ruvector-mragent 0.1.0

package/agent/memory.mjs

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+// MRAgent FROZEN MODEL — the Cue-Tag-Content associative memory substrate.
+//
+// Per the Meta-Harness invariant ("freeze the model, evolve the harness"), this
+// file is NEVER mutated by Darwin. It is the RuVector-backed memory store. In
+// production the nodes, embeddings, and edges live in a RuVector `.rvf` index and
+// traversal is a Cypher query:
+//
+//   MATCH (c:Cue)-[:LINKED_TO*1..N]->(t:Tag)-[:REFERENCES]->(m:Content)
+//   WHERE c.id IN $cueIds RETURN m
+//
+// To keep this example runnable with ZERO native dependencies (and fully
+// deterministic for CI), the store is reimplemented in-process with the same
+// semantics: hybrid (sparse+dense RRF) cue search and bounded-depth, prunable
+// graph reconstruction. If the real `ruvector` package is installed it is used
+// for embeddings; otherwise a deterministic hashed embedding is used. Either way
+// the GRAPH SEMANTICS are identical, so the harness genome evolved here transfers
+// to a live RuVector deployment unchanged.
+
+import { createRequire } from "node:module";
+import { NUM_CONCEPTS, conceptOf, syn } from "./concepts.mjs";
+const require = createRequire(import.meta.url);
+
+// Runtime-optional production backend. The example never *requires* it.
+let RuVector = null;
+try { RuVector = require("ruvector"); } catch { /* deterministic fallback */ }
+
+// Dense embedding = concept-projected semantics + a small lexical hash tail.
+// The concept block (first NUM_CONCEPTS dims) makes paraphrases dense-close even
+// with zero shared tokens; the hash tail keeps unique tokens distinguishable.
+const HASH_TAIL = 64;
+export const EMBED_DIM = NUM_CONCEPTS + HASH_TAIL;
+export const usingRuVector = !!RuVector;
+
+const STOP = new Set(["the", "a", "an", "to", "of", "is", "are", "and", "in", "into", "does", "do", "what", "which", "how", "with", "from", "for", "that"]);
+
+export function tokenize(text) {
+  return String(text)
+    .toLowerCase()
+    .replace(/[^a-z0-9]+/g, " ")
+    .split(" ")
+    .filter((w) => w.length > 1 && !STOP.has(w));
+}
+
+// Deterministic FNV-1a hash → stable across runs/platforms (no Math.random here).
+function hash32(str) {
+  let h = 0x811c9dc5;
+  for (let i = 0; i < str.length; i++) {
+    h ^= str.charCodeAt(i);
+    h = Math.imul(h, 0x01000193) >>> 0;
+  }
+  return h >>> 0;
+}
+
+// Deterministic concept-projected embedding. Stands in for an ONNX MiniLM dense
+// vector: tokens sharing a concept (synonyms) land on the same concept dim, so
+// paraphrases are dense-close WITHOUT lexical overlap. Identifier-like tokens
+// only hit the hash tail, so they are semantically generic (sparse decides them).
+export function embed(text) {
+  const v = new Float32Array(EMBED_DIM);
+  const toks = tokenize(text);
+  for (const t of toks) {
+    const c = conceptOf(t);
+    if (c >= 0) {
+      v[c] += 1; // concept dimension (dense semantics)
+    } else {
+      // lexical-only token → hash tail (after the concept block)
+      v[NUM_CONCEPTS + (hash32(t) % HASH_TAIL)] += 0.6;
+      v[NUM_CONCEPTS + (hash32("salt:" + t) % HASH_TAIL)] += 0.3;
+    }
+  }
+  let norm = 0;
+  for (let i = 0; i < EMBED_DIM; i++) norm += v[i] * v[i];
+  norm = Math.sqrt(norm) || 1;
+  for (let i = 0; i < EMBED_DIM; i++) v[i] /= norm;
+  return v;
+}
+
+function cosine(a, b) {
+  let dot = 0;
+  for (let i = 0; i < a.length; i++) dot += a[i] * b[i];
+  return dot; // both are L2-normalized
+}
+
+// Sparse term-overlap score (BM25-lite): shared tokens / sqrt(len product).
+function sparseScore(queryToks, docToks) {
+  if (!queryToks.length || !docToks.length) return 0;
+  const q = new Set(queryToks);
+  let shared = 0;
+  for (const t of docToks) if (q.has(t)) shared++;
+  return shared / Math.sqrt(queryToks.length * docToks.length);
+}
+
+// ── Graph builder ───────────────────────────────────────────────────────────
+// Builds the Cue-Tag-Content graph from the eval corpus, plus cross-task
+// distractor cues/contents so every gene is load-bearing.
+//
+// Texts are SYNTHESIZED from each task's structured signal spec (concept names +
+// lexical identifiers) so that dense/sparse separation, ranking-distractors and
+// multi-hop bridges are guaranteed, not dependent on fragile English wording.
+//
+//   query        = qConcepts(variant0) + qLex
+//   correct cue  = cue.concepts(variant1) + cue.lex      (same concepts, diff tokens)
+//   correct text = qConcepts(variant0) + expected_fact + cue.lex
+//   distractor   = query echoed twice (out-ranks correct on raw sim, no fact)
+//   decoy cue    = decoy.concepts/lex → wrong tag → wrong content
+//
+// Edge model:
+//   Cue -LINKED_TO-> [bridge0 -> … ->] { relevantTag, corroborateTag }
+//   Tag -REFERENCES-> Content
+function synth(concepts = [], lex = [], variant = 0) {
+  return [...concepts.map((c) => syn(c, variant)), ...lex].join(" ");
+}
+
+/** Synthesize the query string for a task spec (used at retrieval time). */
+export function queryTextFor(spec) {
+  return synth(spec.qConcepts || [], spec.qLex || [], 0);
+}
+
+export function buildGraph(specs) {
+  const cues = new Map();
+  const tags = new Map();
+  const content = new Map();
+  const queries = new Map();
+
+  const mkTag = (name) => {
+    const id = `tag:${name}`;
+    const t = { id, name, text: name.replace(/-/g, " "), toks: tokenize(name), vec: embed(name.replace(/-/g, " ")), content: [], next: [] };
+    tags.set(id, t);
+    return t;
+  };
+  const mkContent = (id, text, taskId) => {
+    content.set(id, { id, text, toks: tokenize(text), vec: embed(text), taskId });
+    return id;
+  };
+
+  for (const spec of specs) {
+    queries.set(spec.id, queryTextFor(spec));
+
+    // Unanswerable task: NO correct content exists — the only honest answer is to
+    // abstain. We still create the cue + decoys so the agent has something to chase
+    // and must judge that the reconstructed evidence is too weak (low confidence).
+    const answerable = spec.answerable !== false;
+
+    let entry;
+    if (answerable) {
+      // Correct content: relevant to the query (shares query concepts) + the fact.
+      const cid = `content:${spec.id}`;
+      mkContent(cid, [synth(spec.qConcepts, [], 0), spec.expected_fact, ...(spec.cue?.lex || [])].join(" "), spec.id);
+
+      // Relevant tag references the correct content (+ ranking-distractor contents).
+      const rel = mkTag(`${spec.id}-rel`);
+      rel.content.push(cid);
+      for (let d = 0; d < (spec.distractors || 0); d++) {
+        // Echoes the query MORE than the correct content → higher raw sim, but no
+        // expected_fact. Only rerank (corroboration) or a wide window survives it.
+        const did = mkContent(`content:${spec.id}:d${d}`,
+          [synth(spec.qConcepts, spec.qLex, 0), synth(spec.qConcepts, [], 0), (spec.qLex || []).join(" ")].join(" "),
+          `${spec.id}-distractor`);
+        rel.content.push(did);
+      }
+
+      // Corroborating tag references the SAME correct content via a second path.
+      // Only surfaces with rerank="gnn" (corroboration boost) AND tagFanout>=2.
+      const tail = [rel];
+      if (spec.corroborate) {
+        const corr = mkTag(`${spec.id}-corr`);
+        corr.content.push(cid);
+        tail.push(corr);
+      }
+
+      // Bridge chain: cue -> b0 -> … -> tail. k bridges ⇒ need traversalDepth k+1.
+      const bridges = [];
+      for (let b = 0; b < (spec.bridges || 0); b++) bridges.push(mkTag(`${spec.id}-b${b}`));
+      for (let b = 0; b < bridges.length; b++) {
+        const nxt = b + 1 < bridges.length ? [bridges[b + 1]] : tail;
+        for (const t of nxt) bridges[b].next.push(t.id);
+      }
+      entry = bridges.length ? [bridges[0]] : tail;
+    } else {
+      // Only a weak tag with a low-similarity placeholder → confidence stays low.
+      const weak = mkTag(`${spec.id}-weak`);
+      const wid = mkContent(`content:${spec.id}:weak`, ["tangential unrelated note", spec.id].join(" "), `${spec.id}-none`);
+      weak.content.push(wid);
+      entry = [weak];
+    }
+
+    // Correct cue (concepts via variant-1 surface tokens, so dense-close to query
+    // but lexically distinct; shares cue.lex with the query for the sparse signal).
+    mkCue(cues, `cue:${spec.id}:correct`,
+      synth(spec.cue?.concepts || [], spec.cue?.lex || [], 1), answerable ? spec.id : `${spec.id}-none`, entry.map((t) => t.id));
+
+    // Decoy cues → wrong tag → wrong content. Concepts use variant-2 surface tokens
+    // so a concept-decoy is dense-close to the query but shares NO token with it —
+    // the correct cue is only retrievable with the right fusion weight.
+    (spec.decoys || []).forEach((dec, di) => {
+      const wc = mkContent(`content:${spec.id}:w${di}`, ["wrong decoy", synth(dec.concepts || [], dec.lex || [], 2)].join(" "), `${spec.id}-decoy`);
+      const wt = mkTag(`${spec.id}-w${di}`);
+      wt.content.push(wc);
+      mkCue(cues, `cue:${spec.id}:decoy${di}`, synth(dec.concepts || [], dec.lex || [], 2), `${spec.id}-decoy`, [wt.id]);
+    });
+  }
+
+  return { cues, tags, content, queries };
+}
+
+function mkCue(cues, id, text, taskId, links) {
+  cues.set(id, { id, text, toks: tokenize(text), vec: embed(text), taskId, links });
+}
+
+// ── MemoryStore: hybrid cue search + bounded-depth reconstruction ─────────────
+export class MemoryStore {
+  constructor(tasks) {
+    this.tasks = tasks;
+    this.graph = buildGraph(tasks);
+    this.cueList = [...this.graph.cues.values()];
+  }
+
+  /** Synthesized query string for a task id (the text actually issued at search). */
+  queryText(taskId) {
+    return this.graph.queries.get(taskId) ?? "";
+  }
+
+  /**
+   * Stage 1 — find entry cues with hybrid (sparse + dense) search + RRF.
+   * `efSearch` bounds the dense candidate pool (HNSW recall proxy): a small
+   * efSearch can drop the correct cue before fusion ever sees it.
+   */
+  hybridSearch(queryText, { cueK = 5, efSearch = 64, hybridAlpha = 0.5, fusion = "rrf" } = {}) {
+    const qTok = tokenize(queryText);
+    const qVec = embed(queryText);
+
+    const dense = this.cueList
+      .map((c) => ({ c, s: cosine(qVec, c.vec) }))
+      .sort((a, b) => b.s - a.s)
+      .slice(0, Math.max(1, efSearch)); // HNSW recall ceiling
+
+    const sparse = this.cueList
+      .map((c) => ({ c, s: sparseScore(qTok, c.toks) }))
+      .sort((a, b) => b.s - a.s)
+      .slice(0, Math.max(1, efSearch));
+
+    const fused = fuse(dense, sparse, { hybridAlpha, fusion });
+    return fused.slice(0, Math.max(1, cueK)).map((e) => e.c.id);
+  }
+
+  /**
+   * Stage 2 — ACTIVE RECONSTRUCTION. From cue ids, traverse LINKED_TO up to
+   * `traversalDepth` hops (expanding <= tagFanout tags per frontier node),
+   * scoring each path by query relevance with per-hop decay, pruning paths
+   * below `pruneThreshold`, and collecting REFERENCES content (capped maxContent).
+   * Returns ordered content + reconstruction stats.
+   */
+  reconstruct(queryText, cueIds, { traversalDepth = 2, tagFanout = 4, pruneThreshold = 0.15, maxContent = 10, decay = 0.7, haltConfidence = 1.1 } = {}) {
+    const qVec = embed(queryText);
+    const qTok = tokenize(queryText);
+    const { tags, content } = this.graph;
+
+    // Per content: best single-path score AND # of corroborating paths.
+    const acc = new Map(); // contentId -> { best, paths }
+    let nodesVisited = 0;
+    let hops = 0;
+    let halted = false;
+    const seenTag = new Set();
+
+    let frontier = [];
+    for (const cueId of cueIds) {
+      const cue = this.graph.cues.get(cueId);
+      if (!cue) continue;
+      for (const tagId of cue.links.slice(0, tagFanout)) frontier.push({ tagId, evidence: 1 });
+    }
+
+    for (let depth = 0; depth < traversalDepth && frontier.length; depth++) {
+      hops = depth + 1;
+      const next = [];
+      for (const { tagId, evidence } of frontier) {
+        if (seenTag.has(tagId)) continue;
+        seenTag.add(tagId);
+        const tag = tags.get(tagId);
+        if (!tag) continue;
+        nodesVisited++;
+
+        // Cue→Tag links are ASSOCIATIVE (structural), not semantic. Path strength
+        // is the carried cue evidence, decayed per hop.
+        const carried = evidence * decay ** depth;
+
+        for (const cid of tag.content) {
+          const c = content.get(cid);
+          if (!c) continue;
+          const contentSim = 0.6 * cosine(qVec, c.vec) + 0.4 * sparseScore(qTok, c.toks);
+          const pathScore = carried * contentSim;
+          if (pathScore < pruneThreshold) continue; // prune irrelevant path
+          const e = acc.get(cid) ?? { best: 0, sim: 0, paths: 0 };
+          e.best = Math.max(e.best, pathScore);     // decayed — for ranking competition
+          e.sim = Math.max(e.sim, contentSim);      // raw relevance — for abstention confidence
+          e.paths += 1; // corroboration: distinct paths reaching this content
+          acc.set(cid, e);
+        }
+
+        for (const nxt of tag.next.slice(0, tagFanout)) next.push({ tagId: nxt, evidence });
+      }
+      frontier = next;
+
+      // ADAPTIVE DEPTH (beyond MRAgent): halt once a genuinely relevant answer
+      // exists, spending traversal only on hard queries (ACT-style adaptive
+      // computation). Uses RAW relevance (sim), not the decayed score, so a deep-
+      // but-relevant answer can trigger halt while a mediocre shallow one cannot.
+      let top = 0;
+      for (const e of acc.values()) top = Math.max(top, e.sim);
+      if (top >= haltConfidence) { halted = true; break; }
+    }
+
+    const ordered = [...acc.entries()]
+      .map(([id, e]) => ({ id, score: e.best, sim: e.sim, paths: e.paths, taskId: content.get(id)?.taskId, text: content.get(id)?.text }))
+      .sort((a, b) => b.score - a.score)
+      .slice(0, Math.max(1, maxContent));
+
+    // Abstention confidence = the chosen content's RAW relevance to the query, not
+    // its decayed path score — so a deep-but-relevant answer is not mistaken for a
+    // weak one. This keeps the abstain threshold robust across traversal depths.
+    const confidence = ordered.length ? ordered[0].sim : 0;
+    return { content: ordered, stats: { hops, nodesVisited, candidates: acc.size, halted, confidence } };
+  }
+}
+
+// Reciprocal Rank Fusion (and linear / dbsf variants) over two ranked lists.
+function fuse(dense, sparse, { hybridAlpha, fusion }) {
+  const k = 60;
+  const acc = new Map(); // cueId -> { c, s }
+  const add = (id, c, s) => {
+    const e = acc.get(id) ?? { c, s: 0 };
+    e.s += s;
+    acc.set(id, e);
+  };
+  if (fusion === "linear") {
+    const dMax = Math.max(1e-9, ...dense.map((e) => e.s));
+    const sMax = Math.max(1e-9, ...sparse.map((e) => e.s));
+    dense.forEach((e) => add(e.c.id, e.c, hybridAlpha * (e.s / dMax)));
+    sparse.forEach((e) => add(e.c.id, e.c, (1 - hybridAlpha) * (e.s / sMax)));
+  } else if (fusion === "dbsf") {
+    // distribution-based score fusion: z-normalize then weight
+    const z = (arr) => {
+      const m = arr.reduce((a, e) => a + e.s, 0) / (arr.length || 1);
+      const sd = Math.sqrt(arr.reduce((a, e) => a + (e.s - m) ** 2, 0) / (arr.length || 1)) || 1;
+      return new Map(arr.map((e) => [e.c.id, (e.s - m) / sd]));
+    };
+    const zd = z(dense), zs = z(sparse);
+    dense.forEach((e) => add(e.c.id, e.c, hybridAlpha * (zd.get(e.c.id) ?? 0)));
+    sparse.forEach((e) => add(e.c.id, e.c, (1 - hybridAlpha) * (zs.get(e.c.id) ?? 0)));
+  } else {
+    // rrf (default)
+    dense.forEach((e, i) => add(e.c.id, e.c, hybridAlpha * (1 / (k + i + 1))));
+    sparse.forEach((e, i) => add(e.c.id, e.c, (1 - hybridAlpha) * (1 / (k + i + 1))));
+  }
+  return [...acc.values()].sort((a, b) => b.s - a.s);
+}

package/benchmark.mjs

@@ -0,0 +1,63 @@
+// MRAgent benchmark (v2): baseline vs Darwin-evolved harness over the frozen
+// Cue-Tag-Content corpus, plus the consolidation (replay) pass. Reports the three
+// beyond-SOTA dimensions: helpfulness (accuracy), calibration (risk + halluc), and
+// reconstruction cost (latency/hops/context). Picks up the evolved genome from
+// optimize.report.json if present.
+//
+// Run: npm run benchmark
+
+import fs from "node:fs";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+import { MemoryStore, baselineGenome, evaluate } from "./agent/harness.mjs";
+import { consolidate } from "./agent/consolidate.mjs";
+
+const __dirname = path.dirname(fileURLToPath(import.meta.url));
+const corpus = JSON.parse(fs.readFileSync(path.join(__dirname, "data", "eval-set.json"), "utf8"));
+const tasks = corpus.tasks;
+
+const baseline = baselineGenome();
+// Evolved genome: from a prior `npm run optimize`, else a calibrated reference.
+let evolved = { ...baseline, fusion: "linear", traversalDepth: 3, abstainThreshold: 0.4, haltConfidence: 0.5, maxContent: 6, tagFanout: 3 };
+const reportPath = path.join(__dirname, "optimize.report.json");
+if (fs.existsSync(reportPath)) {
+  try {
+    const rep = JSON.parse(fs.readFileSync(reportPath, "utf8"));
+    if (rep?.evolved?.genome) evolved = rep.evolved.genome;
+  } catch { /* keep reference */ }
+}
+
+const base = evaluate(baseline, new MemoryStore(tasks), tasks);
+const evoStore = new MemoryStore(tasks);
+const evo = evaluate(evolved, evoStore, tasks);
+
+// Consolidation pass (self-reorganizing memory) on the evolved harness.
+const evoPre = evaluate(evolved, evoStore, tasks);
+const cons = consolidate(evoStore, tasks, evolved);
+const evoPost = evaluate(evolved, evoStore, tasks);
+
+console.log("== MRAgent benchmark (v2 — beyond MRAgent) ==");
+console.log(`corpus: ${tasks.length} Cue-Tag-Content tasks (semantic/lexical/hybrid/bridge/distractor/unanswerable)\n`);
+console.log("config            accuracy  risk   halluc  latency  hops  context");
+const row = (name, m) =>
+  console.log(`${name.padEnd(17)} ${(m.accuracy * 100).toFixed(1).padStart(5)}%  ${m.riskScore.toFixed(3)}  ${m.hallucinationRate.toFixed(2)}   ${m.avgLatencyMs.toFixed(2).padStart(5)}   ${m.avgHops.toFixed(2)}  ${m.avgContext.toFixed(1)}`);
+row("baseline", base);
+row("evolved", evo);
+row("evolved+replay", evoPost);
+
+const dAcc = (evo.accuracy - base.accuracy) * 100;
+const dRisk = evo.riskScore - base.riskScore;
+const dHops = ((evoPre.avgHops - evoPost.avgHops) / Math.max(evoPre.avgHops, 1e-9)) * 100;
+console.log(`\nevolved vs baseline: accuracy ${dAcc >= 0 ? "+" : ""}${dAcc.toFixed(1)}pt · risk ${dRisk >= 0 ? "+" : ""}${dRisk.toFixed(3)} · hallucination ${base.hallucinationRate.toFixed(2)} → ${evo.hallucinationRate.toFixed(2)}`);
+console.log(`consolidation: ${cons.consolidated} shortcuts → ${dHops.toFixed(1)}% fewer hops at ${(evoPost.accuracy * 100).toFixed(1)}% accuracy`);
+
+const report = {
+  frozenModel: "RuVector Cue-Tag-Content graph (frozen)",
+  corpusSize: tasks.length,
+  baseline: { genome: baseline, metrics: base },
+  evolved: { genome: evolved, metrics: evo },
+  consolidated: { shortcuts: cons.consolidated, metrics: evoPost },
+  deltas: { accuracyPoints: dAcc, riskDelta: dRisk, hopsReductionPct: dHops },
+};
+fs.writeFileSync(path.join(__dirname, "benchmark.report.json"), JSON.stringify(report, null, 2));
+console.log(`\nreport -> ${path.join(__dirname, "benchmark.report.json")}`);