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

Training and Inference

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

MCP Server

• Server - Main server implementation
• Config Manager - Configuration management
• Config Validators - Input validation
• Model Manager - Model lifecycle management

Utilities

• Sequence Utils - DNA sequence processing
• Logger - Logging configuration
• Support - Helper functions