@graphty/algorithms 1.0.1 → 1.2.0

package/dist/src/clustering/mcl.js

@@ -0,0 +1,343 @@
+/**
+ * Perform Markov Clustering on a graph
+ */
+export function markovClustering(graph, options = {}) {
+    const { expansion = 2, inflation = 2, maxIterations = 100, tolerance = 1e-6, pruningThreshold = 1e-5, selfLoops = true, } = options;
+    const nodes = Array.from(graph.nodes());
+    const nodeIds = nodes.map((node) => node.id);
+    const n = nodeIds.length;
+    if (n === 0) {
+        return {
+            communities: [],
+            attractors: new Set(),
+            iterations: 0,
+            converged: true,
+        };
+    }
+    // Build initial transition matrix
+    let matrix = buildTransitionMatrix(graph, nodeIds, selfLoops);
+    let converged = false;
+    let iteration = 0;
+    for (iteration = 0; iteration < maxIterations; iteration++) {
+        const oldMatrix = matrix.map((row) => [...row]);
+        // Expansion step (matrix multiplication)
+        matrix = matrixPower(matrix, expansion);
+        // Inflation step (element-wise powering and column normalization)
+        matrix = inflate(matrix, inflation);
+        // Pruning step (remove small values)
+        matrix = prune(matrix, pruningThreshold);
+        // Check for convergence
+        if (hasConverged(oldMatrix, matrix, tolerance)) {
+            converged = true;
+            break;
+        }
+    }
+    // Extract clusters from final matrix
+    const { communities, attractors } = extractClusters(matrix, nodeIds);
+    return {
+        communities,
+        attractors,
+        iterations: iteration + 1,
+        converged,
+    };
+}
+/**
+ * Build initial transition matrix from graph
+ */
+function buildTransitionMatrix(graph, nodeIds, selfLoops) {
+    const n = nodeIds.length;
+    const matrix = Array.from({ length: n }, () => Array(n).fill(0));
+    const nodeToIndex = new Map();
+    nodeIds.forEach((id, index) => nodeToIndex.set(id, index));
+    // Fill adjacency values
+    for (let i = 0; i < n; i++) {
+        const nodeId = nodeIds[i];
+        if (!nodeId) {
+            continue;
+        }
+        const neighbors = graph.neighbors(nodeId);
+        for (const neighbor of neighbors) {
+            const j = nodeToIndex.get(neighbor);
+            if (j !== undefined) {
+                const edge = graph.getEdge(nodeId, neighbor);
+                const weight = edge?.weight ?? 1;
+                const row = matrix[i];
+                if (!row) {
+                    continue;
+                }
+                row[j] = weight;
+            }
+        }
+        // Add self-loops
+        if (selfLoops) {
+            const row = matrix[i];
+            if (!row) {
+                continue;
+            }
+            row[i] = 1;
+        }
+    }
+    // Column-normalize the matrix
+    for (let j = 0; j < n; j++) {
+        let colSum = 0;
+        for (let i = 0; i < n; i++) {
+            const val = matrix[i]?.[j];
+            if (val !== undefined) {
+                colSum += val;
+            }
+        }
+        if (colSum > 0) {
+            for (let i = 0; i < n; i++) {
+                const row = matrix[i];
+                if (!row) {
+                    continue;
+                }
+                const val = row[j];
+                if (val !== undefined) {
+                    row[j] = val / colSum;
+                }
+            }
+        }
+    }
+    return matrix;
+}
+/**
+ * Raise matrix to a power (for expansion step)
+ */
+function matrixPower(matrix, power) {
+    if (power === 1) {
+        return matrix;
+    }
+    if (power === 2) {
+        return matrixMultiply(matrix, matrix);
+    }
+    let result = matrix;
+    for (let i = 1; i < power; i++) {
+        result = matrixMultiply(result, matrix);
+    }
+    return result;
+}
+/**
+ * Multiply two matrices
+ */
+function matrixMultiply(a, b) {
+    const n = a.length;
+    const m = b[0]?.length ?? 0;
+    const p = b.length;
+    const result = Array.from({ length: n }, () => Array(m).fill(0));
+    for (let i = 0; i < n; i++) {
+        for (let j = 0; j < m; j++) {
+            for (let k = 0; k < p; k++) {
+                const aVal = a[i]?.[k] ?? 0;
+                const bVal = b[k]?.[j] ?? 0;
+                const resultRow = result[i];
+                if (!resultRow) {
+                    continue;
+                }
+                const prevVal = resultRow[j];
+                if (prevVal !== undefined) {
+                    resultRow[j] = prevVal + (aVal * bVal);
+                }
+            }
+        }
+    }
+    return result;
+}
+/**
+ * Inflation step: element-wise powering and column normalization
+ */
+function inflate(matrix, inflation) {
+    const n = matrix.length;
+    const result = Array.from({ length: n }, () => Array(n).fill(0));
+    // Element-wise powering
+    for (let i = 0; i < n; i++) {
+        for (let j = 0; j < n; j++) {
+            const val = matrix[i]?.[j];
+            if (val !== undefined) {
+                const resultRow = result[i];
+                if (resultRow) {
+                    resultRow[j] = Math.pow(val, inflation);
+                }
+            }
+        }
+    }
+    // Column normalization
+    for (let j = 0; j < n; j++) {
+        let colSum = 0;
+        for (let i = 0; i < n; i++) {
+            const val = result[i]?.[j];
+            if (val !== undefined) {
+                colSum += val;
+            }
+        }
+        if (colSum > 0) {
+            for (let i = 0; i < n; i++) {
+                const row = result[i];
+                if (!row) {
+                    continue;
+                }
+                const val = row[j];
+                if (val !== undefined) {
+                    row[j] = val / colSum;
+                }
+            }
+        }
+    }
+    return result;
+}
+/**
+ * Pruning step: remove small values
+ */
+function prune(matrix, threshold) {
+    const n = matrix.length;
+    const result = Array.from({ length: n }, () => Array(n).fill(0));
+    for (let i = 0; i < n; i++) {
+        for (let j = 0; j < n; j++) {
+            const matrixRow = matrix[i];
+            if (!matrixRow) {
+                continue;
+            }
+            const matrixVal = matrixRow[j];
+            if (matrixVal !== undefined && matrixVal >= threshold) {
+                const resultRow = result[i];
+                if (resultRow) {
+                    resultRow[j] = matrixVal;
+                }
+            }
+        }
+    }
+    // Re-normalize columns after pruning
+    for (let j = 0; j < n; j++) {
+        let colSum = 0;
+        for (let i = 0; i < n; i++) {
+            const resultRow = result[i];
+            if (!resultRow) {
+                continue;
+            }
+            const val = resultRow[j];
+            if (val !== undefined) {
+                colSum += val;
+            }
+        }
+        if (colSum > 0) {
+            for (let i = 0; i < n; i++) {
+                const resultRow = result[i];
+                if (!resultRow) {
+                    continue;
+                }
+                const val = resultRow[j];
+                if (val !== undefined) {
+                    resultRow[j] = val / colSum;
+                }
+            }
+        }
+    }
+    return result;
+}
+/**
+ * Check if the algorithm has converged
+ */
+function hasConverged(oldMatrix, newMatrix, tolerance) {
+    const n = oldMatrix.length;
+    for (let i = 0; i < n; i++) {
+        for (let j = 0; j < n; j++) {
+            const oldRow = oldMatrix[i];
+            const newRow = newMatrix[i];
+            if (!oldRow || !newRow) {
+                continue;
+            }
+            const oldVal = oldRow[j];
+            const newVal = newRow[j];
+            if (oldVal !== undefined && newVal !== undefined && Math.abs(oldVal - newVal) > tolerance) {
+                return false;
+            }
+        }
+    }
+    return true;
+}
+/**
+ * Extract clusters from the final matrix
+ */
+function extractClusters(matrix, nodeIds) {
+    const n = matrix.length;
+    const attractors = new Set();
+    const communities = [];
+    const nodeToCluster = new Map();
+    // Find attractors (columns with non-zero diagonal elements)
+    for (let i = 0; i < n; i++) {
+        const matrixRow = matrix[i];
+        if (!matrixRow) {
+            continue;
+        }
+        const diagonalVal = matrixRow[i];
+        const nodeId = nodeIds[i];
+        if (diagonalVal !== undefined && diagonalVal > 0 && nodeId !== undefined) {
+            attractors.add(nodeId);
+        }
+    }
+    // Assign nodes to clusters based on columns
+    let clusterIndex = 0;
+    for (let j = 0; j < n; j++) {
+        // Find nodes that belong to this cluster (column)
+        const clusterNodes = [];
+        for (let i = 0; i < n; i++) {
+            const matrixRow = matrix[i];
+            if (!matrixRow) {
+                continue;
+            }
+            const val = matrixRow[j];
+            if (val !== undefined && val > 0 && !nodeToCluster.has(i)) {
+                clusterNodes.push(i);
+                nodeToCluster.set(i, clusterIndex);
+            }
+        }
+        if (clusterNodes.length > 0) {
+            communities.push(clusterNodes.map((idx) => {
+                const nodeId = nodeIds[idx];
+                return nodeId;
+            }).filter((node) => node !== undefined));
+            clusterIndex++;
+        }
+    }
+    // Handle isolated nodes
+    for (let i = 0; i < n; i++) {
+        if (!nodeToCluster.has(i)) {
+            const nodeId = nodeIds[i];
+            if (nodeId !== undefined) {
+                communities.push([nodeId]);
+            }
+            nodeToCluster.set(i, clusterIndex++);
+        }
+    }
+    return { communities, attractors };
+}
+/**
+ * Calculate modularity of MCL clustering result
+ */
+export function calculateMCLModularity(graph, communities) {
+    const m = graph.totalEdgeCount;
+    if (m === 0) {
+        return 0;
+    }
+    let modularity = 0;
+    const communityMap = new Map();
+    // Build community map
+    communities.forEach((community, index) => {
+        community.forEach((nodeId) => {
+            communityMap.set(nodeId, index);
+        });
+    });
+    // Calculate modularity
+    for (const edge of graph.edges()) {
+        const sourceCommunity = communityMap.get(edge.source);
+        const targetCommunity = communityMap.get(edge.target);
+        if (sourceCommunity !== undefined && targetCommunity !== undefined && sourceCommunity === targetCommunity) {
+            modularity += 1;
+        }
+        const sourceDegree = graph.degree(edge.source);
+        const targetDegree = graph.degree(edge.target);
+        modularity -= (sourceDegree * targetDegree) / (2 * m);
+    }
+    return modularity / (2 * m);
+}
+//# sourceMappingURL=mcl.js.map

package/dist/src/clustering/mcl.js.map

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package/dist/src/clustering/spectral.d.ts

@@ -0,0 +1,28 @@
+import type { Graph } from "../core/graph.js";
+import type { NodeId } from "../types/index.js";
+/**
+ * Spectral Clustering implementation
+ *
+ * Uses eigenvalues and eigenvectors of the graph Laplacian matrix to perform clustering.
+ * Particularly effective for finding non-convex clusters and communities in graphs.
+ *
+ * Time complexity: O(V³) for eigendecomposition
+ * Space complexity: O(V²)
+ */
+export interface SpectralClusteringOptions {
+    k: number;
+    laplacianType?: "unnormalized" | "normalized" | "randomWalk";
+    maxIterations?: number;
+    tolerance?: number;
+}
+export interface SpectralClusteringResult {
+    communities: NodeId[][];
+    clusterAssignments: Map<NodeId, number>;
+    eigenvalues?: number[];
+    eigenvectors?: number[][];
+}
+/**
+ * Perform spectral clustering on a graph
+ */
+export declare function spectralClustering(graph: Graph, options: SpectralClusteringOptions): SpectralClusteringResult;
+//# sourceMappingURL=spectral.d.ts.map

package/dist/src/clustering/spectral.d.ts.map

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