@ninebix/nmt-system 1.0.0

package/dist/extensions/clustering/community-detection.js

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+/**
+ * Community Detection - Graph-based neuron community analysis
+ * @module extensions/clustering/community-detection
+ */
+import { generateUUID } from '../../utils/uuid.js';
+/**
+ * Community Detection Service
+ */
+export class CommunityDetectionService {
+    neuronStore;
+    communities;
+    constructor(neuronStore) {
+        this.neuronStore = neuronStore;
+        this.communities = new Map();
+    }
+    /**
+     * Louvain community detection algorithm
+     */
+    async louvain(options = {}) {
+        const { resolution = 1.0, minCommunitySize = 1, maxIterations = 100 } = options;
+        // Build adjacency data
+        const { nodes, edges, weights, totalWeight } = await this.buildGraph();
+        if (nodes.length === 0) {
+            return { communities: [], modularity: 0, coverage: 0 };
+        }
+        // Initialize: each node in its own community
+        let communityAssignment = new Map();
+        nodes.forEach((id, idx) => communityAssignment.set(id, idx));
+        // Degree of each node
+        const degree = new Map();
+        for (const nodeId of nodes) {
+            let deg = 0;
+            const nodeEdges = edges.get(nodeId) ?? [];
+            for (const [, weight] of nodeEdges) {
+                deg += weight;
+            }
+            degree.set(nodeId, deg);
+        }
+        const hierarchy = [];
+        let improved = true;
+        let iteration = 0;
+        let currentNodes = [...nodes];
+        let currentEdges = new Map(edges);
+        let currentDegree = new Map(degree);
+        let currentTotalWeight = totalWeight;
+        while (improved && iteration < maxIterations) {
+            improved = false;
+            // Phase 1: Local moving
+            const localResult = this.localMoving(currentNodes, currentEdges, currentDegree, communityAssignment, currentTotalWeight, resolution);
+            improved = localResult.improved;
+            communityAssignment = localResult.assignment;
+            // Build communities for this level
+            const levelCommunities = this.buildCommunitiesFromAssignment(currentNodes, currentEdges, communityAssignment);
+            hierarchy.push(levelCommunities);
+            if (improved) {
+                // Phase 2: Aggregation
+                const aggregated = this.aggregate(currentNodes, currentEdges, communityAssignment);
+                currentNodes = aggregated.nodes;
+                currentEdges = aggregated.edges;
+                currentDegree = aggregated.degree;
+                // Reset assignment for aggregated nodes
+                communityAssignment = new Map();
+                currentNodes.forEach((id, idx) => communityAssignment.set(id, idx));
+            }
+            iteration++;
+        }
+        // Find best level by modularity
+        let bestModularity = -Infinity;
+        let bestLevel = 0;
+        for (let l = 0; l < hierarchy.length; l++) {
+            const levelMod = this.calculateLevelModularity(hierarchy[l]);
+            if (levelMod > bestModularity) {
+                bestModularity = levelMod;
+                bestLevel = l;
+            }
+        }
+        // Get communities from best level, filter by size
+        const finalCommunities = hierarchy[bestLevel]
+            .filter(c => c.members.length >= minCommunitySize);
+        // Expand aggregated communities back to original nodes if needed
+        const expandedCommunities = await this.expandCommunities(finalCommunities, nodes);
+        // Calculate overall metrics
+        const modularity = this.calculateModularity(nodes, edges, expandedCommunities, totalWeight);
+        const coverage = expandedCommunities.reduce((sum, c) => sum + c.members.length, 0) / nodes.length;
+        // Store communities
+        for (const community of expandedCommunities) {
+            this.communities.set(community.id, community);
+        }
+        return {
+            communities: expandedCommunities,
+            modularity,
+            coverage,
+            hierarchy: {
+                levels: hierarchy,
+                bestLevel
+            }
+        };
+    }
+    /**
+     * Label Propagation community detection
+     */
+    async labelPropagation(options = {}) {
+        const { maxIterations = 100, minCommunitySize = 1 } = options;
+        const { nodes, edges, totalWeight } = await this.buildGraph();
+        if (nodes.length === 0) {
+            return { communities: [], modularity: 0, coverage: 0 };
+        }
+        // Initialize labels
+        const labels = new Map();
+        nodes.forEach((id, idx) => labels.set(id, idx));
+        let changed = true;
+        let iteration = 0;
+        while (changed && iteration < maxIterations) {
+            changed = false;
+            // Shuffle nodes for random order
+            const shuffled = [...nodes].sort(() => Math.random() - 0.5);
+            for (const nodeId of shuffled) {
+                const neighborLabels = new Map();
+                const nodeEdges = edges.get(nodeId) ?? [];
+                // Count neighbor labels weighted by edge weight
+                for (const [neighborId, weight] of nodeEdges) {
+                    const neighborLabel = labels.get(neighborId);
+                    neighborLabels.set(neighborLabel, (neighborLabels.get(neighborLabel) ?? 0) + weight);
+                }
+                if (neighborLabels.size === 0)
+                    continue;
+                // Find most common label
+                let maxWeight = 0;
+                let bestLabels = [];
+                for (const [label, weight] of neighborLabels) {
+                    if (weight > maxWeight) {
+                        maxWeight = weight;
+                        bestLabels = [label];
+                    }
+                    else if (weight === maxWeight) {
+                        bestLabels.push(label);
+                    }
+                }
+                // Random tie-breaking
+                const newLabel = bestLabels[Math.floor(Math.random() * bestLabels.length)];
+                const currentLabel = labels.get(nodeId);
+                if (newLabel !== currentLabel) {
+                    labels.set(nodeId, newLabel);
+                    changed = true;
+                }
+            }
+            iteration++;
+        }
+        // Build communities from labels
+        const labelGroups = new Map();
+        for (const [nodeId, label] of labels) {
+            if (!labelGroups.has(label)) {
+                labelGroups.set(label, []);
+            }
+            labelGroups.get(label).push(nodeId);
+        }
+        const communities = [];
+        for (const members of labelGroups.values()) {
+            if (members.length >= minCommunitySize) {
+                communities.push(await this.buildCommunity(members, edges, 'label-propagation'));
+            }
+        }
+        const modularity = this.calculateModularity(nodes, edges, communities, totalWeight);
+        const coverage = communities.reduce((sum, c) => sum + c.members.length, 0) / nodes.length;
+        // Store communities
+        for (const community of communities) {
+            this.communities.set(community.id, community);
+        }
+        return { communities, modularity, coverage };
+    }
+    /**
+     * Get community by ID
+     */
+    getCommunity(id) {
+        return this.communities.get(id);
+    }
+    /**
+     * Get all communities
+     */
+    getAllCommunities() {
+        return Array.from(this.communities.values());
+    }
+    /**
+     * Find community for a neuron
+     */
+    findCommunityForNeuron(neuronId) {
+        for (const community of this.communities.values()) {
+            if (community.members.includes(neuronId)) {
+                return community;
+            }
+        }
+        return undefined;
+    }
+    /**
+     * Get bridge nodes (connect multiple communities)
+     */
+    async getBridgeNodes() {
+        const bridges = [];
+        const ids = await this.neuronStore.getAllNeuronIds();
+        for (const id of ids) {
+            const outgoing = await this.neuronStore.getOutgoingSynapses(id);
+            const incoming = await this.neuronStore.getIncomingSynapses(id);
+            const myCommunity = this.findCommunityForNeuron(id);
+            if (!myCommunity)
+                continue;
+            const connectedCommunities = new Set();
+            for (const synapse of [...outgoing, ...incoming]) {
+                const otherId = synapse.sourceId === id ? synapse.targetId : synapse.sourceId;
+                const otherCommunity = this.findCommunityForNeuron(otherId);
+                if (otherCommunity && otherCommunity.id !== myCommunity.id) {
+                    connectedCommunities.add(otherCommunity.id);
+                }
+            }
+            if (connectedCommunities.size > 0) {
+                bridges.push(id);
+            }
+        }
+        return bridges;
+    }
+    // ==================== Private Methods ====================
+    async buildGraph() {
+        const nodes = await this.neuronStore.getAllNeuronIds();
+        const edges = new Map();
+        const weights = new Map();
+        let totalWeight = 0;
+        for (const nodeId of nodes) {
+            edges.set(nodeId, []);
+        }
+        for (const nodeId of nodes) {
+            const outgoing = await this.neuronStore.getOutgoingSynapses(nodeId);
+            for (const synapse of outgoing) {
+                const edgeKey = [nodeId, synapse.targetId].sort().join('-');
+                if (!weights.has(edgeKey)) {
+                    weights.set(edgeKey, synapse.weight);
+                    edges.get(nodeId).push([synapse.targetId, synapse.weight]);
+                    edges.get(synapse.targetId).push([nodeId, synapse.weight]);
+                    totalWeight += synapse.weight;
+                }
+            }
+        }
+        return { nodes, edges, weights, totalWeight };
+    }
+    localMoving(nodes, edges, degree, assignment, totalWeight, resolution) {
+        let improved = false;
+        const newAssignment = new Map(assignment);
+        // Shuffle for random order
+        const shuffled = [...nodes].sort(() => Math.random() - 0.5);
+        for (const nodeId of shuffled) {
+            const currentCommunity = newAssignment.get(nodeId);
+            const nodeDegree = degree.get(nodeId) ?? 0;
+            // Calculate delta Q for moving to each neighbor's community
+            const neighborCommunities = new Map();
+            const nodeEdges = edges.get(nodeId) ?? [];
+            for (const [neighborId, weight] of nodeEdges) {
+                const neighborCommunity = newAssignment.get(neighborId);
+                neighborCommunities.set(neighborCommunity, (neighborCommunities.get(neighborCommunity) ?? 0) + weight);
+            }
+            let bestCommunity = currentCommunity;
+            let bestDelta = 0;
+            for (const [community, edgeWeight] of neighborCommunities) {
+                if (community === currentCommunity)
+                    continue;
+                // Calculate community totals
+                let currentTotal = 0;
+                let targetTotal = 0;
+                for (const [nId, comm] of newAssignment) {
+                    const nDeg = degree.get(nId) ?? 0;
+                    if (comm === currentCommunity)
+                        currentTotal += nDeg;
+                    if (comm === community)
+                        targetTotal += nDeg;
+                }
+                // Delta Q for moving from current to target
+                const deltaQ = (edgeWeight - (neighborCommunities.get(currentCommunity) ?? 0)) / totalWeight
+                    - resolution * nodeDegree * (targetTotal - currentTotal + nodeDegree) / (2 * totalWeight * totalWeight);
+                if (deltaQ > bestDelta) {
+                    bestDelta = deltaQ;
+                    bestCommunity = community;
+                }
+            }
+            if (bestCommunity !== currentCommunity) {
+                newAssignment.set(nodeId, bestCommunity);
+                improved = true;
+            }
+        }
+        return { improved, assignment: newAssignment };
+    }
+    aggregate(nodes, edges, assignment) {
+        // Map communities to super-nodes
+        const communityToSuper = new Map();
+        const superNodes = [];
+        for (const [, community] of assignment) {
+            if (!communityToSuper.has(community)) {
+                const superId = generateUUID();
+                communityToSuper.set(community, superId);
+                superNodes.push(superId);
+            }
+        }
+        // Build super-edges
+        const superEdges = new Map();
+        const superWeights = new Map();
+        for (const superId of superNodes) {
+            superEdges.set(superId, []);
+        }
+        for (const nodeId of nodes) {
+            const nodeComm = assignment.get(nodeId);
+            const superNode = communityToSuper.get(nodeComm);
+            const nodeEdges = edges.get(nodeId) ?? [];
+            for (const [neighborId, weight] of nodeEdges) {
+                const neighborComm = assignment.get(neighborId);
+                const neighborSuper = communityToSuper.get(neighborComm);
+                if (superNode !== neighborSuper) {
+                    const edgeKey = [superNode, neighborSuper].sort().join('-');
+                    superWeights.set(edgeKey, (superWeights.get(edgeKey) ?? 0) + weight);
+                }
+            }
+        }
+        // Add aggregated edges
+        for (const [edgeKey, weight] of superWeights) {
+            const [a, b] = edgeKey.split('-');
+            superEdges.get(a).push([b, weight]);
+            superEdges.get(b).push([a, weight]);
+        }
+        // Calculate degrees
+        const superDegree = new Map();
+        for (const superId of superNodes) {
+            let deg = 0;
+            for (const [, weight] of superEdges.get(superId)) {
+                deg += weight;
+            }
+            superDegree.set(superId, deg);
+        }
+        return {
+            nodes: superNodes,
+            edges: superEdges,
+            degree: superDegree
+        };
+    }
+    buildCommunitiesFromAssignment(nodes, edges, assignment) {
+        const groups = new Map();
+        for (const nodeId of nodes) {
+            const comm = assignment.get(nodeId);
+            if (!groups.has(comm)) {
+                groups.set(comm, []);
+            }
+            groups.get(comm).push(nodeId);
+        }
+        const communities = [];
+        for (const [, members] of groups) {
+            // Calculate density
+            let internalEdges = 0;
+            for (const nodeId of members) {
+                for (const [neighborId] of edges.get(nodeId) ?? []) {
+                    if (members.includes(neighborId)) {
+                        internalEdges++;
+                    }
+                }
+            }
+            internalEdges /= 2; // Each edge counted twice
+            const maxEdges = (members.length * (members.length - 1)) / 2;
+            const density = maxEdges > 0 ? internalEdges / maxEdges : 0;
+            communities.push({
+                id: generateUUID(),
+                members,
+                modularity: 0, // Will be calculated later
+                density,
+                bridgeNodes: [],
+                metadata: {
+                    createdAt: new Date().toISOString(),
+                    algorithm: 'louvain'
+                }
+            });
+        }
+        return communities;
+    }
+    async buildCommunity(members, edges, algorithm) {
+        // Calculate density
+        let internalEdges = 0;
+        for (const nodeId of members) {
+            for (const [neighborId] of edges.get(nodeId) ?? []) {
+                if (members.includes(neighborId)) {
+                    internalEdges++;
+                }
+            }
+        }
+        internalEdges /= 2;
+        const maxEdges = (members.length * (members.length - 1)) / 2;
+        const density = maxEdges > 0 ? internalEdges / maxEdges : 0;
+        // Find bridge nodes
+        const bridgeNodes = [];
+        for (const nodeId of members) {
+            for (const [neighborId] of edges.get(nodeId) ?? []) {
+                if (!members.includes(neighborId)) {
+                    bridgeNodes.push(nodeId);
+                    break;
+                }
+            }
+        }
+        return {
+            id: generateUUID(),
+            members,
+            modularity: 0,
+            density,
+            bridgeNodes,
+            metadata: {
+                createdAt: new Date().toISOString(),
+                algorithm
+            }
+        };
+    }
+    calculateLevelModularity(communities) {
+        // Simplified modularity based on density
+        return communities.reduce((sum, c) => sum + c.density * c.members.length, 0) /
+            communities.reduce((sum, c) => sum + c.members.length, 0);
+    }
+    calculateModularity(nodes, edges, communities, totalWeight) {
+        if (totalWeight === 0)
+            return 0;
+        let Q = 0;
+        const m = totalWeight;
+        // Calculate degree for each node
+        const degree = new Map();
+        for (const nodeId of nodes) {
+            let deg = 0;
+            for (const [, weight] of edges.get(nodeId) ?? []) {
+                deg += weight;
+            }
+            degree.set(nodeId, deg);
+        }
+        for (const community of communities) {
+            for (const i of community.members) {
+                for (const j of community.members) {
+                    if (i === j)
+                        continue;
+                    // Check if edge exists
+                    let aij = 0;
+                    for (const [neighborId, weight] of edges.get(i) ?? []) {
+                        if (neighborId === j) {
+                            aij = weight;
+                            break;
+                        }
+                    }
+                    const ki = degree.get(i) ?? 0;
+                    const kj = degree.get(j) ?? 0;
+                    Q += aij - (ki * kj) / (2 * m);
+                }
+            }
+        }
+        return Q / (2 * m);
+    }
+    async expandCommunities(communities, originalNodes) {
+        // If communities already contain original nodes, return as-is
+        const allMembers = new Set(communities.flatMap(c => c.members));
+        const originalSet = new Set(originalNodes);
+        const needsExpansion = ![...allMembers].every(m => originalSet.has(m));
+        if (!needsExpansion) {
+            return communities;
+        }
+        // For hierarchical expansion, we'd need to track the aggregation mapping
+        // For now, return communities as-is
+        return communities;
+    }
+}
+/**
+ * Create a CommunityDetectionService instance
+ */
+export function createCommunityDetectionService(neuronStore) {
+    return new CommunityDetectionService(neuronStore);
+}
+//# sourceMappingURL=community-detection.js.map

package/dist/extensions/clustering/community-detection.js.map

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package/dist/extensions/clustering/index.d.ts

@@ -0,0 +1,114 @@
+/**
+ * Clustering Module - Automatic neuron grouping and topic modeling
+ * @module extensions/clustering
+ */
+import type { UUID, INeuronStore } from '../../types/index.js';
+/**
+ * Cluster definition
+ */
+export interface Cluster {
+    id: UUID;
+    name?: string;
+    centroid: Float32Array;
+    members: UUID[];
+    avgSimilarity: number;
+    metadata: {
+        createdAt: string;
+        updatedAt: string;
+        algorithmUsed: string;
+    };
+}
+/**
+ * Clustering result
+ */
+export interface ClusteringResult {
+    clusters: Cluster[];
+    noise?: UUID[];
+    iterations?: number;
+    silhouetteScore?: number;
+}
+/**
+ * K-means options
+ */
+export interface KMeansOptions {
+    k: number;
+    maxIterations?: number;
+    tolerance?: number;
+    initMethod?: 'random' | 'kmeans++';
+}
+/**
+ * DBSCAN options
+ */
+export interface DBSCANOptions {
+    eps: number;
+    minPts: number;
+}
+/**
+ * Community detection options
+ */
+export interface CommunityOptions {
+    resolution?: number;
+    minCommunitySize?: number;
+}
+/**
+ * Clustering Service
+ */
+export declare class ClusteringService {
+    private neuronStore;
+    private clusters;
+    constructor(neuronStore: INeuronStore);
+    /**
+     * K-means clustering
+     */
+    kmeans(options: KMeansOptions): Promise<ClusteringResult>;
+    /**
+     * DBSCAN clustering
+     */
+    dbscan(options: DBSCANOptions): Promise<ClusteringResult>;
+    /**
+     * Hierarchical clustering (Agglomerative)
+     */
+    hierarchical(targetClusters: number, linkage?: 'single' | 'complete' | 'average'): Promise<ClusteringResult>;
+    /**
+     * Get cluster by ID
+     */
+    getCluster(id: UUID): Cluster | undefined;
+    /**
+     * Get all clusters
+     */
+    getAllClusters(): Cluster[];
+    /**
+     * Find cluster for a neuron
+     */
+    findClusterForNeuron(neuronId: UUID): Cluster | undefined;
+    /**
+     * Assign new neuron to nearest cluster
+     */
+    assignToCluster(neuronId: UUID): Promise<Cluster | null>;
+    /**
+     * Get cluster statistics
+     */
+    getStats(): {
+        totalClusters: number;
+        avgClusterSize: number;
+        largestCluster: number;
+        smallestCluster: number;
+    };
+    private getAllNeurons;
+    private getNeuronsByIds;
+    private initRandom;
+    private initKMeansPlusPlus;
+    private findNearestCentroid;
+    private updateCentroids;
+    private buildClusters;
+    private calculateAvgSimilarity;
+    private calculateSilhouette;
+    private regionQuery;
+    private expandCluster;
+    private calculateLinkage;
+}
+/**
+ * Create a ClusteringService instance
+ */
+export declare function createClusteringService(neuronStore: INeuronStore): ClusteringService;
+//# sourceMappingURL=index.d.ts.map

package/dist/extensions/clustering/index.d.ts.map

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