Adaptive Graph of Thoughts
A scientific reasoning framework that leverages graph structures and the Model Context Protocol (MCP) to process complex scientific queries through an Advanced Scientific Reasoning Graph-of-Thoughts (ASR-GoT) approach.
What is Adaptive Graph of Thoughts?
Adaptive Graph of Thoughts is a Model Context Protocol (MCP) server that allows AI assistants like Claude, Cursor, and VS Code to scientific reasoning framework that leverages graph structures and the model context protocol (mcp) to process complex scientific queries through an advanced scientific reasoning graph-of-thoughts (as...
A scientific reasoning framework that leverages graph structures and the Model Context Protocol (MCP) to process complex scientific queries through an Advanced Scientific Reasoning Graph-of-Thoughts (ASR-GoT) approach.
This server falls under the Coding Agents category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- A scientific reasoning framework that leverages graph struct
Use Cases
Maintainer
Works with
Installation
Manual Installation
npx adaptive-graph-of-thoughts-mcp-serverConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use Adaptive Graph of Thoughts
The Adaptive Graph of Thoughts MCP Server implements an Advanced Scientific Reasoning Graph-of-Thoughts (ASR-GoT) framework that processes complex scientific queries by building and traversing knowledge graphs in Neo4j. It exposes tools for hypothesis evaluation, scientific claim validation, and relationship mapping between concepts — all backed by LLM reasoning chains stored as graph structures. Researchers and scientists can use it to analyze research questions, explore interdisciplinary connections, and build structured reasoning traces for complex domains.
Prerequisites
- Python 3.11 or higher with Poetry installed
- Neo4j 5.x database instance running with the APOC library installed
- An OpenAI API key (OPENAI_API_KEY) for LLM reasoning operations
- An MCP-compatible client such as Claude Desktop
- Docker and Docker Compose (optional, for containerized deployment)
Set up Neo4j with APOC
Install and start a Neo4j instance with the APOC plugin enabled. The APOC library is required for graph operations used by the reasoning framework.
# Using Docker for Neo4j with APOC
docker run -d \
--name neo4j \
-p 7474:7474 -p 7687:7687 \
-e NEO4J_AUTH=neo4j/password \
-e NEO4J_PLUGINS='["apoc"]' \
neo4j:5Clone the repository and install dependencies
Clone the repository and install all Python dependencies using Poetry.
git clone https://github.com/SaptaDey/Adaptive-Graph-of-Thoughts-MCP-server.git
cd Adaptive-Graph-of-Thoughts-MCP-server
poetry install
poetry shellConfigure environment variables
Set the required environment variables for Neo4j connectivity and LLM API access.
export NEO4J_URI=bolt://localhost:7687
export NEO4J_USER=neo4j
export NEO4J_PASSWORD=password
export OPENAI_API_KEY=your_openai_api_key
export LOG_LEVEL=INFO
export API_HOST=0.0.0.0
export API_PORT=8000Start the server
Launch the FastAPI-based MCP server. It will be available at http://localhost:8000 with the MCP endpoint at /mcp.
python src/adaptive_graph_of_thoughts/main.pyConfigure Claude Desktop
Add the server to your Claude Desktop configuration pointing to the running HTTP server endpoint.
{
"mcpServers": {
"adaptive-graph-of-thoughts": {
"command": "python",
"args": ["/path/to/Adaptive-Graph-of-Thoughts-MCP-server/src/adaptive_graph_of_thoughts/main.py"],
"env": {
"NEO4J_URI": "bolt://localhost:7687",
"NEO4J_USER": "neo4j",
"NEO4J_PASSWORD": "password",
"OPENAI_API_KEY": "your_openai_api_key",
"LOG_LEVEL": "INFO"
}
}
}
}Adaptive Graph of Thoughts Examples
Client configuration
Claude Desktop configuration for the Adaptive Graph of Thoughts MCP server with Neo4j and OpenAI credentials.
{
"mcpServers": {
"adaptive-graph-of-thoughts": {
"command": "python",
"args": ["/path/to/Adaptive-Graph-of-Thoughts-MCP-server/src/adaptive_graph_of_thoughts/main.py"],
"env": {
"NEO4J_URI": "bolt://localhost:7687",
"NEO4J_USER": "neo4j",
"NEO4J_PASSWORD": "your_neo4j_password",
"OPENAI_API_KEY": "sk-your_openai_api_key",
"LOG_LEVEL": "INFO",
"API_HOST": "0.0.0.0",
"API_PORT": "8000"
}
}
}
}Prompts to try
Example prompts for scientific reasoning, hypothesis analysis, and concept relationship exploration.
- "Analyze the relationship between microbiome diversity and cancer progression using graph-of-thoughts reasoning"
- "Evaluate this hypothesis with confidence scoring: increased neuroplasticity in adults is correlated with intermittent fasting"
- "Explore the scientific relationships between CRISPR gene editing, off-target effects, and therapeutic safety"
- "Validate the claim that mRNA vaccines produce lasting T-cell immunity against COVID-19 variants"
- "Map the interdisciplinary connections between quantum computing and drug discovery"Troubleshooting Adaptive Graph of Thoughts
Server fails to start with Neo4j connection refused errors
Verify Neo4j is running and accessible at the bolt:// URI specified in NEO4J_URI. Check that the APOC plugin is installed — without APOC, several graph operations will fail. You can verify APOC is loaded by running 'RETURN apoc.version()' in Neo4j Browser at http://localhost:7474.
Scientific reasoning queries timeout or return incomplete graphs
Complex multi-hop reasoning can take 30-60 seconds for large queries. Increase your MCP client timeout if requests are being cut off. Also check that your OPENAI_API_KEY has sufficient quota — the reasoning framework makes multiple LLM calls per query.
Poetry install fails with dependency conflicts
Ensure you have Python 3.11 or higher active in your shell before running poetry install. Use 'poetry env use python3.11' to explicitly set the Python version. Delete any existing .venv directory and retry.
Frequently Asked Questions about Adaptive Graph of Thoughts
What is Adaptive Graph of Thoughts?
Adaptive Graph of Thoughts is a Model Context Protocol (MCP) server that scientific reasoning framework that leverages graph structures and the model context protocol (mcp) to process complex scientific queries through an advanced scientific reasoning graph-of-thoughts (asr-got) approach. It connects AI assistants to external tools and data sources through a standardized interface.
How do I install Adaptive Graph of Thoughts?
Follow the installation instructions on the Adaptive Graph of Thoughts GitHub repository. Clone the repo, install dependencies, and add the server config to your AI client.
Which AI clients work with Adaptive Graph of Thoughts?
Adaptive Graph of Thoughts works with all major MCP-compatible AI clients including Claude Desktop, Claude Code, Cursor, VS Code (GitHub Copilot), Windsurf, and Cline.
Is Adaptive Graph of Thoughts free to use?
Yes, Adaptive Graph of Thoughts is open source and available under the MIT License license. You can use it freely in both personal and commercial projects.
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