@graphty/algorithms 1.0.1 → 1.1.0

package/dist/src/clustering/k-core.js

@@ -0,0 +1,377 @@
+/**
+ * K-Core Decomposition Algorithm
+ *
+ * Finds the k-core subgraph where each node has at least k neighbors
+ * within the subgraph. Used for identifying cohesive groups and
+ * understanding graph structure.
+ */
+/**
+ * K-Core decomposition algorithm
+ * Finds all k-cores in the graph and assigns coreness values to nodes
+ *
+ * @param graph - Undirected graph as adjacency list
+ * @returns K-core decomposition results
+ *
+ * Time Complexity: O(V + E)
+ * Space Complexity: O(V)
+ */
+export function kCoreDecomposition(graph) {
+    if (graph.size === 0) {
+        return { cores: new Map(), coreness: new Map(), maxCore: 0 };
+    }
+    const n = graph.size;
+    const nodes = Array.from(graph.keys());
+    const nodeToIndex = new Map();
+    nodes.forEach((node, i) => nodeToIndex.set(node, i));
+    // Initialize data structures
+    const degree = new Array(n).fill(0);
+    const pos = new Array(n).fill(0);
+    const vert = new Array(n).fill(0);
+    const coreness = new Map();
+    // Initialize coreness for all nodes to 0
+    for (let i = 0; i < n; i++) {
+        const node = nodes[i];
+        if (node !== undefined) {
+            coreness.set(node, 0);
+        }
+    }
+    // Compute initial degrees
+    let maxDegree = 0;
+    for (let i = 0; i < n; i++) {
+        const node = nodes[i];
+        if (!node) {
+            continue;
+        }
+        const neighbors = graph.get(node);
+        const nodeSize = neighbors ? neighbors.size : 0;
+        degree[i] = nodeSize;
+        maxDegree = Math.max(maxDegree, nodeSize);
+    }
+    // Count nodes of each degree
+    const bin = new Array(maxDegree + 1).fill(0);
+    for (let i = 0; i < n; i++) {
+        const deg = degree[i];
+        if (deg !== undefined && deg >= 0 && deg < bin.length) {
+            const currentCount = bin[deg];
+            if (currentCount !== undefined) {
+                bin[deg] = currentCount + 1;
+            }
+        }
+    }
+    // Starting position of each degree in sorted array
+    let start = 0;
+    for (let d = 0; d <= maxDegree; d++) {
+        const temp = bin[d] ?? 0;
+        bin[d] = start;
+        start += temp;
+    }
+    // Sort nodes by degree
+    for (let i = 0; i < n; i++) {
+        const deg = degree[i];
+        if (deg !== undefined && deg >= 0 && deg < bin.length) {
+            const posIndex = bin[deg] ?? 0;
+            pos[i] = posIndex;
+            vert[posIndex] = i;
+            const currentBin = bin[deg];
+            if (currentBin !== undefined) {
+                bin[deg] = currentBin + 1;
+            }
+        }
+        else {
+            // If we can't properly place the node in vert, set its position to -1
+            // This shouldn't happen with our fixes, but just in case
+            pos[i] = -1;
+        }
+    }
+    // Recover starting positions
+    for (let d = maxDegree; d > 0; d--) {
+        bin[d] = bin[d - 1] ?? 0;
+    }
+    bin[0] = 0;
+    // Main algorithm
+    for (let i = 0; i < n; i++) {
+        const v = vert[i];
+        if (v === undefined) {
+            continue;
+        }
+        const node = nodes[v];
+        if (node === undefined) {
+            continue;
+        }
+        const degreeV = degree[v];
+        if (degreeV !== undefined) {
+            coreness.set(node, degreeV);
+        }
+        // Process neighbors
+        const neighbors = graph.get(node);
+        if (!neighbors) {
+            // Node has no neighbors, skip neighbor processing but coreness is already set
+            continue;
+        }
+        for (const neighbor of neighbors) {
+            const u = nodeToIndex.get(neighbor);
+            if (u === undefined) {
+                continue;
+            }
+            const degreeU = degree[u];
+            const degreeV = degree[v];
+            if (degreeU !== undefined && degreeV !== undefined && degreeU > degreeV) {
+                const du = degreeU;
+                const pu = pos[u];
+                const pw = bin[du] ?? 0;
+                const w = vert[pw];
+                if (u !== w && w !== undefined && pw < n && pu !== undefined) {
+                    // Swap u and w in the sorted order
+                    vert[pu] = w;
+                    vert[pw] = u;
+                    pos[u] = pw;
+                    pos[w] = pu;
+                }
+                const currentBin = bin[du];
+                if (currentBin !== undefined) {
+                    bin[du] = currentBin + 1;
+                }
+                degree[u] = degreeU - 1;
+            }
+        }
+    }
+    // Build cores map
+    const cores = new Map();
+    let maxCore = 0;
+    for (const [node, core] of coreness) {
+        if (!cores.has(core)) {
+            cores.set(core, new Set());
+        }
+        const coreSet = cores.get(core);
+        if (coreSet) {
+            coreSet.add(node);
+        }
+        maxCore = Math.max(maxCore, core);
+    }
+    return { cores, coreness, maxCore };
+}
+/**
+ * Extract the k-core subgraph
+ * Returns nodes that belong to k-core or higher
+ *
+ * @param graph - Undirected graph
+ * @param k - Core number
+ * @returns Set of nodes in k-core or higher
+ */
+export function getKCore(graph, k) {
+    const { coreness } = kCoreDecomposition(graph);
+    const kCore = new Set();
+    for (const [node, core] of coreness) {
+        if (core >= k) {
+            kCore.add(node);
+        }
+    }
+    return kCore;
+}
+/**
+ * Get the induced subgraph for k-core
+ * Returns the actual subgraph containing only k-core nodes
+ *
+ * @param graph - Original graph
+ * @param k - Core number
+ * @returns K-core subgraph
+ */
+export function getKCoreSubgraph(graph, k) {
+    const kCoreNodes = getKCore(graph, k);
+    const subgraph = new Map();
+    for (const node of kCoreNodes) {
+        const neighbors = graph.get(node);
+        if (neighbors) {
+            const coreNeighbors = new Set();
+            for (const neighbor of neighbors) {
+                if (kCoreNodes.has(neighbor)) {
+                    coreNeighbors.add(neighbor);
+                }
+            }
+            subgraph.set(node, coreNeighbors);
+        }
+    }
+    return subgraph;
+}
+/**
+ * Degeneracy ordering of the graph
+ * Orders nodes by their coreness values
+ *
+ * @param graph - Undirected graph
+ * @returns Array of nodes ordered by degeneracy
+ */
+export function degeneracyOrdering(graph) {
+    const degree = new Map();
+    const remaining = new Map();
+    const ordering = [];
+    // Initialize
+    for (const [node, neighbors] of graph) {
+        degree.set(node, neighbors.size);
+        remaining.set(node, new Set(neighbors));
+    }
+    // Build ordering
+    while (ordering.length < graph.size) {
+        // Find minimum degree node
+        let minDegree = Infinity;
+        let minNode;
+        for (const [node, deg] of degree) {
+            if (!ordering.includes(node) && deg < minDegree) {
+                minDegree = deg;
+                minNode = node;
+            }
+        }
+        if (minNode === undefined) {
+            break;
+        }
+        ordering.push(minNode);
+        // Update neighbors
+        const neighbors = remaining.get(minNode);
+        if (neighbors) {
+            for (const neighbor of neighbors) {
+                const neighborDegree = degree.get(neighbor);
+                if (neighborDegree !== undefined) {
+                    degree.set(neighbor, neighborDegree - 1);
+                }
+                remaining.get(neighbor)?.delete(minNode);
+            }
+        }
+    }
+    return ordering;
+}
+/**
+ * Find k-truss subgraph (triangular k-cores)
+ * Each edge must be part of at least k-2 triangles
+ *
+ * @param graph - Undirected graph
+ * @param k - Truss number (k >= 2)
+ * @returns Edges in k-truss
+ */
+export function kTruss(graph, k) {
+    if (k < 2) {
+        throw new Error("k must be at least 2 for k-truss");
+    }
+    // Count triangles for each edge
+    const edgeTriangles = new Map();
+    const edges = new Set();
+    // Initialize edges
+    for (const [u, neighbors] of graph) {
+        for (const v of neighbors) {
+            if (u < v) { // Avoid duplicates
+                const edge = `${String(u)},${String(v)}`;
+                edges.add(edge);
+                edgeTriangles.set(edge, 0);
+            }
+        }
+    }
+    // Count triangles
+    for (const [u, uNeighbors] of graph) {
+        for (const v of uNeighbors) {
+            if (u < v) {
+                const vNeighbors = graph.get(v);
+                if (vNeighbors) {
+                    // Find common neighbors (triangles)
+                    for (const w of uNeighbors) {
+                        if (v < w && vNeighbors.has(w)) {
+                            // Triangle found: u-v-w
+                            const edge1 = `${String(u)},${String(v)}`;
+                            const edge2 = `${String(u)},${String(w)}`;
+                            const edge3 = `${String(v)},${String(w)}`;
+                            const edge1Count = edgeTriangles.get(edge1);
+                            const edge2Count = edgeTriangles.get(edge2);
+                            const edge3Count = edgeTriangles.get(edge3);
+                            if (edge1Count !== undefined) {
+                                edgeTriangles.set(edge1, edge1Count + 1);
+                            }
+                            if (edge2Count !== undefined) {
+                                edgeTriangles.set(edge2, edge2Count + 1);
+                            }
+                            if (edge3Count !== undefined) {
+                                edgeTriangles.set(edge3, edge3Count + 1);
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+    // Remove edges with insufficient triangles
+    const kTrussEdges = new Set(edges);
+    let changed = true;
+    while (changed) {
+        changed = false;
+        const toRemove = new Set();
+        for (const edge of kTrussEdges) {
+            const triangleCount = edgeTriangles.get(edge);
+            if (triangleCount !== undefined && triangleCount < k - 2) {
+                toRemove.add(edge);
+                changed = true;
+            }
+        }
+        // Remove edges and update triangle counts
+        for (const edge of toRemove) {
+            kTrussEdges.delete(edge);
+            const parts = edge.split(",");
+            if (parts.length < 2) {
+                continue;
+            }
+            const [u, v] = parts;
+            if (!u || !v) {
+                continue;
+            }
+            // Update triangle counts for affected edges
+            const uNode = u;
+            const vNode = v;
+            const uNeighbors = graph.get(uNode);
+            const vNeighbors = graph.get(vNode);
+            if (uNeighbors && vNeighbors) {
+                for (const w of uNeighbors) {
+                    if (vNeighbors.has(w)) {
+                        const edge1 = uNode < w ? `${String(uNode)},${String(w)}` : `${String(w)},${String(uNode)}`;
+                        const edge2 = vNode < w ? `${String(vNode)},${String(w)}` : `${String(w)},${String(vNode)}`;
+                        if (kTrussEdges.has(edge1)) {
+                            const edge1Count = edgeTriangles.get(edge1);
+                            if (edge1Count !== undefined) {
+                                edgeTriangles.set(edge1, edge1Count - 1);
+                            }
+                        }
+                        if (kTrussEdges.has(edge2)) {
+                            const edge2Count = edgeTriangles.get(edge2);
+                            if (edge2Count !== undefined) {
+                                edgeTriangles.set(edge2, edge2Count - 1);
+                            }
+                        }
+                    }
+                }
+            }
+        }
+    }
+    return kTrussEdges;
+}
+/**
+ * Convert directed graph to undirected for k-core analysis
+ */
+export function toUndirected(directedGraph) {
+    const undirected = new Map();
+    // Initialize all nodes
+    for (const node of directedGraph.keys()) {
+        undirected.set(node, new Set());
+    }
+    // Add edges in both directions
+    for (const [u, neighbors] of directedGraph) {
+        for (const v of neighbors.keys()) {
+            const uNeighbors = undirected.get(u);
+            if (uNeighbors) {
+                uNeighbors.add(v);
+            }
+            if (!undirected.has(v)) {
+                undirected.set(v, new Set());
+            }
+            const vNeighbors = undirected.get(v);
+            if (vNeighbors) {
+                vNeighbors.add(u);
+            }
+        }
+    }
+    return undirected;
+}
+//# sourceMappingURL=k-core.js.map

package/dist/src/clustering/k-core.js.map

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

@@ -0,0 +1,36 @@
+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)
+ */
+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;
+}
+/**
+ * Perform Markov Clustering on a graph
+ */
+export declare function markovClustering(graph: Graph, options?: MCLOptions): MCLResult;
+/**
+ * Calculate modularity of MCL clustering result
+ */
+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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