@graphty/algorithms 2.1.2 → 2.2.0

package/dist/src/clustering/mcl-legacy.js

@@ -0,0 +1,386 @@
+/**
+ * Perform Markov Clustering on a graph
+ * @param graph - The input graph to cluster
+ * @param options - MCL algorithm options (expansion, inflation, iterations, etc.)
+ * @returns MCL clustering result with communities, attractors, and convergence info
+ */
+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
+ * @param graph - The input graph
+ * @param nodeIds - Array of node IDs in the graph
+ * @param selfLoops - Whether to add self-loops to the matrix
+ * @returns Column-normalized transition matrix
+ */
+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 === undefined) {
+            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)
+ * @param matrix - Input square matrix
+ * @param power - Power to raise the matrix to
+ * @returns Matrix raised to the specified power
+ */
+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
+ * @param a - First matrix
+ * @param b - Second matrix
+ * @returns Product matrix a * b
+ */
+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
+ * @param matrix - Input matrix to inflate
+ * @param inflation - Inflation parameter for element-wise powering
+ * @returns Inflated and column-normalized matrix
+ */
+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
+ * @param matrix - Input matrix to prune
+ * @param threshold - Values below this threshold are set to zero
+ * @returns Pruned and re-normalized matrix
+ */
+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
+ * @param oldMatrix - Matrix from previous iteration
+ * @param newMatrix - Matrix from current iteration
+ * @param tolerance - Convergence tolerance threshold
+ * @returns True if the maximum difference between matrices is below tolerance
+ */
+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
+ * @param matrix - Final converged MCL matrix
+ * @param nodeIds - Array of node IDs corresponding to matrix indices
+ * @returns Object containing communities and attractor nodes
+ */
+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 (columns) to clusters based on which attractor (row) they flow to
+    // After MCL convergence, matrix[i][j] > 0 means node j belongs to attractor i's cluster
+    const attractorToCommunity = new Map();
+    for (let j = 0; j < n; j++) {
+        // Find the attractor for this column (node j)
+        // Look for the row with the highest non-zero value in column j
+        let maxVal = 0;
+        let attractorRow = -1;
+        for (let i = 0; i < n; i++) {
+            const matrixRow = matrix[i];
+            if (!matrixRow) {
+                continue;
+            }
+            const val = matrixRow[j];
+            if (val !== undefined && val > maxVal) {
+                maxVal = val;
+                attractorRow = i;
+            }
+        }
+        if (attractorRow >= 0) {
+            // Node j belongs to the cluster of attractor at row attractorRow
+            let community = attractorToCommunity.get(attractorRow);
+            if (!community) {
+                community = [];
+                attractorToCommunity.set(attractorRow, community);
+            }
+            community.push(j);
+            nodeToCluster.set(j, attractorRow);
+        }
+    }
+    // Convert attractor communities to node ID arrays
+    for (const [, memberIndices] of attractorToCommunity) {
+        communities.push(memberIndices
+            .map((idx) => {
+            const nodeId = nodeIds[idx];
+            return nodeId;
+        })
+            .filter((node) => node !== undefined));
+    }
+    // Handle isolated nodes (nodes with all-zero columns)
+    for (let j = 0; j < n; j++) {
+        if (!nodeToCluster.has(j)) {
+            const nodeId = nodeIds[j];
+            if (nodeId !== undefined) {
+                communities.push([nodeId]);
+            }
+        }
+    }
+    return { communities, attractors };
+}
+/**
+ * Calculate modularity of MCL clustering result
+ * @param graph - The original graph that was clustered
+ * @param communities - Array of communities (each community is an array of node IDs)
+ * @returns Modularity score between -0.5 and 1.0
+ */
+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-legacy.js.map

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

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

@@ -1,30 +1,14 @@
-import type { Graph } from "../core/graph.js";
-import type { NodeId } from "../types/index.js";
 /**
- * Markov Clustering (MCL) algorithm implementation
- *
- * MCL simulates flow in graphs and finds clusters based on the notion that
- * random walks stay within clusters and rarely move between clusters.
- * The algorithm alternates between expansion (matrix squaring) and
- * inflation (element-wise powering and normalization).
- *
- * Time complexity: O(V³) per iteration
- * Space complexity: O(V²)
+ * Markov Clustering (MCL) over a legacy `Graph`. `markovClustering` delegates to
+ * `indexed.markovClustering` through `toSnapshot`, with the graph's exact f64 weights; the result
+ * equals the pre-migration implementation in `mcl-legacy.ts` exactly. Parameters or weights the port
+ * refuses (a fractional expansion, a negative, infinite or NaN weight, an undirected edge whose two
+ * stored halves carry different weights, ...) keep the old code.
  */
-export interface MCLOptions {
-    expansion?: number;
-    inflation?: number;
-    maxIterations?: number;
-    tolerance?: number;
-    pruningThreshold?: number;
-    selfLoops?: boolean;
-}
-export interface MCLResult {
-    communities: NodeId[][];
-    attractors: Set<NodeId>;
-    iterations: number;
-    converged: boolean;
-}
+import type { Graph } from "../core/graph.js";
+import { type MCLOptions, type MCLResult } from "./mcl-legacy.js";
+export type { MCLOptions, MCLResult } from "./mcl-legacy.js";
+export { calculateMCLModularity } from "./mcl-legacy.js";
 /**
  * Perform Markov Clustering on a graph
  * @param graph - The input graph to cluster
@@ -32,11 +16,4 @@ export interface MCLResult {
  * @returns MCL clustering result with communities, attractors, and convergence info
  */
 export declare function markovClustering(graph: Graph, options?: MCLOptions): MCLResult;
-/**
- * Calculate modularity of MCL clustering result
- * @param graph - The original graph that was clustered
- * @param communities - Array of communities (each community is an array of node IDs)
- * @returns Modularity score between -0.5 and 1.0
- */
-export declare function calculateMCLModularity(graph: Graph, communities: NodeId[][]): number;
 //# sourceMappingURL=mcl.d.ts.map

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

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