API Reference

This section provides auto-generated API documentation for all DNALLM modules.

Core Modules

Configuration - Configuration management classes and loaders
Models - Model loading and utilities
- Automatic Loading - Auto model detection and loading
- Classification Heads - Task-specific classification heads
- Tokenizers - DNA tokenization utilities
- Special Models - Specialized model implementations
  - Basenji2 - Basenji-2 model support
  - Borzoi - Borzoi model support
  - DNABERT2 - DNABERT-2 model support
  - EVO - EVO-1/EVO-2 model support
  - Enformer - Enformer model support
  - GPN - GPN model support
  - LucaOne - LucaOne model support
  - megaDNA - megaDNA model support
  - MutBERT - MutBERT model support
  - Omni-DNA - Omni-DNA model support
  - SPACE - SPACE model support
Data Handling - Dataset management
- Automatic Builders - Auto dataset creation
Tasks - Task definitions and evaluation
- Metrics - Evaluation metrics

Fine-tuning - Training pipeline and utilities
Inference - Prediction engine
- Benchmark - Multi-model comparison
- Mutagenesis - In-silico mutation analysis
- Interpretation - Model interpretation
- Visualization - Plotting utilities