    --data molecules.csv \
    --task-type regression \
    --targets activity \
    --epochs 100

3. `transfer_learning.py`

Fine-tune pretrained models (ChemBERTa, GROVER) on molecular property prediction tasks.

bash
# Fine-tune ChemBERTa on BBBP
python scripts/transfer_learning.py --model chemberta --dataset bbbp

# Fine-tune GROVER on custom data
python scripts/transfer_learning.py \
    --model grover \
    --data small_dataset.csv \
    --target activity \
    --task-type classification \
    --epochs 20

Common Patterns and Best Practices

Pattern 1: Always Use Scaffold Splitting for Molecules

python
# GOOD: Prevents data leakage
splitter = dc.splits.ScaffoldSplitter()
train, test = splitter.train_test_split(dataset)

# BAD: Similar molecules in train and test
splitter = dc.splits.RandomSplitter()
train, test = splitter.train_test_split(dataset)

Pattern 2: Normalize Features and Targets

python
transformers = [
    dc.trans.NormalizationTransformer(
        transform_y=True,  # Also normalize target values
        dataset=train
    )
]
for transformer in transformers:
    train = transformer.transform(train)
    test = transformer.transform(test)

Pattern 3: Start Simple, Then Scale

Start with Random Forest + CircularFingerprint (fast baseline)
Try XGBoost/LightGBM if RF works well
Move to deep learning (MultitaskRegressor) if you have >5K samples
Try GNNs if you have >10K samples
Use transfer learning for small datasets or novel scaffolds

Pattern 4: Handle Imbalanced Data

python
# Option 1: Balancing transformer
transformer = dc.trans.BalancingTransformer(dataset=train)
train = transformer.transform(train)

# Option 2: Use balanced metrics
metric = dc.metrics.Metric(dc.metrics.balanced_accuracy_score)

Pattern 5: Avoid Memory Issues

python
# Use DiskDataset for large datasets
dataset = dc.data.DiskDataset.from_numpy(X, y, w, ids)

# Use smaller batch sizes
model = dc.models.GCNModel(batch_size=32)  # Instead of 128

Common Pitfalls

Issue 1: Data Leakage in Drug Discovery

Problem: Using random splitting allows similar molecules in train/test sets. Solution: Always use ScaffoldSplitter for molecular datasets.

Issue 2: GNN Underperforming vs Fingerprints

Problem: Graph neural networks perform worse than simple fingerprints. Solutions:

Ensure dataset is large enough (>10K samples typically)
Increase training epochs (50-100)
Try different architectures (AttentiveFP, DMPNN instead of GCN)
Use pretrained models (GROVER)

Issue 3: Overfitting on Small Datasets

Problem: Model memorizes training data. Solutions:

Use stronger regularization (increase dropout to 0.5)
Use simpler models (Random Forest instead of deep learning)
Apply transfer learning (ChemBERTa, GROVER)
Collect more data

Issue 4: Import Errors

Problem: Module not found errors. Solution: Ensure DeepChem is installed with required dependencies:

bash
uv pip install deepchem
# For PyTorch models
uv pip install deepchem[torch]
# For all features
uv pip install deepchem[all]

Reference Documentation

This skill includes comprehensive reference documentation:

`references/api_reference.md`

Complete API documentation including:

All data loaders and their use cases
Dataset classes and when to use each
Complete featurizer catalog with selection guide
Model catalog organized by category (50+ models)
MoleculeNet dataset descriptions
Metrics and evaluation functions
Common code patterns

When to reference: Search this file when you need specific API details, parameter names, or want to explore available options.

`references/workflows.md`

Eight detailed end-to-end workflows:

Molecular property prediction from SMILES
Using MoleculeNet benchmarks
Hyperparameter optimization
Transfer learning with pretrained models
Molecular generation with GANs
Materials property prediction
Protein sequence analysis
Custom model integration

When to reference: Use these workflows as templates for implementing complete solutions.

Installation Notes

Basic installation:

bash
uv pip install deepchem

For PyTorch models (GCN, GAT, etc.):

bash
uv pip install deepchem[torch]

For all features:

bash
uv pip install deepchem[all]

If import errors occur, the user may need specific dependencies. Check the DeepChem documentation for detailed installation instructions.

Additional Resources

Official documentation: https://deepchem.readthedocs.io/
GitHub repository: https://github.com/deepchem/deepchem
Tutorials: https://deepchem.readthedocs.io/en/latest/get_started/tutorials.html
Paper: "MoleculeNet: A Benchmark for Molecular Machine Learning"

Publisher	jimmc414
Repository	`Kosmos`
Skill name	`deepchem`
Stars	585
Forks	105
Bundled files	5
Links	Skill source Repository

Overview

Installation

Install in TypingMind

Install in another agent

Use it in TypingMind

Works with any AI model

Skill instructions

DeepChem

Overview

When to Use This Skill

Core Capabilities

1. Molecular Data Loading and Processing

2. Molecular Featurization

Decision Tree for Featurizer Selection

Example Featurization

3. Data Splitting

4. Model Selection and Training

Quick Model Selection Guide

Example: Traditional ML

Example: Deep Learning

Example: Graph Neural Networks

5. MoleculeNet Benchmarks

6. Transfer Learning

7. Model Evaluation

8. Making Predictions

Typical Workflows

Workflow A: Quick Benchmark Evaluation

Workflow B: Custom Data Prediction

Workflow C: Transfer Learning on Small Dataset

Example Scripts

1. predict_solubility.py

2. graph_neural_network.py

3. transfer_learning.py

Common Patterns and Best Practices

Pattern 1: Always Use Scaffold Splitting for Molecules

Pattern 2: Normalize Features and Targets

Pattern 3: Start Simple, Then Scale

Pattern 4: Handle Imbalanced Data

Pattern 5: Avoid Memory Issues

Common Pitfalls

Issue 1: Data Leakage in Drug Discovery

Issue 2: GNN Underperforming vs Fingerprints

Issue 3: Overfitting on Small Datasets

Issue 4: Import Errors

Reference Documentation

references/api_reference.md

references/workflows.md

Installation Notes

Additional Resources

Bundled files

Frequently asked questions

Related AI Skills

Set up your own AI workspace now

1. `predict_solubility.py`

2. `graph_neural_network.py`

3. `transfer_learning.py`

`references/api_reference.md`

`references/workflows.md`