neuro-cortex-memory 3.4.2

Scientifically-grounded memory system based on computational neuroscience research

Cortex

Persistent memory for Claude Code — built on neuroscience research, not guesswork

Memory that learns, consolidates, forgets intelligently, and surfaces the right context at the right time. Works standalone or with a team of specialized agents.

Getting Started | How It Works | Neural Graph | Agent Integration | Benchmarks | Scientific Foundation

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Getting Started

Prerequisites

• Python 3.10+
• PostgreSQL 15+ with pgvector and pg_trgm extensions
• Claude Code CLI or desktop app

Option A — Claude Code Marketplace (recommended)

claude plugin marketplace add cdeust/Cortex
claude plugin install cortex

Restart your Claude Code session, then run:

/cortex-setup-project

This handles everything: PostgreSQL + pgvector installation, database creation, embedding model download, cognitive profile building from session history, codebase seeding, conversation import, and hook registration. Zero manual steps.

Using Claude Cowork? Install Cortex-cowork instead — uses SQLite, no PostgreSQL required.

claude plugin marketplace add cdeust/Cortex-cowork
claude plugin install cortex-cowork

Option B — Standalone Clone

git clone https://github.com/cdeust/Cortex.git
cd Cortex
bash scripts/setup.sh

Same setup from a local clone. Installs PostgreSQL + pgvector (via Homebrew on macOS, apt/dnf on Linux), creates the database, downloads the embedding model (~100 MB), and registers hooks in ~/.claude/settings.json. Restart Claude Code after setup.

Option C — Docker

git clone https://github.com/cdeust/Cortex.git
cd Cortex

docker build -t cortex-runtime -f docker/Dockerfile .
docker run -it \
  -v $(pwd):/workspace \
  -v cortex-pgdata:/var/lib/postgresql/17/data \
  -v ~/.claude:/home/cortex/.claude-host:ro \
  -v ~/.claude.json:/home/cortex/.claude-host-json/.claude.json:ro \
  cortex-runtime

The container includes PostgreSQL 17, pgvector, the embedding model, and Claude Code. Data persists via the cortex-pgdata volume.

Option C — Manual Setup

Step-by-step instructions

1. Install PostgreSQL + pgvector

# macOS
brew install postgresql@17 pgvector
brew services start postgresql@17

# Ubuntu/Debian
sudo apt-get install postgresql postgresql-server-dev-all
sudo apt-get install postgresql-17-pgvector
sudo systemctl start postgresql

2. Create the database

createdb cortex
psql cortex -c "CREATE EXTENSION IF NOT EXISTS vector;"
psql cortex -c "CREATE EXTENSION IF NOT EXISTS pg_trgm;"

3. Install Python dependencies

pip install -e ".[postgresql]"
pip install sentence-transformers flashrank

4. Initialize schema

export DATABASE_URL=postgresql://localhost:5432/cortex
python3 -c "
from mcp_server.infrastructure.pg_schema import get_all_ddl
from mcp_server.infrastructure.pg_store import PgStore
import asyncio
asyncio.run(PgStore(database_url='$DATABASE_URL').initialize())
"

5. Pre-cache the embedding model

python3 -c "from sentence_transformers import SentenceTransformer; SentenceTransformer('all-MiniLM-L6-v2')"

6. Install hooks

python3 scripts/install_hooks.py --plugin-root $(pwd)

Restart Claude Code to activate.

Verify Installation

After setup, open Claude Code in any project. The SessionStart hook should inject context automatically. You can also test manually:

python3 -m mcp_server  # Should start on stdio without errors

Configuration

Cortex reads DATABASE_URL from the environment (default: postgresql://localhost:5432/cortex). All tunable parameters use the CORTEX_MEMORY_ prefix:

Variable	Default	What It Controls
DATABASE_URL	postgresql://localhost:5432/cortex	PostgreSQL connection string
CORTEX_RUNTIME	auto-detected	cli (strict) or cowork (SQLite fallback)
CORTEX_MEMORY_DECAY_FACTOR	0.95	Per-session heat decay rate
CORTEX_MEMORY_HOT_THRESHOLD	0.7	Heat level considered "hot"
CORTEX_MEMORY_WRRF_VECTOR_WEIGHT	1.0	Vector similarity weight in fusion
CORTEX_MEMORY_WRRF_FTS_WEIGHT	0.5	Full-text search weight in fusion
CORTEX_MEMORY_WRRF_HEAT_WEIGHT	0.3	Thermodynamic heat weight in fusion
CORTEX_MEMORY_DEFAULT_RECALL_LIMIT	10	Max memories returned per query

See mcp_server/infrastructure/memory_config.py for the full list (~40 parameters).

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How It Works

Cortex runs as an MCP server alongside Claude Code. It captures what you work on, consolidates it while you're away, and resurfaces the right context when you need it.

Memory is Invisible

You don't manage memory. Cortex does.

Session start — hot memories, anchored decisions, and team context inject automatically. No manual recall needed.

During work — PostToolUse hooks capture significant actions (edits, commands, test results). Decisions are auto-detected and protected from forgetting. File edits prime related memories via spreading activation so they surface in subsequent recall.

Session end — a "dream" cycle runs automatically: decay old memories, compress verbose ones, and for long sessions, consolidate episodic memories into semantic knowledge (CLS).

Between sessions — memories cool naturally (Ebbinghaus forgetting curve). Important ones stay hot. Protected decisions never decay.

Retrieval Pipeline

Five signals fused server-side in PostgreSQL, then reranked client-side:

Signal	Source	Paper
Vector similarity	pgvector HNSW (384-dim)	Bruch et al. 2023
Full-text search	tsvector + ts_rank_cd	Bruch et al. 2023
Trigram similarity	pg_trgm	Bruch et al. 2023
Thermodynamic heat	Ebbinghaus decay model	Ebbinghaus 1885
Recency	Exponential time decay	—

Hooks

Seven hooks integrate with Claude Code's lifecycle:

Hook	Event	What It Does
SessionStart	Session opens	Injects anchors + hot memories + team decisions + checkpoint
UserPromptSubmit	Before response	Auto-recalls relevant memories based on user's prompt
PostToolUse	After Edit/Write/Bash	Auto-captures significant actions as memories
PostToolUse	After Edit/Write/Read	Primes related memories via heat boost (spreading activation)
SessionEnd	Session closes	Runs dream cycle (decay, compress, CLS based on activity)
Compaction	Context compacts	Saves checkpoint; restores context after compaction
SubagentStart	Agent spawned	Briefs agent with prior work + team decisions

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Neural Graph

The unified neural graph renders the entire memory system as an interactive 3D visualization in the browser (/cortex-visualize).

Node Types

Category	Nodes	Color
Structural	Root, categories, domains, agents, entry points	Blue / Cyan
Behavioral	Recurring patterns, tool preferences, behavioral features	Yellow / Orange
Memory	Episodic memories, semantic memories	Green (episodic), Teal (semantic)
Entities	Functions, files, dependencies, decisions, errors, technologies	Varies by type
Discussions	Full conversation sessions linked to domain hubs	Rose (#F43F5E)

Conversation History

Discussion nodes represent every Claude Code session. Each links to its parent domain via keyword matching. Clicking a discussion node opens a detail panel showing timeline, duration, tools used, and keywords.

Full Conversation Viewer — the "View Full Conversation" button opens a modal with the complete session transcript: timestamped user/assistant messages with collapsible tool call details (input/output).

Filters

Domain, emotion, and consolidation stage dropdowns. Toggle buttons for methodology, memories, knowledge, emotional nodes, protected/hot/global memories, and discussions.

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Agent Integration

Cortex is designed to work with a team of specialized agents. Each agent has scoped memory (agent_topic) while sharing critical decisions across the team.

Transactive Memory System

Based on Wegner 1987: teams store more knowledge than individuals because each member specializes, and a shared directory tells everyone who knows what.

Specialization — each agent writes to its own topic. Engineer's debugging notes don't clutter tester's recall.

Coordination — decisions auto-protect and propagate. When engineer decides "use Redis over Memcached," every agent sees it at next session start.

Directory — entity-based queries span all topics. "What do we know about the reranker?" returns results from engineer, tester, and researcher.

Agent Briefing

When the orchestrator spawns a specialist agent, the SubagentStart hook automatically:

1. Extracts task keywords from the prompt
2. Queries agent-scoped prior work (FTS, no embedding load needed)
3. Fetches team decisions (protected + global memories from other agents)
4. Injects as context prefix — agent starts with knowledge

Compatible Agent Team

Works with any custom Claude Code agents. See zetetic-team-subagents for a reference team of 18 specialists:

Agent	Specialty	Memory Topic
orchestrator	Parallel agent execution, coordination, merge	orchestrator
engineer	Clean Architecture, SOLID, any language/stack	engineer
architect	Module decomposition, layer boundaries, refactoring	architect
code-reviewer	Clean Architecture enforcement, SOLID violations	code-reviewer
test-engineer	Testing, CI verification, wiring checks	test-engineer
dba	Schema design, query optimization, migrations	dba
research-scientist	Benchmark improvement, neuroscience/IR papers	research-scientist
frontend-engineer	React/TypeScript, component design, accessibility	frontend-engineer
security-auditor	Threat modeling, OWASP, defense-in-depth	security-auditor
devops-engineer	CI/CD, Docker, PostgreSQL provisioning	devops-engineer
ux-designer	Usability, accessibility, design systems	ux-designer
data-scientist	EDA, feature engineering, data quality, bias auditing	data-scientist
experiment-runner	Ablation studies, hyperparameter search, statistical rigor	experiment-runner
mlops	Training pipelines, model serving, GPU optimization	mlops
paper-writer	Research paper structure, narrative flow, venue conventions	paper-writer
reviewer-academic	Peer review simulation (NeurIPS/CVPR/ICML style)	reviewer-academic
professor	Concept explanation, mental models, adaptive teaching	professor
latex-engineer	LaTeX templates, figures, TikZ, bibliographies	latex-engineer

Skills

Cortex ships as a Claude Code plugin with 14 skills:

Skill	Command	What It Does
cortex-remember	/cortex-remember	Store a memory with full write gate
cortex-recall	/cortex-recall	Search memories with intent-adaptive retrieval
cortex-consolidate	/cortex-consolidate	Run maintenance (decay, compress, CLS)
cortex-explore-memory	/cortex-explore-memory	Navigate memory by entity/domain
cortex-navigate-knowledge	/cortex-navigate-knowledge	Traverse knowledge graph
cortex-debug-memory	/cortex-debug-memory	Diagnose memory system health
cortex-visualize	/cortex-visualize	Launch 3D neural graph in browser
cortex-profile	/cortex-profile	View cognitive methodology profile
cortex-setup-project	/cortex-setup-project	Bootstrap a new project
cortex-develop	/cortex-develop	Memory-assisted development workflow
cortex-automate	/cortex-automate	Create prospective triggers

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Benchmarks

All scores are retrieval-only — no LLM reader in the evaluation loop. We measure whether retrieval places correct evidence in the top results.

Benchmark	Metric	Cortex	Best in Paper	Paper
LongMemEval	R@10	98.0%	78.4%	Wang et al., ICLR 2025
LongMemEval	MRR	0.880	—
LoCoMo	R@10	97.7%	—	Maharana et al., ACL 2024
LoCoMo	MRR	0.840	—
BEAM	Overall MRR	0.627	0.329 (LIGHT)	Tavakoli et al., ICLR 2026

Per-category breakdowns

BEAM (10 abilities, 400 questions)

Ability	MRR	R@10
contradiction_resolution	0.879	100.0%
knowledge_update	0.867	97.5%
temporal_reasoning	0.857	97.5%
multi_session_reasoning	0.738	92.5%
information_extraction	0.542	72.5%
summarization	0.359	69.4%
preference_following	0.356	62.5%
event_ordering	0.353	62.5%
instruction_following	0.242	52.5%
abstention	0.125	12.5%

LongMemEval (6 categories, 500 questions)

Category	MRR	R@10
Single-session (assistant)	0.970	100.0%
Multi-session reasoning	0.917	100.0%
Temporal reasoning	0.887	97.7%
Knowledge updates	0.884	100.0%
Single-session (user)	0.793	91.4%
Single-session (preference)	0.706	96.7%

LoCoMo (5 categories, 1986 questions)

Category	MRR	R@10
adversarial	0.809	89.0%
open_domain	0.817	91.1%
multi_hop	0.736	84.1%
single_hop	0.714	91.8%
temporal	0.538	76.1%

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Architecture

Clean Architecture with strict dependency rules. Inner layers never import outer layers.

Layer	Modules	Rule
core/	118	Pure business logic. Zero I/O. Imports only shared/.
infrastructure/	33	All I/O: PostgreSQL, embeddings, file system.
handlers/	62 tools	Composition roots wiring core + infrastructure.
hooks/	7	Lifecycle automation (SessionStart/End, PostToolUse, etc.)
shared/	12	Pure utilities. Python stdlib only.

Storage: PostgreSQL 15+ with pgvector (HNSW) and pg_trgm. All retrieval in PL/pgSQL stored procedures.

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Scientific Foundation

The Zetetic Standard

Every algorithm, constant, and threshold traces to a published paper, a measured ablation, or documented engineering source. Nothing is guessed. Where engineering defaults exist, they are labeled as such.

Paper Index (41 citations)

Information Retrieval

Paper	Year	Venue	Module
Bruch et al. "Fusion Functions for Hybrid Retrieval"	2023	ACM TOIS	pg_schema.py
Nogueira & Cho "Passage Re-ranking with BERT"	2019	arXiv	reranker.py
Joren et al. "Sufficient Context"	2025	ICLR	reranker.py
Collins & Loftus "Spreading-activation theory"	1975	Psych. Review	spreading_activation.py

Neuroscience — Encoding (5 papers)

Paper	Year	Module
Friston "A theory of cortical responses"	2005	hierarchical_predictive_coding.py
Bastos et al. "Canonical microcircuits for predictive coding"	2012	hierarchical_predictive_coding.py
Wang & Bhatt "Emotional modulation of memory"	2024	emotional_tagging.py
Doya "Metalearning and neuromodulation"	2002	coupled_neuromodulation.py
Schultz "Prediction and reward"	1997	coupled_neuromodulation.py

Neuroscience — Consolidation (6 papers)

Paper	Year	Module
Kandel "Molecular biology of memory storage"	2001	cascade.py
McClelland et al. "Complementary learning systems"	1995	dual_store_cls.py
Frey & Morris "Synaptic tagging"	1997	synaptic_tagging.py
Josselyn & Tonegawa "Memory engrams"	2020	engram.py
Dudai "The restless engram"	2012	reconsolidation.py
Borbely "Two-process model of sleep"	1982	session_lifecycle.py

Neuroscience — Retrieval & Navigation (4 papers)

Paper	Year	Module
Behrouz et al. "Titans: Learning to Memorize at Test Time"	2025	titans_memory.py
Stachenfeld et al. "Hippocampus as predictive map"	2017	cognitive_map.py
Ramsauer et al. "Hopfield Networks is All You Need"	2021	hopfield.py
Kanerva "Hyperdimensional computing"	2009	hdc_encoder.py

Neuroscience — Plasticity & Maintenance (14 papers)

Paper	Year	Module
Hasselmo "Hippocampal theta rhythm"	2005	oscillatory_clock.py
Buzsaki "Hippocampal sharp wave-ripple"	2015	oscillatory_clock.py
Leutgeb et al. "Pattern separation in dentate gyrus"	2007	pattern_separation.py
Yassa & Stark "Pattern separation in hippocampus"	2011	pattern_separation.py
Turrigiano "The self-tuning neuron"	2008	homeostatic_plasticity.py
Abraham & Bear "Metaplasticity"	1996	homeostatic_plasticity.py
Tse et al. "Schemas and memory consolidation"	2007	schema_engine.py
Gilboa & Marlatte "Neurobiology of schemas"	2017	schema_engine.py
Hebb The Organization of Behavior	1949	synaptic_plasticity.py
Bi & Poo "Synaptic modifications"	1998	synaptic_plasticity.py
Perea et al. "Tripartite synapses"	2009	tripartite_synapse.py
Kastellakis et al. "Synaptic clustering"	2015	dendritic_clusters.py
Wang et al. "Microglia-mediated synapse elimination"	2020	microglial_pruning.py
Ebbinghaus Memory	1885	thermodynamics.py

Team Memory & Preemptive Retrieval (6 papers)

Paper	Year	Module
Wegner "Transactive memory"	1987	memory_ingest.py, session_start.py
Zhang et al. "Collaboration Mechanisms for LLM Agents"	2024	memory_ingest.py
McGaugh "Amygdala modulates consolidation"	2004	memory_ingest.py
Adcock et al. "Reward-motivated learning"	2006	memory_ingest.py
Bar "The proactive brain"	2007	preemptive_context.py
Smith & Vela "Context-dependent memory"	2001	agent_briefing.py

Ablation Data

All ablation results committed to benchmarks/beam/ablation_results.json.

Parameter	Tested Values	Optimal	Source
rerank_alpha	0.30, 0.50, 0.55, 0.70	0.70	BEAM 100K ablation
FTS weight	0.0, 0.3, 0.5, 0.7, 1.0	0.0 (BEAM), 0.5 (balanced)	Cross-benchmark
Heat weight	0.0, 0.1, 0.3, 0.5, 0.7	0.7 (BEAM), 0.3 (balanced)	Cross-benchmark
Adaptive alpha	CE spread QPP	Rejected	Regressed LoCoMo -5.1pp R@10

Engineering Defaults

Values without paper backing, explicitly documented:

Constant	Value	Location	Status
FTS weight	0.5	pg_recall.py	Balanced across benchmarks
Heat weight	0.3	pg_recall.py	Balanced across benchmarks
CE gate threshold	0.15	reranker.py	Engineering default
Titans eta/theta	0.9/0.01	titans_memory.py	Paper uses learned params

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Security

Cortex runs locally (MCP over stdio, PostgreSQL on localhost, visualization on 127.0.0.1). No data leaves your machine unless you explicitly configure an external database.

Audit Score: 91/100

Category	Score	Notes
Data Flow	90	No external data exfiltration. Embeddings computed locally.
SQL Injection	95	All queries parameterized (psycopg %s). Dynamic columns use sql.Identifier().
Auth & Access Control	85	Docker PG uses scram-sha-256 on localhost. MCP over stdio (no network auth needed).
Dependency Health	80	Floor-pinned deps. Background install version-bounded.
Network Behavior	92	Model download on first run only. Viz servers bind 127.0.0.1 with same-origin CORS.
Code Quality	90	Pydantic validation on all tools. Input length limits on remember/recall. Path traversal protected.
Prompt Injection	88	Memory content escaped in HTML rendering. Session injection uses data delimiters.
Secrets Management	90	.env/credentials in .gitignore. No hardcoded secrets. Docker credentials via env vars.

Hardening measures

• SQL parameterization across all 7 pg_store modules (psycopg %s placeholders)
• sql.Identifier() for dynamic column names (no f-string SQL)
• ILIKE patterns escape %, _, \ from user input
• CORS restricted to http://127.0.0.1 (no wildcard)
• Docker PostgreSQL uses scram-sha-256 auth on 127.0.0.1/32
• trust_remote_code removed from embedding model loading
• Input length validation: remember content capped at 50KB, queries at 10KB
• Path traversal protection via .resolve() in sync_instructions
• HTML escaping (esc()) on all user-generated content in visualization
• Background pip install version-bounded (>=2.2.0,<4.0.0)
• Secrets patterns (.env, *.credentials.json, *.pem, *.key) in .gitignore

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Development

pytest                    # 2080 tests
ruff check .              # Lint
ruff format --check .     # Format

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License

MIT

Citation

@software{cortex2026,
  title={Cortex: Persistent Memory for Claude Code},
  author={Deust, Clement},
  year={2026},
  url={https://github.com/cdeust/Cortex}
}