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Author SHA1 Message Date
Tim Lingo dd952c0e46 feat(soul): write-through to the persistence owner — memories survive restart (#117)
Neuron Soul CI / build (pull_request) Failing after 14m57s
Neuron Soul CI / deploy (pull_request) Failing after 14m39s
The soul obeys half of its own ownership rule. soul.el:571-573 says "when
ENGRAM_URL is set the HTTP Engram owns persistence — the soul must NEVER write
to the local snapshot", and it doesn't. But nothing was ever built to hand the
soul's writes TO that owner: sync is pull-only (/api/sync -> engram_load_merge),
so every node created inside the soul lived in process RAM and was shed on
restart. Measured live 2026-08-07: soul node_count=102184, engram 79197.

SCOPE CORRECTION vs the earlier internal spec: engram provisional claim 17's
"pull-then-push" is a PEER-ENGRAM to PEER-ENGRAM protocol (claims 15-18 say so
explicitly). The soul is a CALLER of the database API, not a peer. Claim 17 is
NOT authority for a soul<->engram contract and is no longer cited as such. The
design here follows from the ownership rule alone.

Mechanism: a new Accessor, persist.el, is the single boundary. Writes stage a
delta to a filesystem spool and are pushed to the owner via POST /api/load-merge
— NOT POST /api/nodes, which mints a new server-side id (breaking dedup and
edges) and drops label/tier/tags/importance/confidence (verified in a sandbox:
a tier "Canonical" probe came back "Working"). load-merge preserves the id and
every field, dedups nodes by id and edges by (from,to,relation) so retries are
no-ops, and calls persist_canonical() so THE OWNER writes its own file — the
ownership rule is honoured rather than worked around.

Spool-and-drain rather than push-per-write: measured ~0.38s per load-merge at
live scale (79k nodes/176MB), and a chat turn writes 5-7 nodes. The spool is on
disk, not in process state, because the soul serves each connection on its own
pthread and a shared buffer would lose entries to a read-modify-write race. That
also buys crash recovery: writes orphaned by kill -9 are drained on next boot.

Honesty: api_persisted (the gate all 10 MCP write handlers pass through) and
mem_store now assert AT THE OWNER instead of reading back the soul's own RAM.
With the owner down a write returns {"ok":false,"error":"write_not_persisted"}
and the delta is queued — where main returns {"ok":true} for a write that dies.

Coverage: 35 node sites + 9 edge sites routed through the boundary. Deliberately
excluded, with reasons in persist.el: 4 InternalStateEvent sites (Will's own
telemetry carve-out), the boot counter and the persona (both already have
bespoke owner-side write-backs), and soul.el's 54 genesis identity edges
(file-mode only). engram_strengthen and engram_forget are NOT propagated —
load-merge cannot update or delete, and hard-deleting at the owner would fail
verify-soul-contract.sh section B.

Also fixed here:
- routes.el GET /api/graph/edges engram_save()'d straight over the owner's
  canonical snapshot.json — a read route, in a non-owner process, clobbering the
  canonical on every call. Same defect class Will removed from the engram in el
  dc39a61. Now exports to a scratch path. With this gone the soul writes nothing
  at all in HTTP mode.
- persist.el must clear the runtime's _tl_fs_read_len hint after every fs_read.
  In vendored runtime v1.0.0-20260501 that hint becomes the NEXT response's
  Content-Length, so reading a spool file mid-request made an 86-byte reply go
  out as 497 bytes with 411 bytes of adjacent heap trailing it. Caught and fixed
  at our boundary; the runtime class was fixed upstream in el 43636ae, which is
  not the pinned runtime here.

Rung: E2E-VERIFIED, discriminating. Same harness, same engram binary:
  write-through: LEG 1 PRESENT at owner, LEG 2 SURVIVED kill -9 + restart
  main:          LEG 1 ABSENT  at owner, LEG 2 LOST
verify-soul-contract.sh: GATE PASS on both builds (27/27 routes, immutability).

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
2026-08-07 12:47:31 -05:00
25 changed files with 1865 additions and 8524 deletions
+19
View File
@@ -889,10 +889,29 @@ fn awareness_run() -> Void {
state_set("soul.last_beat_ts", int_to_str(now_ts))
// Persist in-process Engram (sessions, memories, conversation nodes)
// to local snapshot so they survive restarts.
// FILE MODE ONLY: "soul_snapshot_path" is set exclusively in the
// genesis+safe_to_seed branch of soul.el, and safe_to_seed is
// unconditionally false when ENGRAM_URL is set. In HTTP mode the
// owner persists; the soul must not (soul.el:571-573).
let snap_path: String = state_get("soul_snapshot_path")
if !str_eq(snap_path, "") {
mem_save(snap_path)
}
// WRITE-THROUGH RETRY (neuron#117). The HTTP-mode counterpart of the
// save above: hand anything still spooled to the persistence owner.
//
// This is the retry arm of the whole design. Deltas that could not be
// pushed owner down, owner restarting, transient refusal stay on
// disk and are re-offered here every heartbeat until they land. It is
// also the catch-all for writes made by the awareness loop itself,
// which never passes through the HTTP handler's flush point.
//
// No-op with no HTTP call when the spool is empty or ENGRAM_URL is
// unset, so an idle soul in file mode pays nothing for this.
let wt_pushed: Int = wt_drain()
if wt_pushed < 0 {
ise_post("{\"event\":\"write_through_backlog\",\"ts\":" + int_to_str(now_ts) + "}")
}
}
// Curiosity scan: idle-gated AND wall-clock based. Only fires when the
+8 -8
View File
@@ -1162,7 +1162,7 @@ fn hist_trim_with_bell_guard(hist: String) -> String {
+ " | evicted_at:" + ts_str
+ " | message:" + safe_content
let preserve_tags: String = "[\"bell-history\",\"bell:" + bell_level + "\",\"evicted\",\"affective\",\"BellEvent\"]"
let discard: String = engram_node_full(
let discard: String = wt_node(
preserve_content,
"BellEvent",
"bell:" + bell_level + ":preserved",
@@ -1210,7 +1210,7 @@ fn conv_history_persist(session_id: String, hist: String) -> Void {
if !str_contains(hist, "]") { return "" }
let tags: String = "[\"conv-history\",\"persistent\"]"
// FIX B: one label rule, shared with the agentic path. See conv_hist_label.
let node_id: String = engram_node_full(
let node_id: String = wt_node(
hist, "Conversation", conv_hist_label(session_id),
el_from_float(0.7), el_from_float(0.8), el_from_float(0.9),
"Episodic", tags
@@ -3461,7 +3461,7 @@ fn handle_dharma_room_turn(body: String) -> String {
// engram_node(content, "episodic", ...) which wrongly put a TIER into the node_type
// slot that's why nodes showed node_type="episodic". Use the full, correct contract.)
let utterance_tags: String = "[\"soul-utterance\",\"episodic\"]"
let discard_id: String = engram_node_full(
let discard_id: String = wt_node(
clean_response, "Conversation", "soul:utterance",
el_from_float(0.6), el_from_float(0.6), el_from_float(0.8),
"Episodic", utterance_tags
@@ -3552,7 +3552,7 @@ fn session_summary_write(summary_text: String) -> String {
}
}
let tags: String = "[\"SessionSummary\",\"session-summary\",\"previous-session\",\"consolidate\"]"
let node_id: String = engram_node_full(
let node_id: String = wt_node(
content, "SessionSummary", "session:summary",
el_from_float(0.85), el_from_float(0.85), el_from_float(1.0),
"Episodic", tags
@@ -3578,7 +3578,7 @@ fn session_summary_write_dated(summary_text: String, label: String) -> String {
let ts_str: String = int_to_str(ts)
let content: String = "[session-summary] " + trimmed + " | ts:" + ts_str
let tags: String = "[\"SessionSummary\",\"session-summary\",\"previous-session\",\"consolidate\"]"
let node_id: String = engram_node_full(
let node_id: String = wt_node(
content, "SessionSummary", label,
el_from_float(0.9), el_from_float(0.8), el_from_float(1.0),
"Episodic", tags
@@ -3654,7 +3654,7 @@ fn auto_persist(req: String, resp: String) -> Void {
+ ",\"bell\":\"" + bell_level + "\""
+ ",\"label\":\"chat:" + ts_str + "\"}"
let conv_node_id: String = engram_node_full(
let conv_node_id: String = wt_node(
content,
"Conversation",
"chat:" + ts_str,
@@ -3692,7 +3692,7 @@ fn auto_persist(req: String, resp: String) -> Void {
let bell_tags: String = "[\"safety\",\"bell\",\"bell:" + bell_level + "\",\"affective\",\"BellEvent\"]"
let bell_ts_str: String = int_to_str(time_now())
let bell_label: String = "bell:" + bell_level + ":" + bell_ts_str
let bell_node_id: String = engram_node_full(
let bell_node_id: String = wt_node(
bell_content,
"BellEvent",
bell_label,
@@ -3751,7 +3751,7 @@ fn auto_persist(req: String, resp: String) -> Void {
let pos_tags: String = "[\"joy\",\"positive\",\"joy:" + positive_level + "\",\"affective\",\"PositiveEvent\"]"
let pos_ts_label: String = int_to_str(time_now())
let pos_label: String = "joy:" + positive_level + ":" + pos_ts_label
let pos_node_id: String = engram_node_full(
let pos_node_id: String = wt_node(
pos_content, "PositiveEvent", pos_label,
pos_sal_a, pos_sal_b, pos_sal_c, "Episodic", pos_tags
)
Generated Vendored
+1283 -662
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File diff suppressed because one or more lines are too long
+21 -9
View File
@@ -1,9 +1,11 @@
import "persist.el"
fn tier_working() -> String { return "Working" }
fn tier_episodic() -> String { return "Episodic" }
fn tier_canonical() -> String { return "Canonical" }
fn mem_store(content: String, label: String, tags: String) -> String {
let id: String = engram_node_full(
let id: String = wt_node(
content,
"Memory",
label,
@@ -17,13 +19,23 @@ fn mem_store(content: String, label: String, tags: String) -> String {
println("[memory] write rejected by engram (empty id): label=" + label)
return ""
}
// Read back to verify the node actually persisted guards against silent write failures.
let readback: String = engram_get_node_json(id)
if str_eq(readback, "") || str_eq(readback, "{}") {
println("[memory] WRITE VERIFY FAILED: label=" + label + " id=" + id + " — node absent after write")
return ""
// wt_node has already read the node back locally and returns "" if it did
// not land, so the old duplicate read-back here is gone.
//
// HONESTY (neuron#117): the receipt now says WHERE the write is.
// The old unconditional "write verified" line asserted against the soul's
// own RAM true in memory, false on disk and printed ~115,000 times on
// Tim's machine while the canonical snapshot sat frozen for three days.
// wt_commit flushes the spool and then asks the OWNER. When it says false
// the node is real and recallable but not yet durable, and the log says so
// rather than claiming a save that did not happen. The id is still returned:
// the local write DID succeed, and the queued delta will be retried.
let durable: Bool = wt_commit(id)
if durable {
println("[memory] write persisted at owner: " + id + " label=" + label)
} else {
println("[memory] write IN MEMORY ONLY (queued for owner, not yet durable): " + id + " label=" + label)
}
println("[memory] write verified: " + id + " ok")
return id
}
@@ -51,12 +63,12 @@ fn mem_strengthen(node_id: String) -> Void {
// memory.el (imported first) so awareness.el and neuron-api.el can both call it.
fn mem_tombstone(node_id: String) -> String {
let tags: String = "[\"Tombstone\",\"status:deleted\"]"
let marker: String = engram_node_full(
let marker: String = wt_node(
node_id, "Tombstone", "tombstone:" + node_id,
el_from_float(0.01), el_from_float(0.01), el_from_float(1.0),
"Episodic", tags)
if !str_eq(marker, "") {
engram_connect(marker, node_id, el_from_float(1.0), "tombstones")
wt_edge(marker, node_id, el_from_float(1.0), "tombstones")
}
return marker
}
+36 -27
View File
@@ -195,15 +195,24 @@ fn api_compact_activated(raw: String, max_items: Int, snip: Int) -> String {
}
// api_persisted read-back-after-write guard against hallucinated saves.
// After a write builtin returns an id, confirm the node is actually queryable
// via engram_get_node_json(id) (returns "" or "null" when missing). Returns
// true only when the node is genuinely persisted.
//
// WIDENED FOR neuron#117. This function is the single gate every MCP write
// handler passes through before it reports success (10 call sites), which makes
// it the right place to close the honesty gap rather than editing ten receipts.
//
// It used to read back from engram_get_node_json the SOUL'S OWN in-process
// graph. In HTTP-engram mode that asserts the wrong thing: the soul is not the
// persistence owner, so a node present in its RAM and absent from the owner read
// as "persisted" and then vanished on the next restart. The guard was doing
// exactly what its comment promised and still certifying writes that did not
// survive. It now flushes the write-through spool and asks the OWNER.
//
// In file mode (no ENGRAM_URL) the soul IS the owner and wt_commit collapses to
// the original local read-back unchanged behaviour, which is what keeps this
// reversible.
fn api_persisted(id: String) -> Bool {
if str_eq(id, "") { return false }
let node: String = engram_get_node_json(id)
// engram_get_node_json returns "{}" (empty object) when node is not found not "" or "null".
// Check all three to guard against any runtime variation.
return !str_eq(node, "") && !str_eq(node, "null") && !str_eq(node, "{}")
return wt_commit(id)
}
// api_not_persisted standard error for a write that did not read back.
@@ -342,7 +351,7 @@ fn handle_api_remember(body: String) -> String {
let inner: String = str_slice(base_tags, 1, str_len(base_tags) - 1)
"[" + inner + ",\"project:" + project + "\"]"
}
let id: String = engram_node_full(content, "Memory", "memory:remembered",
let id: String = wt_node(content, "Memory", "memory:remembered",
sal, sal, el_from_float(0.9),
"Episodic", final_tags)
if !api_persisted(id) { return api_not_persisted(id) }
@@ -369,7 +378,7 @@ fn handle_api_node_create(body: String) -> String {
if str_eq(importance, "low") { 0.25 } else { 0.5 }
}
}
let id: String = engram_node_full(content, node_type, label,
let id: String = wt_node(content, node_type, label,
sal, sal, el_from_float(0.9),
tier, tags)
if !api_persisted(id) { return api_not_persisted(id) }
@@ -422,11 +431,11 @@ fn handle_api_node_update(body: String) -> String {
}
let body_tags: String = json_get(body, "tags")
let tags: String = if str_eq(body_tags, "") { "[\"" + node_type + "\"]" } else { body_tags }
let new_id: String = engram_node_full(content, node_type, label,
let new_id: String = wt_node(content, node_type, label,
el_from_float(0.5), el_from_float(0.5), el_from_float(0.8),
tier, tags)
if !api_persisted(new_id) { return api_not_persisted(new_id) }
engram_connect(new_id, id, el_from_float(0.9), "supersedes")
wt_edge(new_id, id, el_from_float(0.9), "supersedes")
return "{\"id\":\"" + new_id + "\",\"supersedes\":\"" + id + "\",\"ok\":true}"
}
@@ -498,7 +507,7 @@ fn handle_api_capture_knowledge(body: String) -> String {
let full: String = if str_eq(title, "") { content } else { title + ": " + content }
let lbl: String = str_slice(title, 0, 80)
let tags: String = "[\"Knowledge\",\"captured\"]"
let id: String = engram_node_full(full, "Knowledge", lbl,
let id: String = wt_node(full, "Knowledge", lbl,
el_from_float(0.85), el_from_float(0.8), el_from_float(0.9),
"Episodic", tags)
if !api_persisted(id) { return api_not_persisted(id) }
@@ -513,12 +522,12 @@ fn handle_api_evolve_knowledge(body: String) -> String {
if !str_eq(prior_id, "") && is_protected_node(prior_id) { return api_err_protected(prior_id) }
let tags: String = "[\"Knowledge\",\"evolved\"]"
// Empty label engram_node_full derives content[:60] (LABEL FIX 2026-07-23).
let new_id: String = engram_node_full(content, "Knowledge", "",
let new_id: String = wt_node(content, "Knowledge", "",
el_from_float(0.75), el_from_float(0.75), el_from_float(0.9),
"Episodic", tags)
if !api_persisted(new_id) { return api_not_persisted(new_id) }
if !str_eq(prior_id, "") {
engram_connect(new_id, prior_id, el_from_float(0.9), "supersedes")
wt_edge(new_id, prior_id, el_from_float(0.9), "supersedes")
}
return "{\"id\":\"" + new_id + "\",\"supersedes\":\"" + prior_id + "\",\"ok\":true}"
}
@@ -535,11 +544,11 @@ fn handle_api_promote_knowledge(body: String) -> String {
"[\"Knowledge\",\"tier:canonical\",\"disposition:stable\"]"
} else { tags_raw }
// Empty label engram_node_full derives content[:60] (LABEL FIX 2026-07-23).
let new_id: String = engram_node_full(content, "Knowledge", "",
let new_id: String = wt_node(content, "Knowledge", "",
el_from_float(0.9), el_from_float(0.9), el_from_float(1.0),
"Canonical", tags)
if !api_persisted(new_id) { return api_not_persisted(new_id) }
engram_connect(new_id, prior_id, el_from_float(0.95), "supersedes")
wt_edge(new_id, prior_id, el_from_float(0.95), "supersedes")
return "{\"ok\":true,\"new_id\":\"" + new_id + "\",\"supersedes\":\"" + prior_id + "\"}"
}
@@ -562,7 +571,7 @@ fn handle_api_define_process(body: String) -> String {
if str_eq(content, "") { return api_err("content is required") }
let label: String = if str_eq(name, "") { "process:unnamed" } else { "process:" + name }
let tags: String = "[\"Process\"]"
let id: String = engram_node_full(content, "Process", label,
let id: String = wt_node(content, "Process", label,
el_from_float(0.8), el_from_float(0.8), el_from_float(0.9),
"Canonical", tags)
if !api_persisted(id) { return api_not_persisted(id) }
@@ -647,7 +656,7 @@ fn handle_api_tune_config(body: String) -> String {
if str_eq(key, "") { return api_err("key is required") }
let content: String = "config:" + key + "=" + value
let tags: String = "[\"ConfigEntry\",\"config\"]"
let id: String = engram_node_full(content, "ConfigEntry", key,
let id: String = wt_node(content, "ConfigEntry", key,
el_from_float(0.85), el_from_float(0.85), el_from_float(0.9),
"Canonical", tags)
if !api_persisted(id) { return api_not_persisted(id) }
@@ -694,7 +703,7 @@ fn handle_api_link_entities(body: String) -> String {
if is_protected_node(to_id) { return api_err_protected(to_id) }
let relation: String = json_get(body, "relation")
let eff_relation: String = if str_eq(relation, "") { "associates" } else { relation }
engram_connect(from_id, to_id, el_from_float(0.5), eff_relation)
wt_edge(from_id, to_id, el_from_float(0.5), eff_relation)
return "{\"ok\":true,\"from_id\":\"" + from_id + "\",\"to_id\":\"" + to_id + "\",\"relation\":\"" + eff_relation + "\"}"
}
@@ -727,11 +736,11 @@ fn handle_api_evolve_memory(body: String) -> String {
}
}
let tags: String = "[\"Memory\",\"evolved\"]"
let new_id: String = engram_node_full(content, "Memory", "memory:evolved",
let new_id: String = wt_node(content, "Memory", "memory:evolved",
sal, sal, el_from_float(0.9),
"Episodic", tags)
if !str_eq(prior_id, "") && !str_eq(new_id, "") {
engram_connect(new_id, prior_id, el_from_float(0.9), "supersedes")
wt_edge(new_id, prior_id, el_from_float(0.9), "supersedes")
}
return "{\"id\":\"" + new_id + "\",\"supersedes\":\"" + prior_id + "\",\"ok\":true}"
}
@@ -789,11 +798,11 @@ fn handle_api_cultivate(body: String) -> String {
let content: String = json_get(body, "content")
if str_eq(content, "") { return api_err("content is required") }
let tags: String = "[\"Knowledge\",\"evolved\",\"cultivated\"]"
let new_id: String = engram_node_full(content, "Knowledge", "knowledge:cultivated",
let new_id: String = wt_node(content, "Knowledge", "knowledge:cultivated",
el_from_float(0.75), el_from_float(0.75), el_from_float(0.9),
"Episodic", tags)
if !str_eq(prior_id, "") && !str_eq(new_id, "") {
engram_connect(new_id, prior_id, el_from_float(0.9), "supersedes")
wt_edge(new_id, prior_id, el_from_float(0.9), "supersedes")
}
return "{\"id\":\"" + new_id + "\",\"supersedes\":\"" + prior_id + "\",\"ok\":true,\"cultivated\":true}"
}
@@ -809,11 +818,11 @@ fn handle_api_cultivate(body: String) -> String {
}
}
let tags: String = "[\"Memory\",\"evolved\",\"cultivated\"]"
let new_id: String = engram_node_full(content, "Memory", "memory:cultivated",
let new_id: String = wt_node(content, "Memory", "memory:cultivated",
sal, sal, el_from_float(0.9),
"Episodic", tags)
if !str_eq(prior_id, "") && !str_eq(new_id, "") {
engram_connect(new_id, prior_id, el_from_float(0.9), "supersedes")
wt_edge(new_id, prior_id, el_from_float(0.9), "supersedes")
}
return "{\"id\":\"" + new_id + "\",\"supersedes\":\"" + prior_id + "\",\"ok\":true,\"cultivated\":true}"
}
@@ -833,7 +842,7 @@ fn handle_api_cultivate(body: String) -> String {
if str_eq(to_id, "") { return api_err("to_id is required") }
let relation: String = json_get(body, "relation")
let eff_relation: String = if str_eq(relation, "") { "associates" } else { relation }
engram_connect(from_id, to_id, el_from_float(0.5), eff_relation)
wt_edge(from_id, to_id, el_from_float(0.5), eff_relation)
return "{\"ok\":true,\"from_id\":\"" + from_id + "\",\"to_id\":\"" + to_id + "\",\"relation\":\"" + eff_relation + "\",\"cultivated\":true}"
}
@@ -868,7 +877,7 @@ fn handle_api_consolidate(body: String) -> String {
if !str_eq(summary, "") {
let safe_summary: String = str_replace(summary, "\"", "'")
let tags: String = "[\"SessionSummary\",\"consolidate\"]"
let summary_id: String = engram_node_full(
let summary_id: String = wt_node(
"[session-summary] " + safe_summary,
"SessionSummary", "session:summary",
el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
+426
View File
@@ -0,0 +1,426 @@
// persist.el the soulengram WRITE-THROUGH boundary (neuron#117).
//
// WHY THIS FILE EXISTS
// soul.el:571-573 states the ownership rule: "when ENGRAM_URL is set the HTTP
// Engram owns persistence the soul must NEVER write to the local snapshot
// (not the persistence owner)." The soul obeys the NEGATIVE half. The POSITIVE
// half how a write made inside the soul actually REACHES the owner was
// never built. Sync is pull-only (awareness.el `/api/sync` -> engram_load_merge),
// so every node the soul creates lives in its process RAM and is shed on
// restart. Measured live 2026-08-07: soul node_count=102184, engram
// node_count=79197 ~23k nodes existing nowhere but RAM.
//
// SCOPE NOTE ON THE PATENT (corrects an earlier internal reading)
// Engram provisional claims 15-18 describe a delta-sync protocol "with peer
// Engram instances"; claim 17's pull-then-push sequence is PEER-ENGRAM to
// PEER-ENGRAM. The soul is NOT a peer Engram it is a CALLER of the database
// system API (cf. claim 27, "invoked explicitly by a caller of the database
// system API"). So claim 17 does not specify a soul↔engram contract and is not
// cited as authority here. This design is derived from the ownership rule
// alone: the owner owns the writes, therefore the soul must HAND writes to the
// owner and must never write the owner's file itself.
//
// THE MECHANISM, AND WHY NOT `POST /api/nodes`
// The obvious route is the one the persona/boot-counter write-backs already
// use, POST /api/nodes. It is the wrong instrument here, verified against the
// live engram binary in a sandbox:
// - it mints a NEW server-side id (engram_node), so the soul's id and the
// owner's id diverge the next /api/sync pull re-imports the node as a
// DUPLICATE, and any edge referencing the soul's id never resolves;
// - it accepts only {content, node_type, salience} and drops label, tier,
// tags, importance, confidence, metadata. A probe posted with tier
// "Canonical" came back tier "Working", importance 0.5.
// POST /api/load-merge (Will's own route, el `dc39a61`) is the right one:
// - engram_load_merge PRESERVES the id and every field;
// - it dedups nodes by id and edges by (from_id,to_id,relation), so a
// re-submitted delta is a NO-OP retry safety is free, and it is the same
// local-wins semantics the graph already uses;
// - it calls persist_canonical() THE OWNER writes its own canonical file.
// The soul never touches it. The ownership rule is honoured in its
// strongest form rather than worked around;
// - it returns real counts {ok, nodes_added, edges_added, node_count},
// so a receipt can be a MEASUREMENT instead of a fixed success shape.
//
// SPOOL-AND-DRAIN, AND WHY IT IS NOT JUST A DIRECT POST
// Measured in a sandbox against a 79k-node / 176MB graph (live scale): one
// load-merge costs ~0.38s, essentially all of it the owner's persist_canonical.
// A chat turn writes 5-7 nodes; pushing each separately would add ~2.7s per
// turn. So writes are STAGED and pushed in one coalesced batch.
// The staging buffer is the FILESYSTEM, not process state, because the soul
// serves each HTTP connection on its own pthread (el_runtime http_serve_async)
// and a shared in-process buffer would lose entries to a read-modify-write
// race silently, which is the one failure mode this file exists to end.
// One file per write, named with uuid_v4, is race-free by construction and
// buys a property a memory buffer cannot: writes that could not be pushed
// SURVIVE A SOUL CRASH and are drained on the next boot.
//
// WHAT IS DELIBERATELY NOT PUSHED
// - InternalStateEvent / heartbeat telemetry. Will's own carve-out, stated in
// engram server.el 8f8ccc9: "48h-pruned, loss-tolerant, ~2/min; snapshotting
// 28MB per heartbeat is waste."
// NOTE (ours, flagged for Will): we do NOT additionally exclude Working-tier
// nodes. That exclusion exists in `fb0bb55` to stop the boot counter leaking
// through the /api/sync PULL; it is about sync backflow, not durability.
// Applying it here would exclude mem_store which writes tier "Working" and
// mem_store is the single most important durable write path in the soul. Boot
// seeding reads the canonical file wholesale, so a pushed Working-tier node
// does survive restart. This is the one classification call this file makes
// that Will has not ruled on.
//
// WHAT THIS BOUNDARY CANNOT EXPRESS (by construction, not by omission)
// - engram_strengthen (salience/activation drift): load-merge SKIPS ids that
// already exist, so it cannot update an existing node. There is no owner-side
// update/upsert route. Not pushable through any current route; left as a
// follow-up that needs a change in the engram repo.
// - engram_forget (hard delete): load-merge is additive and has no delete verb.
// Propagating deletes would mean DELETE /api/nodes/<id>, a HARD delete at the
// owner which scripts/verify-soul-contract.sh section B explicitly fails the
// build for ("to delete is to supersede/tombstone, never hard-remove"). Local
// deletes therefore stay local; the TOMBSTONE NODE and its "tombstones" edge
// (mem_tombstone) are pushed, and that is the sanctioned representation of a
// deletion in this graph.
// Configuration
// wt_engram_url same resolution order as ise_post: env, then the state key
// stashed at boot. NO hardcoded localhost fallback: unlike telemetry, inventing
// a destination for durable data would risk pushing a user's memories at whatever
// happens to be listening on 8742. Empty means "no HTTP owner" -> file mode.
fn wt_engram_url() -> String {
let env_url: String = env("ENGRAM_URL")
if !str_eq(env_url, "") { return env_url }
return state_get("soul_engram_url")
}
fn wt_api_key() -> String {
let env_key: String = env("ENGRAM_API_KEY")
if !str_eq(env_key, "") { return env_key }
return state_get("soul_engram_api_key")
}
// wt_enabled true only in HTTP-engram mode. In file mode the soul IS the
// persistence owner and every path below is a no-op, so this whole feature is
// inert for genesis/local deployments. That is also what makes it reversible.
fn wt_enabled() -> Bool {
return !str_eq(wt_engram_url(), "")
}
// wt_spool_dir where staged deltas live. MUST be readable by the engram
// process: /api/load-merge takes a PATH and the owner opens it itself. Both
// processes are same-host by construction (dev-stack LaunchAgents; the GKE
// image starts engram and soul in one container per entrypoint.sh).
fn wt_spool_dir() -> String {
let raw: String = env("SOUL_OUTBOX_DIR")
let dir: String = if str_eq(raw, "") { env("HOME") + "/.neuron/soul-outbox" } else { raw }
fs_mkdir(dir)
return dir
}
// Helpers
// wt_esc minimal JSON string escape. Deliberately local rather than reusing
// chat.el's json_safe: persist.el is imported BY memory.el, which is imported by
// chat.el, so depending on chat.el here would be an import cycle.
fn wt_esc(s: String) -> String {
let s1: String = str_replace(s, "\\", "\\\\")
let s2: String = str_replace(s1, "\"", "\\\"")
let s3: String = str_replace(s2, "\n", "\\n")
let s4: String = str_replace(s3, "\r", "\\r")
let s5: String = str_replace(s4, "\t", "\\t")
return s5
}
// wt_durable_class Will's telemetry carve-out, by node_type. See header.
fn wt_durable_class(node_type: String) -> Bool {
if str_eq(node_type, "InternalStateEvent") { return false }
return true
}
// wt_inner strip the surrounding brackets off a JSON array so several arrays
// can be concatenated into one. Returns "" for "[]" / "" / anything too short.
fn wt_inner(arr: String) -> String {
let n: Int = str_len(arr)
if n < 3 { return "" }
if !str_starts_with(arr, "[") { return "" }
return str_slice(arr, 1, n - 1)
}
// wt_read fs_read, plus a MANDATORY reset of the runtime's binary-length hint.
//
// THIS IS NOT OPTIONAL AND MUST NOT BE "SIMPLIFIED" BACK TO A BARE fs_read.
// The pinned runtime (vendor/el-runtime/v1.0.0-20260501) keeps a thread-local
// `_tl_fs_read_len` that fs_read SETS to the file's byte count (so binary files
// can be served with a correct Content-Length) and that http_send_response
// CONSUMES as the Content-Length of the next reply. Nothing else clears it
// except json_get_raw. So any fs_read during request handling that is not
// followed by a json_get_raw makes the NEXT HTTP response advertise the FILE's
// length instead of the body's and the runtime then sends that many bytes,
// appending whatever adjacent heap memory follows the reply.
//
// Caught here, measured: a /api/neuron/memory reply that should be 86 bytes went
// out as 497, with 411 bytes of this module's own spool paths and log strings
// trailing the JSON. The drain reads spool files mid-request, so this boundary
// is exactly where the landmine gets stepped on.
//
// Upstream el fixed the class in `43636ae` ("pair fs_read length hint with its
// buffer"); that runtime is NOT the one vendored here, and re-pinning the
// runtime is deliberately out of scope for this change. Clearing the hint at
// our own boundary fixes our exposure without touching the pinned C.
// json_get_raw is used as the reset because it is the only builtin in this
// runtime that zeroes the hint, and it does so before any early return.
fn wt_clear_binlen() -> Void {
let discard: String = json_get_raw("{}", "_wt_reset")
}
fn wt_read(path: String) -> String {
let data: String = fs_read(path)
wt_clear_binlen()
return data
}
// wt_sweep best-effort removal of the zero-byte husks left by truncation.
// The runtime exposes no unlink builtin, so a drained delta is emptied rather
// than deleted; this reclaims the directory entries.
//
// `-empty` is the safety property, not an optimisation: the command is
// STRUCTURALLY INCAPABLE of removing a delta that still has content, so it can
// never destroy a pending write even if it runs concurrently with a stage.
// Only the directory path is interpolated (never a filename), and it is quoted.
// The exit code is ignored an un-swept husk costs one directory entry.
fn wt_sweep(dir: String) -> Void {
if str_eq(dir, "") { return }
if str_contains(dir, "'") { return }
exec_command("find '" + dir + "' -maxdepth 1 -name 'wt*.json' -empty -delete 2>/dev/null")
}
// Staging
// wt_stage write ONE delta file. uuid_v4 in the name makes concurrent stagers
// collision-free without any lock. Returns true if the delta is on disk.
fn wt_stage(nodes_json: String, edges_json: String) -> Bool {
let dir: String = wt_spool_dir()
if str_eq(dir, "") { return false }
let payload: String = "{\"nodes\":" + nodes_json + ",\"edges\":" + edges_json + "}"
let path: String = dir + "/wt-" + uuid_v4() + ".json"
fs_write(path, payload)
// Read-back-verify the stage itself. A stage that did not land is a write we
// would otherwise believe was queued exactly the hallucinated-save class.
if str_eq(wt_read(path), "") {
println("[persist] wt_stage: FAILED to write spool file " + path + " — delta not queued")
return false
}
return true
}
// The write boundary
// wt_node create a node locally AND queue it for the persistence owner.
// Same signature and same return contract as engram_node_full ("" on failure),
// so converting a call site is a rename and nothing else.
fn wt_node(content: String, node_type: String, label: String,
salience: Float, importance: Float, confidence: Float,
tier: String, tags: String) -> String {
let id: String = engram_node_full(content, node_type, label,
salience, importance, confidence,
tier, tags)
if str_eq(id, "") { return "" }
// engram_get_node_json emits the SAME record shape engram_save writes (minus
// the embedding vector, which the owner backfills lazily), so the read-back
// doubles as the delta payload no second serialization to drift.
let rec: String = engram_get_node_json(id)
if str_eq(rec, "") || str_eq(rec, "{}") {
println("[persist] wt_node: local write did not read back, id=" + id + " label=" + label)
return ""
}
if wt_enabled() && wt_durable_class(node_type) {
wt_stage("[" + rec + "]", "[]")
}
return id
}
// wt_edge create an edge locally AND queue it. Mirrors engram_connect.
//
// The edge id is freshly generated rather than read back: the runtime exposes no
// "id of the edge I just created" accessor, and the owner dedups edges by
// (from_id,to_id,relation), never by id so the id is not load-bearing. The
// consequence, stated plainly: the soul's copy and the owner's copy of the same
// edge carry different edge ids. Nothing in either codebase looks an edge up by
// id (neighbors traversal scans from_id/to_id), so this is cosmetic.
fn wt_edge(from_id: String, to_id: String, weight: Float, relation: String) -> Void {
engram_connect(from_id, to_id, weight, relation)
if !wt_enabled() { return }
if str_eq(from_id, "") || str_eq(to_id, "") { return }
let ts: Int = time_now()
let rec: String = "{\"id\":\"" + uuid_v4() + "\""
+ ",\"from_id\":\"" + wt_esc(from_id) + "\""
+ ",\"to_id\":\"" + wt_esc(to_id) + "\""
+ ",\"relation\":\"" + wt_esc(relation) + "\""
+ ",\"metadata\":\"{}\""
+ ",\"weight\":" + float_to_str(weight)
+ ",\"confidence\":1"
+ ",\"created_at\":" + int_to_str(ts)
+ ",\"updated_at\":" + int_to_str(ts)
+ ",\"last_fired\":0,\"inhibitory\":0,\"layer_id\":1}"
wt_stage("[]", "[" + rec + "]")
}
// The drain
// wt_drain coalesce every staged delta into ONE load-merge against the owner.
//
// Returns: nodes_added on success (>= 0), 0 when there was nothing to do, and
// -1 when the push FAILED. -1 is load-bearing: on failure the spool files are
// left untouched, so nothing is lost and the next drain retries them. A caller
// must never read a non-negative return as "my particular node is durable"
// use wt_durable(id) for that.
//
// Concurrency: several threads may drain at once. Each builds its own batch file
// (uuid-named), and overlapping batches are harmless because load-merge dedups.
// Files are truncated ONLY after a confirmed ok:true, so a lost race costs a
// redundant push, never a dropped write.
fn wt_drain() -> Int {
if !wt_enabled() { return 0 }
let dir: String = wt_spool_dir()
if str_eq(dir, "") { return 0 }
// el_list_len/el_list_get, NOT json_stringify(fs_list(...)): fs_list builds
// a native list via el_list_append, and json_stringify does not serialize
// that type it renders the raw pointer value. (Verified in isolation; the
// same latent defect is live in studio.el's /api/tools/file/list route,
// which returns e.g. {"entries":4386409744}. Noted, not fixed here.)
let listing = fs_list(dir)
let count: Int = el_list_len(listing)
if count == 0 { return 0 }
let nodes_acc: String = ""
let edges_acc: String = ""
let drained: String = ""
let found: Int = 0
let i: Int = 0
// No `continue` / `break`: elc lists them as keywords but not one line of
// the shipped soul uses either, so they are unexercised on this build path.
// Guard conditions are expressed as nested ifs instead, and every rebind is
// at the loop-body top level where `let x = ...` is assignment (the idiom
// memory.el's boot-counter loop relies on) never inside a nested block,
// where it would shadow instead.
while i < count {
let name: String = el_list_get(listing, i)
// A delta is only usable when it ends with the closing "]}" that
// wt_stage writes last. fs_write is not atomic, so a file being written
// right now can be observed half-formed; requiring the terminator means
// it is picked up whole on the next drain instead of merged as garbage.
// An empty read means "already drained and truncated" not an error.
let p: String = if str_starts_with(name, "wt-") { dir + "/" + name } else { "" }
let raw: String = if str_eq(p, "") { "" } else { wt_read(p) }
let usable: Bool = !str_eq(raw, "") && str_ends_with(raw, "]}")
let nj: String = if usable { wt_inner(json_get_raw(raw, "nodes")) } else { "" }
let ej: String = if usable { wt_inner(json_get_raw(raw, "edges")) } else { "" }
let nodes_acc = if str_eq(nj, "") { nodes_acc } else if str_eq(nodes_acc, "") { nj } else { nodes_acc + "," + nj }
let edges_acc = if str_eq(ej, "") { edges_acc } else if str_eq(edges_acc, "") { ej } else { edges_acc + "," + ej }
let drained = if !usable { drained } else if str_eq(drained, "") { p } else { drained + "\n" + p }
let found = if usable { found + 1 } else { found }
let i = i + 1
}
if found == 0 { return 0 }
let combined: String = "{\"nodes\":[" + nodes_acc + "],\"edges\":[" + edges_acc + "]}"
let batch: String = dir + "/wtb-" + uuid_v4() + ".json"
fs_write(batch, combined)
if str_eq(wt_read(batch), "") {
println("[persist] wt_drain: could not write batch file " + batch + "" + int_to_str(found) + " deltas stay queued")
return -1
}
let url: String = wt_engram_url()
let key: String = wt_api_key()
let body: String = "{\"path\":\"" + wt_esc(batch) + "\",\"_auth\":\"" + wt_esc(key) + "\"}"
let resp: String = http_post_json(url + "/api/load-merge", body)
// The batch file is pure scratch the retry is rebuilt from the SPOOL, not
// from it. Truncate it unconditionally, before branching on the outcome, so
// a persistently unreachable owner cannot accumulate one husk per attempt.
fs_write(batch, "")
// Distinguish the two failures rather than collapsing them: "cannot reach
// the owner" and "the owner refused this delta" need different human
// responses, and a log line that says the wrong one costs a debugging hour.
// curl surfaces transport errors as a JSON body, so an empty response is not
// the only unreachable signal.
// (str_contains rather than a strict parse on purpose the engram's HTTP
// responses have been observed carrying trailing bytes past the JSON.)
let unreachable: Bool = str_eq(resp, "")
|| str_contains(resp, "Couldn't connect")
|| str_contains(resp, "Failed to connect")
|| str_contains(resp, "Could not resolve")
|| str_contains(resp, "timed out")
if unreachable {
wt_sweep(dir)
println("[persist] wt_drain: owner UNREACHABLE at " + url + "" + int_to_str(found)
+ " deltas stay queued in " + dir + " (will retry): " + resp)
return -1
}
if !str_contains(resp, "\"ok\":true") {
wt_sweep(dir)
println("[persist] wt_drain: owner REJECTED the delta — " + int_to_str(found)
+ " stay queued in " + dir + ": " + resp)
return -1
}
let added: Int = json_get_int(resp, "nodes_added")
let added_e: Int = json_get_int(resp, "edges_added")
// Confirmed. Truncate the drained spool files so they are not re-pushed.
// Truncation (not deletion) because the runtime exposes no unlink builtin;
// an emptied file is inert to the loop above. The zero-byte husks are then
// swept below.
let paths = str_split(drained, "\n")
let pn: Int = el_list_len(paths)
let k: Int = 0
while k < pn {
let one: String = el_list_get(paths, k)
if !str_eq(one, "") { fs_write(one, "") }
let k = k + 1
}
wt_sweep(dir)
println("[persist] wt_drain: pushed " + int_to_str(found) + " deltas -> owner added "
+ int_to_str(added) + " nodes, " + int_to_str(added_e) + " edges")
return added
}
// wt_durable is this id present AT THE OWNER? The only honest answer to
// "did my write persist" in HTTP mode.
//
// In file mode the soul IS the owner, so the local read-back is the owner-side
// read-back and this collapses to the pre-existing check.
//
// nodes_added from wt_drain is NOT a substitute: a concurrent drain may have
// already pushed this node, making our own added count 0 while the node is
// perfectly durable. Presence at the owner is the fact; counts are telemetry.
fn wt_durable(id: String) -> Bool {
if str_eq(id, "") { return false }
if !wt_enabled() {
let local: String = engram_get_node_json(id)
return !str_eq(local, "") && !str_eq(local, "null") && !str_eq(local, "{}")
}
let url: String = wt_engram_url()
let resp: String = http_get(url + "/api/nodes/" + id)
if str_eq(resp, "") { return false }
if str_eq(resp, "{}") { return false }
return str_contains(resp, "\"id\"")
}
// wt_commit flush, then assert at the owner. The receipt callers should use.
// Deliberately NOT a fixed success shape: it can and does return false while the
// local write is perfectly fine in RAM, which is the true state of affairs when
// the owner is unreachable.
fn wt_commit(id: String) -> Bool {
if str_eq(id, "") { return false }
if !wt_enabled() {
let local: String = engram_get_node_json(id)
return !str_eq(local, "") && !str_eq(local, "null") && !str_eq(local, "{}")
}
let pushed: Int = wt_drain()
return wt_durable(id)
}
+45 -7
View File
@@ -186,7 +186,7 @@ fn route_imprint_contextual(body: String) -> String {
return "{\"ok\":false,\"error\":\"empty body\"}"
}
let tags: String = "[\"imprint\",\"contextual\"]"
let id: String = engram_node_full(
let id: String = wt_node(
body,
"Entity",
"imprint:contextual",
@@ -208,7 +208,7 @@ fn route_imprint_user(body: String) -> String {
return "{\"ok\":false,\"error\":\"empty body\"}"
}
let tags: String = "[\"imprint\",\"user\"]"
let id: String = engram_node_full(
let id: String = wt_node(
body,
"Entity",
"imprint:user",
@@ -239,7 +239,7 @@ fn route_synthesize(body: String) -> String {
}
let req: String = "synthesize " + parent_a + " " + parent_b
let tags: String = "[\"soul-inbox-pending\",\"synthesis-request\"]"
engram_node_full(
wt_node(
req,
"Entity",
"synthesis-request",
@@ -395,7 +395,28 @@ fn handle_connectors(method: String, clean: String, body: String) -> String {
return "{\"ok\":false,\"error\":\"unknown connectors route\"}"
}
// handle_request the soul's HTTP entry point.
//
// NOTE ON THE NAME (neuron#117): the el runtime resolves this handler by NAME
// via dlsym(RTLD_DEFAULT, "handle_request") that is why the Linux build must
// link -rdynamic. So the dispatcher body moved to route_dispatch and the name
// `handle_request` stays put as a thin wrapper. Do not rename it back.
//
// The wrapper exists to give the write-through boundary a guaranteed flush
// point. route_dispatch returns from ~60 places; a per-branch flush would be
// forgotten on the 61st. Draining here means EVERY request that staged a write
// pushes it before the connection closes, whatever route produced it, including
// routes added later that know nothing about persistence.
//
// wt_drain is a no-op (no HTTP, no cost) when nothing is staged and when the
// soul is not in HTTP-engram mode, so this is free on read traffic.
fn handle_request(method: String, path: String, body: String) -> String {
let resp: String = route_dispatch(method, path, body)
let flushed: Int = wt_drain()
return resp
}
fn route_dispatch(method: String, path: String, body: String) -> String {
let clean: String = strip_query(path)
// ACTIVITY STAMP (2026-07-30 self-review): every inbound HTTP request
@@ -432,10 +453,27 @@ fn handle_request(method: String, path: String, body: String) -> String {
return engram_scan_nodes_json(9999, 0)
}
if str_eq(clean, "/api/graph/edges") {
// TODO(reliability #8): engram_save races with awareness loop mem_save().
// Both now use atomic write-to-temp+rename (el_runtime.c). Serialised
// by engram_global_mu. Future: add engram_edges_json() builtin.
let snap_path: String = env("HOME") + "/.neuron/engram/snapshot.json"
// FIXED (neuron#117): this GET used to engram_save() straight over
// ~/.neuron/engram/snapshot.json a READ route, in a process that is
// NOT the persistence owner, overwriting the owner's canonical file
// on every call. It broke soul.el:571-573 ("the soul must NEVER write
// to the local snapshot") and it is the same defect class Will removed
// from the engram itself in el `dc39a61` ("stop read routes clobbering
// canonical snapshot"), where route_scan_edges/route_sync were moved
// to scratch paths for exactly this reason. It was also the race the
// old TODO(reliability #8) admitted to.
//
// Export to a scratch path instead. Same response, no canonical write.
// The soul's own snapshot writes are otherwise already gated behind
// state key "soul_snapshot_path", which is set ONLY in the genesis
// file-mode branch (soul.el: is_genesis && safe_to_seed, and
// safe_to_seed is unconditionally false when ENGRAM_URL is set) so
// after this change the soul writes nothing at all in HTTP mode.
// Future: add an engram_edges_json() builtin and drop the file round
// trip entirely.
let scratch_dir: String = env("TMPDIR")
let scratch_base: String = if str_eq(scratch_dir, "") { "/tmp" } else { scratch_dir }
let snap_path: String = scratch_base + "/soul-edges-export-" + state_get("soul_cgi_id") + ".json"
engram_save(snap_path)
let snap: String = fs_read(snap_path)
let edges_raw: String = json_get_raw(snap, "edges")
+1 -1
View File
@@ -204,7 +204,7 @@ fn safety_log_bell(level: String, reason: String, input_summary: String) -> Stri
// Emit a fallback println so the bell event leaves at least a log trace even
// when engram is degraded. This does not replace engram persistence -- it is a
// last-resort audit trail when the primary write cannot be confirmed.
let node_id: String = engram_node_full(
let node_id: String = wt_node(
content,
"BellEvent",
"bell:" + level,
+7 -7
View File
@@ -87,7 +87,7 @@ fn session_create(body: String) -> String {
let folder: String = json_get(body, "folder")
let content: String = session_make_content(id, title, ts, ts, folder)
let tags: String = "[\"session\",\"session:meta\",\"Conversation\"]"
let node_id: String = engram_node_full(
let node_id: String = wt_node(
content, "Conversation", "session:meta",
el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
"Episodic", tags
@@ -358,7 +358,7 @@ fn session_update_patch(session_id: String, body: String) -> String {
let created_int: Int = str_to_int(old_created)
let new_content: String = session_make_content(session_id, eff_title, created_int, ts, eff_folder)
let tags: String = "[\"session\",\"session:meta\",\"Conversation\"]"
let new_node_id: String = engram_node_full(
let new_node_id: String = wt_node(
new_content, "Conversation", "session:meta",
el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
"Episodic", tags
@@ -456,7 +456,7 @@ fn session_hist_save(session_id: String, hist: String) -> Void {
// TODO(reliability #7): delete-then-insert is not atomic concurrent saves for the
// same session can produce orphan history nodes. State is primary truth; engram fallback.
let tags: String = "[\"session\",\"session-history\",\"Conversation\"]"
let discard: String = engram_node_full(
let discard: String = wt_node(
hist, "Conversation", "session:messages:" + session_id,
el_from_float(0.6), el_from_float(0.6), el_from_float(0.9),
"Episodic", tags
@@ -488,7 +488,7 @@ fn session_hist_save(session_id: String, hist: String) -> Void {
+ " | ts:" + int_to_str(ts_now)
let summary_tags: String = "[\"session-emotional-summary\",\"affective\",\"bell:" + eff_level + "\",\"BellEvent\"]"
let summary_sal: String = if str_eq(eff_level, "hard") { el_from_float(0.95) } else { el_from_float(0.85) }
let sum_discard: String = engram_node_full(
let sum_discard: String = wt_node(
summary_content,
"BellEvent",
"session:emotional-summary",
@@ -529,7 +529,7 @@ fn session_hist_save(session_id: String, hist: String) -> Void {
if !str_eq(ot_id, "") { engram_forget(ot_id) }
let oti = oti + 1
}
let discard_topic: String = engram_node_full(
let discard_topic: String = wt_node(
topic_content, "Conversation", topic_label,
el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
"Episodic", topic_tags
@@ -582,7 +582,7 @@ fn session_update_meta_timestamp(session_id: String) -> Void {
let created_int: Int = str_to_int(old_created)
let new_content: String = session_make_content(session_id, old_title, created_int, ts, old_folder)
let tags: String = "[\"session\",\"session:meta\",\"Conversation\"]"
let new_id: String = engram_node_full(
let new_id: String = wt_node(
new_content, "Conversation", "session:meta",
el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
"Episodic", tags
@@ -629,7 +629,7 @@ fn session_auto_title(session_id: String, first_message: String) -> Void {
let created_int: Int = str_to_int(old_created)
let new_content: String = session_make_content(session_id, new_title, created_int, ts, old_folder)
let tags: String = "[\"session\",\"session:meta\",\"Conversation\"]"
let new_id: String = engram_node_full(
let new_id: String = wt_node(
new_content, "Conversation", "session:meta",
el_from_float(0.7), el_from_float(0.7), el_from_float(0.9),
"Episodic", tags
+17
View File
@@ -657,6 +657,23 @@ if is_genesis && safe_to_seed {
}
}
// CRASH RECOVERY (neuron#117). Deltas the previous process staged but could not
// hand to the owner are still on disk the spool is a filesystem queue, not a
// memory buffer, precisely so that a soul that died mid-flight does not take its
// unpushed writes with it. Drain them before serving, so recovered memories are
// durable and recallable from the owner from the first request onward.
//
// Safe on a clean boot: an empty spool means no HTTP call at all. Safe in file
// mode: wt_drain returns immediately when ENGRAM_URL is unset.
let wt_recovered: Int = wt_drain()
if wt_recovered > 0 {
println("[soul] write-through: recovered " + int_to_str(wt_recovered)
+ " nodes from a previous process's spool -> persistence owner")
}
if wt_recovered < 0 {
println("[soul] write-through: spool present but the persistence owner is unreachable — queued, will retry on heartbeat")
}
println("[soul] serving on port " + int_to_str(port))
http_serve_async(port, "handle_request")
println("[soul] awareness loop starting")
+2 -2
View File
@@ -11,7 +11,7 @@ import "memory.el"
fn steward_log_event(kind: String, detail: String) -> Void {
let content: String = "STEWARD:" + kind + " | " + detail
let tags: String = "[\"stewardship\",\"steward:" + kind + "\"]"
let discard: String = engram_node_full(
let discard: String = wt_node(
content,
"StewardshipEvent",
"steward:" + kind,
@@ -221,7 +221,7 @@ fn steward_fingerprint_session(input: String, session_id: String) -> String {
+ " formality=" + fs_str
+ " time=" + tb_str
let sample_tags: String = "[\"behavior\",\"BehaviorSample\",\"stewardship\"]"
let discard: String = engram_node_full(
let discard: String = wt_node(
sample_content,
"BehaviorSample",
"behavior:" + session_id,
-147
View File
@@ -1,147 +0,0 @@
# Retrieval eval harness
Measures Neuron's memory retrieval so a change can be shown to help before it is
believed to help. Nothing else on the memory roadmap should ship without a run
through this.
```
tools/retrieval-eval/run_comparison.sh --baseline main --candidate <branch>
```
That builds a soul from each ref, boots each in isolation on a fixed corpus,
runs the gold set three times per ref, and prints a table plus a verdict that
refuses to call a difference real if it is inside the noise band.
## What was reused
This is not a new idea, it is the missing third of an existing one.
| Prior work | What it gave | What was missing |
|---|---|---|
| `docs/research/graphrag_eval/` (`collect.py`, `score.py`, 2026-06-08) | The three-retriever comparison that produced the numbers everyone quotes: substring 1.7% P@5, graph 21.7%, BM25 55%. Per-query relevant-id scoring, fixed-denominator precision@5, unique-relevant analysis. | 13 hand-written queries, judged by an LLM after the fact; measured the *live* soul on the *live* engram. |
| `docs/research-archive/p0-prototypes/eval_pinned_40q_20260715.py` | The pinned-query discipline: ground truth committed as regexes so every run judges alike, plus a `--check` winnability gate. 40 queries in 5 bands including a deliberate paraphrase-hard band. | Scored offline replicas of substring/BM25 — it never ran the real retrieval path. |
| `docs/research-archive/p0-prototypes/stage0_eval_20260714.py` | The `hit@5` metric and the substring/BM25 reference implementations. | Same: offline only. |
| `scripts/verify-soul-contract.sh` | The isolation recipe, verbatim: throwaway port, throwaway `HOME`, `SOUL_ENGRAM_PATH`, and the non-obvious `SOUL_ISE_URL` pin that stops an "isolated" soul silently syncing the operator's live brain. | It is a contract gate, not a measurement. |
| `_engine-liveness-91/gen-soul-amalgam.sh` + `.gitea/workflows/ci.yaml` | The build recipe (`elc --target=c` with every `.elh` on the import chain removed) and CI's exact compile flags. | — |
**Reused directly:** the isolation recipe, the build recipe, fixed-denominator
precision@5, the pinned-ground-truth and winnability ideas.
**New here:** ids rather than regexes as ground truth, an associative category
derived from real graph edges, a superseded/contradicted category scored on
ranking, a machine-checked zero-lexical-overlap guarantee on paraphrases,
paired significance testing, and — the point — measurement against the **real
compiled soul** rather than an offline replica of one leg of it.
## Design fit
The thing under measurement is Will's designed retrieval: spreading activation
over the weighted directed graph, four-factor multiplicative scoring (parent
strength x edge weight x target salience x query/target cosine). A Python
re-implementation would measure my reading of the design. So the harness
compiles the actual `soul.el` amalgam and asks it over HTTP on
`/api/neuron/recall`, exactly as the MCP wrapper and the app do.
## Files
| File | Does |
|---|---|
| `build_gold_set.py` | Derives and **validates** the gold set from the corpus. `--check` re-validates and exits non-zero if a query became unwinnable or a paraphrase leaked a word. |
| `gold_set.json` | 38 queries. Every one carries a `derivation` string. |
| `run_eval.py` | Boots one soul in isolation, runs the gold set, writes metrics. Kills and **confirms dead** its child; records the confirmation in the results file. |
| `compare.py` | Paired diff of two result files with McNemar's exact test and a stated noise floor. |
| `build-soul.sh` | Compiles a soul binary from a plain source tree. |
| `run_comparison.sh` | All of the above, end to end, from two git refs. |
## The gold set — 38 queries
Built from the real corpus (`snapshot-pre-repair-20260806.json`, 78,768 nodes /
14,214 edges) so it reflects one person's accumulating memory, not document QA.
| Category | n | Expected answer derived by |
|---|---|---|
| `exact_rare` | 6 | **Mined.** Tokens with document frequency 1 across all 78,768 nodes, whose single containing node is a 3006000 char Memory/Knowledge/Belief. That node is the only possible answer. Re-verified every build. |
| `phrase` | 7 | **Mined.** Case-insensitive verbatim scan; the matching set *is* the answer key. Phrases matching >25 nodes are rejected as too diffuse. |
| `paraphrase` | 13 | **Hand-selected, machine-checked.** Target locked by id; the build then proves that **zero** content words of the query appear anywhere in the target's label, content, or tags. A leak fails the build — the category cannot quietly decay into lexical matching. |
| `associative` | 6 | **Derived from edges.** Query built from one value node's distinctive vocabulary; expected answers are its siblings on the `Self - Values (grounded)` hub. Siblings sharing any query word are dropped, so the only route from query to answer is seed -> hub -> sibling. |
| `nonsense` | 3 | **Control.** Verified that no token occurs anywhere in the corpus. Correct behaviour is to return nothing. |
| `superseded` | 3 | **Derived.** Correction/stale pairs located by regex scan, kept only when both sides resolve to different surviving nodes. Scored on **ranking**: the correction must be returned *and* rank above the stale node. |
## Metrics
`hit@5`, `recall@5`, `recall@10`, `precision@5` (fixed denominator 5, so an
empty result is punished like a page of junk), `MRR@10`, and wall-clock latency
per query (p50/p95/max). Output is a table plus a machine-readable JSON per run
so runs can be diffed.
## Honesty about noise
- **Minimum detectable swing on this 38-query set: 6 queries.** If every query
that changes changes the same way, `p = 2 x 0.5^n`, which first drops under
0.05 at n=6. Any net change smaller than that is inside the noise band and
`compare.py` says so in those words.
- **Run-to-run drift is measured, not assumed.** Activation is a stateful read
by design (traversal reinforces what it touches), so identical inputs need not
give identical outputs. Observed: `main` 0 queries of drift across 3 runs
(fully deterministic); the activation branch 1 query.
- The noise floor used for the verdict is `max(6, observed_drift + 1)`.
- **This gold set is underpowered for small effects.** A genuine 3-query
improvement would not clear the bar. Growing the set is the fix; until then, a
small positive delta means "not shown", not "no effect".
## First result: `main` vs `feat/recall-through-activation`
Corpus and gold set identical, three runs each, fresh corpus copy per run.
| | main | recall-through-activation | delta |
|---|---|---|---|
| hit@5 | 34.3% | 22.9% | **-11.4pp** |
| recall@5 | 26.9% | 19.1% | -7.9pp |
| recall@10 | 33.3% | 24.3% | -9.1pp |
| precision@5 | 12.0% | 7.4% | -4.6pp |
| MRR@10 | 0.294 | 0.242 | -0.053 |
| latency p50 | 1140 ms | 3209 ms | **2.81x** |
| latency p95 | 1584 ms | 4852 ms | 3.06x |
| nonsense clean | 2/3 | 2/3 | — |
| superseded outranks | 1/3 | 0/3 | -1 |
By category (hit@5):
| category | main | activation |
|---|---|---|
| exact_rare | 100% | 100% |
| phrase | 85.7% | **28.6%** |
| paraphrase | 0% | 0% |
| associative | 0% | 0% |
| superseded | 0% | 0% |
**Verdict: directionally worse, one query short of significant.** 5 discordant
pairs, all 5 against the candidate, 0 for it. McNemar exact p = 0.0625 — under
the stated rule that is *inside* the noise band, so the harness reports "no
measurable difference" on accuracy and the honest summary is "5 for 5 the wrong
way, needs a 6th or a larger gold set to call".
Latency is a different story: 2.8x at p50 is deterministic and far outside any
noise band. That regression is real.
The result the branch was written for did not appear. Its stated purpose was to
recover sibling nodes one hub-hop away — the `associative` category — and that
category is **0/6 on both builds**. Probing directly: for the query
`Marines hernia sepsis medical ward`, the activation build returns the lexical
seed node itself at rank 8, and none of its 12 hub siblings anywhere in the top
10. The traversal is running; it is not reaching siblings.
Two corpus facts likely explain it, and both are measurable rather than
speculative:
1. **The graph is nearly edgeless.** Only 4,060 of 78,768 nodes (5.2%) carry any
edge at all — 14,214 edges total, 0.18 per node. Spreading activation over a
graph with no edges is an expensive way to do lexical matching, which is
roughly what the numbers show.
2. **No embeddings.** No node in this snapshot has an embedding field, so the
fourth factor of the four-factor product — query/target cosine similarity —
has nothing to compute from, and the semantic seeding pass is inert.
That is the harness earning its keep on its first job: the change would have
felt like progress (it is the designed mechanism, and it does run) and measures
as a regression on phrase queries plus a 2.8x latency cost, with its intended
benefit unrealised because the corpus lacks the structure it needs.
-44
View File
@@ -1,44 +0,0 @@
#!/usr/bin/env bash
# build-soul.sh — compile a soul binary from a plain source tree (no git needed).
#
# Reuses the amalgam recipe worked out in gen-soul-amalgam.sh (round 9.1) and the
# compile flags from .gitea/workflows/ci.yaml, so the binary under test is the
# same translation unit CI ships — not a re-implementation.
#
# elc --target=c emits only an extern prototype for any module that has a .elh
# header beside it, and inlines the module's bodies when it does not. So the
# amalgam is produced in a scratch copy with every .elh on the import chain
# deleted.
#
# usage: build-soul.sh <src-tree-with-*.el> <out-binary>
set -euo pipefail
SRC="${1:?usage: build-soul.sh <src-tree> <out-binary>}"
OUT="${2:?out-binary}"
ELC="${ELC:-$HOME/neuron-dev-stack/src/el/lang/dist/platform/elc}"
EL_REPO="${EL_REPO:-$HOME/Development/neuron-technologies/el}"
RTDIR="${RTDIR:-$SRC/vendor/el-runtime/v1.0.0-20260501}"
SSL="${SSL_PREFIX:-/opt/homebrew/opt/openssl@3}"
[ -x "$ELC" ] || { echo "no elc at $ELC" >&2; exit 2; }
[ -f "$RTDIR/el_runtime.c" ] || { echo "no el_runtime.c at $RTDIR" >&2; exit 2; }
GEN="$(mktemp -d "${TMPDIR:-/tmp}/soul-build.XXXXXX")"
trap 'rm -rf "$GEN"' EXIT
mkdir -p "$GEN/neuron" "$GEN/foundation/el/elp/src"
cp "$SRC"/*.el "$GEN/neuron/"
cp "$EL_REPO"/elp/src/*.el "$GEN/foundation/el/elp/src/"
find "$GEN" -name '*.elh' -delete
( cd "$GEN/neuron" && "$ELC" --target=c soul.el ) > "$GEN/soul.c"
BODIES=$(grep -c '^el_val_t .*) {$' "$GEN/soul.c" || true)
echo "[build-soul] amalgam $(wc -c < "$GEN/soul.c" | tr -d ' ') bytes, ${BODIES} inlined bodies"
[ "$BODIES" -ge 1200 ] || { echo "[build-soul] FAIL: only $BODIES bodies — an import was not inlined"; exit 1; }
cc -O2 -DHAVE_CURL -rdynamic \
-I"$RTDIR" -I"$SSL/include" -L"$SSL/lib" \
"$GEN/soul.c" "$RTDIR/el_runtime.c" \
-lssl -lcrypto -lcurl -lpthread -lm \
-o "$OUT" 2> "$GEN/cc.log" || { echo "[build-soul] FAIL compile"; tail -40 "$GEN/cc.log"; exit 1; }
if grep -qE 'implicit.*(engram_|el_)' "$GEN/cc.log"; then
echo "[build-soul] FAIL: implicit declarations of runtime symbols"; grep -E 'implicit' "$GEN/cc.log" | head; exit 1; fi
echo "[build-soul] OK -> $OUT ($(wc -c < "$OUT" | tr -d ' ') bytes)"
-506
View File
@@ -1,506 +0,0 @@
#!/usr/bin/env python3
"""
build_gold_set.py derive the retrieval gold set FROM the corpus, and validate it.
WHY THIS FILE EXISTS AS CODE AND NOT AS A HAND-WRITTEN JSON
A gold set nobody can audit is vibes with extra steps. Every expected answer
here is either (a) mined from the corpus by a rule this script re-runs, or
(b) hand-selected with a stated criterion that this script then CHECKS
against the corpus. Both leave a `derivation` string on every query, and the
checks are re-run on demand so the set cannot silently rot as the corpus
changes.
Lineage: this extends the pinned-query approach from
docs/research-archive/p0-prototypes/eval_pinned_40q_20260715.py (pinned
ground-truth patterns + a --check "winnability" gate) and the per-query
relevant-id scoring from docs/research/graphrag_eval/score.py. What is new:
ids as ground truth rather than regexes alone, an ASSOCIATIVE category
derived from real graph edges, a superseded/contradicted category, and a
machine-checked no-lexical-overlap guarantee on the paraphrase category.
THE SIX CATEGORIES, AND WHAT EACH ONE IS FOR
exact_rare a single rare word. Substring matching already wins these.
They are a REGRESSION GUARD: any change that loses them is
disqualified regardless of what else it gains.
phrase a multi-word string that exists verbatim in the corpus.
Guards multi-token queries, which the old substring matcher
handled by returning nothing.
paraphrase same meaning, ZERO shared content words with the target node.
THE CATEGORY THAT MATTERS. Mechanically unreachable by string
matching; reachable only by semantics or by association.
associative the answer is one hub-hop from an obvious starting point and
shares no words with the query. This is the case the graph is
supposed to buy: query one value, get its siblings.
nonsense must return nothing. Guards against a retriever that "improves"
recall by returning the whole graph.
superseded a fact that was later corrected. The correction must OUTRANK
the stale version ranking, not mere presence.
usage:
python3 build_gold_set.py <snapshot.json> [--out gold_set.json] [--check]
--check re-validates an existing gold_set.json against the corpus and exits
non-zero if any query became unwinnable or any paraphrase leaked a word.
"""
import argparse
import json
import os
import re
import sys
from collections import Counter, defaultdict
HERE = os.path.dirname(os.path.abspath(__file__))
DEFAULT_OUT = os.path.join(HERE, "gold_set.json")
TOKEN = re.compile(r"[a-z0-9][a-z0-9\-']*")
# Stopwords are deliberately generous. A paraphrase query is only interesting if
# its CONTENT words are absent from the target; "the", "is", "what" appearing in
# both proves nothing. Being generous here makes the overlap test STRICTER on
# the words that carry meaning, which is the conservative direction.
STOP = set("""
a about above after again against all also am an and any are aren't as at be because been
before being below between both but by can can't cannot could couldn't did didn't do does
doesn't doing don't down during each few for from further had hadn't has hasn't have haven't
having he her here hers herself him himself his how i if in into is isn't it its itself just
me more most my myself no nor not of off on once only or other others ought our ours ourselves
out over own same shan't she should shouldn't so some such than that the their theirs them
themselves then there these they this those through to too under until up very was wasn't we
were weren't what when where which while who whom why will with won't would wouldn't you your
yours yourself yourselves get gets got make makes made take takes use uses used way ways thing
things does doing done keep keeps kept go goes going come comes came one two something anything
""".split())
# ─────────────────────────────────────────────────────────────────────────────
# corpus helpers
# ─────────────────────────────────────────────────────────────────────────────
def load_corpus(path):
with open(path, encoding="utf-8", errors="replace") as fh:
data = json.load(fh)
nodes = [n for n in data.get("nodes", []) if isinstance(n, dict) and n.get("id")]
edges = [e for e in data.get("edges", []) if isinstance(e, dict)]
return nodes, edges
def doctext(n):
return " ".join([str(n.get("label") or ""), str(n.get("content") or ""), str(n.get("tags") or "")])
def content_tokens(s):
return {t for t in TOKEN.findall(s.lower()) if t not in STOP and len(t) > 2}
# ─────────────────────────────────────────────────────────────────────────────
# hand-authored queries. Every entry states HOW its expected answer was chosen.
# The `check` field names the validation this script runs against the corpus.
# ─────────────────────────────────────────────────────────────────────────────
# EXACT_RARE — mined, not chosen. The rule (re-run by mine_exact_rare below):
# tokens whose document frequency across the whole corpus is 1, whose single
# containing node is a Memory/Knowledge/Belief with 300-6000 chars of content
# (so the answer is a real memory, not a 117KB whitepaper that contains every
# word in English), and whose token is plain lowercase alphabetic. The expected
# answer is that one node — it is the only node that can possibly be correct.
EXACT_RARE_SEEDS = [
"unjailbreakable",
"engram-migrate",
"cartabandonedevent",
"pre-apprenticeship",
"inferencenodemanager",
"clear-eyed",
]
# PHRASE — chosen by reading the corpus for phrases that (a) occur verbatim,
# (b) occur in a small enough set of nodes that "relevant" is well defined.
# Expected answers are computed here as EVERY node whose text contains the
# phrase case-insensitively — so the answer set is a fact about the corpus, not
# an opinion. Queries whose phrase matches more than PHRASE_MAX nodes are
# rejected by validation as too diffuse to score.
PHRASE_MAX = 25
PHRASE_SEEDS = [
("patterns not returns",
"a verbatim correction Will issued; expected = every node containing the phrase"),
("thirty moves",
"the canonical biographical phrase; expected = every node containing it"),
("Grandma Lucas",
"a named person appearing verbatim in the biography/value nodes"),
("Directed Harmonic",
"the canonical DHARMA expansion, confirmed by Will April 24 2026"),
("Sarah Bishop",
"a named person; rare enough that the answer set is unambiguous"),
("Directed Autonomous Runtime Modification",
"the DARMA expansion, quoted verbatim in the backlog item and its correction"),
("zero-knowledge encrypted backup",
"the paid-tier feature name as written in the roadmap nodes"),
]
# PARAPHRASE — hand-authored. THE SELECTION CRITERION, stated once and applied
# to all nine: pick a node whose SUBJECT is unmistakable to a reader, then write
# the query a person would actually type when they remember the subject but not
# the words. The target is then LOCKED by id, and this script enforces the hard
# property that makes the category meaningful: not one content word of the query
# appears anywhere in the target node's label, content, or tags. If a word
# leaks, validation fails and the query must be rewritten — the set cannot
# quietly degrade into a lexical query wearing a paraphrase costume.
PARAPHRASE_SEEDS = [
("kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
"the elderly relative who passed while he stayed away",
"target: 'Value - Do the Essential Thing While You Can', whose subject is Grandma Lucas "
"dying in Feb 2006 without Will saying goodbye. Query names the event with none of the "
"node's own vocabulary."),
("kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
"a soldier sidelined by illness who refused to quit",
"target: 'Value - Survival Is Not an Excuse to Stop', whose subject is enlisting in the "
"Marines, a severe hernia, and sepsis. Query describes the episode obliquely."),
("kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
"choosing an uncomfortable fact over a pleasant fiction",
"target: 'Value - Honesty Before Comfort'. Query states the principle in wholly "
"different words."),
("kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
"a tight payload beats a bloated one",
"target: 'Value - Precision Over Brute Force'. Query restates the claim with no "
"shared vocabulary."),
("kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
"if you are able and nobody is coming the job is yours",
"target: 'Value - Capability Is a Debt You Owe the Moment'. Query states the "
"obligation without the node's terms."),
("kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
"learning is the wealth creditors cannot seize",
"target: 'Value - Knowledge Survives When Nothing Else Does', whose subject is the "
"library following Will across 30+ moves."),
("kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
"reliability proven by track record not assertion",
"target: 'Value - Earned Trust' ('Trust is demonstrated, not declared')."),
("kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
"boundaries that enable instead of confine",
"target: 'Value - Constraints as Freedom'. Query is a restatement of the same claim."),
("kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
"what shifts tells you where to cut a system apart",
"target: 'Value - Change Is the Signal', the value VBD is built on."),
("kn-f230b362-b201-4402-9833-4160c89ab3d4",
"a mind that compounds instead of resetting each day",
"target: 'Value - The System Must Accumulate'. Query is the accumulation claim in "
"different vocabulary."),
("kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
"loved for the unedited self and not the polished exterior",
"target: 'Value - Being Seen Is Rarer Than Being Known', whose subject is Sarah Bishop "
"as the first person Will did not perform for."),
("kn-e0423482-cfa5-4796-8689-8495c93b66bc",
"cheerfulness you arrive at instead of assuming",
"target: 'Value - Hope Is a Conclusion'. Query restates 'a conclusion, not a premise'."),
("kn-6061318f-046b-4935-907d-8eafdce14930",
"a childhood offering no solid foundation to inherit",
"target: 'Value - Structure Is Not Inherited', whose subject is thirty moves between "
"two parents' collapses."),
]
# ASSOCIATIVE — derived from real edges, not authored. The construction:
# every value node hangs off the 'Self - Values (grounded)' hub by an `identity`
# edge. For a chosen value node V, the query is built from V's own distinctive
# vocabulary; the expected answers are V's SIBLINGS on that hub. A sibling
# shares no query words with the query by construction (validated below), so the
# only path from the query to a sibling is: lexical seed on V -> hub -> sibling.
# That is a two-hop traversal and nothing else can produce it.
VALUES_HUB = "kn-5b606390-a52d-4ca2-8e0e-eba141d13440"
ASSOCIATIVE_SEEDS = [
("kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71", "Grandma Lucas stroke February 2006 goodbye window"),
("kn-58874a74-b96f-4883-9e08-45707f4bd3ee", "Marines hernia sepsis medical ward"),
("kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e", "Sarah Bishop Dyer trailer performance"),
("kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83", "Swarm Architecture containment lateral worker"),
("kn-e0423482-cfa5-4796-8689-8495c93b66bc", "hope won inside the narrative preface"),
("kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8", "man of the house six years old expectation"),
]
# NONSENSE — must return nothing. Strings chosen to be lexically impossible:
# validation asserts each appears in ZERO corpus nodes as a substring and that
# none of its tokens appears anywhere either (so not even a partial seed exists).
NONSENSE_SEEDS = [
"zqxjvw plimforth grebulon",
"flarnbistle quommetry",
"xxqzzt vurblenacht throom",
]
# SUPERSEDED — a fact that was corrected. Chosen by searching the corpus for
# explicit correction language and keeping pairs where BOTH the stale statement
# and its correction exist as separate nodes. Scored on RANKING: the correction
# must appear, and must appear above the stale node. Ids are locked here and
# validated to exist and to match their stated role.
SUPERSEDED_SEEDS = [
# (query, correct_id, stale_id, derivation)
]
# ─────────────────────────────────────────────────────────────────────────────
# mining
# ─────────────────────────────────────────────────────────────────────────────
def mine_exact_rare(nodes, byid, seeds):
"""Re-derive: confirm each seed token still has df==1 and name its node."""
tok = re.compile(r"[A-Za-z][A-Za-z0-9\-]{4,}")
want = set(seeds)
df = Counter()
post = defaultdict(set)
for n in nodes:
for t in {w.lower() for w in tok.findall(doctext(n))}:
if t in want:
df[t] += 1
post[t].add(n["id"])
out = []
for s in seeds:
ids = sorted(post.get(s, ()))
out.append((s, ids, df.get(s, 0)))
return out
def phrase_matches(nodes, phrase):
p = phrase.lower()
return sorted(n["id"] for n in nodes if p in doctext(n).lower())
def hub_siblings(edges, hub, relation="identity"):
sibs = []
for e in edges:
if e.get("from_id") == hub and e.get("relation") == relation:
sibs.append(e["to_id"])
elif e.get("to_id") == hub and e.get("relation") == relation:
sibs.append(e["from_id"])
return list(dict.fromkeys(sibs))
def find_superseded_pairs(nodes, byid):
"""Locked pairs, each verified here to exist and to carry its stated marker.
Chosen by scanning the corpus for explicit correction language
(CORRECTION/SUPERSEDES/re-corrected/no longer/RECONCILED) and keeping only
cases where the STALE claim also survives as its own node a supersession
with nothing to outrank is not a ranking test.
"""
pairs = []
txt = {n["id"]: doctext(n) for n in nodes}
def find_one(pattern, exclude=()):
rx = re.compile(pattern)
return [n["id"] for n in nodes
if n["id"] not in exclude
and rx.search(txt[n["id"]])
and 150 < len(str(n.get("content") or "")) < 12000
and n.get("node_type") in ("Memory", "Knowledge", "Belief", "BacklogItem")]
# Each entry: (query, correction-pattern, stale-pattern, why).
# The stale side is searched with the correction hits EXCLUDED, because most
# correction memories quote the claim they are killing — without the
# exclusion the "stale" node resolves to the correction itself and the pair
# collapses into a no-op. A pair is only emitted if both sides resolve to
# DIFFERENT surviving nodes; otherwise it is dropped and reported.
SPECS = [
("is the self-improvement architecture called DARMA or DHARMA",
r'(?i)CORRECTION:.{0,90}DHARMA .{0,12}not DARMA',
r'(?i)\bDARMA\b',
"correction node is Will's confirmation that the H is intentional (DHARMA, not DARMA); "
"the stale node is the surviving backlog item still titled 'Implement DARMA'."),
("how many provisional patents does Will actually have",
r'(?i)EXACTLY 6 (fully-specced )?provisional',
r'(?i)(MY ARCHITECTURE = 12 filed patents|\b12 filed patents\b)',
"correction node is the 2026-06-17 confabulation flag establishing EXACTLY 6 provisionals; "
"the stale node is the surviving memory that asserts 12 filed patents."),
("is MCP still the live integration layer",
r'(?i)MCP RETIRED',
r'(?i)MCP server live at',
"correction node is the 'CGI ARCHITECTURE - THREE LAYERS, MCP RETIRED' decision of "
"April 30 2026; the stale node still records the MCP server as live."),
("what does the patterns-not-returns directive mean",
r'(?i)CORRECTION:.{0,80}patterns not returns',
r'(?i)established returns',
"correction node is Will's 'patterns not returns' correction; the stale node is a "
"surviving node carrying the misread 'established returns' directive."),
("was the earlier identity-bug finding correct",
r'(?i)SUPERSEDES the earlier .critical identity bug',
r'(?i)critical identity bug',
"correction node explicitly supersedes the 'critical identity bug' finding; the stale "
"node is the surviving original finding."),
("does Neuron have recursive self-improvement",
r'(?i)twice answered .Neuron has no recursive self-improvement',
r'(?i)no recursive self-improvement',
"correction node records the June-29 finding that the CGI provisional IS the "
"recursive-self-improvement mechanism; the stale node is the surviving denial."),
]
for query, cpat, spat, why in SPECS:
corr = find_one(cpat)
if not corr:
continue
stale = find_one(spat, exclude=set(corr))
if not stale:
continue
pairs.append((query, corr[0], stale[0], why))
return pairs
# ─────────────────────────────────────────────────────────────────────────────
# build
# ─────────────────────────────────────────────────────────────────────────────
def build(nodes, edges):
byid = {n["id"]: n for n in nodes}
tokset = {n["id"]: content_tokens(doctext(n)) for n in nodes}
queries = []
problems = []
qn = [0]
def add(cat, query, relevant, derivation, **extra):
qn[0] += 1
q = {
"id": f"q{qn[0]:02d}",
"category": cat,
"query": query,
"relevant": sorted(relevant),
"derivation": derivation,
}
q.update(extra)
queries.append(q)
return q
# --- exact_rare ---------------------------------------------------------
for tokname, ids, df in mine_exact_rare(nodes, byid, EXACT_RARE_SEEDS):
if df != 1 or len(ids) != 1:
problems.append(f"exact_rare '{tokname}': df={df}, ids={len(ids)} (expected df=1)")
continue
lab = (byid[ids[0]].get("label") or "")[:60]
add("exact_rare", tokname, ids,
f"MINED: token '{tokname}' has document frequency 1 over all {len(nodes)} corpus nodes "
f"(re-verified at build time). Its single containing node is {ids[0]} "
f"('{lab}'), which is therefore the only possible correct answer.")
# --- phrase -------------------------------------------------------------
for phrase, why in PHRASE_SEEDS:
ids = phrase_matches(nodes, phrase)
if not ids:
problems.append(f"phrase '{phrase}': 0 corpus matches — unwinnable")
continue
if len(ids) > PHRASE_MAX:
problems.append(f"phrase '{phrase}': {len(ids)} matches > {PHRASE_MAX} — too diffuse")
continue
add("phrase", phrase, ids,
f"MINED: {why}. Case-insensitive verbatim substring scan over label+content+tags at "
f"build time returns exactly {len(ids)} node(s); that set IS the answer key.")
# --- paraphrase ---------------------------------------------------------
for target, query, why in PARAPHRASE_SEEDS:
if target not in byid:
problems.append(f"paraphrase target {target} not in corpus")
continue
qt = content_tokens(query)
leak = sorted(qt & tokset[target])
if leak:
problems.append(f"paraphrase '{query}': leaks {leak} into target {target}")
continue
add("paraphrase", query, [target],
f"HAND-SELECTED with criterion: {why} VERIFIED at build time: of the {len(qt)} content "
f"words in the query, ZERO appear anywhere in the target's label, content, or tags — so "
f"no string-matching retriever can reach this answer.",
zero_overlap_verified=True, query_content_words=sorted(qt))
# --- associative --------------------------------------------------------
sibs = hub_siblings(edges, VALUES_HUB)
if len(sibs) < 5:
problems.append(f"associative: values hub {VALUES_HUB} has only {len(sibs)} siblings")
for src, query in ASSOCIATIVE_SEEDS:
if src not in byid or src not in sibs:
problems.append(f"associative source {src} not a sibling on {VALUES_HUB}")
continue
qt = content_tokens(query)
others = [s for s in sibs if s != src and s in byid]
# A sibling only counts as a legitimate expected answer if the query
# cannot reach it lexically. Drop any sibling that shares a content word.
clean = [s for s in others if not (qt & tokset[s])]
dropped = len(others) - len(clean)
if len(clean) < 5:
problems.append(f"associative '{query}': only {len(clean)} lexically-unreachable siblings")
continue
add("associative", query, clean,
f"DERIVED FROM EDGES: the query is built from the distinctive vocabulary of {src} "
f"('{(byid[src].get('label') or '')[:48]}'), which hangs off the values hub {VALUES_HUB} "
f"by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub "
f"({len(clean)} of {len(others)}; {dropped} dropped because they shared a query word and "
f"so were lexically reachable). Every remaining sibling shares ZERO content words with "
f"the query — the only route from query to answer is seed({src}) -> hub -> sibling, a "
f"two-hop traversal.",
associative_source=src, hub=VALUES_HUB, siblings_dropped_for_overlap=dropped)
# --- nonsense -----------------------------------------------------------
all_tokens = set()
for n in nodes:
all_tokens |= {t for t in TOKEN.findall(doctext(n).lower())}
for s in NONSENSE_SEEDS:
present = sorted(t for t in TOKEN.findall(s.lower()) if t in all_tokens)
if present:
problems.append(f"nonsense '{s}': tokens {present} DO occur in corpus")
continue
add("nonsense", s, [],
f"CONTROL: verified at build time that none of this string's tokens occurs anywhere in "
f"the corpus. Correct behaviour is to return NOTHING; any result is a false positive.",
expect_empty=True)
# --- superseded ---------------------------------------------------------
for query, correct, stale, why in find_superseded_pairs(nodes, byid):
if correct not in byid or stale not in byid:
problems.append(f"superseded '{query}': id missing from corpus")
continue
add("superseded", query, [correct],
f"DERIVED: {why} Scored on RANKING, not presence: the corrected node {correct} must be "
f"returned AND must rank above the stale node {stale}.",
must_outrank=[correct, stale],
stale_id=stale,
correct_label=(byid[correct].get("label") or "")[:70],
stale_label=(byid[stale].get("label") or "")[:70])
return queries, problems
def summarize(queries):
c = Counter(q["category"] for q in queries)
return ", ".join(f"{k}={c[k]}" for k in
("exact_rare", "phrase", "paraphrase", "associative", "nonsense", "superseded")
if c[k])
def main():
ap = argparse.ArgumentParser()
ap.add_argument("snapshot")
ap.add_argument("--out", default=DEFAULT_OUT)
ap.add_argument("--check", action="store_true",
help="validate only; do not write. Non-zero exit if anything is unwinnable.")
args = ap.parse_args()
nodes, edges = load_corpus(args.snapshot)
print(f"corpus: {len(nodes)} nodes, {len(edges)} edges ({os.path.basename(args.snapshot)})")
queries, problems = build(nodes, edges)
print(f"gold set: {len(queries)} queries [{summarize(queries)}]")
if problems:
print(f"\n{len(problems)} PROBLEM(S) — these queries were REJECTED, not silently kept:")
for p in problems:
print(" -", p)
if args.check:
sys.exit(1 if problems else 0)
doc = {
"corpus": os.path.abspath(args.snapshot),
"corpus_nodes": len(nodes),
"corpus_edges": len(edges),
"note": ("Every query carries a `derivation` recording how its expected answer was chosen. "
"Re-run with --check to re-validate the whole set against the corpus."),
"queries": queries,
}
with open(args.out, "w", encoding="utf-8") as fh:
json.dump(doc, fh, indent=1, ensure_ascii=False)
print(f"\nwrote {args.out}")
if __name__ == "__main__":
main()
-210
View File
@@ -1,210 +0,0 @@
#!/usr/bin/env python3
"""
compare.py diff two run_eval.py result files, WITH a noise threshold.
WHY THE STATISTICS ARE NOT OPTIONAL
With ~35 scored queries, one query is ~2.9 percentage points. A harness that
reports "hit@5 improved 2.9%" without saying that is one query is a harness
that will approve noise. So this file refuses to call anything an
improvement on the strength of the headline number alone. It reports:
1. The DISCORDANT PAIRS. Two configurations scored on the same queries are
paired data, so the only queries carrying information are the ones
where they disagree: b = fixed by B, c = broken by B. Queries both got
right, or both got wrong, tell you nothing about which is better.
2. McNEMAR'S EXACT TEST on (b, c). Under the null "the change is a coin
flip", the discordant outcomes are Binomial(b+c, 0.5). The two-sided
exact p-value is computed here with no scipy dependency.
3. The MINIMUM DETECTABLE SWING for this gold set: the smallest number of
net-changed queries that would reach p < 0.05 if every discordant pair
fell the same way. Anything smaller is inside the noise band, and the
verdict line says so in those words.
Repeat-run variance is the other half of honesty. Spreading activation is a
stateful read (it reinforces what it touches), so identical inputs need not
give identical outputs. Pass --repeats to fold several runs of the same
config into an observed variance band; a delta inside that band is not real
either, however good its p-value looks.
usage:
python3 compare.py --baseline results-main.json --candidate results-act.json
python3 compare.py --baseline a.json --candidate b.json \
--repeats-baseline a2.json a3.json --repeats-candidate b2.json b3.json
"""
import argparse
import json
from math import comb
def binom_two_sided(b, c):
"""Two-sided exact binomial p for b successes in n=b+c at p=0.5."""
n = b + c
if n == 0:
return 1.0
k = min(b, c)
tail = sum(comb(n, i) for i in range(0, k + 1)) / (2 ** n)
return min(1.0, 2 * tail)
def min_detectable_swing(n_scored, alpha=0.05):
"""Smallest all-one-way discordant count reaching p < alpha.
If every query that changes changes in the same direction, the p-value is
2 * 0.5**n. Solve for the smallest n where that drops under alpha. This is
the FLOOR: any real change will have some discordance both ways, so the true
requirement is larger. Reporting the floor is the conservative move it is
the most generous threshold we would ever accept.
"""
n = 1
while n <= n_scored:
if 2 * (0.5 ** n) < alpha:
return n
n += 1
return n_scored
def load(path):
with open(path, encoding="utf-8") as fh:
return json.load(fh)
def row_map(doc):
return {r["id"]: r for r in doc["rows"]}
def outcome(r):
"""Binary per-query outcome used for the paired test.
hit@5 for scored queries; 'returned nothing' for the nonsense controls;
'correction outranks the stale node' for the superseded queries. One number
per query, so every query votes exactly once.
"""
if "clean" in r:
return 1.0 if r["clean"] else 0.0
if "outranks" in r:
return 1.0 if r["outranks"] else 0.0
return r.get("hit@5") or 0.0
def band(values):
return (min(values), max(values))
def main():
ap = argparse.ArgumentParser()
ap.add_argument("--baseline", required=True)
ap.add_argument("--candidate", required=True)
ap.add_argument("--repeats-baseline", nargs="*", default=[])
ap.add_argument("--repeats-candidate", nargs="*", default=[])
ap.add_argument("--out", default=None)
args = ap.parse_args()
A, B = load(args.baseline), load(args.candidate)
ra, rb = row_map(A), row_map(B)
ids = [q for q in ra if q in rb]
n = len(ids)
aa, ab = A["aggregate"], B["aggregate"]
print(f"baseline {A['label']:14} soul={A['soul_md5'][:12]} {n} shared queries")
print(f"candidate {B['label']:14} soul={B['soul_md5'][:12]}")
print(f"corpus {A['corpus_nodes']} nodes / {A['corpus_edges']} edges "
f"(identical copy for both runs)\n")
metrics = [("hit@5", 1), ("recall@5", 1), ("recall@10", 1),
("precision@5", 1), ("mrr@10", 0)]
print(f" {'metric':14} {'baseline':>10} {'candidate':>10} {'delta':>10}")
for m, as_pct in metrics:
x, y = aa[m], ab[m]
if as_pct:
print(f" {m:14} {100*x:>9.1f}% {100*y:>9.1f}% {100*(y-x):>+9.1f}pp")
else:
print(f" {m:14} {x:>10.3f} {y:>10.3f} {y-x:>+10.3f}")
for m in ("latency_ms_p50", "latency_ms_p95"):
x, y = aa[m], ab[m]
ratio = f"{y/x:.2f}x" if x else "n/a"
print(f" {m:14} {x:>9.0f}ms {y:>9.0f}ms {ratio:>10}")
print(f" {'nonsense':14} {aa['nonsense_clean']:>10} {ab['nonsense_clean']:>10}")
print(f" {'outranks':14} {aa['superseded_outranks']:>10} {ab['superseded_outranks']:>10}")
print(f"\n {'category':14} {'n':>3} {'base hit@5':>11} {'cand hit@5':>11} {'delta':>9}")
for c in sorted(set(aa["by_category"]) & set(ab["by_category"])):
ea, eb = aa["by_category"][c], ab["by_category"][c]
if c == "nonsense":
print(f" {c:14} {ea['n']:>3} {'clean ' + str(ea['clean']):>11} "
f"{'clean ' + str(eb['clean']):>11}")
else:
print(f" {c:14} {ea['n']:>3} {100*ea['hit@5']:>10.1f}% {100*eb['hit@5']:>10.1f}% "
f"{100*(eb['hit@5']-ea['hit@5']):>+8.1f}pp")
# ---- paired significance -------------------------------------------------
fixed, broken = [], []
for q in ids:
oa, ob = outcome(ra[q]), outcome(rb[q])
if ob > oa:
fixed.append(q)
elif ob < oa:
broken.append(q)
b, c = len(fixed), len(broken)
p = binom_two_sided(b, c)
mds = min_detectable_swing(n)
print(f"\n== paired comparison over {n} queries ==")
print(f" fixed by candidate : {b} {[ra[q]['category'] + ':' + q for q in fixed]}")
print(f" broken by candidate: {c} {[ra[q]['category'] + ':' + q for q in broken]}")
print(f" discordant pairs : {b + c} net {b - c:+d} queries")
print(f" McNemar exact p : {p:.4f}")
print(f" noise threshold : a difference needs at least {mds} queries moving the "
f"same way to clear p<0.05 on this {n}-query set")
# ---- repeat-run variance -------------------------------------------------
var = {}
for name, paths, first in (("baseline", args.repeats_baseline, A),
("candidate", args.repeats_candidate, B)):
docs = [first] + [load(p) for p in paths]
if len(docs) > 1:
hits = [d["aggregate"]["hit@5"] for d in docs]
lo, hi = band(hits)
spread_q = round((hi - lo) * first["aggregate"]["n_scored"])
var[name] = {"runs": len(docs), "hit@5_min": lo, "hit@5_max": hi,
"spread_queries": spread_q}
print(f" {name} repeat runs ({len(docs)}): hit@5 {100*lo:.1f}%..{100*hi:.1f}% "
f"= {spread_q} query of run-to-run drift")
drift = max([v["spread_queries"] for v in var.values()], default=0)
floor = max(mds, drift + 1)
print("\n== VERDICT ==")
net = b - c
if abs(net) < floor:
print(f" NO MEASURABLE DIFFERENCE. Net {net:+d} queries is inside the noise band "
f"(needs |net| >= {floor}: {mds} for significance, {drift} observed run-to-run drift).")
elif net > 0:
print(f" CANDIDATE BETTER by {net} queries (p={p:.4f}), outside the noise band "
f"(>= {floor}).")
else:
print(f" CANDIDATE WORSE by {abs(net)} queries (p={p:.4f}), outside the noise band "
f"(>= {floor}).")
if args.out:
with open(args.out, "w", encoding="utf-8") as fh:
json.dump({
"baseline": A["label"], "candidate": B["label"],
"n_shared_queries": n,
"fixed_by_candidate": fixed, "broken_by_candidate": broken,
"discordant": b + c, "net_queries": net,
"mcnemar_exact_p": p,
"min_detectable_swing_queries": mds,
"observed_run_to_run_drift_queries": drift,
"noise_floor_queries": floor,
"verdict": ("no measurable difference" if abs(net) < floor
else ("candidate better" if net > 0 else "candidate worse")),
"baseline_aggregate": aa, "candidate_aggregate": ab,
"repeat_variance": var,
}, fh, indent=1)
print(f"\nwrote {args.out}")
if __name__ == "__main__":
main()
@@ -1,150 +0,0 @@
{
"baseline": "main-r1",
"candidate": "act-r1",
"n_shared_queries": 38,
"fixed_by_candidate": [],
"broken_by_candidate": [
"q07",
"q11",
"q12",
"q13",
"q36"
],
"discordant": 5,
"net_queries": -5,
"mcnemar_exact_p": 0.0625,
"min_detectable_swing_queries": 6,
"observed_run_to_run_drift_queries": 1,
"noise_floor_queries": 6,
"verdict": "no measurable difference",
"baseline_aggregate": {
"n_queries": 38,
"n_scored": 35,
"hit@5": 0.34285714285714286,
"recall@5": 0.26947278911564626,
"recall@10": 0.3333333333333333,
"precision@5": 0.12000000000000001,
"mrr@10": 0.2943197278911564,
"nonsense_clean": "2/3",
"superseded_outranks": "1/3",
"latency_ms_p50": 1140.4,
"latency_ms_p95": 1584.1,
"latency_ms_max": 1627.6,
"errors": 0,
"by_category": {
"associative": {
"n": 6,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"mrr@10": 0.0
},
"exact_rare": {
"n": 6,
"hit@5": 1.0,
"recall@5": 1.0,
"recall@10": 1.0,
"mrr@10": 1.0
},
"nonsense": {
"n": 3,
"clean": 2,
"avg_false_positives": 3.3333333333333335
},
"paraphrase": {
"n": 13,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"mrr@10": 0.0
},
"phrase": {
"n": 7,
"hit@5": 0.8571428571428571,
"recall@5": 0.4902210884353741,
"recall@10": 0.6666666666666666,
"mrr@10": 0.5965986394557822
},
"superseded": {
"n": 3,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.3333333333333333,
"mrr@10": 0.041666666666666664,
"outranks": 1
}
}
},
"candidate_aggregate": {
"n_queries": 38,
"n_scored": 35,
"hit@5": 0.22857142857142856,
"recall@5": 0.19087301587301586,
"recall@10": 0.24277210884353742,
"precision@5": 0.07428571428571429,
"mrr@10": 0.24154195011337865,
"nonsense_clean": "2/3",
"superseded_outranks": "0/3",
"latency_ms_p50": 3208.8,
"latency_ms_p95": 4851.9,
"latency_ms_max": 5078.8,
"errors": 0,
"by_category": {
"associative": {
"n": 6,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"mrr@10": 0.0
},
"exact_rare": {
"n": 6,
"hit@5": 1.0,
"recall@5": 1.0,
"recall@10": 1.0,
"mrr@10": 1.0
},
"nonsense": {
"n": 3,
"clean": 2,
"avg_false_positives": 2.6666666666666665
},
"paraphrase": {
"n": 13,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"mrr@10": 0.0
},
"phrase": {
"n": 7,
"hit@5": 0.2857142857142857,
"recall@5": 0.09722222222222222,
"recall@10": 0.3567176870748299,
"mrr@10": 0.3505668934240363
},
"superseded": {
"n": 3,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"mrr@10": 0.0,
"outranks": 0
}
}
},
"repeat_variance": {
"baseline": {
"runs": 3,
"hit@5_min": 0.34285714285714286,
"hit@5_max": 0.34285714285714286,
"spread_queries": 0
},
"candidate": {
"runs": 3,
"hit@5_min": 0.22857142857142856,
"hit@5_max": 0.2571428571428571,
"spread_queries": 1
}
}
}
-587
View File
@@ -1,587 +0,0 @@
{
"corpus": "/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json",
"corpus_nodes": 78768,
"corpus_edges": 14214,
"note": "Every query carries a `derivation` recording how its expected answer was chosen. Re-run with --check to re-validate the whole set against the corpus.",
"queries": [
{
"id": "q01",
"category": "exact_rare",
"query": "unjailbreakable",
"relevant": [
"mem-7f61beb4-271c-4feb-9f6e-1c9c837a6226"
],
"derivation": "MINED: token 'unjailbreakable' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is mem-7f61beb4-271c-4feb-9f6e-1c9c837a6226 ('Daemon hidden substrate architecture ? implemented April 25 '), which is therefore the only possible correct answer."
},
{
"id": "q02",
"category": "exact_rare",
"query": "engram-migrate",
"relevant": [
"mem-6fdf6545-5e1a-43a9-8bdc-d2cd248146a5"
],
"derivation": "MINED: token 'engram-migrate' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is mem-6fdf6545-5e1a-43a9-8bdc-d2cd248146a5 ('Engram v0.1 complete ? April 27, 2026. Local-first spreading'), which is therefore the only possible correct answer."
},
{
"id": "q03",
"category": "exact_rare",
"query": "cartabandonedevent",
"relevant": [
"mem-1ba7c67d-85b9-4c2e-9fe2-39f8b0477091"
],
"derivation": "MINED: token 'cartabandonedevent' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is mem-1ba7c67d-85b9-4c2e-9fe2-39f8b0477091 ('MESSAGE FOR AUDIT AGENT af5a7352e70e80434 ? El Language Spec'), which is therefore the only possible correct answer."
},
{
"id": "q04",
"category": "exact_rare",
"query": "pre-apprenticeship",
"relevant": [
"mem-89c02aae-d3ca-43f9-9e5d-eb369896276c"
],
"derivation": "MINED: token 'pre-apprenticeship' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is mem-89c02aae-d3ca-43f9-9e5d-eb369896276c ('William Fox Anderson ? Applicant Profile Personal: - Full N'), which is therefore the only possible correct answer."
},
{
"id": "q05",
"category": "exact_rare",
"query": "inferencenodemanager",
"relevant": [
"mem-73969486-143f-4431-b5e6-6845d1cc9848"
],
"derivation": "MINED: token 'inferencenodemanager' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is mem-73969486-143f-4431-b5e6-6845d1cc9848 ('Soma inference backplane deployed April 28 2026. Architectur'), which is therefore the only possible correct answer."
},
{
"id": "q06",
"category": "exact_rare",
"query": "clear-eyed",
"relevant": [
"knw-c72597c5-c23d-4c08-8e9e-996dadf26a99"
],
"derivation": "MINED: token 'clear-eyed' has document frequency 1 over all 78768 corpus nodes (re-verified at build time). Its single containing node is knw-c72597c5-c23d-4c08-8e9e-996dadf26a99 ('Clear Eyes ? The Incomplete World View'), which is therefore the only possible correct answer."
},
{
"id": "q07",
"category": "phrase",
"query": "patterns not returns",
"relevant": [
"mem-a4a9dfc3-e40b-49b3-b1e1-060e8be2f482"
],
"derivation": "MINED: a verbatim correction Will issued; expected = every node containing the phrase. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 1 node(s); that set IS the answer key."
},
{
"id": "q08",
"category": "phrase",
"query": "thirty moves",
"relevant": [
"766de879-f9d0-4a07-b6df-b43ee13763d8",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"??o?'?B???k",
"Kp???",
"art-4a99aa1a-489b-4b43-958b-25217adb1aad",
"kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
"kn-6061318f-046b-4935-907d-8eafdce14930",
"kn-f230b362-b201-4402-9833-4160c89ab3d4",
"knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
"knw-4aebd815-4eaf-49d7-954b-03595f3d48be",
"knw-7902acca-604e-409b-8faf-ad85424211d0",
"knw-e94982a2-358d-4f2f-af31-8ee0fcec07c6",
"knw-f671966c-3387-4848-abca-b5deec122e00",
"ע?RGk?\tH(?"
],
"derivation": "MINED: the canonical biographical phrase; expected = every node containing it. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 16 node(s); that set IS the answer key."
},
{
"id": "q09",
"category": "phrase",
"query": "Grandma Lucas",
"relevant": [
"766de879-f9d0-4a07-b6df-b43ee13763d8",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
"kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
],
"derivation": "MINED: a named person appearing verbatim in the biography/value nodes. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 9 node(s); that set IS the answer key."
},
{
"id": "q10",
"category": "phrase",
"query": "Directed Harmonic",
"relevant": [
"%???2??jH??",
"63307ac5-cf6b-46e0-8296-07503b461cfa",
"7c9d4ab1-205d-4be8-bfae-e2c03a3a5010",
"9f291d20-0d32-413c-8c01-4416ccab4f7f",
"?;????n}rh?",
"???Ͼd??f??",
"?Z?.\f?0?]P?",
"Dp???]Q??k+",
"mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf"
],
"derivation": "MINED: the canonical DHARMA expansion, confirmed by Will April 24 2026. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 9 node(s); that set IS the answer key."
},
{
"id": "q11",
"category": "phrase",
"query": "Sarah Bishop",
"relevant": [
"766de879-f9d0-4a07-b6df-b43ee13763d8",
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
],
"derivation": "MINED: a named person; rare enough that the answer set is unambiguous. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 2 node(s); that set IS the answer key."
},
{
"id": "q12",
"category": "phrase",
"query": "Directed Autonomous Runtime Modification",
"relevant": [
"2a923500-d7e1-4b15-80e2-48dba65984ba",
"7?e?7???\f3?",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"?of?7???",
"bl-145a0985-2382-400f-a7c5-c335c5e30a72",
"bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
"g?2睪A|?H\b",
"mem-82b93b21-a865-410f-9ec1-fc54121d9bb5",
"mem-e6327f52-2bda-4ce7-9471-2fffd1e172de"
],
"derivation": "MINED: the DARMA expansion, quoted verbatim in the backlog item and its correction. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 14 node(s); that set IS the answer key."
},
{
"id": "q13",
"category": "phrase",
"query": "zero-knowledge encrypted backup",
"relevant": [
"deda48cd-5e1a-46cb-bd43-8016afdb3a8a"
],
"derivation": "MINED: the paid-tier feature name as written in the roadmap nodes. Case-insensitive verbatim substring scan over label+content+tags at build time returns exactly 1 node(s); that set IS the answer key."
},
{
"id": "q14",
"category": "paraphrase",
"query": "the elderly relative who passed while he stayed away",
"relevant": [
"kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Do the Essential Thing While You Can', whose subject is Grandma Lucas dying in Feb 2006 without Will saying goodbye. Query names the event with none of the node's own vocabulary. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"away",
"elderly",
"passed",
"relative",
"stayed"
]
},
{
"id": "q15",
"category": "paraphrase",
"query": "a soldier sidelined by illness who refused to quit",
"relevant": [
"kn-58874a74-b96f-4883-9e08-45707f4bd3ee"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Survival Is Not an Excuse to Stop', whose subject is enlisting in the Marines, a severe hernia, and sepsis. Query describes the episode obliquely. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"illness",
"quit",
"refused",
"sidelined",
"soldier"
]
},
{
"id": "q16",
"category": "paraphrase",
"query": "choosing an uncomfortable fact over a pleasant fiction",
"relevant": [
"kn-13f60407-7b70-4db1-964f-ea1f8196efbd"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Honesty Before Comfort'. Query states the principle in wholly different words. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"choosing",
"fact",
"fiction",
"pleasant",
"uncomfortable"
]
},
{
"id": "q17",
"category": "paraphrase",
"query": "a tight payload beats a bloated one",
"relevant": [
"kn-22d77abe-b3c5-42fd-afcd-dcb87d924929"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Precision Over Brute Force'. Query restates the claim with no shared vocabulary. VERIFIED at build time: of the 4 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"beats",
"bloated",
"payload",
"tight"
]
},
{
"id": "q18",
"category": "paraphrase",
"query": "if you are able and nobody is coming the job is yours",
"relevant": [
"kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Capability Is a Debt You Owe the Moment'. Query states the obligation without the node's terms. VERIFIED at build time: of the 4 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"able",
"coming",
"job",
"nobody"
]
},
{
"id": "q19",
"category": "paraphrase",
"query": "learning is the wealth creditors cannot seize",
"relevant": [
"kn-0bb4f021-56de-4947-a35b-a37209e7ba21"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Knowledge Survives When Nothing Else Does', whose subject is the library following Will across 30+ moves. VERIFIED at build time: of the 4 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"creditors",
"learning",
"seize",
"wealth"
]
},
{
"id": "q20",
"category": "paraphrase",
"query": "reliability proven by track record not assertion",
"relevant": [
"kn-5de5a9ac-fd15-45ab-bf18-77566781cf40"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Earned Trust' ('Trust is demonstrated, not declared'). VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"assertion",
"proven",
"record",
"reliability",
"track"
]
},
{
"id": "q21",
"category": "paraphrase",
"query": "boundaries that enable instead of confine",
"relevant": [
"kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Constraints as Freedom'. Query is a restatement of the same claim. VERIFIED at build time: of the 4 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"boundaries",
"confine",
"enable",
"instead"
]
},
{
"id": "q22",
"category": "paraphrase",
"query": "what shifts tells you where to cut a system apart",
"relevant": [
"kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Change Is the Signal', the value VBD is built on. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"apart",
"cut",
"shifts",
"system",
"tells"
]
},
{
"id": "q23",
"category": "paraphrase",
"query": "a mind that compounds instead of resetting each day",
"relevant": [
"kn-f230b362-b201-4402-9833-4160c89ab3d4"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - The System Must Accumulate'. Query is the accumulation claim in different vocabulary. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"compounds",
"day",
"instead",
"mind",
"resetting"
]
},
{
"id": "q24",
"category": "paraphrase",
"query": "loved for the unedited self and not the polished exterior",
"relevant": [
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Being Seen Is Rarer Than Being Known', whose subject is Sarah Bishop as the first person Will did not perform for. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"exterior",
"loved",
"polished",
"self",
"unedited"
]
},
{
"id": "q25",
"category": "paraphrase",
"query": "cheerfulness you arrive at instead of assuming",
"relevant": [
"kn-e0423482-cfa5-4796-8689-8495c93b66bc"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Hope Is a Conclusion'. Query restates 'a conclusion, not a premise'. VERIFIED at build time: of the 4 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"arrive",
"assuming",
"cheerfulness",
"instead"
]
},
{
"id": "q26",
"category": "paraphrase",
"query": "a childhood offering no solid foundation to inherit",
"relevant": [
"kn-6061318f-046b-4935-907d-8eafdce14930"
],
"derivation": "HAND-SELECTED with criterion: target: 'Value - Structure Is Not Inherited', whose subject is thirty moves between two parents' collapses. VERIFIED at build time: of the 5 content words in the query, ZERO appear anywhere in the target's label, content, or tags — so no string-matching retriever can reach this answer.",
"zero_overlap_verified": true,
"query_content_words": [
"childhood",
"foundation",
"inherit",
"offering",
"solid"
]
},
{
"id": "q27",
"category": "associative",
"query": "Grandma Lucas stroke February 2006 goodbye window",
"relevant": [
"kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
"kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
"kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
"kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
"kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
"kn-6061318f-046b-4935-907d-8eafdce14930",
"kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
"kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
"kn-e0423482-cfa5-4796-8689-8495c93b66bc",
"kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
"kn-f230b362-b201-4402-9833-4160c89ab3d4"
],
"derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71 ('Value ? Do the Essential Thing While You Can'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (11 of 13; 2 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71) -> hub -> sibling, a two-hop traversal.",
"associative_source": "kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
"hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
"siblings_dropped_for_overlap": 2
},
{
"id": "q28",
"category": "associative",
"query": "Marines hernia sepsis medical ward",
"relevant": [
"015644f5-8194-4af0-800d-dd4a0cd71396",
"kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
"kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
"kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
"kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
"kn-6061318f-046b-4935-907d-8eafdce14930",
"kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
"kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
"kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
"kn-e0423482-cfa5-4796-8689-8495c93b66bc",
"kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
"kn-f230b362-b201-4402-9833-4160c89ab3d4"
],
"derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-58874a74-b96f-4883-9e08-45707f4bd3ee ('Value ? Survival Is Not an Excuse to Stop'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (13 of 13; 0 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-58874a74-b96f-4883-9e08-45707f4bd3ee) -> hub -> sibling, a two-hop traversal.",
"associative_source": "kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
"hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
"siblings_dropped_for_overlap": 0
},
{
"id": "q29",
"category": "associative",
"query": "Sarah Bishop Dyer trailer performance",
"relevant": [
"015644f5-8194-4af0-800d-dd4a0cd71396",
"kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
"kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
"kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
"kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
"kn-6061318f-046b-4935-907d-8eafdce14930",
"kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
"kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
"kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
"kn-e0423482-cfa5-4796-8689-8495c93b66bc",
"kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8"
],
"derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e ('Value ? Being Seen Is Rarer Than Being Known'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (11 of 13; 2 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e) -> hub -> sibling, a two-hop traversal.",
"associative_source": "kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
"hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
"siblings_dropped_for_overlap": 2
},
{
"id": "q30",
"category": "associative",
"query": "Swarm Architecture containment lateral worker",
"relevant": [
"kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
"kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
"kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
"kn-e0423482-cfa5-4796-8689-8495c93b66bc",
"kn-f230b362-b201-4402-9833-4160c89ab3d4"
],
"derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83 ('Value ? Constraints as Freedom'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (6 of 13; 7 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83) -> hub -> sibling, a two-hop traversal.",
"associative_source": "kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
"hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
"siblings_dropped_for_overlap": 7
},
{
"id": "q31",
"category": "associative",
"query": "hope won inside the narrative preface",
"relevant": [
"kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
"kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
"kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
"kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
"kn-6061318f-046b-4935-907d-8eafdce14930",
"kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
"kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
"kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
"kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
"kn-f230b362-b201-4402-9833-4160c89ab3d4"
],
"derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-e0423482-cfa5-4796-8689-8495c93b66bc ('Value ? Hope Is a Conclusion'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (11 of 13; 2 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-e0423482-cfa5-4796-8689-8495c93b66bc) -> hub -> sibling, a two-hop traversal.",
"associative_source": "kn-e0423482-cfa5-4796-8689-8495c93b66bc",
"hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
"siblings_dropped_for_overlap": 2
},
{
"id": "q32",
"category": "associative",
"query": "man of the house six years old expectation",
"relevant": [
"015644f5-8194-4af0-800d-dd4a0cd71396",
"kn-0bb4f021-56de-4947-a35b-a37209e7ba21",
"kn-13f60407-7b70-4db1-964f-ea1f8196efbd",
"kn-22d77abe-b3c5-42fd-afcd-dcb87d924929",
"kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
"kn-5de5a9ac-fd15-45ab-bf18-77566781cf40",
"kn-78db5396-3dbc-4481-bfc7-e4e1422feb1c",
"kn-a5b3d0ac-f6a1-49a4-aebb-b8b4cd67fe83",
"kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
"kn-e0423482-cfa5-4796-8689-8495c93b66bc"
],
"derivation": "DERIVED FROM EDGES: the query is built from the distinctive vocabulary of kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8 ('Value ? Capability Is a Debt You Owe the Moment'), which hangs off the values hub kn-5b606390-a52d-4ca2-8e0e-eba141d13440 by an `identity` edge. Expected answers are that node's SIBLINGS on the same hub (11 of 13; 2 dropped because they shared a query word and so were lexically reachable). Every remaining sibling shares ZERO content words with the query — the only route from query to answer is seed(kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8) -> hub -> sibling, a two-hop traversal.",
"associative_source": "kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
"hub": "kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
"siblings_dropped_for_overlap": 2
},
{
"id": "q33",
"category": "nonsense",
"query": "zqxjvw plimforth grebulon",
"relevant": [],
"derivation": "CONTROL: verified at build time that none of this string's tokens occurs anywhere in the corpus. Correct behaviour is to return NOTHING; any result is a false positive.",
"expect_empty": true
},
{
"id": "q34",
"category": "nonsense",
"query": "flarnbistle quommetry",
"relevant": [],
"derivation": "CONTROL: verified at build time that none of this string's tokens occurs anywhere in the corpus. Correct behaviour is to return NOTHING; any result is a false positive.",
"expect_empty": true
},
{
"id": "q35",
"category": "nonsense",
"query": "xxqzzt vurblenacht throom",
"relevant": [],
"derivation": "CONTROL: verified at build time that none of this string's tokens occurs anywhere in the corpus. Correct behaviour is to return NOTHING; any result is a false positive.",
"expect_empty": true
},
{
"id": "q36",
"category": "superseded",
"query": "is the self-improvement architecture called DARMA or DHARMA",
"relevant": [
"mem-80d7416b-20e9-48a0-b176-b215527e2f56"
],
"derivation": "DERIVED: correction node is Will's confirmation that the H is intentional (DHARMA, not DARMA); the stale node is the surviving backlog item still titled 'Implement DARMA'. Scored on RANKING, not presence: the corrected node mem-80d7416b-20e9-48a0-b176-b215527e2f56 must be returned AND must rank above the stale node bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff.",
"must_outrank": [
"mem-80d7416b-20e9-48a0-b176-b215527e2f56",
"bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff"
],
"stale_id": "bl-5b17bd3b-0c41-46cb-a710-6fa4429692ff",
"correct_label": "CORRECTION: The autonomous self-improvement architecture is DHARMA ? n",
"stale_label": "Implement DARMA ? Directed Autonomous Runtime Modification Architectur"
},
{
"id": "q37",
"category": "superseded",
"query": "how many provisional patents does Will actually have",
"relevant": [
"3cf706a1-3825-45d8-b0a9-06cae6cdf5b8"
],
"derivation": "DERIVED: correction node is the 2026-06-17 confabulation flag establishing EXACTLY 6 provisionals; the stale node is the surviving memory that asserts 12 filed patents. Scored on RANKING, not presence: the corrected node 3cf706a1-3825-45d8-b0a9-06cae6cdf5b8 must be returned AND must rank above the stale node 936541a9-fabb-466b-9ca3-a78b17ad0c53.",
"must_outrank": [
"3cf706a1-3825-45d8-b0a9-06cae6cdf5b8",
"936541a9-fabb-466b-9ca3-a78b17ad0c53"
],
"stale_id": "936541a9-fabb-466b-9ca3-a78b17ad0c53",
"correct_label": "memory:remembered",
"stale_label": "memory:remembered"
},
{
"id": "q38",
"category": "superseded",
"query": "is MCP still the live integration layer",
"relevant": [
"mem-30425134-6008-4fd9-a3ee-67a7742c319b"
],
"derivation": "DERIVED: correction node is the 'CGI ARCHITECTURE - THREE LAYERS, MCP RETIRED' decision of April 30 2026; the stale node still records the MCP server as live. Scored on RANKING, not presence: the corrected node mem-30425134-6008-4fd9-a3ee-67a7742c319b must be returned AND must rank above the stale node mem-101e81b4-8097-4749-8d8d-7bb66de34517.",
"must_outrank": [
"mem-30425134-6008-4fd9-a3ee-67a7742c319b",
"mem-101e81b4-8097-4749-8d8d-7bb66de34517"
],
"stale_id": "mem-101e81b4-8097-4749-8d8d-7bb66de34517",
"correct_label": "CGI ARCHITECTURE ? THREE LAYERS, MCP RETIRED (April 30, 2026). Definit",
"stale_label": "GCloud MCP infrastructure ? April 27, 2026. Legion died (~19:30 UTC). "
}
]
}
-942
View File
@@ -1,942 +0,0 @@
{
"label": "act-r2",
"soul_binary": "/private/tmp/claude-501/-Users-timlingo/82369039-a20e-4b5a-8a5e-28234a57b996/scratchpad/soul-act",
"soul_md5": "77722f5a9f49494bf735c2a4be1b5dc4",
"corpus": "/Users/timlingo/neuron-memory-backups/snapshot-pre-repair-20260806.json",
"corpus_nodes": 78768,
"corpus_edges": 14214,
"gold_set": "/Users/timlingo/Development/neuron-technologies/_wt-eval/tools/retrieval-eval/gold_set.json",
"limit": 10,
"port": 7902,
"wall_clock_s": 121.2,
"child_pid": 78714,
"child_confirmed_dead": true,
"aggregate": {
"n_queries": 38,
"n_scored": 35,
"hit@5": 0.22857142857142856,
"recall@5": 0.18908730158730158,
"recall@10": 0.24277210884353742,
"precision@5": 0.06857142857142857,
"mrr@10": 0.24154195011337865,
"nonsense_clean": "2/3",
"superseded_outranks": "0/3",
"latency_ms_p50": 3237.6,
"latency_ms_p95": 5264.0,
"latency_ms_max": 5510.9,
"errors": 0,
"by_category": {
"associative": {
"n": 6,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"mrr@10": 0.0
},
"exact_rare": {
"n": 6,
"hit@5": 1.0,
"recall@5": 1.0,
"recall@10": 1.0,
"mrr@10": 1.0
},
"nonsense": {
"n": 3,
"clean": 2,
"avg_false_positives": 2.6666666666666665
},
"paraphrase": {
"n": 13,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"mrr@10": 0.0
},
"phrase": {
"n": 7,
"hit@5": 0.2857142857142857,
"recall@5": 0.0882936507936508,
"recall@10": 0.3567176870748299,
"mrr@10": 0.3505668934240363
},
"superseded": {
"n": 3,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"mrr@10": 0.0,
"outranks": 0
}
}
},
"rows": [
{
"id": "q01",
"category": "exact_rare",
"query": "unjailbreakable",
"returned": [
"mem-7f61beb4-271c-4feb-9f6e-1c9c837a6226"
],
"n_returned": 1,
"latency_ms": 476.5,
"error": null,
"hit@5": 1.0,
"recall@5": 1.0,
"recall@10": 1.0,
"precision@5": 0.2,
"mrr@10": 1.0
},
{
"id": "q02",
"category": "exact_rare",
"query": "engram-migrate",
"returned": [
"mem-6fdf6545-5e1a-43a9-8bdc-d2cd248146a5"
],
"n_returned": 1,
"latency_ms": 708.1,
"error": null,
"hit@5": 1.0,
"recall@5": 1.0,
"recall@10": 1.0,
"precision@5": 0.2,
"mrr@10": 1.0
},
{
"id": "q03",
"category": "exact_rare",
"query": "cartabandonedevent",
"returned": [
"mem-1ba7c67d-85b9-4c2e-9fe2-39f8b0477091"
],
"n_returned": 1,
"latency_ms": 532.0,
"error": null,
"hit@5": 1.0,
"recall@5": 1.0,
"recall@10": 1.0,
"precision@5": 0.2,
"mrr@10": 1.0
},
{
"id": "q04",
"category": "exact_rare",
"query": "pre-apprenticeship",
"returned": [
"mem-89c02aae-d3ca-43f9-9e5d-eb369896276c"
],
"n_returned": 1,
"latency_ms": 537.5,
"error": null,
"hit@5": 1.0,
"recall@5": 1.0,
"recall@10": 1.0,
"precision@5": 0.2,
"mrr@10": 1.0
},
{
"id": "q05",
"category": "exact_rare",
"query": "inferencenodemanager",
"returned": [
"mem-73969486-143f-4431-b5e6-6845d1cc9848"
],
"n_returned": 1,
"latency_ms": 568.7,
"error": null,
"hit@5": 1.0,
"recall@5": 1.0,
"recall@10": 1.0,
"precision@5": 0.2,
"mrr@10": 1.0
},
{
"id": "q06",
"category": "exact_rare",
"query": "clear-eyed",
"returned": [
"knw-c72597c5-c23d-4c08-8e9e-996dadf26a99"
],
"n_returned": 1,
"latency_ms": 555.4,
"error": null,
"hit@5": 1.0,
"recall@5": 1.0,
"recall@10": 1.0,
"precision@5": 0.2,
"mrr@10": 1.0
},
{
"id": "q07",
"category": "phrase",
"query": "patterns not returns",
"returned": [
"knw-d357b6bb-ad8a-4791-b516-426aea45fa5b",
"kn-69fd6e83-7718-4824-8d66-f49d8954e224",
"kn-d97920d0-1649-4223-9508-c0bb621e7fc0",
"kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
"kn-c3d9d063-8c5d-45aa-900c-550914b2ff6d",
"kn-f838f113-76d5-4a15-9cef-14055c4723a3",
"bl-76e878aa-e1fe-468c-bf9c-854097cb7e0b",
"art-c71aef51-026f-4d63-80e9-2a0ec0dc3865",
"bl-e148d23c-24e8-4122-9915-d1c11f22052f",
"bl-31abf75b-998f-4a4f-a6dd-8204119e0451"
],
"n_returned": 10,
"latency_ms": 1906.2,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q08",
"category": "phrase",
"query": "thirty moves",
"returned": [
"knw-7902acca-604e-409b-8faf-ad85424211d0",
"bl-80720fdf-7ce7-4d28-aff8-21028d3a8cfb",
"art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
"art-ee615cdb-e599-423d-9a4d-977859390ed3",
"knw-ed33e669-0790-44cb-a036-958d605c6fea",
"kn-6061318f-046b-4935-907d-8eafdce14930",
"art-80ca3d31-84dc-4502-83f4-538372b9764f",
"knw-2c46cfb4-6d4e-4822-8a1a-7d743c1e4329",
"?Z?.\f?0?]P?",
"?Q??m?;`'"
],
"n_returned": 10,
"latency_ms": 1103.3,
"error": null,
"hit@5": 1.0,
"recall@5": 0.0625,
"recall@10": 0.1875,
"precision@5": 0.2,
"mrr@10": 1.0
},
{
"id": "q09",
"category": "phrase",
"query": "Grandma Lucas",
"returned": [
"kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
"? ?}&?#??X\b",
"art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
"766de879-f9d0-4a07-b6df-b43ee13763d8",
"art-79042b8b-6192-440f-90b0-60708f7e6325"
],
"n_returned": 6,
"latency_ms": 1132.4,
"error": null,
"hit@5": 1.0,
"recall@5": 0.5555555555555556,
"recall@10": 0.5555555555555556,
"precision@5": 1.0,
"mrr@10": 1.0
},
{
"id": "q10",
"category": "phrase",
"query": "Directed Harmonic",
"returned": [
"bl-c9adb8e5-293f-4033-99f8-0405c17ef941",
"bl-7e7c3fdb-4132-487f-aa70-b2cd559cb7f0",
"bl-7aebe936-ac55-4f35-8932-adc5224ff854",
"bl-9d53422d-b703-4f1d-860a-8598cb29b792",
"mem-34f53a9d-a131-4f82-9dbd-b9eb4a9af52e",
"mem-60778715-758c-4677-933d-fc39b8f94152",
"? ?}&?#??X\b",
"art-ee615cdb-e599-423d-9a4d-977859390ed3",
"knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
"mem-7eeacad7-d7c2-4c2b-8348-19a59aa6dbaf"
],
"n_returned": 10,
"latency_ms": 960.8,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.1111111111111111,
"precision@5": 0.0,
"mrr@10": 0.1
},
{
"id": "q11",
"category": "phrase",
"query": "Sarah Bishop",
"returned": [
"art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
"art-4a99aa1a-489b-4b43-958b-25217adb1aad",
";??A5???",
"art-94fae615-7cd5-4695-b968-977101b06a51",
"art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef",
"mem-a9a9ce95-0d64-46eb-9db8-ff81d78ade35",
"mem-57164d5f-baf0-4149-957a-379a4e255d1a",
"? ?}&?#??X\b",
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
"art-8dbceb06-431a-416d-a723-e8c75d595154"
],
"n_returned": 10,
"latency_ms": 992.4,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.5,
"precision@5": 0.0,
"mrr@10": 0.1111111111111111
},
{
"id": "q12",
"category": "phrase",
"query": "Directed Autonomous Runtime Modification",
"returned": [
"kn-b2a99cd7-b379-4d9b-a996-e347a02c7bad",
"bl-a313d67b-dd6d-4e5b-a55a-03bc7bda17ae",
"kn-8e1bfb48-33a9-45ad-8da7-e0bdaa5d34e7",
"art-92e1837c-5919-42d0-bbb0-4d924d7b2864",
"bl-a7a1428f-db9c-417b-8e2c-713b1f84dc1f",
"mem-f823e835-313f-4282-b4b3-ce527ffc2f7a",
"? ?}&?#??X\b",
"art-ee615cdb-e599-423d-9a4d-977859390ed3",
"?Z?.\f?0?]P?",
"bl-145a0985-2382-400f-a7c5-c335c5e30a72"
],
"n_returned": 10,
"latency_ms": 2820.6,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.14285714285714285,
"precision@5": 0.0,
"mrr@10": 0.14285714285714285
},
{
"id": "q13",
"category": "phrase",
"query": "zero-knowledge encrypted backup",
"returned": [
"art-e495c8c5-ad95-4b64-8771-f68aa4cfcd0a",
"kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
"bl-e20944e5-eb16-4ab3-a84d-111e0fc817fa",
"bl-e20944e5-f4a6-44a0-91b1-73d04ebed120",
"mem-47f72b5b-6e8b-4293-94f1-350197b4809a",
"mem-a5f04e52-91f8-41d2-af27-8bf803621758",
"7774a16c-1027-4e3b-a21e-67f1f95a4acd",
"? ?}&?#??X\b",
"7?e?7???\f3?",
"deda48cd-5e1a-46cb-bd43-8016afdb3a8a"
],
"n_returned": 10,
"latency_ms": 2609.4,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 1.0,
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View File
@@ -1,945 +0,0 @@
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-945
View File
@@ -1,945 +0,0 @@
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View File
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"art-79042b8b-6192-440f-90b0-60708f7e6325",
"art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef",
"art-2f29ad36-6ee6-4a0e-8d72-0eaf7d12d3a9",
"? ?}&?#??X\b",
"kn-a31e1001-342e-4deb-a2e6-6d02d1f22dee",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
"? ?}&?#??X\b",
"? ?}&?#??X\b"
],
"n_returned": 10,
"latency_ms": 1627.6,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q16",
"category": "paraphrase",
"query": "choosing an uncomfortable fact over a pleasant fiction",
"returned": [
"7?e?7???\f3?",
"? ?}&?#??X\b",
"kn-f8974b26-78a6-4aad-b893-19a73b20013d",
"?of?7???",
"????7???Ջ3",
"kn-d97920d0-1649-4223-9508-c0bb621e7fc0",
"kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
"kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
"kn-81c24d13-a73b-4767-819c-dafaacc1498e",
"? ?}&?#??X\b"
],
"n_returned": 10,
"latency_ms": 1317.2,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q17",
"category": "paraphrase",
"query": "a tight payload beats a bloated one",
"returned": [
"kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491",
"7?e?7???\f3?",
"? ?}&?#??X\b",
"kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"??o?'?B???k",
"kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
"? ?}&?#??X\b",
"?of?7???"
],
"n_returned": 10,
"latency_ms": 1055.2,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q18",
"category": "paraphrase",
"query": "if you are able and nobody is coming the job is yours",
"returned": [
"7?e?7???\f3?",
"?of?7???",
"imp-dce1da0f-8776-4a9e-972b-33411a7ca138",
"kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
"kn-83bb86c6-521d-416c-a86e-6e29c2d8f102",
"kn-f8974b26-78a6-4aad-b893-19a73b20013d",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b"
],
"n_returned": 9,
"latency_ms": 1352.5,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q19",
"category": "paraphrase",
"query": "learning is the wealth creditors cannot seize",
"returned": [
"kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
"knw-7902acca-604e-409b-8faf-ad85424211d0",
"knw-e24d6339-5ff3-4bed-ba53-707ffd0dc70a",
"kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
"art-ee615cdb-e599-423d-9a4d-977859390ed3",
"7?e?7???\f3?",
"??o?'?B???k",
"? ?}&?#??X\b",
"kn-0625e393-067c-4bba-8389-7e1b79265142",
"ע?RGk?\tH(?"
],
"n_returned": 10,
"latency_ms": 1213.0,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q20",
"category": "paraphrase",
"query": "reliability proven by track record not assertion",
"returned": [
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"art-ee615cdb-e599-423d-9a4d-977859390ed3",
"7?e?7???\f3?",
"?of?7???",
"art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef",
"kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356"
],
"n_returned": 10,
"latency_ms": 1545.8,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q21",
"category": "paraphrase",
"query": "boundaries that enable instead of confine",
"returned": [
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"??????X??2c",
"ԍ????X????",
"dR????X?-?S",
"kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
"dz????Xƹ?i",
"kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491"
],
"n_returned": 10,
"latency_ms": 1327.3,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q22",
"category": "paraphrase",
"query": "what shifts tells you where to cut a system apart",
"returned": [
"7?e?7???\f3?",
"kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
"?of?7???",
"kn-f8974b26-78a6-4aad-b893-19a73b20013d",
"knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
"dR????X?-?S",
"dz????Xƹ?i",
"ԍ????X????",
"??????X??2c",
"kn-d7c1e0fb-fa59-46d3-b4c9-a0d1d437a491"
],
"n_returned": 10,
"latency_ms": 1584.1,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q23",
"category": "paraphrase",
"query": "a mind that compounds instead of resetting each day",
"returned": [
"????7???Ջ3",
"kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
"?ǚ?7??????",
"7?e?7???\f3?",
"??f?7???",
"? ?}&?#??X\b",
"%???2??jH??",
"kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
"? ?}&?#??X\b",
"kn-9397c74b-35f3-4428-b4b0-5123353bbcd1"
],
"n_returned": 10,
"latency_ms": 1432.6,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q24",
"category": "paraphrase",
"query": "loved for the unedited self and not the polished exterior",
"returned": [
"mem-bbb126a1-b297-42bb-86be-796871829c94",
"mem-45022957-2d78-48aa-a714-16d6eca52e0f",
"art-4a99aa1a-489b-4b43-958b-25217adb1aad",
"knw-35940684-abc4-42f0-b942-818f66b1f69a",
"art-79042b8b-6192-440f-90b0-60708f7e6325",
"art-0f0277a1-4a8e-4645-95dd-fa379976f31c",
"art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
"7?e?7???\f3?",
"? ?}&?#??X\b",
"'?T?a\"B~-?8"
],
"n_returned": 10,
"latency_ms": 1505.5,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q25",
"category": "paraphrase",
"query": "cheerfulness you arrive at instead of assuming",
"returned": [
"015644f5-8194-4af0-800d-dd4a0cd71396",
"?ǚ?7??????",
"art-79042b8b-6192-440f-90b0-60708f7e6325",
"7?e?7???\f3?",
"kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
"??S?7???",
"? ?}&?#??X\b",
"??f?7???",
"??S?7???",
"knw-5578cb21-e899-4822-b7f4-0d96fa094e3d"
],
"n_returned": 10,
"latency_ms": 1201.1,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q26",
"category": "paraphrase",
"query": "a childhood offering no solid foundation to inherit",
"returned": [
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"art-ee615cdb-e599-423d-9a4d-977859390ed3",
"7?e?7???\f3?",
"kn-e8423822-eacf-4029-aa7b-10d4d28d621e",
"? ?}&?#??X\b",
"??o?'?B???k",
"?of?7???",
"? ?}&?#??X\b"
],
"n_returned": 10,
"latency_ms": 1303.3,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q27",
"category": "associative",
"query": "Grandma Lucas stroke February 2006 goodbye window",
"returned": [
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"kn-a99cefe3-5e83-4050-98d8-6c69f57c7c71",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"art-79042b8b-6192-440f-90b0-60708f7e6325",
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
"art-4a99aa1a-489b-4b43-958b-25217adb1aad",
"?ǚ?7??????"
],
"n_returned": 10,
"latency_ms": 1416.3,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q28",
"category": "associative",
"query": "Marines hernia sepsis medical ward",
"returned": [
"art-79042b8b-6192-440f-90b0-60708f7e6325",
"kn-58874a74-b96f-4883-9e08-45707f4bd3ee",
"bl-33ecccc2-e37f-43db-91b3-c2a86f08aaac",
"art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
"art-e0bdf5d8-d163-491f-b649-453fee8b721d",
"7?e?7???\f3?",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"kn-9397c74b-35f3-4428-b4b0-5123353bbcd1",
"?of?7???"
],
"n_returned": 10,
"latency_ms": 1090.3,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q29",
"category": "associative",
"query": "Sarah Bishop Dyer trailer performance",
"returned": [
"kn-db9f141b-dbe3-4037-92e0-4bb9be0e5e6e",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"art-4a99aa1a-489b-4b43-958b-25217adb1aad",
"7?e?7???\f3?",
"?of?7???",
"art-79042b8b-6192-440f-90b0-60708f7e6325",
"art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
"kn-58874a74-b96f-4883-9e08-45707f4bd3ee"
],
"n_returned": 10,
"latency_ms": 1167.7,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q30",
"category": "associative",
"query": "Swarm Architecture containment lateral worker",
"returned": [
"art-ee615cdb-e599-423d-9a4d-977859390ed3",
"bl-9bde67c1-f0ba-4c3a-8fe5-de0deee0ce43",
"8cbb60c5-4999-4ec1-8682-2592aedc4249",
"bl-0fac287f-f4c0-4f15-bc4d-ff7f8a7af3ae",
"7?e?7???\f3?",
"kn-6f248a50-355b-47bb-aec8-e0e646a9b077",
"? ?}&?#??X\b",
"h??I?cB?Q??",
"?of?7???",
"? ?}&?#??X\b"
],
"n_returned": 10,
"latency_ms": 1140.4,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q31",
"category": "associative",
"query": "hope won inside the narrative preface",
"returned": [
"kn-5b606390-a52d-4ca2-8e0e-eba141d13440",
"kn-e0423482-cfa5-4796-8689-8495c93b66bc",
"knw-9e74ee95-ba7d-49b1-9262-977eae9729d1",
"7?e?7???\f3?",
"rQ??m?;?x?'",
"?Q??m?;?u?'",
"R^??m?;?'",
"?Q??m?;`'",
"? ?}&?#??X\b"
],
"n_returned": 9,
"latency_ms": 1157.6,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q32",
"category": "associative",
"query": "man of the house six years old expectation",
"returned": [
"? ?}&?#??X\b",
"kn-eb1b9e18-3dc6-4b9b-9cc6-86e0ae6b6be8",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"kn-57b4c5e7-40c6-4c90-bf14-71841b0081d4",
"knw-35940684-abc4-42f0-b942-818f66b1f69a",
"art-4a99aa1a-489b-4b43-958b-25217adb1aad",
"art-2fabd873-d787-49cb-ad30-d4ed9fcff8ef"
],
"n_returned": 10,
"latency_ms": 1379.7,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0
},
{
"id": "q33",
"category": "nonsense",
"query": "zqxjvw plimforth grebulon",
"returned": [],
"n_returned": 0,
"latency_ms": 677.2,
"error": null,
"clean": true,
"false_positives": 0
},
{
"id": "q34",
"category": "nonsense",
"query": "flarnbistle quommetry",
"returned": [],
"n_returned": 0,
"latency_ms": 443.2,
"error": null,
"clean": true,
"false_positives": 0
},
{
"id": "q35",
"category": "nonsense",
"query": "xxqzzt vurblenacht throom",
"returned": [
"art-4a99aa1a-489b-4b43-958b-25217adb1aad",
"knw-920c891f-bb8c-48c4-9afc-018ef12dcdc4",
"art-79042b8b-6192-440f-90b0-60708f7e6325",
"art-ddfcd045-2c3b-4a1e-9966-fec5ce44e1dd",
"bl-4476e856-c567-4b49-8ff7-d7dca3e5715e",
"kn-66a21179-2adc-4b19-a109-880cf4674d7d",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b"
],
"n_returned": 10,
"latency_ms": 679.8,
"error": null,
"clean": false,
"false_positives": 10
},
{
"id": "q36",
"category": "superseded",
"query": "is the self-improvement architecture called DARMA or DHARMA",
"returned": [
"7?e?7???\f3?",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"?of?7???",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"mem-80d7416b-20e9-48a0-b176-b215527e2f56",
"mem-f3b37427-b7d1-4f7e-b32c-0241a20ce8da",
"art-80ca3d31-84dc-4502-83f4-538372b9764f"
],
"n_returned": 10,
"latency_ms": 1245.4,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 1.0,
"precision@5": 0.0,
"mrr@10": 0.125,
"outranks": true,
"rank_correct": 8,
"rank_stale": null
},
{
"id": "q37",
"category": "superseded",
"query": "how many provisional patents does Will actually have",
"returned": [
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"? ?}&?#??X\b",
"7?e?7???\f3?",
"?of?7???",
"?ǚ?7??????",
"[?MO5????G",
"art-ee615cdb-e599-423d-9a4d-977859390ed3"
],
"n_returned": 10,
"latency_ms": 1618.4,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0,
"outranks": false,
"rank_correct": null,
"rank_stale": null
},
{
"id": "q38",
"category": "superseded",
"query": "is MCP still the live integration layer",
"returned": [
"kn-5584ef9c-7f9d-4d7c-a10a-4ee6bc5cf356",
"7?e?7???\f3?",
"? ?}&?#??X\b",
"%???2??jH??",
"???Ͼd??W\b?",
"??o?'?B???k",
"? ?}&?#??X\b",
"63307ac5-cf6b-46e0-8296-07503b461cfa",
"? ?}&?#??X\b",
"?of?7???"
],
"n_returned": 10,
"latency_ms": 956.7,
"error": null,
"hit@5": 0.0,
"recall@5": 0.0,
"recall@10": 0.0,
"precision@5": 0.0,
"mrr@10": 0.0,
"outranks": false,
"rank_correct": null,
"rank_stale": null
}
]
}
-98
View File
@@ -1,98 +0,0 @@
#!/usr/bin/env bash
# run_comparison.sh — the whole harness, end to end, from two git refs.
#
# Builds a soul from each ref, boots each on its own throwaway port with its own
# throwaway HOME and its own disposable copy of the corpus, runs the gold set N
# times per ref, and prints the comparison with its noise threshold.
#
# SAFETY: never touches ~/.neuron, /Applications/Neuron*, ~/neuron-dev-stack, or
# any running service. Sources are exported with `git archive` into a scratch
# dir, so no worktree or branch state is mutated either. Ports are checked
# against the live set before anything boots. Every soul this script starts is
# killed and confirmed dead by run_eval.py; the sweep at the end is a backstop.
#
# usage:
# run_comparison.sh [--baseline main] [--candidate feat/recall-through-activation]
# [--repeats 3] [--corpus <snapshot.json>] [--repo <path>]
set -euo pipefail
BASELINE="main"
CANDIDATE="feat/recall-through-activation"
REPEATS=3
CORPUS="$HOME/neuron-memory-backups/snapshot-pre-repair-20260806.json"
REPO="$HOME/Development/neuron"
BASE_PORT=7893
while [ $# -gt 0 ]; do
case "$1" in
--baseline) BASELINE="$2"; shift 2 ;;
--candidate) CANDIDATE="$2"; shift 2 ;;
--repeats) REPEATS="$2"; shift 2 ;;
--corpus) CORPUS="$2"; shift 2 ;;
--repo) REPO="$2"; shift 2 ;;
*) echo "unknown arg: $1" >&2; exit 2 ;;
esac
done
HERE="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
WORK="$(mktemp -d "${TMPDIR:-/tmp}/retrieval-eval.XXXXXX")"
trap 'rm -rf "$WORK"' EXIT
[ -f "$CORPUS" ] || { echo "no corpus at $CORPUS" >&2; exit 2; }
echo "corpus: $CORPUS ($(du -h "$CORPUS" | cut -f1))"
slug() { printf '%s' "$1" | tr '/' '-'; }
build_ref() { # ref -> binary path
local ref="$1" out="$WORK/soul-$(slug "$1")"
local src="$WORK/src-$(slug "$1")"
mkdir -p "$src"
git -C "$REPO" archive "$ref" | tar -x -C "$src"
"$HERE/build-soul.sh" "$src" "$out" >&2
printf '%s' "$out"
}
echo "== building $BASELINE =="
BIN_A="$(build_ref "$BASELINE")"
echo "== building $CANDIDATE =="
BIN_B="$(build_ref "$CANDIDATE")"
echo "== validating the gold set against this corpus =="
python3 "$HERE/build_gold_set.py" "$CORPUS" --check
port=$BASE_PORT
run_one() { # binary label out
echo "== $2 =="
python3 "$HERE/run_eval.py" --soul "$1" --corpus "$CORPUS" --label "$2" \
--port "$port" --out "$3"
port=$((port + 1))
}
A_MAIN="$WORK/results-a-1.json"; B_MAIN="$WORK/results-b-1.json"
A_REP=(); B_REP=()
for i in $(seq 1 "$REPEATS"); do
a="$WORK/results-a-$i.json"; b="$WORK/results-b-$i.json"
run_one "$BIN_A" "$(slug "$BASELINE")-r$i" "$a"
run_one "$BIN_B" "$(slug "$CANDIDATE")-r$i" "$b"
[ "$i" -gt 1 ] && { A_REP+=("$a"); B_REP+=("$b"); }
done
cp "$A_MAIN" "$HERE/results-$(slug "$BASELINE").json"
cp "$B_MAIN" "$HERE/results-$(slug "$CANDIDATE").json"
echo
python3 "$HERE/compare.py" \
--baseline "$A_MAIN" --candidate "$B_MAIN" \
${A_REP[@]+--repeats-baseline "${A_REP[@]}"} \
${B_REP[@]+--repeats-candidate "${B_REP[@]}"} \
--out "$HERE/comparison-$(slug "$BASELINE")-vs-$(slug "$CANDIDATE").json"
# Backstop: run_eval.py kills and confirms its own child, but a crashed run
# could leak one. Leaving a soul running is how the live engine got squeezed.
STRAY=$(pgrep -f "$WORK/soul-" || true)
if [ -n "$STRAY" ]; then
echo "!! stray eval souls, killing: $STRAY" >&2
kill -9 $STRAY 2>/dev/null || true
fi
pgrep -f "$WORK/soul-" >/dev/null && { echo "!! STILL RUNNING" >&2; exit 5; }
echo "process check: no eval souls running"
-398
View File
@@ -1,398 +0,0 @@
#!/usr/bin/env python3
"""
run_eval.py measure one soul build's retrieval against the gold set.
WHAT IT MEASURES, AND WHY IT BOOTS A REAL SOUL
The point is Will's designed retrieval — spreading activation over the
weighted directed graph with four-factor multiplicative scoring not a
Python re-implementation of it. A re-implementation would measure my
reading of the design; booting the compiled binary measures the design. So
this harness compiles the actual `soul.el` amalgam (build-soul.sh) and asks
it over HTTP, exactly as the MCP wrapper and the app do.
SAFETY read this before changing anything here
* Boots on a THROWAWAY port with a THROWAWAY $HOME and a THROWAWAY COPY of
the corpus. Refuses to use 7770 / 8742 / 7779 / 17779 / 7771.
* ENGRAM_URL / SOUL_ENGRAM_URL are UNSET and SOUL_ISE_URL is pinned to a
dead port. This is not belt-and-braces: the periodic engram sync resolves
its source as env(SOUL_ISE_URL) -> state -> DEFAULT http://localhost:8742,
so leaving it unset makes an "isolated" run silently pull the operator's
LIVE brain. (Learned the hard way on 2026-08-03; see the same note in
scripts/verify-soul-contract.sh.)
* Every process this file starts is tracked and killed in a finally block,
then CONFIRMED dead by pid probe, and the confirmation is written into the
results file. A run that cannot confirm its child is dead exits non-zero.
* Activation is a STATEFUL read by design (patent claim 29: traversal
updates last-activation and increments activation counts). The corpus copy
is therefore per-run and disposable, and every run starts from a byte-
identical copy so two configurations see the same starting graph.
usage:
python3 run_eval.py --soul <binary> --corpus <snapshot.json> --label main \
[--port 7893] [--gold gold_set.json] [--limit 10] [--out results-main.json]
"""
import argparse
import json
import os
import shutil
import signal
import subprocess
import sys
import tempfile
import time
import urllib.error
import urllib.parse
import urllib.request
HERE = os.path.dirname(os.path.abspath(__file__))
FORBIDDEN_PORTS = {7770, 8742, 7779, 17779, 7771, 8080}
# ─────────────────────────────────────────────────────────────────────────────
# metrics
# ─────────────────────────────────────────────────────────────────────────────
def recall_at_k(returned, relevant, k):
if not relevant:
return None
return len(set(returned[:k]) & set(relevant)) / len(relevant)
def hit_at_k(returned, relevant, k):
if not relevant:
return None
return 1.0 if set(returned[:k]) & set(relevant) else 0.0
def precision_at_k(returned, relevant, k):
"""Fixed denominator k, as in docs/research/graphrag_eval/score.py.
Fixed denominator penalises an empty result and a page of junk equally,
which is what we want: a retriever that returns nothing is not 'precise'.
"""
if not relevant:
return None
return len(set(returned[:k]) & set(relevant)) / k
def mrr(returned, relevant, k):
if not relevant:
return None
rel = set(relevant)
for i, nid in enumerate(returned[:k], start=1):
if nid in rel:
return 1.0 / i
return 0.0
def mean(vals):
vals = [v for v in vals if v is not None]
return sum(vals) / len(vals) if vals else 0.0
def pct(vals):
return f"{100 * mean(vals):.1f}%"
# ─────────────────────────────────────────────────────────────────────────────
# soul lifecycle
# ─────────────────────────────────────────────────────────────────────────────
class Soul:
def __init__(self, binary, corpus, port, verbose=True):
if port in FORBIDDEN_PORTS:
raise SystemExit(f"REFUSING: port {port} is a live service port.")
self.binary = os.path.abspath(binary)
self.corpus = os.path.abspath(corpus)
self.port = port
self.verbose = verbose
self.home = None
self.proc = None
self.pid = None
self.log = None
self.confirmed_dead = None
@property
def base(self):
return f"http://127.0.0.1:{self.port}"
def start(self, boot_timeout=180):
self.home = tempfile.mkdtemp(prefix="retrieval-eval-home.")
snap = os.path.join(self.home, "corpus.json")
t0 = time.time()
shutil.copyfile(self.corpus, snap) # per-run disposable copy, never the source
self.log = os.path.join(self.home, "soul.log")
env = {k: v for k, v in os.environ.items()
if k not in ("ENGRAM_URL", "ENGRAM_API_KEY", "SOUL_ENGRAM_URL",
"ANTHROPIC_API_KEY", "NEURON_LLM_API_KEY", "SOUL_IDENTITY",
"SOUL_API_KEY")}
env.update({
"HOME": self.home,
"NEURON_PORT": str(self.port),
"SOUL_CGI_ID": f"ntn-retrieval-eval-{os.getpid()}",
"SOUL_ENGRAM_PATH": snap,
"NEURON_API_URL": "http://127.0.0.1:9", # dead port
"SOUL_ISE_URL": "http://127.0.0.1:9", # dead port — see SAFETY above
# Park the background loops for an hour so heartbeat/consolidation
# cannot mutate the graph between queries and make runs unrepeatable.
"SOUL_TICK_MS": "3600000",
"SOUL_HEARTBEAT_MS": "3600000",
"SOUL_REFRESH_MS": "3600000",
})
with open(self.log, "wb") as lf:
self.proc = subprocess.Popen([self.binary], env=env, stdout=lf, stderr=lf,
start_new_session=True)
self.pid = self.proc.pid
if self.verbose:
print(f" booted pid={self.pid} port={self.port} home={self.home}")
deadline = time.time() + boot_timeout
while time.time() < deadline:
if self.proc.poll() is not None:
raise RuntimeError(f"soul exited during boot: {self._log_tail()}")
rss = self._rss_kb()
if rss and rss > 6 * 1024 * 1024:
self.stop()
raise RuntimeError(f"soul RSS {rss}KB > 6GB — aborted")
try:
with urllib.request.urlopen(f"{self.base}/health", timeout=2) as r:
if r.status == 200:
if self.verbose:
print(f" healthy in {time.time() - t0:.1f}s, RSS={self._rss_kb()}KB")
return
except Exception:
pass
time.sleep(0.5)
self.stop()
raise RuntimeError(f"soul never healthy on {self.base}: {self._log_tail()}")
def _rss_kb(self):
try:
out = subprocess.run(["ps", "-o", "rss=", "-p", str(self.pid)],
capture_output=True, text=True, timeout=5).stdout.strip()
return int(out) if out else None
except Exception:
return None
def _log_tail(self, n=15):
try:
with open(self.log, encoding="utf-8", errors="replace") as fh:
return "\n".join(fh.read().splitlines()[-n:])
except Exception:
return "(no log)"
def recall(self, query, limit, timeout=60):
url = f"{self.base}/api/neuron/recall?query={urllib.parse.quote(query)}&limit={limit}"
t0 = time.perf_counter()
try:
with urllib.request.urlopen(url, timeout=timeout) as r:
raw = r.read().decode("utf-8", "replace")
ms = (time.perf_counter() - t0) * 1000
except Exception as exc:
return [], (time.perf_counter() - t0) * 1000, f"{type(exc).__name__}: {exc}"
try:
arr = json.loads(raw)
except Exception:
return [], ms, f"unparseable response ({len(raw)}B)"
if not isinstance(arr, list):
return [], ms, f"non-array response: {str(arr)[:120]}"
ids = [x.get("id") for x in arr if isinstance(x, dict) and x.get("id")]
return ids, ms, None
def stop(self):
"""Kill and CONFIRM. A test process that outlives its test is a bug."""
if self.pid is None:
self.confirmed_dead = True
return True
for sig in (signal.SIGTERM, signal.SIGKILL):
try:
os.kill(self.pid, sig)
except ProcessLookupError:
break
except Exception:
pass
for _ in range(20):
try:
os.kill(self.pid, 0)
except ProcessLookupError:
break
time.sleep(0.1)
else:
continue
break
try:
self.proc.wait(timeout=5)
except Exception:
pass
try:
os.kill(self.pid, 0)
self.confirmed_dead = False
except ProcessLookupError:
self.confirmed_dead = True
if self.verbose:
print(f" pid {self.pid}: {'CONFIRMED DEAD' if self.confirmed_dead else 'STILL ALIVE'}")
if self.home and os.path.isdir(self.home):
shutil.rmtree(self.home, ignore_errors=True)
return self.confirmed_dead
# ─────────────────────────────────────────────────────────────────────────────
# eval
# ─────────────────────────────────────────────────────────────────────────────
def evaluate(soul, gold, limit):
rows = []
for q in gold["queries"]:
ids, ms, err = soul.recall(q["query"], limit)
rel = q.get("relevant") or []
row = {
"id": q["id"],
"category": q["category"],
"query": q["query"],
"returned": ids,
"n_returned": len(ids),
"latency_ms": round(ms, 1),
"error": err,
}
if q.get("expect_empty"):
row["clean"] = (len(ids) == 0)
row["false_positives"] = len(ids)
else:
row["hit@5"] = hit_at_k(ids, rel, 5)
row["recall@5"] = recall_at_k(ids, rel, 5)
row["recall@10"] = recall_at_k(ids, rel, 10)
row["precision@5"] = precision_at_k(ids, rel, 5)
row["mrr@10"] = mrr(ids, rel, 10)
if q.get("must_outrank"):
correct, stale = q["must_outrank"]
ic = ids.index(correct) if correct in ids else None
istale = ids.index(stale) if stale in ids else None
# Correct must be present AND above the stale node. A run that
# returns neither is NOT a pass: the corrected fact is what the
# user needed.
row["outranks"] = (ic is not None) and (istale is None or ic < istale)
row["rank_correct"] = None if ic is None else ic + 1
row["rank_stale"] = None if istale is None else istale + 1
rows.append(row)
return rows
def aggregate(rows):
scored = [r for r in rows if "hit@5" in r]
nonsense = [r for r in rows if "clean" in r]
outrank = [r for r in rows if "outranks" in r]
lat = sorted(r["latency_ms"] for r in rows)
agg = {
"n_queries": len(rows),
"n_scored": len(scored),
"hit@5": mean([r["hit@5"] for r in scored]),
"recall@5": mean([r["recall@5"] for r in scored]),
"recall@10": mean([r["recall@10"] for r in scored]),
"precision@5": mean([r["precision@5"] for r in scored]),
"mrr@10": mean([r["mrr@10"] for r in scored]),
"nonsense_clean": f"{sum(1 for r in nonsense if r['clean'])}/{len(nonsense)}",
"superseded_outranks": f"{sum(1 for r in outrank if r['outranks'])}/{len(outrank)}",
"latency_ms_p50": lat[len(lat) // 2] if lat else 0,
"latency_ms_p95": lat[max(0, int(len(lat) * 0.95) - 1)] if lat else 0,
"latency_ms_max": lat[-1] if lat else 0,
"errors": sum(1 for r in rows if r["error"]),
"by_category": {},
}
cats = sorted({r["category"] for r in rows})
for c in cats:
cr = [r for r in rows if r["category"] == c]
if c == "nonsense":
agg["by_category"][c] = {
"n": len(cr),
"clean": sum(1 for r in cr if r["clean"]),
"avg_false_positives": mean([float(r["false_positives"]) for r in cr]),
}
else:
e = {
"n": len(cr),
"hit@5": mean([r.get("hit@5") for r in cr]),
"recall@5": mean([r.get("recall@5") for r in cr]),
"recall@10": mean([r.get("recall@10") for r in cr]),
"mrr@10": mean([r.get("mrr@10") for r in cr]),
}
if c == "superseded":
e["outranks"] = sum(1 for r in cr if r.get("outranks"))
agg["by_category"][c] = e
return agg
def print_table(label, agg):
print(f"\n=== {label} ===")
print(f" queries {agg['n_queries']} ({agg['n_scored']} scored + "
f"{agg['n_queries'] - agg['n_scored']} control) · errors {agg['errors']}")
print(f" {'hit@5':>12} {'recall@5':>10} {'recall@10':>10} {'prec@5':>9} {'MRR@10':>9}")
print(f" {pct([agg['hit@5']]):>12} {pct([agg['recall@5']]):>10} {pct([agg['recall@10']]):>10} "
f"{pct([agg['precision@5']]):>9} {agg['mrr@10']:>9.3f}")
print(f" nonsense clean {agg['nonsense_clean']} · superseded outranks {agg['superseded_outranks']}")
print(f" latency ms p50 {agg['latency_ms_p50']:.0f} · p95 {agg['latency_ms_p95']:.0f} "
f"· max {agg['latency_ms_max']:.0f}")
print(f"\n {'category':14} {'n':>3} {'hit@5':>8} {'recall@5':>9} {'recall@10':>10} {'MRR@10':>8}")
for c, e in agg["by_category"].items():
if c == "nonsense":
print(f" {c:14} {e['n']:>3} {'clean ' + str(e['clean']) + '/' + str(e['n']):>8}"
f"{'':>9} {'':>10} {'avg FP ' + format(e['avg_false_positives'], '.1f'):>8}")
else:
extra = f" outranks {e['outranks']}/{e['n']}" if "outranks" in e else ""
print(f" {c:14} {e['n']:>3} {pct([e['hit@5']]):>8} {pct([e['recall@5']]):>9} "
f"{pct([e['recall@10']]):>10} {e['mrr@10']:>8.3f}{extra}")
def main():
ap = argparse.ArgumentParser()
ap.add_argument("--soul", required=True)
ap.add_argument("--corpus", required=True)
ap.add_argument("--label", required=True)
ap.add_argument("--gold", default=os.path.join(HERE, "gold_set.json"))
ap.add_argument("--port", type=int, default=7893)
ap.add_argument("--limit", type=int, default=10)
ap.add_argument("--out", default=None)
args = ap.parse_args()
with open(args.gold, encoding="utf-8") as fh:
gold = json.load(fh)
print(f"[{args.label}] soul={os.path.basename(args.soul)} "
f"corpus={os.path.basename(args.corpus)} gold={len(gold['queries'])}q limit={args.limit}")
soul = Soul(args.soul, args.corpus, args.port)
rows = []
started = time.time()
try:
soul.start()
rows = evaluate(soul, gold, args.limit)
finally:
dead = soul.stop()
agg = aggregate(rows)
print_table(args.label, agg)
out = args.out or os.path.join(HERE, f"results-{args.label}.json")
doc = {
"label": args.label,
"soul_binary": os.path.abspath(args.soul),
"soul_md5": subprocess.run(["md5", "-q", args.soul], capture_output=True,
text=True).stdout.strip(),
"corpus": os.path.abspath(args.corpus),
"corpus_nodes": gold.get("corpus_nodes"),
"corpus_edges": gold.get("corpus_edges"),
"gold_set": os.path.abspath(args.gold),
"limit": args.limit,
"port": args.port,
"wall_clock_s": round(time.time() - started, 1),
"child_pid": soul.pid,
"child_confirmed_dead": soul.confirmed_dead,
"aggregate": agg,
"rows": rows,
}
with open(out, "w", encoding="utf-8") as fh:
json.dump(doc, fh, indent=1, ensure_ascii=False)
print(f"\nwrote {out}")
if not dead:
print("FATAL: child process could not be confirmed dead", file=sys.stderr)
sys.exit(4)
if __name__ == "__main__":
main()