Mnemex

CortexGraph: Temporal Memory for AI

A Model Context Protocol (MCP) server providing human-like memory dynamics for AI assistants. Memories naturally fade over time unless reinforced through use, mimicking the Ebbinghaus forgetting curve.

[License: AGPL-3.0] [Python 3.10+] [Tests] [Security Scanning] [codecov] [SBOM: CycloneDX]

[!NOTE] About the Name & Version

This project was originally developed as mnemex (published to PyPI up to v0.6.0). In November 2025, it was transferred to Prefrontal Systems and renamed to CortexGraph to better reflect its role within a broader cognitive architecture for AI systems.

Version numbering starts at 0.1.0 for the cortexgraph package to signal a fresh start under the new name, while acknowledging the mature, well-tested codebase (791 tests, 98%+ coverage) inherited from mnemex. The mnemex package remains frozen at v0.6.0 on PyPI.

This versioning approach:

• Signals "new package" to PyPI users discovering cortexgraph
• Gives room to evolve the brand, API, and organizational integration before 1.0
• Maintains continuity: users can migrate from pip install mnemex → pip install cortexgraph
• Reflects that while the code is mature, the cortexgraph identity is just beginning

[!IMPORTANT] 🔬 RESEARCH ARTIFACT - NOT FOR PRODUCTION

This software is a Proof of Concept (PoC) and reference implementation for research purposes. It exists to validate theoretical frameworks in cognitive architecture and AI safety (specifically the STOPPER Protocol and CortexGraph).

It is NOT a commercial product. It is not maintained for general production use, may contain breaking changes, and offers no guarantees of stability or support. Use it to study the concepts, but build your own production implementations.

📖 New to this project? Start with the ELI5 Guide for a simple explanation of what this does and how to use it.

What is CortexGraph?

CortexGraph gives AI assistants like Claude a human-like memory system.

The Problem

When you chat with Claude, it forgets everything between conversations. You tell it "I prefer TypeScript" or "I'm allergic to peanuts," and three days later, you have to repeat yourself. This is frustrating and wastes time.

What CortexGraph Does

CortexGraph makes AI assistants remember things naturally, just like human memory:

• 🧠 Remembers what matters - Your preferences, decisions, and important facts
• ⏰ Forgets naturally - Old, unused information fades away over time (like the Ebbinghaus forgetting curve)
• 💪 Gets stronger with use - The more you reference something, the longer it's remembered
• 📦 Saves important things permanently - Frequently used memories get promoted to long-term storage

How It Works (Simple Version)

1. You talk naturally - "I prefer dark mode in all my apps"
2. Memory is saved automatically - No special commands needed
3. Time passes - Memory gradually fades if not used
4. You reference it again - "Make this app dark mode"
5. Memory gets stronger - Now it lasts even longer
6. Important memories promoted - Used 5+ times? Saved permanently to your Obsidian vault

No flashcards. No explicit review. Just natural conversation.

Why It's Different

Most memory systems are dumb:

• ❌ "Delete after 7 days" (doesn't care if you used it 100 times)
• ❌ "Keep last 100 items" (throws away important stuff just because it's old)

CortexGraph is smart:

• ✅ Combines recency (when?), frequency (how often?), and importance (how critical?)
• ✅ Memories fade naturally like human memory
• ✅ Frequently used memories stick around longer
• ✅ You can mark critical things to "never forget"

Technical Overview

This repository contains research, design, and a complete implementation of a short-term memory system that combines:

• Novel temporal decay algorithm based on cognitive science
• Reinforcement learning through usage patterns
• Two-layer architecture (STM + LTM) for working and permanent memory
• Smart prompting patterns for natural LLM integration
• Git-friendly storage with human-readable JSONL
• Knowledge graph with entities and relations

Module Organization

CortexGraph follows a modular architecture:

• cortexgraph.core: Foundational algorithms (decay, similarity, clustering, consolidation, search validation)
• cortexgraph.agents: Multi-agent consolidation pipeline and storage utilities
• cortexgraph.storage: JSONL and SQLite storage backends with batch operations
• cortexgraph.tools: MCP tool implementations

Why CortexGraph?

🔒 Privacy & Transparency

All data stored locally on your machine - no cloud services, no tracking, no data sharing.

• Short-term memory:

  • JSONL (default): Human-readable, git-friendly files (~/.config/cortexgraph/jsonl/)
  • SQLite: Robust database storage for larger datasets (~/.config/cortexgraph/cortexgraph.db)

• Long-term memory: Markdown files optimized for Obsidian

  • YAML frontmatter with metadata
  • Wikilinks for connections
  • Permanent storage you control

• Export: Built-in utility to export memories to Markdown for portability.

You own your data. You can read it, edit it, delete it, or version control it - all without any special tools.

Core Algorithm

The temporal decay scoring function:

$$ \Large \text{score}(t) = (n_{\text{use}})^\beta \cdot e^{-\lambda \cdot \Delta t} \cdot s $$

Where:

• $\large n_{\text{use}}$ - Use count (number of accesses)
• $\large \beta$ (beta) - Sub-linear use count weighting (default: 0.6)
• $\large \lambda = \frac{\ln(2)}{t_{1/2}}$ (lambda) - Decay constant; set via half-life (default: 3-day)
• $\large \Delta t$ - Time since last access (seconds)
• $\large s$ - Strength parameter $\in [0, 2]$ (importance multiplier)

Thresholds:

• $\large \tau_{\text{forget}}$ (default 0.05) — if score < this, forget
• $\large \tau_{\text{promote}}$ (default 0.65) — if score ≥ this, promote (or if $\large n_{\text{use}}\ge5$ in 14 days)

Decay Models:

• Power‑Law (default): heavier tail; most human‑like retention
• Exponential: lighter tail; forgets sooner
• Two‑Component: fast early forgetting + heavier tail

See detailed parameter reference, model selection, and worked examples in docs/scoring_algorithm.md.

Tuning Cheat Sheet

• Balanced (default)
  • Half-life: 3 days (λ ≈ 2.67e-6)
  • β = 0.6, τ_forget = 0.05, τ_promote = 0.65, use_count≥5 in 14d
  • Strength: 1.0 (bump to 1.3–2.0 for critical)
• High‑velocity context (ephemeral notes, rapid switching)
  • Half-life: 12–24 hours (λ ≈ 1.60e-5 to 8.02e-6)
  • β = 0.8–0.9, τ_forget = 0.10–0.15, τ_promote = 0.70–0.75
• Long retention (research/archival)
  • Half-life: 7–14 days (λ ≈ 1.15e-6 to 5.73e-7)
  • β = 0.3–0.5, τ_forget = 0.02–0.05, τ_promote = 0.50–0.60
• Preference/decision heavy assistants
  • Half-life: 3–7 days; β = 0.6–0.8
  • Strength defaults: 1.3–1.5 for preferences; 1.8–2.0 for decisions
• Aggressive space control
  • Raise τ_forget to 0.08–0.12 and/or shorten half-life; schedule weekly GC
• Environment template
  • CORTEXGRAPH_DECAY_LAMBDA=2.673e-6, CORTEXGRAPH_DECAY_BETA=0.6
  • CORTEXGRAPH_FORGET_THRESHOLD=0.05, CORTEXGRAPH_PROMOTE_THRESHOLD=0.65
  • CORTEXGRAPH_PROMOTE_USE_COUNT=5, CORTEXGRAPH_PROMOTE_TIME_WINDOW=14

Decision thresholds:

• Forget: $\text{score} < 0.05$ → delete memory
• Promote: $\text{score} \geq 0.65$ OR $n_{\text{use}} \geq 5$ within 14 days → move to LTM

Key Innovations

1. Temporal Decay with Reinforcement

Unlike traditional caching (TTL, LRU), Mnemex scores memories continuously by combining recency (exponential decay), frequency (sub-linear use count), and importance (adjustable strength). See Core Algorithm for the mathematical formula. This creates memory dynamics that closely mimic human cognition.

2. Smart Prompting System + Natural Language Activation (v0.6.0+)

Patterns for making AI assistants use memory naturally, now enhanced with automatic entity extraction and importance scoring:

Auto-Enrichment (NEW in v0.6.0)

When you save memories, CortexGraph automatically:

• Extracts entities (people, technologies, organizations) using spaCy NER
• Calculates importance/strength based on content markers
• Detects save/recall intent from natural language phrases

# Before v0.6.0 - manual entity specificationsave_memory(content="Use JWT for auth", entities=["JWT", "auth"])
# v0.6.0+ - automatic extractionsave_memory(content="Use JWT for auth")# Entities auto-extracted: ["jwt", "auth"]# Strength auto-calculated based on content

Auto-Save

User: "Remember: I prefer TypeScript over JavaScript"→ Detected save phrase: "Remember"→ Automatically saved with:   - Entities: [typescript, javascript]   - Strength: 1.5 (importance marker detected)   - Tags: [preferences, programming]

Auto-Recall

User: "What did I say about TypeScript?"→ Detected recall phrase: "what did I say about"→ Automatically searches for TypeScript memories→ Retrieves preferences and conventions

Auto-Reinforce

User: "Yes, still using TypeScript"→ Memory strength increased, decay slowed

Decision Support Tools (v0.6.0+)

Two new tools help Claude decide when to save/recall:

• analyze_message - Detects memory-worthy content, suggests entities and strength
• analyze_for_recall - Detects recall intent, suggests search queries

No explicit memory commands needed - just natural conversation.

3. Natural Spaced Repetition

Inspired by how concepts naturally reinforce across different contexts (the "Maslow effect" - remembering Maslow's hierarchy better when it appears in history, economics, and sociology classes).

No flashcards. No explicit review sessions. Just natural conversation.

How it works:

1. Review Priority Calculation - Memories in the "danger zone" (0.15-0.35 decay score) get highest priority
2. Cross-Domain Detection - Detects when memories are used in different contexts (tag Jaccard similarity <30%)
3. Automatic Reinforcement - Memories strengthen naturally when used, especially across domains
4. Blended Search - Review candidates appear in 30% of search results (configurable)

Usage pattern:

User: "Can you help with authentication in my API?"→ System searches, retrieves JWT preference memory→ System uses memory to answer question→ System calls observe_memory_usage with context tags [api, auth, backend]→ Cross-domain usage detected (original tags: [security, jwt, preferences])→ Memory automatically reinforced, strength boosted→ Next search naturally surfaces memories needing review

Configuration:

CORTEXGRAPH_REVIEW_BLEND_RATIO=0.3           # 30% review candidates in searchCORTEXGRAPH_REVIEW_DANGER_ZONE_MIN=0.15      # Lower bound of danger zoneCORTEXGRAPH_REVIEW_DANGER_ZONE_MAX=0.35      # Upper bound of danger zoneCORTEXGRAPH_AUTO_REINFORCE=true              # Auto-reinforce on observe

See docs/prompts/ for LLM system prompt templates that enable natural memory usage.

4. Two-Layer Architecture

graph TD    STM["<b>Short-Term Memory</b><br/>- JSONL storage<br/>- Temporal decay<br/>- Hours to weeks retention"]    LTM["<b>LTM (Long-Term Memory)</b><br/>- Markdown files Obsidian<br/>- Permanent storage<br/>- Git version control"]        STM -->|Automatic promotion| LTM        style STM fill:#e1f5ff,stroke:#01579b,stroke-width:2px    style LTM fill:#f3e5f5,stroke:#4a148c,stroke-width:2px

5. Multi-Agent Consolidation Pipeline

Automated memory maintenance through five specialized agents:

graph LR    decay["<b>DecayAnalyzer</b><br/>Find at-risk<br/>memories"]    cluster["<b>ClusterDetector</b><br/>Find similar<br/>groups"]    merge["<b>SemanticMerge</b><br/>Combine<br/>similar groups"]    promote["<b>LTMPromoter</b><br/>Promote<br/>to LTM"]    relations["<b>RelationshipDiscovery</b><br/>Discover cross-<br/>domain links"]        decay --> cluster    cluster --> merge    merge --> promote    promote --> relations    relations -.->|feedback| decay        style decay fill:#ffebee,stroke:#b71c1c,stroke-width:2px    style cluster fill:#fff3e0,stroke:#e65100,stroke-width:2px    style merge fill:#f3e5f5,stroke:#4a148c,stroke-width:2px    style promote fill:#e8f5e9,stroke:#1b5e20,stroke-width:2px    style relations fill:#e1f5fe,stroke:#01579b,stroke-width:2px

The Five Agents:

Key Features:

• Dry-run mode: Preview changes without modifying data
• Rate limiting: Configurable operations per minute (default: 60)
• Audit trail: Every decision tracked via beads issue tracking
• Human override: Review and approve decisions before execution

Usage:

from cortexgraph.agents import Scheduler
# Preview what would change (dry run)scheduler = Scheduler(dry_run=True)preview = scheduler.run_pipeline()
# Run full pipelinescheduler = Scheduler(dry_run=False)results = scheduler.run_pipeline()
# Run single agentdecay_results = scheduler.run_agent("decay")

CLI:

# Dry run (preview)cortexgraph-consolidate --dry-run
# Run specific agentcortexgraph-consolidate --agent decay --dry-run
# Scheduled execution (with interval)cortexgraph-consolidate --scheduled --interval-hours 1

See docs/agents.md for complete documentation including configuration, beads integration, and troubleshooting.

Quick Start

Installation

Recommended: UV Tool Install (from PyPI)

# Install from PyPI (recommended - fast, isolated, includes all 7 CLI commands)uv tool install cortexgraph

This installs cortexgraph and all 7 CLI commands in an isolated environment.

Alternative Installation Methods

# Using pipx (similar isolation to uv)pipx install cortexgraph
# Using pip (traditional, installs in current environment)pip install cortexgraph
# From GitHub (latest development version)uv tool install git+https://github.com/simplemindedbot/cortexgraph.git

For Development (Editable Install)

# Clone and install in editable modegit clone https://github.com/simplemindedbot/cortexgraph.gitcd cortexgraphuv pip install -e ".[dev]"

Configuration

IMPORTANT: Configuration location depends on installation method:

Method 1: .env file (Works for all installation methods)

Create ~/.config/cortexgraph/.env:

# Create config directorymkdir -p ~/.config/cortexgraph
# Option A: Copy from cloned repocp .env.example ~/.config/cortexgraph/.env
# Option B: Download directlycurl -o ~/.config/cortexgraph/.env https://raw.githubusercontent.com/simplemindedbot/cortexgraph/main/.env.example

Edit ~/.config/cortexgraph/.env with your settings:

# StorageCORTEXGRAPH_STORAGE_PATH=~/.config/cortexgraph/jsonl
# Decay model (power_law | exponential | two_component)CORTEXGRAPH_DECAY_MODEL=power_law
# Power-law parameters (default model)CORTEXGRAPH_PL_ALPHA=1.1CORTEXGRAPH_PL_HALFLIFE_DAYS=3.0
# Exponential (if selected)# CORTEXGRAPH_DECAY_LAMBDA=2.673e-6  # 3-day half-life
# Two-component (if selected)# CORTEXGRAPH_TC_LAMBDA_FAST=1.603e-5  # ~12h# CORTEXGRAPH_TC_LAMBDA_SLOW=1.147e-6  # ~7d# CORTEXGRAPH_TC_WEIGHT_FAST=0.7
# Common parametersCORTEXGRAPH_DECAY_LAMBDA=2.673e-6CORTEXGRAPH_DECAY_BETA=0.6
# ThresholdsCORTEXGRAPH_FORGET_THRESHOLD=0.05CORTEXGRAPH_PROMOTE_THRESHOLD=0.65
# Long-term memory (optional)LTM_VAULT_PATH=~/Documents/Obsidian/Vault

Where cortexgraph looks for .env files:

1. Primary: ~/.config/cortexgraph/.env ← Use this for uv tool install / uvx
2. Fallback: ./.env (current directory) ← Only works for editable installs

MCP Configuration

Recommended: Use absolute path (works everywhere)

Add to ~/Library/Application Support/Claude/claude_desktop_config.json:

{  "mcpServers": {    "cortexgraph": {      "command": "/Users/yourusername/.local/bin/cortexgraph"    }  }}

Find your actual path:

which cortexgraph# Example output: /Users/yourusername/.local/bin/cortexgraph

Use that path in your config. Replace yourusername with your actual username.

Why absolute path? GUI apps like Claude Desktop don't inherit your shell's PATH configuration (.zshrc, .bashrc). Using the full path ensures it always works.

For development (editable install):

{  "mcpServers": {    "cortexgraph": {      "command": "uv",      "args": ["--directory", "/path/to/cortexgraph", "run", "cortexgraph"],      "env": {"PYTHONPATH": "/path/to/cortexgraph/src"}    }  }}

Configuration can be loaded from ./.env in the project directory OR ~/.config/cortexgraph/.env.

Troubleshooting: Command Not Found

If Claude Desktop shows spawn cortexgraph ENOENT errors, the cortexgraph command isn't in Claude Desktop's PATH.

macOS/Linux: GUI apps don't inherit shell PATH

GUI applications on macOS and Linux don't see your shell's PATH configuration (.zshrc, .bashrc, etc.). Claude Desktop only searches:

• /usr/local/bin
• /opt/homebrew/bin (macOS)
• /usr/bin
• /bin
• /usr/sbin
• /sbin

If uv tool install placed cortexgraph in ~/.local/bin/ or another custom location, Claude Desktop can't find it.

Solution: Use absolute path

# Find where cortexgraph is installedwhich cortexgraph# Example output: /Users/username/.local/bin/cortexgraph

Update your Claude config with the absolute path:

{  "mcpServers": {    "cortexgraph": {      "command": "/Users/username/.local/bin/cortexgraph"    }  }}

Replace /Users/username/.local/bin/cortexgraph with your actual path from which cortexgraph.

Maintenance

Use the maintenance CLI to inspect and compact JSONL storage:

# Show storage stats (active counts, file sizes, compaction hints)cortexgraph-maintenance stats
# Compact JSONL (rewrite without tombstones/duplicates)cortexgraph-maintenance compact

Migrating to UV Tool Install

If you're currently using an editable install (uv pip install -e .), you can switch to the simpler UV tool install:

# 1. Uninstall editable versionuv pip uninstall cortexgraph
# 2. Install as UV tooluv tool install git+https://github.com/simplemindedbot/cortexgraph.git
# 3. Update Claude Desktop config to just:#    {"command": "cortexgraph"}#    Remove the --directory, run, and PYTHONPATH settings

Your data is safe! This only changes how the command is installed. Your memories in ~/.config/cortexgraph/ are untouched.

CLI Commands

The server includes 7 command-line tools:

cortexgraph                  # Run MCP servercortexgraph-migrate          # Migrate from old STM setupcortexgraph-index-ltm        # Index Obsidian vaultcortexgraph-backup           # Git backup operationscortexgraph-vault            # Vault markdown operationscortexgraph-search           # Unified STM+LTM searchcortexgraph-maintenance      # JSONL storage stats and compaction

Visualization

Interactive graph visualization using PyVis:

# Install visualization dependenciespip install "cortexgraph[visualization]"# or with uvuv pip install "cortexgraph[visualization]"
# Or install dependencies manuallypip install pyvis networkx
# Generate interactive HTML visualizationpython scripts/visualize_graph.py
# Custom output locationpython scripts/visualize_graph.py --output ~/Desktop/memory_graph.html
# Custom data pathspython scripts/visualize_graph.py --memories ~/data/memories.jsonl --relations ~/data/relations.jsonl

Features:

• Interactive network graph with pan/zoom
• Node colors by status (active=blue, promoted=green, archived=gray)
• Node size based on use count
• Edge colors by relation type
• Hover tooltips showing full content, tags, and entities
• Physics controls for layout adjustment

The visualization reads directly from your JSONL files and creates a standalone HTML file you can open in any browser.

MCP Tools

13 tools for AI assistants to manage memories:

Example: Unified Search

Search across STM and LTM with the CLI:

cortexgraph-search "typescript preferences" --tags preferences --limit 5 --verbose

Example: Reinforce (Touch) Memory

Boost a memory's recency/use count to slow decay:

{  "memory_id": "mem-123",  "boost_strength": true}

Sample response:

{  "success": true,  "memory_id": "mem-123",  "old_score": 0.41,  "new_score": 0.78,  "use_count": 5,  "strength": 1.1}

Example: Promote Memory

Suggest and promote high-value memories to the Obsidian vault.

Auto-detect (dry run):

{  "auto_detect": true,  "dry_run": true}

Promote a specific memory:

{  "memory_id": "mem-123",  "dry_run": false,  "target": "obsidian"}

As an MCP tool (request body):

{  "query": "typescript preferences",  "tags": ["preferences"],  "limit": 5,  "verbose": true}

Example: Consolidate Similar Memories

Find and merge duplicate or highly similar memories to reduce clutter:

Auto-detect candidates (preview):

{  "auto_detect": true,  "mode": "preview",  "cohesion_threshold": 0.75}

Apply consolidation to detected clusters:

{  "auto_detect": true,  "mode": "apply",  "cohesion_threshold": 0.80}

The tool will:

• Merge content intelligently (preserving unique information)
• Combine tags and entities (union)
• Calculate strength based on cluster cohesion
• Preserve earliest created_at and latest last_used timestamps
• Create tracking relations showing consolidation history

Mathematical Details

Decay Curves

For a memory with $n_{\text{use}}=1$, $s=1.0$, and $\lambda = 2.673 \times 10^{-6}$ (3-day half-life):

Use Count Impact

With $\beta = 0.6$ (sub-linear weighting):

Frequent access significantly extends retention.

Documentation

• MCP Tools Reference - Comprehensive documentation for all 18 MCP tools
• API Quick Reference - Minimal tool signatures and usage examples
• Scoring Algorithm - Complete mathematical model with LaTeX formulas
• Smart Prompting - Patterns for natural LLM integration
• Architecture - System design and implementation
• Multi-Agent System - Consolidation agents and pipeline architecture
• Bear Integration - Guide to using Bear app as an LTM store
• Graph Features - Knowledge graph usage

Use Cases

Personal Assistant (Balanced)

• 3-day half-life
• Remember preferences and decisions
• Auto-promote frequently referenced information

Development Environment (Aggressive)

• 1-day half-life
• Fast context switching
• Aggressive forgetting of old context

Research / Archival (Conservative)

• 14-day half-life
• Long retention
• Comprehensive knowledge preservation

License

AGPL-3.0 License - See LICENSE for details.

This project uses the GNU Affero General Public License v3.0, which requires that modifications to this software be made available as source code when used to provide a network service.

Related Work

• Model Context Protocol - MCP specification
• Ebbinghaus Forgetting Curve - Cognitive science foundation
• Basic Memory - Primary inspiration for the integration layer. CortexGraph extends this concept by adding the Ebbinghaus forgetting curve, temporal decay algorithms, short-term memory in JSONL storage, and natural spaced repetition.
• Additional research inspired by: mem0, Neo4j Graph Memory

Citation

If you use this work in research, please cite:

@software{cortexgraph_2025,  title = {Mnemex: Temporal Memory for AI},  author = {simplemindedbot},  year = {2025},  url = {https://github.com/simplemindedbot/cortexgraph},  version = {0.5.3}}

Contributing

Contributions are welcome! See CONTRIBUTING.md for detailed instructions.

🚨 Help Needed: Windows & Linux Testers!

I develop on macOS and need help testing on Windows and Linux. If you have access to these platforms, please:

• Try the installation instructions
• Run the test suite
• Report what works and what doesn't

See the Help Needed section in CONTRIBUTING.md for details.

General Contributions

For all contributors, see CONTRIBUTING.md for:

• Platform-specific setup (Windows, Linux, macOS)
• Development workflow
• Testing guidelines
• Code style requirements
• Pull request process

Quick start:

1. Read CONTRIBUTING.md for platform-specific setup
2. Understand the Architecture docs
3. Review the Scoring Algorithm
4. Follow existing code patterns
5. Add tests for new features
6. Update documentation

Status

Version: 1.0.0 Status: Research implementation - functional but evolving

Phase 1 (Complete) ✅

• 14 MCP tools
• Temporal decay algorithm
• Knowledge graph

Phase 2 (Complete) ✅

• JSONL storage
• LTM index
• Git integration
• Smart prompting documentation
• Maintenance CLI
• Memory consolidation (algorithmic merging)

Phase 3 (Complete) ✅

• Multi-Agent Consolidation Pipeline
  • DecayAnalyzer, ClusterDetector, SemanticMerge, LTMPromoter, RelationshipDiscovery
  • Scheduler for orchestration
  • Beads issue tracking integration
  • Dry-run and rate limiting support
• Natural language activation (v0.6.0+)
• Auto-enrichment for entity extraction

Future Work

• Adaptive decay parameters
• Performance benchmarks
• LLM-assisted consolidation (optional enhancement)

Built with Claude Code 🤖