Adaptive Graph of Thoughts
LLM Reasoning Framework for Scientific Research
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 llm reasoning framework for scientific research
LLM Reasoning Framework for Scientific Research
This server falls under the Coding Agents category on MCPgee, the world's largest MCP server directory with 33,000+ servers.
Features
- LLM Reasoning Framework for Scientific Research
Use Cases
Maintainer
Works with
Installation
Manual Installation
npx adaptive-graph-of-thoughts-mcpConfiguration
Configuration Details
claude_desktop_config.json
Performance
Response Metrics
Resource Usage
How to Set Up and Use Adaptive Graph of Thoughts
Adaptive Graph of Thoughts (AGT) is a sophisticated MCP server that implements a graph-based reasoning framework for scientific research, backed by a Neo4j graph database. It models scientific knowledge as an interconnected graph and exposes tools for hypothesis analysis, semantic relationship exploration, evidence-based claim validation, and complex scientific reasoning queries with full reasoning traces. Researchers and AI engineers working on knowledge-intensive scientific tasks will benefit from its structured approach to multi-step reasoning.
Prerequisites
- Python 3.11+ and Poetry package manager installed
- Neo4j database running (locally or remotely) with URI, username, and password available
- An Anthropic API key (ANTHROPIC_API_KEY) or OpenAI API key (OPENAI_API_KEY) for LLM integration
- An MCP-compatible client such as Claude Desktop or VS Code with MCP extension
- Git for cloning the repository
Clone the repository and install dependencies
Clone the AGT MCP server 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 installSet up Neo4j
Install and start Neo4j (Desktop, Docker, or AuraDB cloud). Note your connection URI (bolt://localhost:7687 for local), username (default: neo4j), and password.
# Docker quickstart for Neo4j:
docker run -d \
--name neo4j \
-p 7474:7474 -p 7687:7687 \
-e NEO4J_AUTH=neo4j/yourpassword \
neo4j:latestConfigure environment variables
Copy the example env file and fill in your Neo4j credentials and LLM API key. Set MCP_TRANSPORT_TYPE to 'stdio' for use with Claude Desktop.
cp .env.example .env
# Edit .env with your values:
# NEO4J_URI=bolt://localhost:7687
# NEO4J_USER=neo4j
# NEO4J_PASSWORD=yourpassword
# ANTHROPIC_API_KEY=sk-ant-...
# MCP_TRANSPORT_TYPE=stdioRun the setup initializer
Run the AGT setup script to initialize the graph schema and verify database connectivity before connecting an MCP client.
poetry run python -m agt_setupAdd the server to your MCP client configuration
Configure Claude Desktop or VS Code to launch the AGT server, passing your credentials via the env block.
{
"mcpServers": {
"adaptive-graph-of-thoughts": {
"command": "python",
"args": ["-m", "adaptive_graph_of_thoughts.main"],
"env": {
"NEO4J_URI": "bolt://localhost:7687",
"NEO4J_USER": "neo4j",
"NEO4J_PASSWORD": "yourpassword",
"ANTHROPIC_API_KEY": "sk-ant-...",
"MCP_TRANSPORT_TYPE": "stdio"
}
}
}
}Adaptive Graph of Thoughts Examples
Client configuration
Full claude_desktop_config.json entry for the Adaptive Graph of Thoughts MCP server.
{
"mcpServers": {
"adaptive-graph-of-thoughts": {
"command": "python",
"args": ["-m", "adaptive_graph_of_thoughts.main"],
"env": {
"NEO4J_URI": "bolt://localhost:7687",
"NEO4J_USER": "neo4j",
"NEO4J_PASSWORD": "yourpassword",
"ANTHROPIC_API_KEY": "sk-ant-...",
"MCP_TRANSPORT_TYPE": "stdio",
"LOG_LEVEL": "INFO"
}
}
}
}Prompts to try
Scientific reasoning queries you can submit once the server is running.
- "Analyze the relationship between gut microbiome diversity and cancer progression"
- "Evaluate the hypothesis that sleep deprivation accelerates neurodegeneration — provide confidence metrics"
- "Explore semantic relationships between CRISPR gene editing and off-target mutation risks"
- "Validate the claim that high-dose vitamin D supplementation reduces COVID-19 severity with evidence"
- "Run a scientific reasoning query on the links between inflammation and Alzheimer's disease with a full reasoning trace"Troubleshooting Adaptive Graph of Thoughts
Neo4j connection refused or authentication failed
Verify Neo4j is running (check bolt://localhost:7687 or your configured URI) and that NEO4J_USER and NEO4J_PASSWORD match the database credentials. For Docker, ensure the container is started and ports 7687 and 7474 are mapped.
Poetry command not found
Install Poetry with: curl -sSL https://install.python-poetry.org | python3 - then restart your shell and verify with 'poetry --version'.
Module not found errors when starting the server
Ensure you are running commands from inside the cloned repository directory and that 'poetry install' completed without errors. Use 'poetry run python' rather than the system Python to ensure the virtual environment is active.
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 llm reasoning framework for scientific research 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. You can use it freely in both personal and commercial projects.
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