memnest-mcp 0.3.3

Persistent graph memory MCP server for AI agents using LadybugDB

Memnest Memory MCP Server

Persistent graph memory for AI agents using LadybugDB — an embedded graph database with native vector search and full-text search.

Give your AI agent memory that persists across sessions, deduplicates automatically, and models knowledge as a graph with typed relationships.

Why Memnest?

• Graph memory — memories linked via Topic nodes and relationships (RELATED_TO, SUPERSEDES, EXPLAINS) with Cypher queries
• Three-layer auto-dedup — exact hash + semantic similarity + LLM-driven consolidation
• Workspace namespacing — memories scoped per project; global_search opt-out
• HNSW vector search — fast cosine similarity over FastEmbed embeddings
• Topic auto-linking — tags become graph nodes, enabling traversal queries
• Embedded — no Docker, no server process, single database directory
• Zero config — sensible defaults, just install and run
• Importance & access tracking — memories ranked by relevance and usage

Benchmarks

Memnest scores 82.9% on the LOCOMO benchmark — the standard evaluation for long-term conversational memory (ACL 2024).

Category	Score
Single-hop	84.4%
Multi-hop	76.9%
Open-domain	85.7%
Temporal	86.5%
Adversarial	76.6%
Overall	82.9%

Evaluated with Claude Sonnet 4.5 as the answer agent and Haiku 4.5 as the judge, using the industry-standard LLM-as-a-Judge methodology. All 5 LOCOMO categories included.

Architecture advantages

• Zero LLM calls in the server — intelligence lives in the agent, not the memory layer
• Local embeddings — no API key needed (bge-small-en-v1.5, 384-dim)
• Single embedded database — no Docker, no PostgreSQL, no separate vector DB
• Hybrid search — Vector (HNSW) + Full-text (BM25) + Graph (PageRank + Louvain communities)
• 3 agent tools — memory_search, memory_get, calculator. Simple interface, powerful retrieval.

Quick Start

# Run directly with uvx (no install needed)
uvx memnest-mcp

Or install and run:

pip install memnest-mcp
memnest-mcp

MCP Configuration

Add to your MCP client config (Kiro, Claude Desktop, Cursor, etc.):

{
  "mcpServers": {
    "memnest": {
      "command": "uvx",
      "args": ["--prerelease=allow", "memnest-mcp@latest"],
      "env": {
        "FASTMCP_LOG_LEVEL": "ERROR"
      }
    }
  }
}

That's it — zero config required. All settings have sensible defaults.

Tools

Tool	What it does
memory_store	Store a memory (single or batch) with auto-dedup, auto-link to Topic nodes
memory_search	Hybrid semantic + keyword search, ranked by relevance
memory_update	Update content, importance, or tags (single or batch)
memory_delete	Delete one or more memories and their relationships
memory_relate	Create RELATED_TO / SUPERSEDES / EXPLAINS relationships (single or batch)
memory_query	Run any Cypher query — traversals, writes, extension calls (INSTALL/LOAD), table scans
memory_schema	Inspect live DB schema: tables, columns, indexes, extensions
memory_topics	List all topics (tags) with memory counts
memory_stats	Database statistics: counts, categories, topics, top memories
memory_dream	Periodic consolidation — auto-prune stale, auto-merge trivial duplicates, surface clusters for review
memory_graph_html	Generate an interactive HTML visualization of the graph
memory_get	(compat) Get full content of a memory by ID
memory_list	(compat) List memories filtered by recency, category, topic, or importance
memory_traverse	(compat) Read-only Cypher — alias for memory_query(read_only=True)

Graph Data Model

(:Memory)  — content, embedding, category, tags, importance, access_count, timestamps
(:Topic)   — auto-created from tags

(:Memory)-[:ABOUT]->(:Topic)          # memory is about a topic
(:Memory)-[:RELATED_TO]->(:Memory)    # memories are related
(:Memory)-[:SUPERSEDES]->(:Memory)    # newer memory replaces older

Example: Store and Search

# Store a memory (via MCP tool call)
memory_store(
    content="User prefers Python over Node.js for backend tools",
    category="preference",
    tags=["python", "nodejs", "backend"],
    importance=4
)

# Search memories
memory_search(query="what language does the user prefer")

# Traverse the graph
memory_query(
    cypher_query="MATCH (m:Memory)-[:ABOUT]->(t:Topic {name: 'python'}) RETURN m.content"
)

Example: Graph Relationships

# Link related memories
memory_relate(from_id=5, to_id=3, relationship="RELATED_TO")

# Mark a decision as superseded
memory_relate(from_id=8, to_id=2, relationship="SUPERSEDES")

# Find all memories about a topic
memory_query(
    cypher_query="MATCH (m:Memory)-[:ABOUT]->(t:Topic) RETURN t.name, COUNT(m) ORDER BY COUNT(m) DESC"
)

Three-Layer Deduplication

Every memory_store call runs through three dedup layers:

1. Exact hash — SHA256 of normalized content. Identical content is rejected, importance bumped.
2. Semantic similarity — If cosine similarity > 0.92 with an existing memory, merges into it (keeps longer content, merges tags, bumps importance).
3. Consolidation — Periodic via memory_dream. Auto-prunes stale low-importance memories, auto-merges trivial duplicates (similarity ≥ 0.95), surfaces clusters for LLM-driven review.

Categories

Category	Use for
learning	Technical knowledge, facts, how things work
preference	User preferences and choices
decision	Architecture decisions, tool choices
pattern	Recurring workflows, conventions
general	Everything else (default)

Configuration

All settings are optional — defaults work out of the box.

Environment Variable	Default	Description
MEMORY_DB_PATH	.memnest/memory.lbug (in cwd)	LadybugDB database path. Use :memory: for ephemeral testing
MEMORY_DEDUP_THRESHOLD	0.92	Semantic similarity threshold for auto-dedup
MEMORY_EMBEDDING_MODEL	BAAI/bge-small-en-v1.5	FastEmbed model for embeddings
MEMORY_EMBEDDING_DIM	384	Embedding dimension (must match model)
MEMORY_WORKSPACE	cwd	Workspace identifier for memory namespacing
MEMORY_RESPONSE_FORMAT	toon if installed, else json	Response serialization. toon is more token-efficient for LLM context
MEMORY_SEARCH_LIMIT	10	Max results from memory_search
MEMORY_LIST_LIMIT	20	Default page size for memory_list
MEMORY_MAX_CONTENT	500	Content truncation length in search/list results
MEMORY_LATENCY_WARN_MS	200	Log a warning when an op exceeds this (ms)
MEMORY_DREAM_MIN_OPS	10	Min ops since last dream before next runs
MEMORY_DREAM_MIN_HOURS	24	Min hours since last dream before next runs
MEMORY_DREAM_MIN_MEMORIES	20	Min total memories before dream is allowed (skipped otherwise)
MEMORY_DREAM_PRUNE_DAYS	30	Auto-prune memories older than N days (with low importance)
MEMORY_DREAM_PRUNE_MAX_IMP	2	Auto-prune only memories at or below this importance
MEMORY_DREAM_TRIVIAL_THRESHOLD	0.95	Cosine similarity ≥ this is auto-merged in dream
MEMORY_DREAM_CLUSTER_LOW	0.88	Cluster-review window: [low, trivial) is surfaced for agent review
MEMORY_CONSOLIDATE_CLUSTERS	10	Max clusters returned per memory_dream run
MEMORY_CONSOLIDATE_SCAN	1000	Max memories scanned per dream phase
MEMORY_ALLOW_DESTRUCTIVE	false	Allow DELETE/DROP/TRUNCATE through memory_query. Off by default for safety. Opt in with true
MEMORY_GRAPH_MAX_NODES	2000	Max nodes memory_graph_html will render before refusing
MEMORY_EMBED_TIMEOUT_S	30	Soft timeout for embedding model load (warm-up only)

In-Memory Mode (Testing)

"env": { "MEMORY_DB_PATH": ":memory:" }

All data is ephemeral — lost on restart. Useful for testing.

Kiro Power

This repo includes a ready-to-use Kiro Power in the power/memnest/ directory with:

• Pre-configured MCP server (power/memnest/mcp.json)
• Three hooks for automatic memory persistence and recall (power/memnest/hooks/)
  • persist-memory — stores important info when the agent stops
  • recall-memory — searches memory before responding to each prompt
  • auto-dream — manually trigger consolidation (prune + merge + review)
• Steering files with setup guide and Cypher query examples (power/memnest/steering/)

Install in Kiro: Add Custom Power → https://github.com/arunkumars-mf/memnest-mcp/tree/main/power/memnest

Architecture

AI Agent (Kiro, Claude, etc.)
    │
    ├─ memory_store ──→ embed content → dedup check → insert node → link topics
    ├─ memory_search ─→ embed query → HNSW vector search → tag boost → rank
    ├─ memory_query ──→ execute Cypher → return graph results
    │
    └─ LadybugDB (embedded, single directory)
        ├─ Memory nodes (content + FLOAT[384] embeddings)
        ├─ Topic nodes (auto-linked from tags)
        ├─ HNSW vector index (cosine similarity)
        └─ Graph relationships (ABOUT, RELATED_TO, SUPERSEDES, EXPLAINS)

Requirements

• Python 3.10+
• Dependencies installed automatically: real-ladybug, fastembed, mcp
• ~130MB disk for the embedding model (downloaded on first run)

Contributing

Issues and PRs welcome. See LICENSE for terms.

License

MIT

Changelog

0.3.0

• Default database is now per-workspace: .memnest/memory.lbug in the current directory. No more cross-workspace lock conflicts.
• Set MEMORY_DB_PATH to use a custom location (e.g. ~/.memnest/memory.lbug for global shared memory).
• Hybrid search: Vector (HNSW) + Full-text (BM25) + Graph scoring with PageRank, Louvain community detection, and K-Core decomposition.
• LOCOMO benchmark: 82.9% overall score.

0.2.0

Compatibility-preserving redesign with improved safety defaults.

• New tools: memory_query (general Cypher), memory_schema, memory_topics, memory_dream, memory_graph_html. Batch mode added to memory_store, memory_update, memory_relate, memory_delete.
• Breaking: MEMORY_ALLOW_DESTRUCTIVE now defaults to false. Set it to true if you previously relied on memory_query deleting nodes.
• Breaking: tag storage migrated from comma-joined strings to JSON arrays. Old rows are still readable; rewriting (e.g. via memory_update) upgrades them to JSON.
• memory_get, memory_list, memory_traverse from 0.1.x are retained as compatibility aliases. They will be removed in 0.3.0.
• TOON serialization is now the default response format when toon-format is installed; set MEMORY_RESPONSE_FORMAT=json to opt out.
• memory_relate validates that both endpoints exist before returning created (used to silently no-op on typo'd IDs).
• memory_graph_html is now XSS-safe (HTML-escaped tooltips, DOM textContent for the detail panel), refuses to render >MEMORY_GRAPH_MAX_NODES, and rotates snapshots.
• Workspace filter pushed inside the vector index WITH clause so search recall isn't starved across workspaces.
• Dream consolidation: dedupes parallel edges across merges, isolates clusters by workspace, persists state via atomic sidecar JSON.