cozo-memory 1.2.9 → 1.2.11

package/README.md

@@ -7,6 +7,8 @@
 
 > **Why Cozo Memory?**  
 > LLMs have short-term memory limits. Standard RAG retrieves documents but can't connect facts across time. Cozo Memory gives your AI agent **persistent, structured memory** – it remembers past conversations, infers relationships, detects contradictions, and explores its knowledge graph – fully on your machine, with **optional local LLM integration via Ollama** for intelligent actions (cleanup, reflection, summarization, agentic routing).
+>
+> Most memory stacks combine separate databases: SQLite for facts, Chroma for vector search, NetworkX for graphs. **CozoDB replaces all of that with one embedded engine**: relational, graph, vector, and full-text search in a single query language, one file, zero sync lag.
 
 **Local-first memory for Claude & AI agents with hybrid search, Graph-RAG, and time-travel – runs entirely on your machine. Optional [Ollama](https://ollama.ai) integration enables LLM-powered actions (cleanup, reflect, summarize, agentic retrieval).**
 
@@ -51,7 +53,7 @@ Now add the server to your MCP client (e.g. Claude Desktop) – see [Integration
 
 ⏱️ **Time-Travel Queries** - Version all changes via CozoDB Validity; query any point in history with full audit trails
 
-🎯 **GraphRAG-R1 Adaptive Retrieval** - Intelligent system with Progressive Retrieval Attenuation (PRA) and Cost-Aware F1 (CAF) scoring that learns from usage
+🎯 **GraphRAG-R1-Inspired Adaptive Retrieval** - Intelligent system with Progressive Retrieval Attenuation (PRA) and Cost-Aware F1 (CAF) scoring, conceptually inspired by GraphRAG-R1 (Yu et al., WWW 2026) and adapted for CozoDB, that learns from usage
 
 ⏳ **Temporal Conflict Resolution** - Automatic detection and resolution of contradictory observations with semantic analysis and audit preservation
 
@@ -65,17 +67,36 @@ Now add the server to your MCP client (e.g. Claude Desktop) – see [Integration
 
 ## Positioning & Comparison
 
+### Why CozoDB instead of SQLite + Chroma + NetworkX?
+
+A common first question is: *"Why not just combine existing tools?"*
+
+| If you need... | Typical separate stack | CozoDB Memory |
+| :--- | :--- | :--- |
+| Structured data & relations | **SQLite** / PostgreSQL | ✅ Built-in relational engine |
+| Semantic / vector search | **Chroma** / Qdrant / Pinecone | ✅ HNSW + FTS + RRF in one engine |
+| Graph traversal & reasoning | **NetworkX** / Neo4j | ✅ Native graph queries + PageRank |
+| Time-travel / versioning | Custom audit tables | ✅ Built-in `Validity` time-travel |
+| Unified query language | Multiple APIs + glue code | ✅ Single Datalog query across all dimensions |
+
+**The core insight:** Most memory stacks bolt vector search onto a graph DB, or graph search onto a vector DB. CozoDB is different: it is a **single engine** that natively combines relational, graph, vector, and full-text search. That means:
+
+- **One query language** (Datalog) reaches every dimension.
+- **No sync lag** between separate indexes.
+- **No ETL bridge** between "vector results" and "graph expansion."
+- **Smaller operational surface**: one database file, one process, one dependency chain.
+
+### Comparison with other memory solutions
+
 Most "Memory" MCP servers fall into two categories:
 1. **Simple Knowledge Graphs**: CRUD operations on triples, often only text search
 2. **Pure Vector Stores**: Semantic search (RAG), but little understanding of complex relationships
 
-This server fills the gap in between ("Sweet Spot"): A **local, database-backed memory engine** combining vector, graph, and keyword signals.
-
-### Comparison with other solutions
+This server fills the gap in between ("Sweet Spot"): A **local, database-backed memory engine** combining vector, graph, and keyword signals — powered by CozoDB's unified engine rather than a patchwork of separate databases.
 
 | Feature | **CozoDB Memory (This Project)** | **Official Reference (`@modelcontextprotocol/server-memory`)** | **mcp-memory-service (Community)** | **Database Adapters (Qdrant/Neo4j)** |
 | :--- | :--- | :--- | :--- | :--- |
-| **Backend** | **CozoDB** (Graph + Vector + Relational) | JSON file (`memory.jsonl`) | SQLite / Cloudflare | Specialized DB (only Vector or Graph) |
+| **Backend** | **CozoDB** (Graph + Vector + Relational + FTS in one engine) | JSON file (`memory.jsonl`) | SQLite / Cloudflare | Specialized DB (only Vector or Graph) |
 | **Search Logic** | **Agentic (Auto-Route)**: Hybrid + Graph + Summaries | Keyword only / Exact Graph Match | Vector + Keyword | Mostly only one dimension |
 | **Inference** | **Yes**: Built-in engine for implicit knowledge | No | No ("Dreaming" is consolidation) | No (Retrieval only) |
 | **Community** | **Yes**: Hierarchical Community Summaries | No | No | Only clustering (no summary) |
@@ -451,8 +472,8 @@ Built with:
 - [FastMCP](https://github.com/jlowin/fastmcp) - MCP server framework
 
 Research foundations:
-- GraphRAG-R1 (Yu et al., WWW 2026)
+- GraphRAG-R1 (Yu et al., WWW 2026) - conceptual inspiration for adaptive retrieval
 - HopRAG (ACL 2025)
 - T-GRAG (Li et al., 2025)
-- FEEG Framework (Samuel et al., 2026)
+- FEEG Framework (Samuel et al., 2026) - conceptual inspiration for query intent classification
 - Allan-Poe (arXiv:2511.00855)

package/dist/benchmark.js

@@ -8,153 +8,431 @@ const path_1 = __importDefault(require("path"));
 const fs_1 = __importDefault(require("fs"));
 const perf_hooks_1 = require("perf_hooks");
 const BENCHMARK_DB_PATH = path_1.default.join(process.cwd(), "benchmark_db");
-async function runBenchmark() {
-    console.log("🚀 Starting Performance Benchmark...");
-    // Cleanup
+function parseArgs() {
+    const args = process.argv.slice(2);
+    const opts = {
+        format: process.env.BENCH_FORMAT || "text",
+        runs: parseInt(process.env.BENCH_RUNS || "5", 10),
+        warmupRuns: parseInt(process.env.BENCH_WARMUP || "2", 10),
+        enableRerank: (process.env.BENCH_ENABLE_RERANK || "false").toLowerCase() !== "false",
+    };
+    for (let i = 0; i < args.length; i++) {
+        const a = args[i];
+        if (a === "--format" && args[i + 1])
+            opts.format = args[++i];
+        else if (a === "--runs" && args[i + 1])
+            opts.runs = Math.max(1, parseInt(args[++i], 10));
+        else if (a === "--warmup" && args[i + 1])
+            opts.warmupRuns = Math.max(0, parseInt(args[++i], 10));
+        else if (a === "--csv" && args[i + 1])
+            opts.csvPath = args[++i];
+        else if (a === "--enable-rerank")
+            opts.enableRerank = true;
+        else if (a === "--no-rerank")
+            opts.enableRerank = false;
+    }
+    if (!["text", "json", "markdown"].includes(opts.format)) {
+        opts.format = "text";
+    }
+    return opts;
+}
+function percentile(sorted, p) {
+    if (sorted.length === 0)
+        return 0;
+    const pos = (sorted.length - 1) * p;
+    const base = Math.floor(pos);
+    const rest = pos - base;
+    if (sorted[base + 1] !== undefined) {
+        return sorted[base] + rest * (sorted[base + 1] - sorted[base]);
+    }
+    return sorted[base];
+}
+function mean(values) {
+    if (values.length === 0)
+        return 0;
+    return values.reduce((a, b) => a + b, 0) / values.length;
+}
+function median(values) {
+    const sorted = values.slice().sort((a, b) => a - b);
+    return percentile(sorted, 0.5);
+}
+function stddev(values) {
+    if (values.length < 2)
+        return 0;
+    const m = mean(values);
+    const v = values.reduce((s, x) => s + (x - m) ** 2, 0) / (values.length - 1);
+    return Math.sqrt(v);
+}
+function formatNum(n, digits = 2) {
+    return n.toFixed(digits);
+}
+async function time(fn) {
+    const t0 = perf_hooks_1.performance.now();
+    const result = await fn();
+    const t1 = perf_hooks_1.performance.now();
+    return { result, ms: t1 - t0 };
+}
+async function warmupServer(server, times = 2) {
+    const durations = [];
+    for (let i = 0; i < times; i++) {
+        const { ms } = await time(async () => {
+            await server.hybridSearch.search({ query: "warmup benchmark", limit: 5, includeEntities: true, includeObservations: true });
+            await server.hybridSearch.graphRag({ query: "warmup", limit: 5, graphConstraints: { maxDepth: 1 } });
+        });
+        durations.push(ms);
+    }
+    return durations.length ? mean(durations) : 0;
+}
+function computeNDCG(results, expectedNames, k) {
+    const topK = results.slice(0, k);
+    const relevances = topK.map((r) => {
+        const name = (r.name || "").toLowerCase();
+        return expectedNames.some(e => e.toLowerCase() === name) ? 1 : 0;
+    });
+    const ideal = expectedNames.slice(0, k).map(() => 1);
+    const dcg = relevances.reduce((sum, rel, idx) => sum + rel / Math.log2(idx + 2), 0);
+    const idealDcg = ideal.reduce((sum, rel, idx) => sum + rel / Math.log2(idx + 2), 0);
+    return idealDcg === 0 ? 0 : dcg / idealDcg;
+}
+function computeRecall(results, expectedNames, k) {
+    const topK = results.slice(0, k);
+    const found = expectedNames.filter(name => topK.some(r => (r.name || "").toLowerCase() === name.toLowerCase()));
+    return expectedNames.length ? found.length / expectedNames.length : 0;
+}
+function computeMRR(results, expectedNames) {
+    for (let i = 0; i < results.length; i++) {
+        const name = (results[i].name || "").toLowerCase();
+        if (expectedNames.some(e => e.toLowerCase() === name)) {
+            return 1 / (i + 1);
+        }
+    }
+    return 0;
+}
+async function seedData(server) {
+    const entities = [];
+    const addEntity = async (name, type, metadata) => {
+        const entity = await server.createEntity({ name, type, metadata });
+        entities.push(entity);
+        return entity;
+    };
+    const acme = await addEntity("Acme Corp", "Organization", {});
+    const openai = await addEntity("OpenAI", "Organization", {});
+    const google = await addEntity("Google", "Organization", {});
+    const samOpenAI = await addEntity("Sam Altman", "Person", {});
+    const samAcme = await addEntity("Sam Brown", "Person", {});
+    const aliceGoogle = await addEntity("Alice Chen", "Person", {});
+    const aliceAcme = await addEntity("Alice Walker", "Person", {});
+    const bobEngineer = await addEntity("Bob Martinez", "Person", {});
+    const projectX = await addEntity("Project X", "Project", {});
+    const projectY = await addEntity("Project Y", "Project", {});
+    const datalog = await addEntity("Datalog", "Technology", {});
+    const python = await addEntity("Python", "Technology", {});
+    const rust = await addEntity("Rust", "Technology", {});
+    const oldInitiative = await addEntity("Legacy Initiative", "Project", {});
+    const newInitiative = await addEntity("Cloud Initiative", "Project", {});
+    const obs = async (entityId, text, metadata) => server.addObservation({ entity_id: entityId, text, metadata });
+    const rel = async (fromId, toId, relationType, strength = 0.9) => server.createRelation({ from_id: fromId, to_id: toId, relation_type: relationType, strength });
+    await obs(samOpenAI.id, "Sam Altman is the CEO of OpenAI since 2019.", { year: 2019 });
+    await obs(samOpenAI.id, "Sam Altman briefly joined Acme Corp as advisor in 2023.", { year: 2023 });
+    await obs(samOpenAI.id, "Sam Altman returned to OpenAI full-time in late 2023.", { year: 2023 });
+    await obs(samAcme.id, "Sam Brown is the CFO of Acme Corp since 2021.", { year: 2021 });
+    await obs(aliceGoogle.id, "Alice Chen works at Google on search ranking.", { year: 2022 });
+    await obs(aliceGoogle.id, "Alice Chen moved to Acme Corp as VP Engineering in 2024.", { year: 2024 });
+    await obs(aliceAcme.id, "Alice Walker is a product manager at Acme Corp.", { year: 2020 });
+    await obs(bobEngineer.id, "Bob Martinez is a senior engineer on Project X.", { year: 2022 });
+    await obs(bobEngineer.id, "Bob Martinez switched from Python to Rust in 2024.", { year: 2024 });
+    await obs(projectX.id, "Project X is Acme Corp's internal search engine.", { year: 2021 });
+    await obs(projectX.id, "Project X is being rewritten in Rust.", { year: 2024 });
+    await obs(projectY.id, "Project Y is Acme Corp's data lake.", { year: 2022 });
+    await obs(projectY.id, "Project Y was paused in 2024.", { year: 2024 });
+    await obs(acme.id, "Acme Corp acquired a Datalog startup in 2022.", { year: 2022 });
+    await obs(acme.id, "Acme Corp is headquartered in Berlin.", { year: 2020 });
+    await obs(datalog.id, "Datalog is used inside Project X for policy rules.", { year: 2023 });
+    await obs(datalog.id, "Datalog was replaced by SQL in Project Y.", { year: 2024 });
+    await obs(oldInitiative.id, "Legacy Initiative was cancelled in 2023.", { year: 2023 });
+    await obs(newInitiative.id, "Cloud Initiative started in 2024.", { year: 2024 });
+    await rel(samOpenAI.id, openai.id, "works_at", 0.95);
+    await rel(samOpenAI.id, acme.id, "advised", 0.7);
+    await rel(samAcme.id, acme.id, "works_at", 0.95);
+    await rel(aliceGoogle.id, google.id, "works_at", 0.9);
+    await rel(aliceGoogle.id, acme.id, "works_at", 0.95);
+    await rel(aliceAcme.id, acme.id, "works_at", 0.95);
+    await rel(bobEngineer.id, projectX.id, "works_on", 0.95);
+    await rel(bobEngineer.id, projectY.id, "works_on", 0.4);
+    await rel(projectX.id, datalog.id, "uses_tech", 0.9);
+    await rel(projectX.id, rust.id, "uses_tech", 0.85);
+    await rel(projectY.id, python.id, "uses_tech", 0.8);
+    await rel(acme.id, oldInitiative.id, "owns", 0.7);
+    await rel(acme.id, newInitiative.id, "owns", 0.9);
+    const distractors = [];
+    for (let i = 0; i < 220; i++) {
+        distractors.push(`Background note ${i}: noise about ${i % 5 === 0 ? 'Paris' : i % 5 === 1 ? 'Tokyo' : i % 5 === 2 ? 'finance' : i % 5 === 3 ? 'marketing' : 'logistics'} seed ${i}.`);
+    }
+    for (let i = 0; i < distractors.length; i++) {
+        const target = entities[i % entities.length];
+        await server.addObservation({ entity_id: target.id, text: distractors[i] });
+    }
+    return { entities, NUM_ENTITIES: entities.length, NUM_OBSERVATIONS: 265, NUM_RELATIONS: 14 };
+}
+async function measureRecall(server, runs, warmupRuns, opts) {
+    const tasks = [
+        { query: "Who works at OpenAI?", expected: ["Sam Altman", "OpenAI"], type: "factual" },
+        { query: "Current CEO of OpenAI", expected: ["Sam Altman"], type: "factual" },
+        { query: "Alice engineering manager Acme", expected: ["Alice Walker", "Alice Chen"], type: "ambiguous" },
+        { query: "Who is Bob's colleague on the search engine project?", expected: ["Project X"], type: "relational" },
+        { query: "Project using Datalog and Rust", expected: ["Project X"], type: "multi-hop" },
+        { query: "Technology switched by Bob in 2024", expected: ["Rust", "Python"], type: "temporal" },
+        { query: "Current Acme active initiative 2024", expected: ["Cloud Initiative"], type: "temporal" },
+        { query: "Acme acquisition technology 2022", expected: ["Datalog"], type: "multi-hop" },
+        { query: "Sam Altman Acme advisor", expected: ["Sam Altman", "Acme Corp"], type: "relational" },
+        { query: "Person VP Engineering Acme 2024", expected: ["Alice Chen", "Alice Walker"], type: "temporal" },
+    ];
+    const methods = [
+        { name: "Hybrid Search", fn: (q) => server.hybridSearch.search({ query: q, limit: 10, includeEntities: true, includeObservations: true }) },
+        { name: "Graph-RAG", fn: (q) => server.hybridSearch.graphRag({ query: q, limit: 10, graphConstraints: { maxDepth: 2 } }) },
+        { name: "Graph-Walking", fn: (q) => server.graph_walking({ query: q, limit: 10, max_depth: 3 }) },
+        ...(opts.enableRerank ? [
+            { name: "Reranked Search", fn: (q) => server.hybridSearch.search({ query: q, limit: 10, rerank: true, includeEntities: true, includeObservations: true }) },
+            { name: "Graph-RAG (Reranked)", fn: (q) => server.hybridSearch.graphRag({ query: q, limit: 10, graphConstraints: { maxDepth: 2 }, rerank: true }) },
+        ] : []),
+    ];
+    const results = [];
+    for (const method of methods) {
+        const allRunsRecall10 = [];
+        const allRunsRecall3 = [];
+        const allRunsMRR = [];
+        const allRunsNDCG10 = [];
+        const allRunsLatency = [];
+        for (let r = 0; r < warmupRuns + runs; r++) {
+            await server.hybridSearch.clearCache();
+            let r10 = 0, r3 = 0, mrr = 0, ndcg = 0, lat = 0;
+            for (const task of tasks) {
+                const { result, ms } = await time(() => method.fn(task.query));
+                r10 += computeRecall(result, task.expected, 10);
+                r3 += computeRecall(result, task.expected, 3);
+                mrr += computeMRR(result, task.expected);
+                ndcg += computeNDCG(result, task.expected, 10);
+                lat += ms;
+            }
+            const n = tasks.length;
+            if (r >= warmupRuns) {
+                allRunsRecall10.push(r10 / n);
+                allRunsRecall3.push(r3 / n);
+                allRunsMRR.push(mrr / n);
+                allRunsNDCG10.push(ndcg / n);
+                allRunsLatency.push(lat / n);
+            }
+        }
+        results.push({
+            method: method.name,
+            recallAt10: mean(allRunsRecall10),
+            recallAt3: mean(allRunsRecall3),
+            mrr: mean(allRunsMRR),
+            ndcgAt10: mean(allRunsNDCG10),
+            avgLatencyMs: mean(allRunsLatency),
+            p50LatencyMs: median(allRunsLatency),
+            p95LatencyMs: percentile(allRunsLatency.slice().sort((a, b) => a - b), 0.95),
+        });
+    }
+    return results;
+}
+async function runBenchmark(opts) {
+    console.log(`🚀 Starting Performance Benchmark (runs=${opts.runs}, warmup=${opts.warmupRuns}, format=${opts.format})`);
     if (fs_1.default.existsSync(BENCHMARK_DB_PATH + ".db")) {
         fs_1.default.unlinkSync(BENCHMARK_DB_PATH + ".db");
     }
-    // Measure Memory Baseline
     const memStart = process.memoryUsage();
-    // Initialize Server
+    const envStart = perf_hooks_1.performance.now();
     console.log("• Initializing Server & Loading Embedding Model...");
-    const initStart = perf_hooks_1.performance.now();
     const server = new index_1.MemoryServer(BENCHMARK_DB_PATH);
-    // Force embedding model load
-    await server.embeddingService.embed("warmup");
-    const initEnd = perf_hooks_1.performance.now();
-    console.log(`  -> Init Time: ${(initEnd - initStart).toFixed(2)}ms`);
+    await server.initPromise;
+    const embedWarmupStart = perf_hooks_1.performance.now();
+    await server.embeddingService.embed("benchmark-warmup");
+    const embedWarmupEnd = perf_hooks_1.performance.now();
+    const initMs = embedWarmupEnd - envStart;
+    const firstEmbeddingMs = embedWarmupEnd - embedWarmupStart;
+    console.log(`  -> Init + Warmup: ${formatNum(initMs)}ms`);
+    console.log(`  -> First embedding: ${formatNum(firstEmbeddingMs)}ms`);
     const memAfterInit = process.memoryUsage();
-    console.log(`  -> Memory Increase (Init): ${((memAfterInit.rss - memStart.rss) / 1024 / 1024).toFixed(2)} MB RSS`);
-    // Data Generation
-    const NUM_ENTITIES = 50;
-    const NUM_OBSERVATIONS = 200;
-    const NUM_RELATIONS = 100;
-    console.log(`\n• Generating Data (${NUM_ENTITIES} Entities, ${NUM_OBSERVATIONS} Observations, ${NUM_RELATIONS} Relations)...`);
-    const dataStart = perf_hooks_1.performance.now();
-    // Entities
-    const entities = [];
-    for (let i = 0; i < NUM_ENTITIES; i++) {
-        entities.push(await server.createEntity({
-            name: `Entity_${i}`,
-            type: i % 2 === 0 ? "Person" : "Project",
-            metadata: { index: i }
-        }));
-    }
-    // Observations
-    for (let i = 0; i < NUM_OBSERVATIONS; i++) {
-        const entity = entities[i % NUM_ENTITIES];
-        // @ts-ignore
-        await server.addObservation({
-            // @ts-ignore
-            entity_id: entity.id,
-            text: `This is observation number ${i} for entity ${ // @ts-ignore
-            entity.name}. It contains some random keywords like apple, banana, and cherry.`
-        });
-    }
-    // Relations
-    for (let i = 0; i < NUM_RELATIONS; i++) {
-        const from = entities[i % NUM_ENTITIES];
-        const to = entities[(i + 1) % NUM_ENTITIES];
-        // @ts-ignore
-        await server.createRelation({
-            // @ts-ignore
-            from_id: from.id,
-            // @ts-ignore
-            to_id: to.id,
-            relation_type: "related_to",
-            strength: 0.5
-        });
-    }
-    const dataEnd = perf_hooks_1.performance.now();
-    console.log(`  -> Data Ingestion Time: ${(dataEnd - dataStart).toFixed(2)}ms`);
-    console.log(`  -> Avg Time per Operation: ${((dataEnd - dataStart) / (NUM_ENTITIES + NUM_OBSERVATIONS + NUM_RELATIONS)).toFixed(2)}ms`);
+    console.log(`\n• Seeding Data...`);
+    const seedStart = perf_hooks_1.performance.now();
+    const { entities, NUM_ENTITIES, NUM_OBSERVATIONS, NUM_RELATIONS } = await seedData(server);
+    const seedEnd = perf_hooks_1.performance.now();
+    const totalOps = NUM_ENTITIES + NUM_OBSERVATIONS + NUM_RELATIONS;
+    const ingestionTotalMs = seedEnd - seedStart;
+    const ingestionAvgMs = ingestionTotalMs / totalOps;
+    console.log(`  -> Data Ingestion: ${formatNum(ingestionTotalMs)}ms (${formatNum(ingestionAvgMs)} ms/op)`);
     const memAfterData = process.memoryUsage();
-    console.log(`  -> Memory Increase (Data): ${((memAfterData.rss - memAfterInit.rss) / 1024 / 1024).toFixed(2)} MB RSS`);
-    // Query Benchmark
-    console.log("\n• Running Queries (Hybrid Search)...");
+    await warmupServer(server, opts.warmupRuns);
+    console.log("\n• Running Query Benchmarks...");
     const queries = [
         "observation number 10",
-        "apple banana",
-        "Entity_0",
-        "Project related"
+        "alpha beta gamma",
+        `Entity_${NUM_ENTITIES - 1}`,
+        "Project related",
+        "delta observation keywords",
+        "colleague technology",
+        "Bob Alice relation",
+        "works on project",
+        "Senior Engineer Berlin",
+        "graph traversal seed",
     ];
-    const times = [];
-    for (const q of queries) {
-        const t0 = perf_hooks_1.performance.now();
-        await server.hybridSearch.search({
-            query: q,
-            limit: 10,
-            includeEntities: true,
-            includeObservations: true
-        });
-        const t1 = perf_hooks_1.performance.now();
-        times.push(t1 - t0);
-        process.stdout.write(".");
-    }
-    console.log("");
-    const avgQueryTime = times.reduce((a, b) => a + b, 0) / times.length;
-    const minQueryTime = Math.min(...times);
-    const maxQueryTime = Math.max(...times);
-    console.log(`  -> Avg Query Time: ${avgQueryTime.toFixed(2)}ms`);
-    console.log(`  -> Min Query Time: ${minQueryTime.toFixed(2)}ms`);
-    console.log(`  -> Max Query Time: ${maxQueryTime.toFixed(2)}ms`);
-    // RRF Overhead Estimation (Approximation)
-    // We perform a raw vector search (fastest component) and compare with hybrid search
-    // This is a rough proxy because hybrid search does 5 parallel searches + RRF
-    console.log("\n• Estimating RRF/Combination Overhead...");
-    const tVecStart = perf_hooks_1.performance.now();
-    // Access private method via any cast or just simulate a similar query
-    // Since we can't easily access private methods, we will rely on the fact that
-    // Hybrid Search = Promise.all([Vector, Keyword, Graph]) + RRF
-    // We'll run a search with ONLY vector enabled (by setting weights of others to 0? No, they still run)
-    // We will try to run a pure DB query to simulate vector search time
-    const vectorOnlyStart = perf_hooks_1.performance.now();
-    const qEmb = await server.embeddingService.embed("apple");
-    await server.db.run(`
-    ?[id, score] := ~entity:semantic { id | query: vec($qEmb), k: 10, ef: 20 }, score = 1.0
-  `, { qEmb });
-    const vectorOnlyEnd = perf_hooks_1.performance.now();
-    const vectorTime = vectorOnlyEnd - vectorOnlyStart;
-    console.log(`  -> Raw Vector Search Time: ${vectorTime.toFixed(2)}ms`);
-    console.log(`  -> Overhead (Hybrid Logic + RRF): ${(avgQueryTime - vectorTime).toFixed(2)}ms`);
-    // Graph Benchmark
-    console.log("\n• Running Graph Benchmarks (Graph-RAG & Graph-Walking)...");
-    // Graph-RAG
-    const ragStart = perf_hooks_1.performance.now();
-    // @ts-ignore
-    await server.hybridSearch.graphRag({
-        query: "Entity_0",
-        limit: 20,
-        graphConstraints: {
-            maxDepth: 2
+    const runs = { hybrid: [], reranked: [], graphRag: [], graphWalking: [], rawVector: [] };
+    for (let r = 0; r < opts.runs; r++) {
+        await server.hybridSearch.clearCache();
+        for (const q of queries) {
+            const hybridMs = (await time(() => server.hybridSearch.search({
+                query: q,
+                limit: 10,
+                includeEntities: true,
+                includeObservations: true,
+            }))).ms;
+            runs.hybrid.push(hybridMs);
+            if (opts.enableRerank) {
+                const rerankedMs = (await time(() => server.hybridSearch.search({
+                    query: q,
+                    limit: 10,
+                    rerank: true,
+                    includeEntities: true,
+                    includeObservations: true,
+                }))).ms;
+                runs.reranked.push(rerankedMs);
+            }
+            const graphRagMs = (await time(() => server.hybridSearch.graphRag({
+                query: q,
+                limit: 10,
+                graphConstraints: { maxDepth: 2 },
+            }))).ms;
+            runs.graphRag.push(graphRagMs);
+            const startEntityId = entities[r % entities.length].id;
+            const walkMs = (await time(() => server.graph_walking({
+                query: q,
+                start_entity_id: startEntityId,
+                max_depth: 3,
+                limit: 10,
+            }))).ms;
+            runs.graphWalking.push(walkMs);
         }
-    });
-    const ragEnd = perf_hooks_1.performance.now();
-    console.log(`  -> Graph-RAG (2-Hop) Time: ${(ragEnd - ragStart).toFixed(2)}ms`);
-    // Graph-Walking
-    const walkStart = perf_hooks_1.performance.now();
-    // @ts-ignore
-    const startEntityId = entities[0].id;
-    // @ts-ignore
-    await server.graph_walking({
-        query: "related concepts",
-        start_entity_id: startEntityId,
-        max_depth: 3,
-        limit: 10
-    });
-    const walkEnd = perf_hooks_1.performance.now();
-    console.log(`  -> Graph-Walking (Recursive) Time: ${(walkEnd - walkStart).toFixed(2)}ms`);
-    // Final Memory
+        const qEmb = await server.embeddingService.embed("benchmark-vector-baseline");
+        const vectorMs = (await time(() => server.db.run(`?[id, score] := ~entity:semantic { id | query: vec($qEmb), k: 10, ef: 20 }, score = 1.0`, { qEmb }))).ms;
+        runs.rawVector.push(vectorMs);
+    }
+    console.log("\n• Running Recall Evaluation...");
+    const recall = await measureRecall(server, opts.runs, opts.warmupRuns, opts);
     const memFinal = process.memoryUsage();
-    console.log("\n• Final Memory Stats:");
-    console.log(`  -> RSS: ${(memFinal.rss / 1024 / 1024).toFixed(2)} MB`);
-    console.log(`  -> Heap Used: ${(memFinal.heapUsed / 1024 / 1024).toFixed(2)} MB`);
-    // Cleanup
-    // @ts-ignore
+    console.log(`\n• Final Memory Stats:`);
+    console.log(`  -> RSS Init: ${formatNum(memAfterInit.rss / 1024 / 1024)} MB`);
+    console.log(`  -> RSS After Data: ${formatNum(memAfterData.rss / 1024 / 1024)} MB`);
+    console.log(`  -> RSS Final: ${formatNum(memFinal.rss / 1024 / 1024)} MB`);
+    console.log(`  -> Heap Used Final: ${formatNum(memFinal.heapUsed / 1024 / 1024)} MB`);
+    const summary = {
+        environment: {
+            nodeVersion: process.version,
+            platform: process.platform,
+            timestamp: new Date().toISOString(),
+            embeddingModel: process.env.EMBEDDING_MODEL || "Xenova/bge-m3",
+            dbEngine: process.env.DB_ENGINE || "sqlite",
+        },
+        warmup: {
+            initMs,
+            firstEmbeddingMs,
+        },
+        ingestion: {
+            totalMs: ingestionTotalMs,
+            avgPerOpMs: ingestionAvgMs,
+            throughputOpsPerSec: 1000 / ingestionAvgMs,
+        },
+        memory: {
+            rssAfterInitMB: memAfterInit.rss / 1024 / 1024,
+            rssAfterDataMB: memAfterData.rss / 1024 / 1024,
+            rssFinalMB: memFinal.rss / 1024 / 1024,
+            heapUsedFinalMB: memFinal.heapUsed / 1024 / 1024,
+        },
+        queries: {
+            rawVectorMs: { avg: mean(runs.rawVector), p50: median(runs.rawVector), p95: percentile(runs.rawVector.slice().sort((a, b) => a - b), 0.95) },
+            hybrid: { avg: mean(runs.hybrid), p50: median(runs.hybrid), p95: percentile(runs.hybrid.slice().sort((a, b) => a - b), 0.95) },
+            reranked: { avg: mean(runs.reranked), p50: median(runs.reranked), p95: percentile(runs.reranked.slice().sort((a, b) => a - b), 0.95) },
+            graphRag: { avg: mean(runs.graphRag), p50: median(runs.graphRag), p95: percentile(runs.graphRag.slice().sort((a, b) => a - b), 0.95) },
+            graphWalking: { avg: mean(runs.graphWalking), p50: median(runs.graphWalking), p95: percentile(runs.graphWalking.slice().sort((a, b) => a - b), 0.95) },
+        },
+        recall,
+    };
+    const output = renderSummary(summary, opts);
+    if (opts.format === "json") {
+        console.log(JSON.stringify(summary, null, 2));
+    }
+    else if (opts.format === "markdown") {
+        console.log(output);
+    }
+    else {
+        console.log(output);
+    }
+    if (opts.csvPath && recall.length) {
+        const header = ["method", "recall_at_10", "recall_at_3", "mrr", "ndcg_at_10", "avg_latency_ms", "p50_latency_ms", "p95_latency_ms"];
+        const rows = recall.map(r => [r.method, r.recallAt10.toFixed(4), r.recallAt3.toFixed(4), r.mrr.toFixed(4), r.ndcgAt10.toFixed(4), r.avgLatencyMs.toFixed(2), r.p50LatencyMs.toFixed(2), r.p95LatencyMs.toFixed(2)]);
+        const csv = [header.join(","), ...rows.map(r => r.join(","))].join("\n");
+        fs_1.default.writeFileSync(opts.csvPath, csv);
+        console.log(`\n• CSV written to: ${opts.csvPath}`);
+    }
     server.db.close();
     if (fs_1.default.existsSync(BENCHMARK_DB_PATH + ".db")) {
         fs_1.default.unlinkSync(BENCHMARK_DB_PATH + ".db");
     }
 }
-runBenchmark().catch(console.error);
+function renderSummary(s, opts) {
+    const lines = [];
+    lines.push("==================================================");
+    lines.push("CozoDB Memory Benchmark Results");
+    lines.push("==================================================");
+    lines.push(`Environment: ${s.environment.nodeVersion} on ${s.environment.platform}`);
+    lines.push(`Timestamp:   ${s.environment.timestamp}`);
+    lines.push(`Embedding:   ${s.environment.embeddingModel}`);
+    lines.push(`DB Engine:   ${s.environment.dbEngine}`);
+    lines.push(`Runs:        ${opts.runs}  Warmup: ${opts.warmupRuns}`);
+    lines.push("");
+    lines.push("## Warmup");
+    lines.push(`- Init + Warmup:          ${formatNum(s.warmup.initMs)} ms`);
+    lines.push(`- First embedding:       ${formatNum(s.warmup.firstEmbeddingMs)} ms`);
+    lines.push("");
+    lines.push("## Ingestion");
+    lines.push(`- Total ingestion:       ${formatNum(s.ingestion.totalMs)} ms`);
+    lines.push(`- Avg per operation:     ${formatNum(s.ingestion.avgPerOpMs)} ms`);
+    lines.push(`- Throughput:            ${formatNum(s.ingestion.throughputOpsPerSec)} ops/sec`);
+    lines.push("");
+    lines.push("## Memory");
+    lines.push(`- RSS after init:        ${formatNum(s.memory.rssAfterInitMB)} MB`);
+    lines.push(`- RSS after data load:   ${formatNum(s.memory.rssAfterDataMB)} MB`);
+    lines.push(`- RSS final:             ${formatNum(s.memory.rssFinalMB)} MB`);
+    lines.push(`- Heap used final:       ${formatNum(s.memory.heapUsedFinalMB)} MB`);
+    lines.push("");
+    lines.push("## Query Latency (ms)");
+    lines.push("| Method           | Avg      | P50      | P95      |");
+    lines.push("|------------------|----------|----------|----------|");
+    lines.push(`| Raw Vector       | ${formatNum(s.queries.rawVectorMs.avg, 2).padEnd(8)} | ${formatNum(s.queries.rawVectorMs.p50, 2).padEnd(8)} | ${formatNum(s.queries.rawVectorMs.p95, 2).padEnd(8)} |`);
+    lines.push(`| Hybrid Search    | ${formatNum(s.queries.hybrid.avg, 2).padEnd(8)} | ${formatNum(s.queries.hybrid.p50, 2).padEnd(8)} | ${formatNum(s.queries.hybrid.p95, 2).padEnd(8)} |`);
+    if (opts.enableRerank) {
+        lines.push(`| Reranked Search  | ${formatNum(s.queries.reranked.avg, 2).padEnd(8)} | ${formatNum(s.queries.reranked.p50, 2).padEnd(8)} | ${formatNum(s.queries.reranked.p95, 2).padEnd(8)} |`);
+    }
+    lines.push(`| Graph-RAG        | ${formatNum(s.queries.graphRag.avg, 2).padEnd(8)} | ${formatNum(s.queries.graphRag.p50, 2).padEnd(8)} | ${formatNum(s.queries.graphRag.p95, 2).padEnd(8)} |`);
+    lines.push(`| Graph-Walking    | ${formatNum(s.queries.graphWalking.avg, 2).padEnd(8)} | ${formatNum(s.queries.graphWalking.p50, 2).padEnd(8)} | ${formatNum(s.queries.graphWalking.p95, 2).padEnd(8)} |`);
+    lines.push("");
+    lines.push(`## Recall & Quality (Mean across ${opts.runs} runs)`);
+    lines.push("| Method                | Recall@10 | Recall@3 | MRR   | nDCG@10 | Avg Latency | P50 Latency | P95 Latency |");
+    lines.push("|-----------------------|-----------|----------|-------|---------|-------------|-------------|-------------|");
+    for (const r of s.recall) {
+        lines.push(`| ${r.method.padEnd(21)} | ${r.recallAt10.toFixed(3).padStart(9)} | ${r.recallAt3.toFixed(3).padStart(8)} | ${r.mrr.toFixed(3).padStart(5)} | ${r.ndcgAt10.toFixed(3).padStart(7)} | ${formatNum(r.avgLatencyMs, 2).padStart(11)} | ${formatNum(r.p50LatencyMs, 2).padStart(11)} | ${formatNum(r.p95LatencyMs, 2).padStart(11)} |`);
+    }
+    lines.push("");
+    lines.push("## Benchmarking external systems");
+    lines.push("Recall/Quality numbers for Chroma, Qdrant, Mem0 are not generated by this script.");
+    lines.push("Fill the comparison table in docs/BENCHMARKS.md only from published/public benchmarks.");
+    lines.push("Do not insert internal estimates into the publication table.");
+    lines.push("");
+    lines.push("==================================================");
+    return lines.join("\n");
+}
+const opts = parseArgs();
+runBenchmark(opts).catch((err) => {
+    console.error("Benchmark failed:", err);
+    process.exit(1);
+});

package/dist/test-adaptive-retrieval.js

@@ -8,7 +8,7 @@ const embedding_service_1 = require("./embedding-service");
 const adaptive_retrieval_1 = require("./adaptive-retrieval");
 const DB_PATH = 'memory_db.cozo.db';
 async function testAdaptiveRetrieval() {
-    console.log('=== Testing GraphRAG-R1 Adaptive Retrieval ===\n');
+    console.log('=== Testing GraphRAG-R1-Inspired Adaptive Retrieval ===\n');
     const db = new cozo_node_1.CozoDb('sqlite', DB_PATH);
     const embeddingService = new embedding_service_1.EmbeddingService();
     const adaptiveRetrieval = new adaptive_retrieval_1.AdaptiveGraphRetrieval(db, embeddingService, {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cozo-memory",
-  "version": "1.2.9",
+  "version": "1.2.11",
   "mcpName": "io.github.tobs-code/cozo-memory",
   "description": "Local-first persistent memory system for AI agents with hybrid search, graph reasoning, and MCP integration",
   "main": "dist/index.js",