zikkaron 1.3.0

Biologically-inspired persistent memory engine for Claude Code

Zikkaron

Zikkaron (זיכרון) is Hebrew for "memory."

Your AI forgets you every time you close the tab. Every architecture decision you explained, every debugging rabbit hole you went down together, every "remember, we're using Postgres not SQLite" correction. Gone. You start the next session a stranger to your own tools.

Zikkaron is a persistent memory engine for Claude Code built on computational neuroscience. It remembers what you worked on, how you think, what you decided and why. Not as a dumb text dump that gets shoved into context, but as a living memory system that consolidates, forgets intelligently, and reconstructs the right context at the right time.

26 subsystems. 23 MCP tools. Runs entirely on your machine. One SQLite file.

Two minutes to never repeat yourself again

pip install zikkaron

Add to your Claude Code config:

{
  "mcpServers": {
    "zikkaron": {
      "command": "zikkaron"
    }
  }
}

Tell Claude how to use it. Drop this in your global ~/.claude/CLAUDE.md (your home directory, not per-project):

## Memory
- On every new session, call `recall` with the current project name
- Before starting any task, call `get_project_context` for the current directory
- After completing significant work, call `remember` to store decisions and outcomes

Or just let Zikkaron handle it. On every startup, it automatically syncs ~/.claude/CLAUDE.md with the latest instructions via sync_instructions. You set it up once and never think about it again.

What this actually feels like

Monday. You spend an hour debugging a nasty auth token race condition. Claude helps you trace it to a TTL mismatch between Redis and your JWT config. You fix it. Claude stores the memory.

Thursday. A user reports intermittent logouts. You open Claude Code in the same project. Before you even describe the bug, Claude recalls the Redis TTL fix from Monday, checks if it's related, and asks whether the middleware you added is handling the edge case where Redis restarts mid-session.

That's the difference. Not "here's your conversation history." Real recall. The kind where your tools understand the shape of what you've been building, not just the words you typed last time.

Retrieval that actually works

We tested Zikkaron against LoCoMo (Maharana et al., ACL 2024), the standard benchmark for long conversation memory. 10 conversations, 1,986 questions, everything from simple factual lookups to multi-hop reasoning to adversarial trick questions designed to trip you up.

	Zikkaron	What it means
Recall@10	86.8%	The right memory shows up in the top 10 nearly 9 times out of 10
MRR	0.708	The correct answer is usually the first or second result
Single-hop MRR	0.757	Factual questions, almost always nails it on the first try
Temporal MRR	0.712	"When did X happen?" queries, strong time awareness

The thing is, there's no LLM running at query time. No API calls. No billion parameter models. Just a 22MB embedding model, a SQLite file, and a bunch of neuroscience algorithms doing the heavy lifting. Most systems that hit numbers like these need GPT-4 in the loop. Zikkaron gets there with Hopfield energy scoring, spreading activation, and a cross-encoder reranker.

Hippocampal Replay: Context that survives compaction

Here's a problem nobody talks about. Claude Code has a 200K token context window. During long sessions, when that window fills up, it compacts: summarizes older messages, strips tool outputs, paraphrases your instructions. Important nuance evaporates. Decisions you anchored early in the conversation dissolve into vague summaries.

Hippocampal Replay fixes this. Named after the neuroscience phenomenon where your brain replays important experiences during sleep to consolidate them into long-term memory, it treats context compaction as the "sleep" and replays what matters when Claude "wakes up."

How it works:

Before compaction hits, a hook fires. Zikkaron drains your active context: what you were working on, which files were open, what decisions you'd made, what errors were unresolved. It stores all of this as a checkpoint.

After compaction, a second hook fires. Zikkaron reconstructs your context intelligently. Not by dumping everything back in, but by assembling the right pieces: your latest checkpoint, any facts you'd anchored as critical, the hottest project memories, and predictions about what you'll need next based on your usage patterns.

You can also be explicit about what matters:

Tool: anchor
  content: "We're using the event-sourcing pattern. All state changes go through the event bus."
  reason: "Architecture constraint"

Anchored memories get maximum protection. They always survive compaction, no matter what.

One-time setup per project:

Tool: install_hooks
  project_directory: "/path/to/your/project"

After that, everything is automatic. You don't think about it. You don't call anything manually. The hooks fire, the context drains, the context restores. Your long sessions just... work.

Zero-gap memory (v1.3.0)

Previous versions still had gaps. You'd work on something for an hour, making incremental progress, and Zikkaron's write gate would block half of it because each small step looked "unsurprising" relative to the last. You'd make a critical architecture decision and it would slowly decay into a gist. You'd come back to a new session and Claude would have no idea what you were just doing.

v1.3.0 fixes all of this:

Adaptive write gate. The system now tracks your last 10 stored memories. When you're clearly working on the same task — same directory, same timeframe, similar content — it lowers the surprisal threshold so incremental progress gets through. The gate still blocks noise. It just stops blocking your work.

Decision auto-protection. When you say "decided to use Redis instead of Memcached" or "chose the event-sourcing pattern over CRUD," Zikkaron detects the decision pattern and automatically marks it as protected. Protected memories never compress and never decay fast. Your decisions outlive your sessions.

Automatic action capture. A PostToolUse hook fires after every single tool call Claude makes. File edits, bash commands, searches — all captured into a lightweight action log. The consolidation daemon periodically processes these into real memories. You don't call remember for routine work. The system just knows.

Session context injection. A SessionStart hook fires on every new session and injects your project context — hot memories, anchored facts, recent actions, last checkpoint — directly into Claude's context window. Claude starts every session already knowing what you were doing.

Micro-checkpointing. Instead of checkpointing every 50 tool calls, the system now auto-checkpoints on significant events: errors encountered, decisions made, high-surprise information. Critical state transitions are captured the moment they happen.

Session coherence. Memories created within the last 4 hours get a heat bonus that fades linearly. You'll never hit the "I just told you this 10 minutes ago" problem again.

All hooks work in both stdio and HTTP transport modes — they access the SQLite database directly, no server communication needed.

The science under the hood

Zikkaron doesn't store memories the way a database stores rows. It treats them more like a brain treats experiences.

Memories have temperature. Every memory starts hot. If you keep accessing it, it stays hot. If you don't, it cools. Below a threshold, it compresses: first to a gist, then to tags, then eventually it fades entirely. This isn't a bug. It's rate-distortion optimal forgetting, the same mathematical framework your brain uses to decide what's worth keeping. Important memories resist compression. Surprising ones get a heat boost. Boring, redundant ones quietly disappear.

Storage has a gatekeeper. Not everything deserves to be remembered. Zikkaron maintains a predictive model of what it already knows, and only stores information that violates its expectations. Tell it the same thing twice and the write gate blocks the second attempt. This is predictive coding: the same mechanism your neocortex uses to filter sensory input. Only prediction errors get through.

Retrieval changes the memory. When you recall a memory in a new context, it doesn't just passively hand it back. It compares the retrieval context against the storage context, and if there's enough mismatch, it reconsolidates: updates the memory to reflect what's true now. Severe mismatch archives the old version and creates a new one. This is real neuroscience. Nader et al. showed in 2000 that retrieved memories become labile and can be rewritten. Your codebase evolves, and so do Zikkaron's memories of it.

Memories compete for space. A pool of engram slots, each with an excitability score that spikes on use and decays over time. When a new memory arrives, it goes to the most excitable slot. Memories in the same slot get temporally linked, creating chains of related experiences even when their content has nothing in common. This models how real neurons allocate engrams through CREB-dependent excitability.

Background consolidation runs like sleep. When you're idle, an astrocyte daemon wakes up and processes recent experiences. It extracts entities and relationships, builds the knowledge graph, merges near-duplicates, discovers causal chains, and runs "dream replay" where random memory pairs are compared and new connections emerge. Four domain-specialized processes handle different types of knowledge at different rates: code structure, architectural decisions, error patterns, and dependencies.

A cognitive map organizes everything. Successor representations build a 2D map of concept space where memories that get accessed in similar contexts cluster together, even if their content is completely different. Debugging memories cluster near other debugging memories. Architecture decisions cluster together. Navigate this map, and you find related knowledge that keyword search would never surface.

All 23 tools

Tool	Purpose
remember	Store a memory through the predictive coding write gate
recall	Multi-signal retrieval with heat-weighted ranking
forget	Delete a memory
validate_memory	Check staleness against current file state
get_project_context	Get hot memories for a directory
consolidate_now	Force a consolidation cycle
memory_stats	System statistics across all subsystems
rate_memory	Usefulness feedback for metamemory tracking
recall_hierarchical	Query the fractal hierarchy at a specific abstraction level
drill_down	Navigate into a memory cluster
create_trigger	Set prospective triggers that fire on matching context
get_project_story	Autobiographical narrative of a project
add_rule	Neuro-symbolic constraints for filtering and re-ranking
get_rules	List active rules
navigate_memory	Traverse concept space via successor representations
get_causal_chain	Causal ancestors and descendants for an entity
assess_coverage	Evaluate knowledge coverage with gap identification
detect_gaps	Find isolated entities, stale regions, missing connections
checkpoint	Snapshot working state for compaction recovery
restore	Reconstruct context after compaction via Hippocampal Replay
anchor	Mark critical facts as compaction-resistant
install_hooks	Enable auto-capture, context injection, and compaction recovery hooks
sync_instructions	Update CLAUDE.md with latest Zikkaron capabilities

Architecture

Everything runs locally. A single SQLite database with WAL mode, FTS5 full-text search, and sqlite-vec for approximate nearest neighbor vector search.

26 subsystems organized into five layers:

Core Storage and Retrieval

Module	Role
storage.py	SQLite WAL engine, 16 tables, FTS5 indexing, sqlite-vec ANN search
embeddings.py	Sentence-transformer encoding (all-MiniLM-L6-v2), batched operations
retrieval.py	Four-signal fusion: vector similarity, FTS5 BM25, knowledge graph PPR, spreading activation
models.py	Pydantic data models for the full type hierarchy
config.py	Environment-based configuration with ZIKKARON_ prefix

Memory Dynamics

Module	Role
thermodynamics.py	Heat, surprise, importance, emotional valence, temporal decay
reconsolidation.py	Labile retrieval with three outcomes per Nader et al. (2000)
predictive_coding.py	Write gate that filters redundancy via prediction error
engram.py	Competitive slot allocation with CREB-like excitability
compression.py	Rate-distortion optimal forgetting over three compression levels
staleness.py	File-change watchdog via SHA-256 hash comparison

Consolidation and Organization

Module	Role
consolidation.py	Background astrocyte daemon for periodic consolidation
astrocyte_pool.py	Domain-specialized worker processes for code, decisions, errors, deps
sleep_compute.py	Dream replay, Louvain community detection, temporal compression
fractal.py	Multi-scale memory tree with drill-down navigation
cls_store.py	Complementary Learning Systems: fast episodic + slow semantic stores

Knowledge Structure

Module	Role
knowledge_graph.py	Typed entity-relationship graph with Personalized PageRank
causal_discovery.py	PC algorithm for causal DAGs from coding session data
cognitive_map.py	Successor Representation for navigation-based retrieval
narrative.py	Autobiographical project story synthesis
curation.py	Duplicate merging, contradiction detection, cross-reference linking

Frontier Capabilities

Module	Role
hopfield.py	Modern continuous Hopfield networks (Ramsauer et al., 2021)
hdc_encoder.py	Hyperdimensional Computing in 10,000-dimensional bipolar space
metacognition.py	Self-assessment of knowledge coverage and gap detection
rules_engine.py	Hard and soft neuro-symbolic constraints
crdt_sync.py	Multi-agent memory sharing via CRDTs
prospective.py	Future-oriented triggers on directory, keyword, entity, or time
sensory_buffer.py	Episodic capture buffer for raw session content
restoration.py	Hippocampal Replay engine for context compaction resilience

Advanced setup

From source

git clone https://github.com/amanhij/Zikkaron.git
cd Zikkaron
pip install -e .

SSE transport

Run as a persistent background server instead of stdio:

zikkaron --transport sse

Then point Claude Code at the URL:

{
  "mcpServers": {
    "zikkaron": {
      "type": "sse",
      "url": "http://127.0.0.1:8742/sse"
    }
  }
}

Default port is 8742. Override with --port. Database defaults to ~/.zikkaron/memory.db, override with --db-path.

Configuration

All settings use the ZIKKARON_ environment variable prefix:

Variable	Default	What it controls
ZIKKARON_PORT	8742	Server port
ZIKKARON_DB_PATH	~/.zikkaron/memory.db	Database location
ZIKKARON_EMBEDDING_MODEL	all-MiniLM-L6-v2	Sentence-transformer model
ZIKKARON_DECAY_FACTOR	0.95	Heat decay per consolidation cycle
ZIKKARON_COLD_THRESHOLD	0.05	Heat below which memories become archival candidates
ZIKKARON_WRITE_GATE_THRESHOLD	0.4	Minimum surprisal to pass the write gate
ZIKKARON_HOPFIELD_BETA	8.0	Hopfield network sharpness
ZIKKARON_SR_DISCOUNT	0.9	Successor representation discount factor
ZIKKARON_COGNITIVE_LOAD_LIMIT	4	Active context chunk limit (Cowan's 4 +/- 1)

Full list in zikkaron/config.py.

Testing

python -m pytest zikkaron/tests/ -x -q

969 tests across 34 test files covering every subsystem.

References

The papers and books behind the implementation

Ramsauer et al. "Hopfield Networks is All You Need" (ICLR 2021, arXiv:2008.02217)

Nader, Schafe, LeDoux. "Fear memories require protein synthesis in the amygdala for reconsolidation after retrieval" (Nature 406, 2000)

Osan, Tort, Bhatt, Amaral. "Three outcomes of reconsolidation" (PLoS ONE, 2011)

McClelland, McNaughton, O'Reilly. "Why there are complementary learning systems in the hippocampus and neocortex" (Psychological Review 102, 1995)

Sun et al. "Organizing memories for generalization in complementary learning systems" (Nature Neuroscience 26, 2023)

Stachenfeld, Botvinick, Gershman. "The hippocampus as a predictive map" (Nature Neuroscience 20, 2017)

Whittington et al. "The Tolman-Eichenbaum Machine" (Cell 183, 2020)

Spirtes, Glymour, Scheines. Causation, Prediction, and Search (MIT Press, 2000)

Kanerva. Sparse Distributed Memory (MIT Press, 1988)

Frady, Kleyko, Sommer. "Variable Binding for Sparse Distributed Representations" (IEEE TNNLS, 2022)

Toth et al. "Optimal forgetting via rate-distortion theory" (PLoS Computational Biology, 2020)

Josselyn, Frankland. "Memory allocation: mechanisms and function" (Annual Review Neuroscience 41, 2018)

Rashid et al. "Competition between engrams influences fear memory formation and recall" (Science 353, 2016)

Zhou et al. "MetaRAG: Metacognitive Retrieval-Augmented Generation" (ACM Web, 2024)

License

MIT