@ninebix/nmt-system 1.0.0

package/dist/src/extensions/clustering/index.js

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+/**
+ * Clustering Module - Automatic neuron grouping and topic modeling
+ * @module extensions/clustering
+ */
+import { cosineSimilarity, centroid } from '../../utils/similarity.js';
+import { generateUUID } from '../../utils/uuid.js';
+/**
+ * Clustering Service
+ */
+export class ClusteringService {
+    neuronStore;
+    clusters;
+    constructor(neuronStore) {
+        this.neuronStore = neuronStore;
+        this.clusters = new Map();
+    }
+    /**
+     * K-means clustering
+     */
+    async kmeans(options) {
+        const { k, maxIterations = 100, tolerance = 1e-4, initMethod = 'kmeans++' } = options;
+        // Get all neurons
+        const neurons = await this.getAllNeurons();
+        if (neurons.length < k) {
+            throw new Error(`Not enough neurons (${neurons.length}) for ${k} clusters`);
+        }
+        // Initialize centroids
+        let centroids = initMethod === 'kmeans++'
+            ? this.initKMeansPlusPlus(neurons, k)
+            : this.initRandom(neurons, k);
+        let assignments = new Array(neurons.length).fill(-1);
+        let iterations = 0;
+        let converged = false;
+        while (iterations < maxIterations && !converged) {
+            // Assign neurons to nearest centroid
+            const newAssignments = neurons.map(n => this.findNearestCentroid(n.embedding, centroids));
+            // Check convergence
+            converged = assignments.every((a, i) => a === newAssignments[i]);
+            assignments = newAssignments;
+            if (!converged) {
+                // Update centroids
+                const newCentroids = this.updateCentroids(neurons, assignments, k);
+                // Check centroid movement
+                let maxMovement = 0;
+                for (let i = 0; i < k; i++) {
+                    const movement = 1 - cosineSimilarity(centroids[i], newCentroids[i]);
+                    maxMovement = Math.max(maxMovement, movement);
+                }
+                if (maxMovement < tolerance) {
+                    converged = true;
+                }
+                centroids = newCentroids;
+            }
+            iterations++;
+        }
+        // Build clusters
+        const clusters = this.buildClusters(neurons, assignments, centroids, 'kmeans');
+        // Calculate silhouette score
+        const silhouetteScore = this.calculateSilhouette(neurons, assignments, clusters);
+        // Store clusters
+        for (const cluster of clusters) {
+            this.clusters.set(cluster.id, cluster);
+        }
+        return {
+            clusters,
+            iterations,
+            silhouetteScore
+        };
+    }
+    /**
+     * DBSCAN clustering
+     */
+    async dbscan(options) {
+        const { eps, minPts } = options;
+        const neurons = await this.getAllNeurons();
+        const n = neurons.length;
+        // Build distance matrix (using 1 - similarity)
+        const distances = [];
+        for (let i = 0; i < n; i++) {
+            distances[i] = [];
+            for (let j = 0; j < n; j++) {
+                distances[i][j] = 1 - cosineSimilarity(neurons[i].embedding, neurons[j].embedding);
+            }
+        }
+        const labels = new Array(n).fill(-1); // -1 = unvisited
+        const noise = [];
+        let clusterId = 0;
+        for (let i = 0; i < n; i++) {
+            if (labels[i] !== -1)
+                continue; // Already processed
+            // Find neighbors
+            const neighbors = this.regionQuery(distances, i, eps);
+            if (neighbors.length < minPts) {
+                labels[i] = 0; // Mark as noise
+                noise.push(neurons[i].id);
+            }
+            else {
+                // Expand cluster
+                clusterId++;
+                this.expandCluster(distances, labels, i, neighbors, clusterId, eps, minPts);
+            }
+        }
+        // Build clusters from labels
+        const clusterMap = new Map();
+        for (let i = 0; i < n; i++) {
+            if (labels[i] > 0) {
+                if (!clusterMap.has(labels[i])) {
+                    clusterMap.set(labels[i], []);
+                }
+                clusterMap.get(labels[i]).push(neurons[i].id);
+            }
+        }
+        const clusters = [];
+        for (const [, members] of clusterMap) {
+            const memberNeurons = neurons.filter(n => members.includes(n.id));
+            const centroidVec = centroid(memberNeurons.map(n => n.embedding));
+            clusters.push({
+                id: generateUUID(),
+                centroid: centroidVec,
+                members,
+                avgSimilarity: this.calculateAvgSimilarity(memberNeurons),
+                metadata: {
+                    createdAt: new Date().toISOString(),
+                    updatedAt: new Date().toISOString(),
+                    algorithmUsed: 'dbscan'
+                }
+            });
+        }
+        // Store clusters
+        for (const cluster of clusters) {
+            this.clusters.set(cluster.id, cluster);
+        }
+        return {
+            clusters,
+            noise
+        };
+    }
+    /**
+     * Hierarchical clustering (Agglomerative)
+     */
+    async hierarchical(targetClusters, linkage = 'average') {
+        const neurons = await this.getAllNeurons();
+        const n = neurons.length;
+        // Initialize: each neuron is its own cluster
+        let currentClusters = neurons.map((neuron, i) => ({
+            members: [i],
+            centroid: new Float32Array(neuron.embedding)
+        }));
+        // Build similarity matrix
+        const similarities = [];
+        for (let i = 0; i < n; i++) {
+            similarities[i] = [];
+            for (let j = 0; j < n; j++) {
+                similarities[i][j] = cosineSimilarity(neurons[i].embedding, neurons[j].embedding);
+            }
+        }
+        // Merge until target cluster count
+        while (currentClusters.length > targetClusters) {
+            // Find most similar pair
+            let maxSim = -Infinity;
+            let mergeI = 0, mergeJ = 1;
+            for (let i = 0; i < currentClusters.length; i++) {
+                for (let j = i + 1; j < currentClusters.length; j++) {
+                    const sim = this.calculateLinkage(currentClusters[i].members, currentClusters[j].members, similarities, linkage);
+                    if (sim > maxSim) {
+                        maxSim = sim;
+                        mergeI = i;
+                        mergeJ = j;
+                    }
+                }
+            }
+            // Merge clusters
+            const merged = {
+                members: [...currentClusters[mergeI].members, ...currentClusters[mergeJ].members],
+                centroid: centroid([currentClusters[mergeI].centroid, currentClusters[mergeJ].centroid])
+            };
+            // Remove old clusters and add merged
+            currentClusters = currentClusters.filter((_, idx) => idx !== mergeI && idx !== mergeJ);
+            currentClusters.push(merged);
+        }
+        // Build final clusters
+        const clusters = currentClusters.map(c => {
+            const memberNeurons = c.members.map(i => neurons[i]);
+            return {
+                id: generateUUID(),
+                centroid: c.centroid,
+                members: memberNeurons.map(n => n.id),
+                avgSimilarity: this.calculateAvgSimilarity(memberNeurons),
+                metadata: {
+                    createdAt: new Date().toISOString(),
+                    updatedAt: new Date().toISOString(),
+                    algorithmUsed: `hierarchical-${linkage}`
+                }
+            };
+        });
+        // Store clusters
+        for (const cluster of clusters) {
+            this.clusters.set(cluster.id, cluster);
+        }
+        return { clusters };
+    }
+    /**
+     * Get cluster by ID
+     */
+    getCluster(id) {
+        return this.clusters.get(id);
+    }
+    /**
+     * Get all clusters
+     */
+    getAllClusters() {
+        return Array.from(this.clusters.values());
+    }
+    /**
+     * Find cluster for a neuron
+     */
+    findClusterForNeuron(neuronId) {
+        for (const cluster of this.clusters.values()) {
+            if (cluster.members.includes(neuronId)) {
+                return cluster;
+            }
+        }
+        return undefined;
+    }
+    /**
+     * Assign new neuron to nearest cluster
+     */
+    async assignToCluster(neuronId) {
+        const neuron = await this.neuronStore.getNeuron(neuronId);
+        if (!neuron)
+            return null;
+        let bestCluster = null;
+        let bestSimilarity = -Infinity;
+        for (const cluster of this.clusters.values()) {
+            const sim = cosineSimilarity(neuron.embedding, cluster.centroid);
+            if (sim > bestSimilarity) {
+                bestSimilarity = sim;
+                bestCluster = cluster;
+            }
+        }
+        if (bestCluster) {
+            bestCluster.members.push(neuronId);
+            bestCluster.metadata.updatedAt = new Date().toISOString();
+            // Update centroid
+            const memberNeurons = await this.getNeuronsByIds(bestCluster.members);
+            bestCluster.centroid = centroid(memberNeurons.map(n => n.embedding));
+            bestCluster.avgSimilarity = this.calculateAvgSimilarity(memberNeurons);
+        }
+        return bestCluster;
+    }
+    /**
+     * Get cluster statistics
+     */
+    getStats() {
+        const clusters = Array.from(this.clusters.values());
+        const sizes = clusters.map(c => c.members.length);
+        return {
+            totalClusters: clusters.length,
+            avgClusterSize: sizes.length > 0
+                ? sizes.reduce((a, b) => a + b, 0) / sizes.length
+                : 0,
+            largestCluster: sizes.length > 0 ? Math.max(...sizes) : 0,
+            smallestCluster: sizes.length > 0 ? Math.min(...sizes) : 0
+        };
+    }
+    // ==================== Private Methods ====================
+    async getAllNeurons() {
+        const ids = await this.neuronStore.getAllNeuronIds();
+        const neurons = [];
+        for (const id of ids) {
+            const neuron = await this.neuronStore.getNeuron(id);
+            if (neuron)
+                neurons.push(neuron);
+        }
+        return neurons;
+    }
+    async getNeuronsByIds(ids) {
+        const neurons = [];
+        for (const id of ids) {
+            const neuron = await this.neuronStore.getNeuron(id);
+            if (neuron)
+                neurons.push(neuron);
+        }
+        return neurons;
+    }
+    initRandom(neurons, k) {
+        const indices = new Set();
+        while (indices.size < k) {
+            indices.add(Math.floor(Math.random() * neurons.length));
+        }
+        return Array.from(indices).map(i => new Float32Array(neurons[i].embedding));
+    }
+    initKMeansPlusPlus(neurons, k) {
+        const centroids = [];
+        // Choose first centroid randomly
+        const firstIdx = Math.floor(Math.random() * neurons.length);
+        centroids.push(new Float32Array(neurons[firstIdx].embedding));
+        // Choose remaining centroids
+        for (let c = 1; c < k; c++) {
+            const distances = neurons.map(n => {
+                let minDist = Infinity;
+                for (const cent of centroids) {
+                    const dist = 1 - cosineSimilarity(n.embedding, cent);
+                    minDist = Math.min(minDist, dist);
+                }
+                return minDist * minDist; // Square for probability
+            });
+            // Weighted random selection
+            const totalDist = distances.reduce((a, b) => a + b, 0);
+            let random = Math.random() * totalDist;
+            for (let i = 0; i < neurons.length; i++) {
+                random -= distances[i];
+                if (random <= 0) {
+                    centroids.push(new Float32Array(neurons[i].embedding));
+                    break;
+                }
+            }
+        }
+        return centroids;
+    }
+    findNearestCentroid(embedding, centroids) {
+        let maxSim = -Infinity;
+        let nearest = 0;
+        for (let i = 0; i < centroids.length; i++) {
+            const sim = cosineSimilarity(embedding, centroids[i]);
+            if (sim > maxSim) {
+                maxSim = sim;
+                nearest = i;
+            }
+        }
+        return nearest;
+    }
+    updateCentroids(neurons, assignments, k) {
+        const centroids = [];
+        for (let c = 0; c < k; c++) {
+            const members = neurons.filter((_, i) => assignments[i] === c);
+            if (members.length > 0) {
+                centroids.push(centroid(members.map(m => m.embedding)));
+            }
+            else {
+                // Empty cluster - reinitialize randomly
+                const randomIdx = Math.floor(Math.random() * neurons.length);
+                centroids.push(new Float32Array(neurons[randomIdx].embedding));
+            }
+        }
+        return centroids;
+    }
+    buildClusters(neurons, assignments, centroids, algorithm) {
+        const clusters = [];
+        for (let c = 0; c < centroids.length; c++) {
+            const members = neurons
+                .filter((_, i) => assignments[i] === c)
+                .map(n => n.id);
+            const memberNeurons = neurons.filter((_, i) => assignments[i] === c);
+            clusters.push({
+                id: generateUUID(),
+                centroid: centroids[c],
+                members,
+                avgSimilarity: this.calculateAvgSimilarity(memberNeurons),
+                metadata: {
+                    createdAt: new Date().toISOString(),
+                    updatedAt: new Date().toISOString(),
+                    algorithmUsed: algorithm
+                }
+            });
+        }
+        return clusters;
+    }
+    calculateAvgSimilarity(neurons) {
+        if (neurons.length < 2)
+            return 1;
+        let totalSim = 0;
+        let count = 0;
+        for (let i = 0; i < neurons.length; i++) {
+            for (let j = i + 1; j < neurons.length; j++) {
+                totalSim += cosineSimilarity(neurons[i].embedding, neurons[j].embedding);
+                count++;
+            }
+        }
+        return count > 0 ? totalSim / count : 1;
+    }
+    calculateSilhouette(neurons, assignments, clusters) {
+        if (clusters.length < 2)
+            return 0;
+        let totalScore = 0;
+        for (let i = 0; i < neurons.length; i++) {
+            const myCluster = assignments[i];
+            // Calculate a(i) - average distance to same cluster
+            const sameCluster = neurons.filter((_, j) => assignments[j] === myCluster && j !== i);
+            const a = sameCluster.length > 0
+                ? sameCluster.reduce((sum, n) => sum + (1 - cosineSimilarity(neurons[i].embedding, n.embedding)), 0) / sameCluster.length
+                : 0;
+            // Calculate b(i) - minimum average distance to other clusters
+            let b = Infinity;
+            for (let c = 0; c < clusters.length; c++) {
+                if (c === myCluster)
+                    continue;
+                const otherCluster = neurons.filter((_, j) => assignments[j] === c);
+                if (otherCluster.length > 0) {
+                    const avgDist = otherCluster.reduce((sum, n) => sum + (1 - cosineSimilarity(neurons[i].embedding, n.embedding)), 0) / otherCluster.length;
+                    b = Math.min(b, avgDist);
+                }
+            }
+            // Silhouette score for this point
+            const s = Math.max(a, b) > 0 ? (b - a) / Math.max(a, b) : 0;
+            totalScore += s;
+        }
+        return totalScore / neurons.length;
+    }
+    regionQuery(distances, pointIdx, eps) {
+        const neighbors = [];
+        for (let i = 0; i < distances.length; i++) {
+            if (distances[pointIdx][i] <= eps) {
+                neighbors.push(i);
+            }
+        }
+        return neighbors;
+    }
+    expandCluster(distances, labels, pointIdx, neighbors, clusterId, eps, minPts) {
+        labels[pointIdx] = clusterId;
+        const queue = [...neighbors];
+        let i = 0;
+        while (i < queue.length) {
+            const q = queue[i];
+            if (labels[q] === 0) {
+                // Was noise, now border point
+                labels[q] = clusterId;
+            }
+            if (labels[q] !== -1) {
+                i++;
+                continue;
+            }
+            labels[q] = clusterId;
+            const qNeighbors = this.regionQuery(distances, q, eps);
+            if (qNeighbors.length >= minPts) {
+                for (const n of qNeighbors) {
+                    if (!queue.includes(n)) {
+                        queue.push(n);
+                    }
+                }
+            }
+            i++;
+        }
+    }
+    calculateLinkage(cluster1, cluster2, similarities, linkage) {
+        const allSims = [];
+        for (const i of cluster1) {
+            for (const j of cluster2) {
+                allSims.push(similarities[i][j]);
+            }
+        }
+        switch (linkage) {
+            case 'single':
+                return Math.max(...allSims);
+            case 'complete':
+                return Math.min(...allSims);
+            case 'average':
+                return allSims.reduce((a, b) => a + b, 0) / allSims.length;
+        }
+    }
+}
+/**
+ * Create a ClusteringService instance
+ */
+export function createClusteringService(neuronStore) {
+    return new ClusteringService(neuronStore);
+}
+//# sourceMappingURL=index.js.map

package/dist/src/extensions/clustering/index.js.map

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package/dist/src/index.d.ts

@@ -0,0 +1,14 @@
+/**
+ * NMT System - Neuron Merkle Tree
+ * Verifiable Semantic Knowledge Graph System
+ *
+ * @module nmt-system
+ * @version 1.0.0
+ */
+export * from './types/index.js';
+export * from './core/index.js';
+export * from './storage/index.js';
+export * from './services/index.js';
+export * from './api/index.js';
+export * from './utils/index.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/src/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/index.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAGH,cAAc,kBAAkB,CAAC;AAGjC,cAAc,iBAAiB,CAAC;AAGhC,cAAc,oBAAoB,CAAC;AAGnC,cAAc,qBAAqB,CAAC;AAGpC,cAAc,gBAAgB,CAAC;AAG/B,cAAc,kBAAkB,CAAC"}

package/dist/src/index.js

@@ -0,0 +1,20 @@
+/**
+ * NMT System - Neuron Merkle Tree
+ * Verifiable Semantic Knowledge Graph System
+ *
+ * @module nmt-system
+ * @version 1.0.0
+ */
+// Types
+export * from './types/index.js';
+// Core Engines
+export * from './core/index.js';
+// Storage
+export * from './storage/index.js';
+// Services
+export * from './services/index.js';
+// API
+export * from './api/index.js';
+// Utilities
+export * from './utils/index.js';
+//# sourceMappingURL=index.js.map

package/dist/src/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/index.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,QAAQ;AACR,cAAc,kBAAkB,CAAC;AAEjC,eAAe;AACf,cAAc,iBAAiB,CAAC;AAEhC,UAAU;AACV,cAAc,oBAAoB,CAAC;AAEnC,WAAW;AACX,cAAc,qBAAqB,CAAC;AAEpC,MAAM;AACN,cAAc,gBAAgB,CAAC;AAE/B,YAAY;AACZ,cAAc,kBAAkB,CAAC"}

package/dist/src/mcp/server.d.ts

@@ -0,0 +1,43 @@
+/**
+ * NMT MCP Server
+ * Model Context Protocol server for NMT system
+ *
+ * @module mcp/server
+ */
+/**
+ * NMT MCP Server
+ */
+export declare class NMTMCPServer {
+    private server;
+    private dataDir;
+    private chunkEngine;
+    private merkleEngine;
+    private hnswIndex;
+    private chunkStore;
+    private neuronStore;
+    private indexStore;
+    private graphManager;
+    private ingestionService;
+    private queryService;
+    private verifyService;
+    private clusteringService;
+    private initialized;
+    constructor(dataDir?: string);
+    /**
+     * Initialize all components
+     */
+    init(): Promise<void>;
+    /**
+     * Setup MCP handlers
+     */
+    private setupHandlers;
+    /**
+     * Start the MCP server
+     */
+    start(): Promise<void>;
+    /**
+     * Close the server
+     */
+    close(): Promise<void>;
+}
+//# sourceMappingURL=server.d.ts.map

package/dist/src/mcp/server.d.ts.map

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