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ClarkMem

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ClarkMem — the persistent memory engine behind Clark. Typed temporal knowledge-graph memory for AI agents: evidence-counted facts with invalidation history, hybrid entity-anchored recall, multi-tenant, zero-external-services local mode or Neo4j at fleet scale. MCP server for Claude + HTTP for any runtime. Proprietary (Weblyfe); formerly Cognify.

ClarkMem

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The persistent memory engine behind Clark.Give any AI agent durable, structured, temporal memory: drop in documents,notes, or conversation facts — get back a typed knowledge graph with hybridrecall that knows not just what is true, but how strongly evidenced itis and whether it still holds.

Proprietary software by Weblyfe · formerly published as "Cognify" (≤0.5.0, MIT).

Why agents need this

Vector RAG finds similar text. Agents need more: who works where now, whatreplaced what, how facts connect across documents ingested weeks apart.ClarkMem keeps three layers in one engine:

  1. Chunks + embeddings — fuzzy recall over everything ingested.
  2. A typed knowledge graph — entities (Person, Project, Technology, …)and typed relations (WORKS_AT, USES, DEPENDS_ON, …) extracted by acheap LLM at write time, merged across documents.
  3. Time — every fact carries observed_at, an evidence count that growsas more sources assert it, and an invalid_at when the world moves on.Closed facts stay queryable as history; recall hides them by default.

What's inside

Capability How
Temporal facts evidence counting, explicit invalidate, optional one-current-object predicates (CLARKMEM_FUNCTIONAL_PREDICATES), history preserved
Hybrid recall vector search + entity-anchored retrieval (chunks mentioning entities named in the query), fused by reciprocal-rank fusion — no LLM call at recall time
Multi-hop graph expansion hops=1..3 over typed relations, invalidated edges break the chain
Multi-tenant + namespaces every node keyed by tenant; namespaces partition a tenant (docs / memory / transcripts / …)
Stable note identity key= gives an evolving note update-in-place semantics; inline text is otherwise content-addressed
Self-maintenance maintain — integrity pass: dangling chunks, orphan entities, vector/graph reconciliation
Two backends, one API local = ChromaDB + networkx, zero external services, torch-free · neo4j = TurboVec + Neo4j for a shared fleet graph
Claude-native MCP server (clarkmem-mcp) → tools in Claude Code / Claude Desktop
Runtime-agnostic HTTP API (clarkmem-serve) for Hermes, n8n, cron, curl — plus a CLI
Agent skills included skills/ — drop-in SKILL.md files that teach agents to use and to improve ClarkMem

Same 384d embedding space on both backends, so a graph built locally isqueryable on the server and vice versa.

Core technology

  • Python 3.10+ — ~2k lines, src layout, frozen dataclasses, one file per concern
  • ChromaDB (embedded) with its bundled ONNX MiniLM — local vectors, no torch, no services
  • networkx MultiDiGraph — local typed graph, persisted as JSON per tenant
  • Neo4j 5 — fleet-scale property graph (C-prefixed labels, tenant-keyed nodes)
  • TurboVec — per-tenant server-side vector index
  • fastembed / sentence-transformers — one L2-normalized 384d space everywhere (all-MiniLM-L6-v2)
  • FastAPI + Uvicorn — the HTTP surface (multi-bind, constant-time API-key auth)
  • MCP SDK (FastMCP) — native tools for Claude Code / Claude Desktop
  • pypdf for PDF ingestion; numpy and requests are the only hard dependencies
  • Extraction LLM — any OpenAI-compatible endpoint (OpenRouter, OpenAI, vLLM, Ollama) ornative Anthropic Claude; one cheap call per chunk at write time, zero LLM calls at recall

60-second start

./setup.sh local            # venv + deps + .env  (zero external services)
source .venv/bin/activate
echo 'OPENROUTER_API_KEY=sk-or-...' >> .env      # or ANTHROPIC_API_KEY
set -a && . ./.env && set +a

clarkmem ingest examples/sample_docs/acme.md --tenant demo
clarkmem recall "what does Pathfinder run on and who owns it?" --tenant demo
clarkmem stats --tenant demo

Python:

import clarkmem
be = clarkmem.get_backend("local")
clarkmem.ingest(be, "handbook.pdf", tenant="acme", namespace="hr")
clarkmem.ingest(be, "Sam now leads support.", tenant="acme", key="sam-role")  # evolving note
res = clarkmem.recall(be, "who leads support?", tenant="acme")
print(res.chunks, res.relations)                  # facts carry evidence counts
clarkmem.invalidate(be, "Sam", predicate="LEADS", tenant="acme")  # world changed

Recall pipeline

remember ->  Extract   file/text -> heading-aware ~512-token chunks
             Cognize   per chunk, cheap LLM -> typed entities + relations
             Load      embed (384d) -> vectors ; graph merge (evidence++, temporal)
recall   ->  vector top-k  +  entity-anchored chunks   ->  RRF fuse
             -> expand typed graph around hits (1..3 hops, live facts only)
             -> chunks + entities + relations, ready to ground an answer
maintain ->  integrity pass: dangling chunks, orphan entities, vector drift

Use with Claude

pip install 'clarkmem[local,claude]'
claude mcp add clarkmem -- clarkmem-mcp

Claude gets clarkmem_ingest, clarkmem_recall, clarkmem_invalidate,clarkmem_forget, clarkmem_stats. Claude can also BE the extractor — setANTHROPIC_API_KEY and it's auto-detected. Drop skills/clarkmem/ into~/.claude/skills/ to teach agents the memory workflow (recall-first,remember-with-key, invalidate-on-change).

Use with Hermes (and any runtime)

The CLI works as-is for shell-native agents; drop skills/clarkmem/SKILL.mdinto the agent's skills directory. For a shared long-running graph, run theserver:

pip install 'clarkmem[neo4j,serve,fastembed]'
export CLARKMEM_BACKEND=neo4j CLARKMEM_EMBED_PROVIDER=fastembed
export CLARKMEM_HOST=127.0.0.1,100.x.y.z CLARKMEM_API_KEY=$(openssl rand -hex 24)
clarkmem-serve   # /health open; everything else needs x-api-key

curl -s localhost:8799/ingest  -H 'content-type: application/json' \
  -d '{"text":"the refund policy is 14 days","title":"policy","tenant":"acme"}'
curl -s localhost:8799/recall  -H 'content-type: application/json' \
  -d '{"query":"refund policy?","tenant":"acme"}'
curl -s localhost:8799/invalidate -H 'content-type: application/json' \
  -d '{"subject":"Acme","predicate":"OFFERS","tenant":"acme"}'

Server-side {"path": ...} ingestion is off by default; allow it for onedirectory with CLARKMEM_INGEST_ROOT. Text bodies are capped byCLARKMEM_MAX_TEXT. k/hops are clamped engine-wide.

How it compares

ClarkMem Cognee Mem0 Graphiti / Zep LightRAG plain RAG
Typed entity+relation graph ✅ ✅ partial ✅ ✅ ❌
Temporal facts (evidence, invalidation, history) ✅ deterministic ❌ partial ✅ (LLM-driven) ❌ ❌
Graph as a retrieval signal (anchored hybrid recall) ✅ ⚠️ ❌ ✅ ✅ ❌
Zero external services mode ✅ ❌ ❌ ❌ ⚠️ ✅
Torch-free local install ✅ ❌ ❌ ❌ ❌ varies
Same API, swap local ↔ server ✅ ⚠️ ❌ ❌ ❌ n/a
Built-in multi-tenancy ✅ ⚠️ ✅ ✅ ❌ ❌
MCP server for Claude ✅ ✅ ❌ ❌ ❌ ❌
Agent skills shipped in-repo ✅ ❌ ❌ ❌ ❌ ❌
Core small enough to read in a sitting ✅ ~2k lines ❌ ❌ ❌ ⚠️ ✅

Honest edges elsewhere: Zep/Graphiti does LLM-driven contradictiondetection and SOC2/HIPAA compliance; Cognee has more managed connectors; Mem0is the quickest hosted drop-in for pure conversational personalization.ClarkMem wins when you want a real temporal knowledge graph an agent can runanywhere — a laptop, an isolated client box, or a shared fleet server — withone dependency-light install and one API across all of them.

Extraction models

One cheap LLM call per ~2KB chunk at ingest (never at recall). Recommended:openai/gpt-4o-mini via OpenRouter (~$0.20 per 40-doc KB), gemini-2.0-flash,a local Qwen/Llama via Ollama/vLLM (free, point CLARKMEM_LLM_BASE at it), orClaude Haiku (ANTHROPIC_API_KEY, auto-detected — best quality of the cheaptier). Avoid :free OpenRouter variants for bulk (heavy 429s).

Configuration

All via env — see .env.example. Primary prefix CLARKMEM_*; legacyCOGNIFY_* names from the pre-rename era keep working. Key ones:CLARKMEM_BACKEND, CLARKMEM_DATA_DIR, CLARKMEM_LLM_BASE/MODEL/KEY,CLARKMEM_EMBED_PROVIDER (st|fastembed), CLARKMEM_EXTRACT_WORKERS,CLARKMEM_HOST/PORT/API_KEY, CLARKMEM_INGEST_ROOT, CLARKMEM_MAX_TEXT,CLARKMEM_FUNCTIONAL_PREDICATES, NEO4J_URI/USER/PASSWORD.

For agents working on this repo

CLAUDE.md is the operating guide, ARCHITECTURE.md the design,BLUEPRINT.md a from-scratch reconstruction spec, andskills/clarkmem-dev/ the contributor skill (invariants, test harnesses,roadmap). Hand an agent this repo and it can use it, extend it, or rebuild it.

Migrating from Cognify

The GitHub URL redirects. pip install clarkmem replaces cognify-kg(never published to PyPI, so no package migration). Legacy cognify,cognify-serve, cognify-mcp commands and COGNIFY_* env vars still work.On-disk stores are read in place — including ~/.cognify — no data migration.

License

Proprietary — © 2026 Weblyfe. Source available for evaluation and securityreview; production use requires a license (see LICENSE). Versions ≤0.5.0were released under MIT as "Cognify" and remain MIT.

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