GDS Agent

Neither LLMs nor any existing toolings (MCP Servers) are capable of complex reasoning on graphs at the moment.

This MCP Server includes toolings from Neo4j Graph Data Science (GDS) library, which allows you to run all common graph algorithms.

Once the server is running, you are able to ask any graph questions about your Neo4j graph and get answers. LLMs equipped with GDS agent can decide and accurately execute the appropriate parameterised graph algorithms over the graph you have in your Neo4j database.

An example where an LLM with GDS Agent is able to pick shortest path and Yen's algorithm to answer my question about travel plan:

Table of Contents

For Users

• Use GDS Agent

For Developers

• Example dataset

• Start the server

• How to contribute

• Feature request and bug reports

• Additional resource

Use GDS Agent

If you have uvx installed, add the following config to your claude_desktop_config.json

{
    "mcpServers": {
      "neo4j-gds": {
      "command": "/opt/homebrew/bin/uvx",
      "args": [ "gds-agent" ],
      "env": {
        "NEO4J_URI": "bolt://localhost:7687",
        "NEO4J_USERNAME": "neo4j",
        "NEO4J_PASSWORD": ""
      }
    }
    }
}

Replace command with your uvx location. Find out by running which uvx in the command line. Replace NEOJ_URI, NEO4J_USERNAME, NEO4J_PASSWORD with your database login details. You can also optionally specify NEO4J_DATABASE.

By default the server uses STDIO transport for local MCP clients. For HTTP-native clients, run the server with streamable HTTP:

gds-agent --transport http --host 127.0.0.1 --port 8000 --path /mcp

The equivalent environment variables are GDS_AGENT_TRANSPORT, GDS_AGENT_HOST, GDS_AGENT_PORT, and GDS_AGENT_PATH. The Neo4j MCP-style NEO4J_TRANSPORT and NEO4J_MCP_SERVER_* names are also supported.

GDS Aura Graph Analytics (sessions)

The server detects whether the connected Neo4j has the GDS plugin installed or whether to use a GDS Aura Graph Analytics session. Detection runs gds.session.list() on startup; if it succeeds, session mode is used and graph projections fall back to gds.graph.project.remote.

Session mode requires Aura API credentials. Add them to the same .env file (or env block in your MCP config) used for the database credentials:

AURA_API_CLIENT_ID=...
AURA_API_CLIENT_SECRET=...
AURA_API_PROJECT_ID=...
# optional
SESSION_MEMORY_GB=8
SESSION_NAME=mcp_gds_session
SESSION_TTL_HOURS=24

The session is created lazily on the first algorithm/projection call. Three extra tools become available in session mode: list_sessions, delete_session, and recreate_session (the last is useful to bump memory after an OOM).

Example dataset

To load the London underground example dataset:

1. Fork and clone the repository

2. Install necessary packages in your python environment with pip install -r requirements.txt

3. Install the Neo4j database with GDS plugin: Download the Neo4j Desktop from Neo4j Download Center Install the GDS plugin from the Neo4j Desktop Create a new database and start it

4. Populate .env file with necessary credentials:

   NEO4J_URI=bolt://localhost:7687  # or your database URI
   NEO4J_USERNAME=neo4j  # or your db username
   NEO4J_PASSWORD=your_password

5. Load the London Underground dataset with the following command:

   python import_data.py --undirected

Connect to your DB and querying the graph from Neo4j workspace, you should see:

Start the server for dev

1. When inside the /mcp_server directory, run uv sync --dev and run uv run gds-agent to start the MCP server standalone, or run claude to start claude-cli with the agent.

How to contribute

Open a pull request from a branch of your forked repository into the main branch of this repo, for example mygithubid:add-new-algo -> neo4j-contrib:main.

The CI build in github action requires all codestyle checks and tests to pass.

To run and fix codestyle checks locally, in the /mcp_server directory, run:

uv sync --dev

to setup the python environment. And then,

uv run pytest tests -v -s
uv run ruff check
uv run ruff format

for all tests and codestyle fixes.

Feature request and bug reports

To report a bug or a new feature request, raise an issue. If it is a bug, include the full stacktrace and errors. When available, attach relevant logs in mcp_server_neo4j_gds.log. This file is located inside the /mcp_server/src_mcp_server_neo4j_gds directory if the gds agent is running from source, or inside the logging path for Claude (e.g /Library/Logs/Claude for Claude Desktop on Mac). Include relevant minimal dataset that can be used to reproduce the issue if possible.

Additional resources

The GDS agent can be used with other MCP servers, such as those that provide additional Neo4j toolings: https://github.com/neo4j-contrib/mcp-neo4j

Arxiv paper including details about the architecture and benchmark results: https://arxiv.org/abs/2508.20637.