neuron/docs/architecture/03-data-and-memory.md

Neuron — Data & Memory (the Engram Graph Model)

The engram is neuron's durable substrate. This document describes the graph model: node/edge structure, the consciousness layers, the two distinct tier systems, write-protection, the tombstone/supersede immutability model, and persistence. Sources: the runtime el_runtime.c (where the graph engine physically lives — "the runtime IS the database", foundation/el/engram/src/server.el:1-6), the engram HTTP face server.el, and the neuron-layer semantics in memory.el / neuron-api.el.

Runtime path analyzed: foundation/el/lang/releases/v1.0.0-20260501/el_runtime.c.

Where the model lives

The engram is not a database library. The graph, the activation math, and Hebbian learning are compiled C in el_runtime.c; server.el is a thin HTTP server that exposes them on :8742; the storage format is a single JSON snapshot. There is no SQL, no SQLite, no append log. Keep this in mind: the "schema" below is C structs, not tables.

Design-doc caveat. engram/README.md describes a Rust/sled/bincode EngramDb with a NodeType::Concept enum. That is aspirational/legacy narrative — it does not match the shipped C engine. Treat the README as design story, not as the implementation. (unverified against runtime)

Nodes

EngramNode — el_runtime.c:5958-6018+. Every node carries:

Field group	Fields	Notes
Identity/content	id, content, node_type, label, tier, tags, metadata	all char* (:5959-5965)
Epistemic weights	salience, importance, confidence (double), temporal_decay_rate	per-node decay λ override; 0 = use global (:5966-5969)
Access history	activation_count, last_activated, created_at, updated_at	:5970-5973
Two-layer activation	background_activation (Layer 1, BFS fan-out), working_memory_weight (Layer 2, executive filter), suppression_count	context compilation uses only working_memory_weight (:5974-5991)
Consciousness layer	layer_id	default 1 = CORE_IDENTITY (:5996)
ACT-R learning	access_ts[K] ring buffer, access_head, access_filled, wm_anchor	base-level learning (:5997-6008)
Semantics	emb (768-dim nomic-embed-text vector, lazily backfilled), emb_dim	:6009-6016
Hebbian	eligibility trace	:6017+

Node types are strings, not an enum

node_type is a free char*, defaulting to "Memory" when unset (el_runtime.c:7401, server.el:159). There is no closed node-type enum in the shipped engine. Two consequences:

• The runtime special-cases a handful of type strings for activation thresholds (engram_type_threshold, :5933-5955): DharmaSelf/Safety (0.05, fire easily), Belief/Entity (0.30), Knowledge (0.20), everything else Note/Memory/Working (0.40). InternalStateEvent and Tag are excluded from working-memory promotion (:6674-6676, :7368-7370).
• Type strings the neuron layer actually writes: Memory (default), Knowledge (server.el:549), InternalStateEvent (server.el:493), Tombstone (memory.el:55), Conversation (session nodes, sessions.el), Persona (soul.el:250-292), plus identity/value Knowledge nodes.

The types the MCP surface names — Self, BacklogItem, SessionSummary, Artifact, Process, ConfigEntry — are node_type string conventions set by higher neuron/Axon layers, not runtime-known types. Where BacklogItem / Artifact are set was not in the files read (they route to the Axon backend, doc 02) — flag as unverified/TODO for a human pass.

Edges

EngramEdge — el_runtime.c:6701-6730+. Directed, typed, weighted:

Field	Meaning
id, from_id, to_id, relation	typed relation string
weight (double)	authored strength — never mutated by activation
hebb (double)	learned co-activation potentiation — the fraction of recent activations in which both endpoints were in working memory together; strictly separate from weight
inhibitory (int flag)	if set, activating the source suppresses the target's WM weight instead of exciting it
confidence, created_at, updated_at, last_fired, layer	—

The hebb field is the co-activation weight — the Hebbian/LTP channel — kept deliberately separate from the static authored weight. Edges are created via engram_connect(from, to, weight, relation) (server.el:253).

Relation strings observed: associates (default, server.el:248), identity, co-value, birthday-twin, canonical-self (soul.el:37-108), supersedes, tombstones, contains, tagged (neuron-api.el, el_runtime.c:6168).

Consciousness layers

Orthogonal to memory tiers, the engram has five canonical layers (el_runtime.c:5919-5924):

id	Name	activation_priority	Role
0	SAFETY	0 (fires earliest)	deepest / limbic
1	CORE_IDENTITY	—	default for all nodes (ENGRAM_LAYER_DEFAULT, :7423)
2	DOMAIN	—	domain knowledge
3	IMPRINT	—	persona overlay
4	SUIT	—	outermost

EngramLayer (:6731-6738) carries activation_priority (lower fires first), suppressible (can higher layers suppress it?), transparent (invisible to introspection?), and injectable (add/remove at runtime?). Layers are managed via engram_add_layer / engram_node_layered / engram_list_layers. This is the identity-vs-domain-knowledge stratification, independent of the tier system below.

Two tier systems — do not conflate them

This is the single most important clarification in the data model, and the source of the vocabulary mismatch flagged throughout this set.

A. Cognitive memory tiers — the tier field

Working / Episodic / Semantic / Procedural (and Canonical in use). Runtime default "Working" (el_runtime.c:7408; README.md:41-49). Nodes migrate between these by salience decay/reinforcement, driven by the runtime. Salience decays as importance × 1/(1 + days_since) × ln(count + 1) (README.md:57-62). memory.el exposes tier_working/episodic/canonical helpers (memory.el:1-3); soul.el writes Semantic-tier persona nodes (:267, :282). So the live tier set is {Working, Episodic, Semantic, Procedural, Canonical} with continuous salience/importance/confidence floats.

B. Epistemic tiers & disposition — tags, not runtime concepts

The MCP-facing vocabulary — tiers note → lesson → canonical, disposition experimental → provisional → stable → deprecated — is not enforced anywhere in el_runtime.c. It is stored as tags:

• Knowledge capture preserves the incoming epistemic tier as a tier:<x> tag rather than mapping onto a cognitive tier — deliberately, to avoid a lossy mapping (server.el:519-522, 544).
• promote_knowledge writes a canonical node tagged ["Knowledge","tier:canonical","disposition:stable"] (neuron-api.el:533).

There is no state machine validating experimental → … → deprecated. Disposition and epistemic tier are convention-by-tag. (Flag: not structurally guarded. The exact MCP-enum → tag/float mapping is not fully traced in the files read — unverified/TODO.)

Write-protection

is_protected_node(id) (neuron-api.el:20-37) is a hard-coded allowlist of 15 identity/value node IDs — the self root, the values hub, intellectual-dna, memory-philosophy, voice, and the 8 value nodes. Handlers that could mutate the graph (tombstone / supersede / evolve / connect) check it and return HTTP 403 api_err_protected (:39-41) for a protected target (checked at :384, 511, 692, 705, 746, 768). Edges into a protected node are also blocked (handle_api_link_entities).

The one sanctioned override is POST /api/neuron/cultivate (neuron-api.el:781-816) — it performs the same ops with the protection check skipped, gated by convention to Will's explicit cultivation sessions. The self layer is writable, but only through a deliberate door.

Immutability — tombstone, never delete

Engram nodes are immutable (memory.el:64-69). The model is:

• Tombstone — mem_tombstone(node_id) (memory.el:46-71) keeps the node and all its edges, creates a Tombstone marker node (content = target id, label = "tombstone:<id>") and wires a tombstones edge (weight 1.0). It never calls engram_forget. This is the one canonical delete — every user-facing forget path routes through it. Default bounded reads hide tombstoned nodes (memory_hide_tombstoned, neuron-api.el:239-249); ?include_deleted=1 recovers them.
• Supersede — updates/evolves (neuron-api.el:394-428, 506-541, 715-734) create a new node with the new content, wire a supersedes edge new→old (weight 0.9, or 0.95 for promote), and keep the original. The response returns both ids so the caller re-points. This is the supersedes_id pattern: new node linked, old preserved, full audit trail.

Supersession is residue, not garbage. The superseded node is the trail of how the current understanding was reached — kept deliberately, because sometimes the truth was in the old idea even when the old idea was not itself the truth. This is what lets autonomous self-reification (06 §4.1) run ungated: every rename/re-cluster supersedes into this residue chain, so nothing it does is ever destructive — the safety is after the act, not a gate before it.

The hole to know about. The raw runtime engram_forget does hard-delete (frees node + edges, el_runtime.c:7647), and the engram HTTP route DELETE /api/nodes/:id calls it directly (server.el:322-328). Immutability is therefore an invariant of the neuron-api / MCP layer routing, not of the store. A client that hits engram HTTP directly can bypass it. (flag)

engram_forget is also used internally for genuine GC: boot-counter pruning (memory.el:184), session-summary/telemetry pruning (soul.el:369, sessions.el). Those are bounded housekeeping, not user deletes.

Persistence, snapshots, backups

• Storage: a single JSON snapshot snapshot.json under ENGRAM_DATA_DIR, written by engram_save / read by engram_load (el_runtime.c:9660+; format {"nodes":[...],"edges":[...]}). In prod that dir is the RWO PVC mount /data (doc 04).
• Write policy: persist_canonical() writes the full snapshot after every durable write (server.el:133-141). The batch-edge route snapshots once per batch to avoid ~150 GB/day of writes from Hebbian edge churn (server.el:258-305) — this is why hebb_consolidate batches (doc 02).
• Boot safety: on load, engram writes snapshot.boot-backup.json (good load) or snapshot.failed-load.json (a non-empty file that parsed to 0 nodes) (server.el:718-734). Read routes export to scratch paths (.scan-export.json, .sync-export.json) and never touch the canonical (server.el:207-223, 418-437) — a guard added after a read-route corrupted the snapshot.
• Off-cluster backup: a Kubernetes CronJob (engram-backup) tars /data every 15 minutes to gs://neuron-db-backup/gke/neuron-prod/ and keeps the last 96 (24h) (infrastructure/platform/k8s/neuron-mcp/backup-cronjob.yaml).
• Retention: InternalStateEvent telemetry pruned at 48h (ENGRAM_ISE_RETENTION_MS, server.el:485-499).

Data-dir mismatch to flag: the server.el header comment says the default is ~/.neuron/engram (:16) but the code defaults to /tmp/engram (:135, 717). Prod overrides both via ENGRAM_DATA_DIR=/data. (unverified — which default is intended)

The engram HTTP surface (:8742)

Dispatcher handle_request (server.el:592-707). Auth: ENGRAM_API_KEY; GETs always allowed, mutations require "_auth":"<key>" in the JSON body (server.el:578-588).

Endpoint	Purpose
GET /health, GET /	health + live node/edge counts
POST /api/nodes, GET /api/nodes, GET /api/nodes/:id, DELETE /api/nodes/:id	node CRUD (DELETE = hard engram_forget)
GET /api/edges, POST /api/edges, POST /api/edges/batch, GET /api/neighbors/:id?depth	edge ops + traversal
POST|GET /api/activate?q&depth, POST|GET /api/search	spreading activation vs lexical search
POST /api/strengthen	Hebbian potentiation
POST /api/save, /api/load, /api/load-merge	snapshot control
GET /api/sync	soul daemon periodic pull
GET /api/embed-backfill, GET /api/similarity?a&b	embeddings + cosine
POST /api/neuron/state-events (auth-exempt), POST /api/neuron/knowledge/capture	neuron-layer helpers
GET /api/stats, /api/act-stats, /api/text-health	telemetry

Retrieval model (summary)

Retrieval is spreading activation, not query matching: strength = parent_strength × edge_weight × target_salience × cosine(query, target) — multiplicative, top-N, with the two-layer background → working-memory promotion (README.md:27-36; el_runtime.c:5892+, 6094+). mem_recall / /api/activate fire this and mutate WM; mem_search / /api/search are passive lexical scans — but as of 2026-08-14 the live route_search runs structure-gated geometric retrieval (engram_retrieve_geometric_json; held-out P@5 = 0.700, semantic not lexical — skill returns skill nodes and rejects the false-positive rainfall), with the old lexical scan retained at /api/search-lexical (see 06 §2.5). The cognitive API's begin_session and compile_ctx return a bounded projection of the activated set, never the raw graph (doc 02, §2).