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DNALLM Documentation

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zhangtaolab/DNALLM

Introduction
Getting Started
User Guide
API
Concepts
Resources
Examples
FAQ

DNALLM Documentation

zhangtaolab/DNALLM

Introduction
Getting Started
Getting Started
- Quick Start
- Installation
User Guide
User Guide
- Getting Started
- Common Workflows
- Best Practices
- Performance Guide
- Troubleshooting
- Tutorial
  Tutorial
  - End-to-End Workflow
- Data Processing
  Data Processing
- Fine Tuning
  Fine Tuning
- Inference
  Inference
- Benchmark
  Benchmark
- MCP
  MCP
- CLI Tools
  CLI Tools
- Performance Optimization
  Performance Optimization
- Models
- Case Studies
  Case Studies
API
API
- Overview
- Configuration
  Configuration
  - Configs
- Models
  Models
  - Model
  - Auto Loading
  - Tokenizer
  - Classification Heads
  - Special Models
    Special Models
    
    Basenji2
    
    Borzoi
    
    DNABERT2
    
    EVO
    
    Enformer
    
    GPN
    
    LucaOne
    
    megaDNA
    
    MutBERT
    
    Omni-DNA
    
    SPACE
- Datahandling
  Datahandling
  - Data
  - Auto Builders
- Inference
  Inference
- Finetune
  Finetune
  - Trainer
- MCP
  MCP
- Tasks
  Tasks
  - Task
  - Metrics
- Utils
  Utils
  - Sequence
  - Logger
  - Support
Concepts
Concepts
- Biology
  Biology
- Training
- Inference
- MCP
- Architecture
  Architecture
- Technical Guides
  Technical Guides
Resources
Resources
- Model Zoo
- Data Handling
- Model Selection
- Model Troubleshooting
- Model Guides
  Model Guides
Examples
Examples
- Notebooks
  Notebooks
  - Overview
  - Fine-Tuning
    Fine-Tuning
    
    Binary Classification
    
    Multi-Label Classification
    
    NER Fine-tuning
    
    NER Data Generation
    
    Custom Head
    
    Generation
    
    LoRA Fine-tuning
    
    LoRA Inference
  - Inference
    Inference
    
    Basic Inference
    
    EVO Models
    
    MegaDNA Models
    
    Sequence Generation
    
    tRNA Inference
  - Analysis
    Analysis
    
    Mutagenesis
    
    Interpretation
    
    Embedding
  - Benchmarking
    Benchmarking
    
    Benchmark
  - Data Preparation
    Data Preparation
    
    Fine-tuning Data
    
    Prediction Data Preparation
  - MCP Examples
    MCP Examples
    
    DNALLM MCP Client with LangChain Agents
    
    Pydantic AI with Ollama and MCP Server
- Marimo Demos
  Marimo Demos
FAQ
FAQ
- Overview
- Installation
- Models
- Benchmark
- Fine-tuning
- Data Processing
- CLI
- Inference
- MCP

Benchmark Troubleshooting¶

Please see benchmark section for detailed usage, any troubleshooting not recorded will be added here.

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