科学推理图思维框架

    ╔══════════════════════════════════════╗
    ║                                      ║
    ║           🧠 NexusMind 🧠            ║
    ║                                      ║
    ║     Intelligent Scientific           ║
    ║     Reasoning through                ║
    ║     Graph-of-Thoughts                ║
    ║                                      ║
    ╚══════════════════════════════════════╝

graph TD
    A[🌱 Stage 1: Initialization] --> B[🧩 Stage 2: Decomposition]
    B --> C[🔬 Stage 3: Hypothesis/Planning]
    C --> D[📊 Stage 4: Evidence Integration]
    D --> E[✂️ Stage 5: Pruning/Merging]
    E --> F[🔍 Stage 6: Subgraph Extraction]
    F --> G[📝 Stage 7: Composition]
    G --> H[🤔 Stage 8: Reflection]
    
    A1[Create root node<br/>Set initial confidence<br/>Define graph structure] --> A
    B1[Break into dimensions<br/>Identify components<br/>Create dimensional nodes] --> B
    C1[Generate hypotheses<br/>Create reasoning strategy<br/>Set falsification criteria] --> C
    D1[Gather evidence<br/>Link to hypotheses<br/>Update confidence scores] --> D
    E1[Remove low-value elements<br/>Consolidate similar nodes<br/>Optimize structure] --> E
    F1[Identify relevant portions<br/>Focus on high-value paths<br/>Create targeted subgraphs] --> F
    G1[Synthesize findings<br/>Create coherent insights<br/>Generate comprehensive answer] --> G
    H1[Evaluate reasoning quality<br/>Identify improvements<br/>Final confidence assessment] --> H
    
    style A fill:#e1f5fe
    style B fill:#f3e5f5
    style C fill:#e8f5e8
    style D fill:#fff3e0
    style E fill:#ffebee
    style F fill:#f1f8e9
    style G fill:#e3f2fd
    style H fill:#fce4ec

NexusMind/
├── 📁 config/                             # Configuration files
│   ├── settings.yaml                      # Application settings
│   ├── claude_mcp_config.json            # Claude MCP integration config
│   └── logging.yaml                       # Logging configuration
│
├── 📁 src/asr_got_reimagined/            # Main source code
│   ├── 📁 api/                           # API layer
│   │   ├── 📁 routes/                    # API route definitions
│   │   │   ├── mcp.py                    # MCP protocol endpoints
│   │   │   ├── health.py                 # Health check endpoints
│   │   │   └── graph.py                  # Graph query endpoints
│   │   ├── schemas.py                    # API request/response schemas
│   │   └── middleware.py                 # API middleware
│   │
│   ├── 📁 domain/                        # Core business logic
│   │   ├── 📁 models/                    # Domain models
│   │   │   ├── common.py                 # Common types and enums
│   │   │   ├── graph_elements.py         # Node, Edge, Hyperedge models
│   │   │   ├── graph_state.py            # Graph state management
│   │   │   ├── confidence.py             # Confidence vector models
│   │   │   └── metadata.py               # Metadata schemas
│   │   │
│   │   ├── 📁 services/                  # Business services
│   │   │   ├── got_processor.py          # Main GoT processing service
│   │   │   ├── evidence_service.py       # Evidence gathering and assessment
│   │   │   ├── confidence_service.py     # Confidence calculation service
│   │   │   ├── graph_service.py          # Graph manipulation service
│   │   │   └── mcp_service.py            # MCP protocol service
│   │   │
│   │   ├── 📁 stages/                    # 8-Stage pipeline implementation
│   │   │   ├── base_stage.py             # Abstract base stage
│   │   │   ├── stage_1_initialization.py # Stage 1: Graph initialization
│   │   │   ├── stage_2_decomposition.py  # Stage 2: Query decomposition
│   │   │   ├── stage_3_hypothesis.py     # Stage 3: Hypothesis generation
│   │   │   ├── stage_4_evidence.py       # Stage 4: Evidence integration
│   │   │   ├── stage_5_pruning.py        # Stage 5: Pruning and merging
│   │   │   ├── stage_6_extraction.py     # Stage 6: Subgraph extraction
│   │   │   ├── stage_7_composition.py    # Stage 7: Answer composition
│   │   │   └── stage_8_reflection.py     # Stage 8: Quality reflection
│   │   │
│   │   └── 📁 utils/                     # Utility functions
│   │       ├── graph_utils.py            # Graph manipulation utilities
│   │       ├── confidence_utils.py       # Confidence calculation utilities
│   │       ├── statistical_utils.py      # Statistical analysis utilities
│   │       ├── bias_detection.py         # Bias detection algorithms
│   │       └── temporal_analysis.py      # Temporal pattern analysis
│   │
│   ├── 📁 infrastructure/                # Infrastructure layer
│   │   ├── 📁 database/                  # Database integration
│   │   ├── 📁 cache/                     # Caching layer
│   │   └── 📁 external/                  # External service integrations
│   │
│   ├── main.py                           # Application entry point
│   └── app_setup.py                      # Application setup and configuration
│
├── 📁 tests/                             # Test suite
│   ├── 📁 unit/                          # Unit tests
│   │   ├── 📁 stages/                    # Stage-specific tests
│   │   ├── 📁 services/                  # Service tests
│   │   └── 📁 models/                    # Model tests
│   ├── 📁 integration/                   # Integration tests
│   └── 📁 fixtures/                      # Test fixtures and data
│
├── 📁 scripts/                           # Utility scripts
│   ├── setup_dev.py                      # Development setup
│   ├── add_type_hints.py                 # Type hint utilities
│   └── deployment/                       # Deployment scripts
│
├── 📁 docs/                              # Documentation
│   ├── api/                              # API documentation
│   ├── architecture/                     # Architecture diagrams
│   └── examples/                         # Usage examples
│
├── 📁 static/                            # Static assets
│   └── nexusmind-logo.png               # Application logo
│
├── 📄 Docker Files & Config
├── Dockerfile                            # Docker container definition
├── docker-compose.yml                   # Multi-container setup
├── .dockerignore                         # Docker ignore patterns
│
├── 📄 Configuration Files
├── pyproject.toml                        # Python project configuration
├── poetry.lock                           # Dependency lock file
├── mypy.ini                              # Type checking configuration
├── pyrightconfig.json                    # Python type checker config
├── .pre-commit-config.yaml              # Pre-commit hooks
├── .gitignore                            # Git ignore patterns
│
└── 📄 Documentation
    ├── README.md                         # This file
    ├── CHANGELOG.md                      # Version history
    ├── LICENSE                           # Apache 2.0 license
    └── CONTRIBUTING.md                   # Contribution guidelines

graph TB
    subgraph "Development Environment"
        A[👨‍💻 Developer] --> B[🐳 Docker Compose]
    end
    
    subgraph "Container Orchestration"
        B --> C[📦 NexusMind Container]
        B --> D[📊 Monitoring Container]
        B --> E[🗄️ Database Container]
    end
    
    subgraph "NexusMind Application"
        C --> F[⚡ FastAPI Server]
        F --> G[🧠 ASR-GoT Engine]
        F --> H[🔌 MCP Protocol]
    end
    
    subgraph "External Integrations"
        H --> I[🤖 Claude Desktop]
        H --> J[🔗 Other AI Clients]
    end
    
    style A fill:#e1f5fe
    style B fill:#f3e5f5
    style C fill:#e8f5e8
    style F fill:#fff3e0
    style G fill:#ffebee
    style H fill:#f1f8e9

# Run full test suite with coverage
poetry run pytest --cov=src --cov-report=html --cov-report=term

# Run specific test categories
poetry run pytest tests/unit/stages/          # Stage-specific tests
poetry run pytest tests/integration/         # Integration tests
poetry run pytest -k "test_confidence"       # Tests matching pattern

# Type checking and linting
poetry run mypy src/ --strict                # Strict type checking
poetry run ruff check . --fix                # Auto-fix linting issues
poetry run ruff format .                     # Format code

# Pre-commit hooks (recommended)
poetry run pre-commit install                # Install hooks
poetry run pre-commit run --all-files       # Run all hooks

# Core application settings
app:
  name: "NexusMind"
  version: "0.1.0"
  debug: false
  log_level: "INFO"

# API configuration
api:
  host: "0.0.0.0"
  port: 8000
  cors_origins: ["*"]
  
# ASR-GoT Framework settings
asr_got:
  max_stages: 8
  default_confidence_threshold: 0.6
  enable_bias_detection: true
  enable_temporal_analysis: true
  max_hypotheses_per_dimension: 5
  
# Graph settings
graph:
  max_nodes: 10000
  enable_hyperedges: true
  enable_multi_layer: true
  temporal_decay_factor: 0.1

{
  "name": "nexusmind",
  "description": "Advanced Scientific Reasoning with Graph-of-Thoughts",
  "version": "0.1.0",
  "endpoints": {
    "mcp": "http://localhost:8000/mcp"
  },
  "capabilities": [
    "scientific_reasoning",
    "graph_analysis",
    "confidence_assessment",
    "bias_detection"
  ]
}