@graphty/algorithms 2.1.1 → 2.2.0

package/src/research/grsbm-legacy.ts

@@ -0,0 +1,586 @@
+import type { Graph } from "../core/graph.js";
+import type { NodeId } from "../types/index.js";
+import { SeededRandom } from "../utils/math-utilities.js";
+
+/**
+ * Configuration options for the GRSBM (Greedy Recursive Spectral Bisection) algorithm
+ */
+export interface GRSBMConfig {
+    /** Maximum depth of recursive bisection */
+    maxDepth?: number;
+    /** Minimum cluster size to continue splitting */
+    minClusterSize?: number;
+    /** Number of eigenvectors to use for spectral embedding */
+    numEigenvectors?: number;
+    /** Convergence tolerance for eigenvalue computation */
+    tolerance?: number;
+    /** Maximum number of power iterations for eigenvalue computation */
+    maxIterations?: number;
+    /** Random seed for reproducibility */
+    seed?: number;
+}
+
+/**
+ * Represents a cluster in the hierarchical structure
+ */
+export interface GRSBMCluster {
+    /** Unique identifier for this cluster */
+    id: string;
+    /** Node IDs in this cluster */
+    members: Set<NodeId>;
+    /** Left child cluster (if split) */
+    left?: GRSBMCluster;
+    /** Right child cluster (if split) */
+    right?: GRSBMCluster;
+    /** Modularity score of this cluster */
+    modularity: number;
+    /** Depth in the hierarchy */
+    depth: number;
+    /** Spectral embedding quality score */
+    spectralScore: number;
+}
+
+/**
+ * Result of the GRSBM clustering algorithm
+ */
+export interface GRSBMResult {
+    /** Root of the cluster hierarchy */
+    root: GRSBMCluster;
+    /** Flat clustering at leaf level */
+    clusters: Map<NodeId, number>;
+    /** Number of final clusters */
+    numClusters: number;
+    /** Modularity scores for each level */
+    modularityScores: number[];
+    /** Explanation of the clustering structure */
+    explanation: ClusterExplanation[];
+}
+
+/**
+ * Explanation for a cluster split decision
+ */
+export interface ClusterExplanation {
+    /** Cluster that was split */
+    clusterId: string;
+    /** Reason for the split */
+    reason: string;
+    /** Modularity improvement from the split */
+    modularityImprovement: number;
+    /** Key nodes that influenced the split */
+    keyNodes: NodeId[];
+    /** Spectral embedding values */
+    spectralValues: number[];
+}
+
+/**
+ * GRSBM - Greedy Recursive Spectral Bisection with Modularity
+ *
+ * This algorithm performs hierarchical community detection using spectral
+ * bisection guided by modularity optimization. It provides explainable
+ * community structure by tracking the reasoning behind each split.
+ *
+ * Based on: "Explainable Community Detection via Hierarchical Spectral Clustering" (2024)
+ * @param graph - Input graph to cluster
+ * @param config - Configuration options
+ * @returns Hierarchical clustering result with explanations
+ */
+export function grsbm(graph: Graph, config: GRSBMConfig = {}): GRSBMResult {
+    const {
+        maxDepth = 10,
+        minClusterSize = 2, // Reduced default to allow more splits
+        numEigenvectors = 2,
+        tolerance = 1e-6,
+        maxIterations = 100,
+        seed = 42,
+    } = config;
+
+    // Set random seed for reproducibility
+    const rng = SeededRandom.createGenerator(seed);
+    const originalRandom = Math.random;
+    Math.random = rng;
+
+    const nodes = Array.from(graph.nodes());
+    const nodeCount = nodes.length;
+
+    if (nodeCount === 0) {
+        throw new Error("Cannot cluster empty graph");
+    }
+
+    // Initialize root cluster with all nodes
+    const rootMembers = new Set(nodes.map((node) => node.id));
+    const initialModularity = calculateModularity(graph, new Map([...rootMembers].map((id) => [id, 0])));
+
+    const root: GRSBMCluster = {
+        id: "root",
+        members: rootMembers,
+        modularity: initialModularity,
+        depth: 0,
+        spectralScore: 0,
+    };
+
+    const explanations: ClusterExplanation[] = [];
+    const modularityScores: number[] = [initialModularity];
+
+    // Perform recursive bisection
+    const clusterQueue: GRSBMCluster[] = [root];
+    let nextClusterId = 1;
+
+    while (clusterQueue.length > 0) {
+        const currentCluster = clusterQueue.shift();
+        if (!currentCluster) {
+            continue;
+        }
+
+        // Check stopping criteria
+        if (currentCluster.depth >= maxDepth || currentCluster.members.size < minClusterSize * 2) {
+            continue;
+        }
+
+        // Attempt spectral bisection
+        const bisectionResult = spectralBisection(graph, currentCluster, numEigenvectors, tolerance, maxIterations);
+
+        if (!bisectionResult) {
+            continue; // Could not split this cluster
+        }
+
+        const { leftMembers, rightMembers, spectralScore, keyNodes, spectralValues, reason } = bisectionResult;
+
+        // Create child clusters
+        const leftCluster: GRSBMCluster = {
+            id: `cluster_${String(nextClusterId++)}`,
+            members: leftMembers,
+            modularity: 0, // Will be calculated below
+            depth: currentCluster.depth + 1,
+            spectralScore,
+        };
+
+        const rightCluster: GRSBMCluster = {
+            id: `cluster_${String(nextClusterId++)}`,
+            members: rightMembers,
+            modularity: 0, // Will be calculated below
+            depth: currentCluster.depth + 1,
+            spectralScore,
+        };
+
+        // Calculate modularity improvement
+        const newAssignment = new Map<NodeId, number>();
+        for (const nodeId of leftMembers) {
+            newAssignment.set(nodeId, 0);
+        }
+        for (const nodeId of rightMembers) {
+            newAssignment.set(nodeId, 1);
+        }
+
+        const newModularity = calculateModularity(graph, newAssignment);
+        const modularityImprovement = newModularity - currentCluster.modularity;
+
+        // Only split if modularity improves or is neutral (allow small splits)
+        if (modularityImprovement >= -0.01) {
+            // Small tolerance for neutral splits
+            leftCluster.modularity = newModularity;
+            rightCluster.modularity = newModularity;
+
+            currentCluster.left = leftCluster;
+            currentCluster.right = rightCluster;
+
+            // Add explanation
+            explanations.push({
+                clusterId: currentCluster.id,
+                reason,
+                modularityImprovement,
+                keyNodes,
+                spectralValues,
+            });
+
+            modularityScores.push(newModularity);
+
+            // Add children to queue for further processing
+            clusterQueue.push(leftCluster, rightCluster);
+        }
+    }
+
+    // Extract flat clustering from leaf nodes
+    const clusters = new Map<NodeId, number>();
+    let clusterId = 0;
+
+    function assignClusterIds(cluster: GRSBMCluster): void {
+        if (!cluster.left && !cluster.right) {
+            // Leaf node
+            for (const nodeId of cluster.members) {
+                clusters.set(nodeId, clusterId);
+            }
+            clusterId++;
+        } else {
+            // Internal node - traverse children
+            if (cluster.left) {
+                assignClusterIds(cluster.left);
+            }
+
+            if (cluster.right) {
+                assignClusterIds(cluster.right);
+            }
+        }
+    }
+
+    assignClusterIds(root);
+
+    // Restore original random function
+    Math.random = originalRandom;
+
+    return {
+        root,
+        clusters,
+        numClusters: clusterId,
+        modularityScores,
+        explanation: explanations,
+    };
+}
+
+/**
+ * Perform spectral bisection on a cluster
+ * @param graph - The input graph
+ * @param cluster - The cluster to bisect
+ * @param _numEigenvectors - Number of eigenvectors to compute (reserved for future use)
+ * @param tolerance - Convergence tolerance
+ * @param maxIterations - Maximum number of iterations
+ * @returns Bisection result with left/right members, scores, and explanation, or null if bisection failed
+ */
+function spectralBisection(
+    graph: Graph,
+    cluster: GRSBMCluster,
+    _numEigenvectors: number,
+    tolerance: number,
+    maxIterations: number,
+): {
+    leftMembers: Set<NodeId>;
+    rightMembers: Set<NodeId>;
+    spectralScore: number;
+    keyNodes: NodeId[];
+    spectralValues: number[];
+    reason: string;
+} | null {
+    const members = Array.from(cluster.members);
+    const n = members.length;
+
+    if (n < 4) {
+        return null; // Too small to split meaningfully
+    }
+
+    // Create subgraph Laplacian matrix
+    const laplacian = createLaplacianMatrix(graph, members);
+
+    // Compute the second smallest eigenvector (Fiedler vector)
+    const eigenvector = computeFiedlerVector(laplacian, tolerance, maxIterations);
+
+    if (!eigenvector) {
+        return null; // Could not compute eigenvector
+    }
+
+    // Find optimal split point
+    const sortedIndices = eigenvector.map((value, index) => ({ value, index })).sort((a, b) => a.value - b.value);
+
+    let bestSplitIndex = Math.floor(n / 2);
+    let bestModularity = -Infinity;
+
+    // Try different split points
+    for (let splitIndex = Math.floor(n * 0.2); splitIndex <= Math.floor(n * 0.8); splitIndex++) {
+        const leftIndices = sortedIndices.slice(0, splitIndex).map((item) => item.index);
+        const rightIndices = sortedIndices.slice(splitIndex).map((item) => item.index);
+
+        const assignment = new Map<NodeId, number>();
+        for (const idx of leftIndices) {
+            const nodeId = members[idx];
+            if (nodeId !== undefined) {
+                assignment.set(nodeId, 0);
+            }
+        }
+        for (const idx of rightIndices) {
+            const nodeId = members[idx];
+            if (nodeId !== undefined) {
+                assignment.set(nodeId, 1);
+            }
+        }
+
+        const modularity = calculateModularity(graph, assignment);
+
+        if (modularity > bestModularity) {
+            bestModularity = modularity;
+            bestSplitIndex = splitIndex;
+        }
+    }
+
+    // Create final split
+    const leftIndices = sortedIndices.slice(0, bestSplitIndex).map((item) => item.index);
+    const rightIndices = sortedIndices.slice(bestSplitIndex).map((item) => item.index);
+
+    const leftMembers = new Set<NodeId>();
+    const rightMembers = new Set<NodeId>();
+
+    for (const idx of leftIndices) {
+        const nodeId = members[idx];
+        if (nodeId !== undefined) {
+            leftMembers.add(nodeId);
+        }
+    }
+
+    for (const idx of rightIndices) {
+        const nodeId = members[idx];
+        if (nodeId !== undefined) {
+            rightMembers.add(nodeId);
+        }
+    }
+
+    // Identify key nodes (those with extreme spectral values)
+    const extremeThreshold = 0.1;
+    const sortedValues = [...eigenvector].sort((a, b) => Math.abs(b) - Math.abs(a));
+    const threshold = sortedValues[Math.floor(sortedValues.length * extremeThreshold)] ?? 0;
+
+    const keyNodes: NodeId[] = [];
+    for (let i = 0; i < eigenvector.length; i++) {
+        const eigenValue = eigenvector[i];
+        if (eigenValue !== undefined && Math.abs(eigenValue) >= Math.abs(threshold)) {
+            const nodeId = members[i];
+            if (nodeId !== undefined) {
+                keyNodes.push(nodeId);
+            }
+        }
+    }
+
+    // Calculate spectral score (based on eigenvalue gap)
+    const firstValue = sortedValues[0] ?? 0;
+    const lastValue = sortedValues[sortedValues.length - 1] ?? 0;
+    const spectralScore = Math.abs(firstValue - lastValue);
+
+    // Generate explanation
+    const reason = `Spectral bisection based on Fiedler vector with modularity ${bestModularity.toFixed(3)}. Split creates clusters of sizes ${String(leftMembers.size)} and ${String(rightMembers.size)}.`;
+
+    return {
+        leftMembers,
+        rightMembers,
+        spectralScore,
+        keyNodes: keyNodes.slice(0, 5), // Top 5 key nodes
+        spectralValues: eigenvector,
+        reason,
+    };
+}
+
+/**
+ * Create Laplacian matrix for a subgraph
+ * @param graph - The input graph
+ * @param nodes - The nodes to include in the subgraph
+ * @returns The Laplacian matrix as a 2D array
+ */
+function createLaplacianMatrix(graph: Graph, nodes: NodeId[]): number[][] {
+    const n = nodes.length;
+    const nodeIndex = new Map<NodeId, number>();
+
+    // Create node index mapping
+    for (let i = 0; i < n; i++) {
+        const node = nodes[i];
+        if (node !== undefined) {
+            nodeIndex.set(node, i);
+        }
+    }
+
+    // Initialize Laplacian matrix
+    const laplacian = Array.from({ length: n }, () => new Array<number>(n).fill(0));
+
+    // Fill adjacency part and calculate degrees
+    const degrees = new Array<number>(n).fill(0);
+
+    for (let i = 0; i < n; i++) {
+        const nodeId = nodes[i];
+        if (nodeId === undefined) {
+            continue;
+        }
+
+        for (const neighbor of graph.neighbors(nodeId)) {
+            const neighborIdx = nodeIndex.get(neighbor);
+            if (neighborIdx !== undefined && i < laplacian.length && i < degrees.length) {
+                const row = laplacian[i];
+                if (row) {
+                    row[neighborIdx] = -1;
+                    degrees[i] = (degrees[i] ?? 0) + 1;
+                }
+            }
+        }
+    }
+
+    // Set diagonal (degree) values
+    for (let i = 0; i < n; i++) {
+        const row = laplacian[i];
+        const degree = degrees[i];
+        if (row && degree !== undefined) {
+            row[i] = degree;
+        }
+    }
+
+    return laplacian;
+}
+
+/**
+ * Compute the Fiedler vector (second smallest eigenvector) using power iteration
+ * @param laplacian - The Laplacian matrix
+ * @param tolerance - Convergence tolerance
+ * @param maxIterations - Maximum number of iterations
+ * @returns The Fiedler vector, or null if computation failed
+ */
+function computeFiedlerVector(laplacian: number[][], tolerance: number, maxIterations: number): number[] | null {
+    const n = laplacian.length;
+    if (n < 2) {
+        return null;
+    }
+
+    // Initialize random vector orthogonal to the all-ones vector
+    let vector = new Array<number>(n).fill(0);
+    for (let i = 0; i < n; i++) {
+        vector[i] = Math.random() - 0.5;
+    }
+
+    // Make orthogonal to all-ones vector
+    const mean = vector.reduce((sum: number, val: number) => sum + val, 0) / n;
+    for (let i = 0; i < n; i++) {
+        const val = vector[i];
+        if (val !== undefined) {
+            vector[i] = val - mean;
+        }
+    }
+
+    // Normalize
+    const norm = Math.sqrt(vector.reduce((sum: number, val: number) => sum + val * val, 0));
+    if (norm > 0) {
+        for (let i = 0; i < n; i++) {
+            const val = vector[i];
+            if (val !== undefined) {
+                vector[i] = val / norm;
+            }
+        }
+    }
+
+    // Power iteration with deflation for second smallest eigenvalue
+    for (let iter = 0; iter < maxIterations; iter++) {
+        const newVector = new Array<number>(n).fill(0);
+
+        // Matrix-vector multiplication: newVector = L * vector
+        for (let i = 0; i < n; i++) {
+            let sum = 0;
+            const row = laplacian[i];
+            if (row) {
+                for (let j = 0; j < n; j++) {
+                    const matrixVal = row[j];
+                    const vectorVal = vector[j];
+                    if (matrixVal !== undefined && vectorVal !== undefined) {
+                        sum += matrixVal * vectorVal;
+                    }
+                }
+            }
+
+            newVector[i] = sum;
+        }
+
+        // For smallest eigenvalue, we actually want inverse iteration
+        // This is simplified - in practice would solve (L - shift*I)x = vector
+        // For now, use power iteration on -L (approximately)
+        for (let i = 0; i < n; i++) {
+            const val = newVector[i];
+            if (val !== undefined) {
+                newVector[i] = -val;
+            }
+        }
+
+        // Orthogonalize against all-ones vector
+        const newMean = newVector.reduce((sum, val) => sum + val, 0) / n;
+        for (let i = 0; i < n; i++) {
+            const val = newVector[i];
+            if (val !== undefined) {
+                newVector[i] = val - newMean;
+            }
+        }
+
+        // Normalize
+        const newNorm = Math.sqrt(newVector.reduce((sum, val) => sum + val * val, 0));
+        if (newNorm < tolerance) {
+            break; // Converged to zero vector
+        }
+
+        for (let i = 0; i < n; i++) {
+            const val = newVector[i];
+            if (val !== undefined) {
+                newVector[i] = val / newNorm;
+            }
+        }
+
+        // Check convergence
+        let diff = 0;
+        for (let i = 0; i < n; i++) {
+            const newVal = newVector[i];
+            const oldVal = vector[i];
+            if (newVal !== undefined && oldVal !== undefined) {
+                diff += Math.abs(newVal - oldVal);
+            }
+        }
+
+        vector = newVector;
+
+        if (diff < tolerance) {
+            break;
+        }
+    }
+
+    return vector;
+}
+
+/**
+ * Calculate modularity of a graph partitioning
+ * @param graph - The input graph
+ * @param assignment - Map from node ID to community ID
+ * @returns The modularity score
+ */
+function calculateModularity(graph: Graph, assignment: Map<NodeId, number>): number {
+    const totalEdges = graph.uniqueEdgeCount;
+    if (totalEdges === 0) {
+        return 0;
+    }
+
+    let modularity = 0;
+    const communities = new Map<number, Set<NodeId>>();
+
+    // Group nodes by community
+    for (const [nodeId, communityId] of assignment) {
+        if (!communities.has(communityId)) {
+            communities.set(communityId, new Set());
+        }
+
+        const community = communities.get(communityId);
+        if (community) {
+            community.add(nodeId);
+        }
+    }
+
+    // Calculate modularity for each community
+    for (const [, members] of communities) {
+        let internalEdges = 0;
+        let totalDegree = 0;
+
+        for (const nodeId of members) {
+            const nodeDegree = graph.degree(nodeId);
+            totalDegree += nodeDegree;
+
+            // Count internal edges
+            for (const neighbor of graph.neighbors(nodeId)) {
+                if (members.has(neighbor)) {
+                    internalEdges++;
+                }
+            }
+        }
+
+        // Each edge is counted twice in undirected graphs
+        internalEdges /= 2;
+
+        // Modularity contribution for this community
+        const expectedEdges = (totalDegree * totalDegree) / (4 * totalEdges);
+        modularity += (internalEdges - expectedEdges) / totalEdges;
+    }
+
+    return modularity;
+}