lobster-ml
Machine learning and deep learning for biological data analysis and framework export.
Installation
# Basic installation
pip install lobster-ml
# With deep learning dependencies (scVI, PyTorch)
pip install lobster-ml[ml]
Agents
| Agent | Description |
|---|---|
machine_learning_expert |
ML specialist for biological data. Feature engineering, data splitting, framework export, and deep learning embeddings. |
Services
| Service | Purpose |
|---|---|
| MLPreparationService | Feature selection, scaling, and train/test/validation splitting |
| MLTranscriptomicsServiceALPHA | Transcriptomics-specific ML workflows (ALPHA) |
| MLProteomicsServiceALPHA | Proteomics-specific ML workflows (ALPHA) |
| scVIEmbeddingService | Deep learning embeddings using scVI for single-cell data |
Features
ML Readiness Assessment
- Evaluate biological datasets for machine learning suitability
- Check sample size, class balance, and feature quality
- Identify potential data leakage and batch effects
- Recommend preprocessing steps before ML pipeline
Feature Engineering
- Highly variable gene selection for dimensionality reduction
- PCA-based feature extraction with variance thresholds
- Marker gene features from differential expression
- Z-score normalization and scaling
Data Splitting
- Stratified train/test/validation splits
- Configurable split ratios (default: 70/15/15)
- Class balance preservation across splits
- Batch-aware splitting to prevent data leakage
Framework Export
- NumPy arrays for scikit-learn workflows
- CSV export for general ML frameworks
- PyTorch tensor datasets with DataLoader support
- TensorFlow NPZ format for Keras models
Deep Learning Embeddings
- scVI integration for variational autoencoder embeddings
- Latent space visualization and clustering
- Transfer learning from pre-trained models
- GPU acceleration when available
Requirements
- Python 3.12+
- lobster-ai >= 1.0.0
- Optional: torch, scvi-tools (for deep learning features)
Tier Requirement
This is a premium agent. Access is controlled at runtime via Lobster AI's tier system.
Documentation
Full documentation: docs.omics-os.com/docs/agents/ml
License
MIT
1 maintainer
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