@graphty/algorithms 2.1.2 → 2.2.0

package/dist/src/algorithms/centrality/katz.js

@@ -1,3 +1,6 @@
+import { scoresToRecord } from "../../indexed/facade.js";
+import { katzCentrality as indexedKatz } from "../../indexed/katz.js";
+import { needsLegacyCode, toSnapshot } from "../../indexed/to-snapshot.js";
 /**
  * Calculate Katz centrality for all nodes in the graph.
  * Uses iterative method to compute centrality scores.
@@ -6,6 +9,34 @@
  * @returns Object mapping node IDs to their Katz centrality scores
  */
 export function katzCentrality(graph, options = {}) {
+    const { alpha = 0.1, beta = 1.0 } = options;
+    // A negative alpha or beta can leave every score negative, and the legacy rescale measures the
+    // maximum from 0 rather than from the largest score.
+    if (alpha < 0 || beta < 0) {
+        return legacyKatzCentrality(graph, options);
+    }
+    if (needsLegacyCode(graph)) {
+        return legacyKatzCentrality(graph, options);
+    }
+    const s = toSnapshot(graph);
+    const r = indexedKatz(s, {
+        alpha,
+        beta,
+        maxIterations: options.maxIterations,
+        tolerance: options.tolerance,
+        normalized: options.normalized,
+    });
+    return scoresToRecord(s.ids, r.scores);
+}
+/**
+ * The implementation {@link katzCentrality} delegates away from, kept as its differential-test
+ * oracle and for a negative `alpha` or `beta`. Deleted at the removal release.
+ * @param graph - The graph to compute Katz centrality on
+ * @param options - Configuration options for the computation
+ * @returns Object mapping node IDs to their Katz centrality scores
+ * @internal
+ */
+export function legacyKatzCentrality(graph, options = {}) {
     const { alpha = 0.1, beta = 1.0, maxIterations = 100, tolerance = 1e-6, normalized = true } = options;
     const centrality = {};
     const nodes = Array.from(graph.nodes());

package/dist/src/algorithms/centrality/katz.js.map

@@ -1 +1 @@
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package/dist/src/algorithms/centrality/pagerank.d.ts

@@ -35,9 +35,8 @@ export interface PageRankOptions {
      */
     weight?: string;
     /**
-     * Use delta-based optimization for faster convergence.
-     * Defaults to true for graphs with >100 nodes, false for smaller graphs.
-     * Set explicitly to override automatic heuristic.
+     * Accepted and ignored. It once chose between two engines that compute the same iteration, so
+     * it never changed the result, and now there is one engine.
      */
     useDelta?: boolean;
 }
@@ -61,21 +60,22 @@ export interface PageRankResult {
 /**
  * Calculate PageRank for all nodes in the graph
  *
- * Uses delta-based optimization by default for improved performance on larger graphs.
- * Automatically falls back to standard algorithm for very small graphs.
- *
- * The delta-based approach provides significant speedup for:
- * - Incremental updates after graph modifications
- * - Graphs with localized changes
- * - Early convergence detection per vertex
- *
- * For initial computation on small-medium graphs, standard algorithm may be faster
- * due to lower overhead.
+ * Power iteration with the dangling mass spread over every node and an L-infinity stopping rule.
+ * `useDelta` is ignored: it chose between two engines that computed the same iteration.
  * @param graph - The directed input graph to analyze
  * @param options - Algorithm configuration options
  * @returns PageRank result containing ranks, iteration count, and convergence status
  */
 export declare function pageRank(graph: Graph, options?: PageRankOptions): PageRankResult;
+/**
+ * The implementation {@link pageRank} delegates away from, kept as its differential-test oracle and
+ * for a personalization naming a node the graph lacks. Deleted at the removal release.
+ * @param graph - The directed input graph to analyze
+ * @param options - Algorithm configuration options
+ * @returns PageRank result containing ranks, iteration count, and convergence status
+ * @internal
+ */
+export declare function legacyPageRank(graph: Graph, options?: PageRankOptions): PageRankResult;
 /**
  * Calculate Personalized PageRank for a specific set of source nodes
  * @param graph - The directed input graph to analyze

package/dist/src/algorithms/centrality/pagerank.d.ts.map

@@ -1 +1 @@
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package/dist/src/algorithms/centrality/pagerank.js

@@ -1,22 +1,59 @@
+import { INVALID_INDEX } from "@graphty/graph-format";
+import { deltaPageRank } from "../../indexed/delta-pagerank.js";
+import { exactArcWeights, scoresToRecord } from "../../indexed/facade.js";
+import { needsLegacyCode, toSnapshot } from "../../indexed/to-snapshot.js";
 import { SimpleDeltaPageRank } from "./delta-pagerank-simple.js";
 /**
  * Calculate PageRank for all nodes in the graph
  *
- * Uses delta-based optimization by default for improved performance on larger graphs.
- * Automatically falls back to standard algorithm for very small graphs.
- *
- * The delta-based approach provides significant speedup for:
- * - Incremental updates after graph modifications
- * - Graphs with localized changes
- * - Early convergence detection per vertex
- *
- * For initial computation on small-medium graphs, standard algorithm may be faster
- * due to lower overhead.
+ * Power iteration with the dangling mass spread over every node and an L-infinity stopping rule.
+ * `useDelta` is ignored: it chose between two engines that computed the same iteration.
  * @param graph - The directed input graph to analyze
  * @param options - Algorithm configuration options
  * @returns PageRank result containing ranks, iteration count, and convergence status
  */
 export function pageRank(graph, options = {}) {
+    if (needsLegacyCode(graph)) {
+        return legacyPageRank(graph, options);
+    }
+    const s = toSnapshot(graph);
+    const { personalization, initialRanks, weight } = options;
+    // The legacy code normalises the personalization over every entry of the Map, so an id the
+    // graph lacks takes a share; the port sees only the graph's nodes.
+    if (personalization !== undefined &&
+        [...personalization.keys()].some((id) => s.ids.indexOf(id) === INVALID_INDEX)) {
+        return legacyPageRank(graph, options);
+    }
+    const perNode = (map, fill) => {
+        if (map === undefined) {
+            return undefined;
+        }
+        const out = new Float64Array(s.nodeCount);
+        for (let i = 0; i < out.length; i++) {
+            out[i] = map.get(s.ids.idOf(i)) ?? fill;
+        }
+        return out;
+    };
+    const r = deltaPageRank(s, {
+        dampingFactor: options.dampingFactor,
+        maxIterations: options.maxIterations,
+        tolerance: options.tolerance,
+        weighted: Boolean(weight),
+        weights: weight ? exactArcWeights(s) : undefined,
+        initialRanks: perNode(initialRanks, 1 / s.nodeCount),
+        personalization: perNode(personalization, 0),
+    });
+    return { ranks: scoresToRecord(s.ids, r.scores), iterations: r.iterations, converged: r.converged };
+}
+/**
+ * The implementation {@link pageRank} delegates away from, kept as its differential-test oracle and
+ * for a personalization naming a node the graph lacks. Deleted at the removal release.
+ * @param graph - The directed input graph to analyze
+ * @param options - Algorithm configuration options
+ * @returns PageRank result containing ranks, iteration count, and convergence status
+ * @internal
+ */
+export function legacyPageRank(graph, options = {}) {
     const { dampingFactor = 0.85, maxIterations = 100, tolerance = 1e-6, initialRanks, personalization, weight, } = options;
     if (!graph.isDirected) {
         throw new Error("PageRank requires a directed graph");

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package/dist/src/algorithms/community/girvan-newman-legacy.d.ts

@@ -0,0 +1,27 @@
+/**
+ * Girvan-Newman as it was before `girvanNewman` delegated to `indexed.girvanNewman`, unchanged. The
+ * facade in `girvan-newman.ts` still calls it for a directed graph, a self-loop, a NaN weight or
+ * ids spelled alike, and its facade test uses it as the oracle.
+ */
+import { Graph } from "../../core/graph.js";
+import type { CommunityResult, GirvanNewmanOptions } from "../../types/index.js";
+/**
+ * Girvan-Newman community detection algorithm
+ *
+ * Implements the Girvan-Newman method for community detection by iteratively
+ * removing edges with the highest betweenness centrality until the graph
+ * splits into disconnected components.
+ *
+ * This is a divisive hierarchical clustering algorithm that produces a
+ * dendrogram of community structures.
+ *
+ * References:
+ * - Girvan, M., & Newman, M. E. J. (2002). Community structure in social
+ * and biological networks. Proceedings of the National Academy of Sciences,
+ * 99(12), 7821-7826.
+ * @param graph - The input graph
+ * @param options - Algorithm options
+ * @returns Array of community detection results representing the dendrogram
+ */
+export declare function girvanNewman(graph: Graph, options?: GirvanNewmanOptions): CommunityResult[];
+//# sourceMappingURL=girvan-newman-legacy.d.ts.map

package/dist/src/algorithms/community/girvan-newman-legacy.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"girvan-newman-legacy.d.ts","sourceRoot":"","sources":["../../../../src/algorithms/community/girvan-newman-legacy.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,KAAK,EAAE,MAAM,qBAAqB,CAAC;AAC5C,OAAO,KAAK,EAAE,eAAe,EAAmB,mBAAmB,EAAU,MAAM,sBAAsB,CAAC;AAG1G;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAgB,YAAY,CAAC,KAAK,EAAE,KAAK,EAAE,OAAO,GAAE,mBAAwB,GAAG,eAAe,EAAE,CAsE/F"}

package/dist/src/algorithms/community/girvan-newman-legacy.js

@@ -0,0 +1,335 @@
+/**
+ * Girvan-Newman as it was before `girvanNewman` delegated to `indexed.girvanNewman`, unchanged. The
+ * facade in `girvan-newman.ts` still calls it for a directed graph, a self-loop, a NaN weight or
+ * ids spelled alike, and its facade test uses it as the oracle.
+ */
+import { connectedComponents } from "../components/connected.js";
+/**
+ * Girvan-Newman community detection algorithm
+ *
+ * Implements the Girvan-Newman method for community detection by iteratively
+ * removing edges with the highest betweenness centrality until the graph
+ * splits into disconnected components.
+ *
+ * This is a divisive hierarchical clustering algorithm that produces a
+ * dendrogram of community structures.
+ *
+ * References:
+ * - Girvan, M., & Newman, M. E. J. (2002). Community structure in social
+ * and biological networks. Proceedings of the National Academy of Sciences,
+ * 99(12), 7821-7826.
+ * @param graph - The input graph
+ * @param options - Algorithm options
+ * @returns Array of community detection results representing the dendrogram
+ */
+export function girvanNewman(graph, options = {}) {
+    const { maxCommunities } = options;
+    const minCommunitySize = options.minCommunitySize ?? 1;
+    const maxIterations = options.maxIterations ?? 100; // Prevent infinite loops
+    const dendrogram = [];
+    const workingGraph = graph.clone();
+    let iterations = 0;
+    // Initial state: one large component
+    let components = getConnectedComponentsResult(workingGraph);
+    dendrogram.push({
+        communities: components.components.filter((community) => community.length >= minCommunitySize),
+        modularity: calculateModularity(graph, components.componentMap),
+    });
+    while (Array.from(workingGraph.edges()).length > 0 && iterations < maxIterations) {
+        iterations++;
+        // Calculate edge betweenness centrality
+        const { betweenness: edgeBetweenness, edgeEndpoints } = calculateEdgeBetweenness(workingGraph);
+        if (edgeBetweenness.size === 0) {
+            break;
+        }
+        // Find edges with maximum betweenness
+        const maxBetweenness = Math.max(...edgeBetweenness.values());
+        const edgesToRemove = [];
+        for (const [edgeKey, centrality] of edgeBetweenness) {
+            if (Math.abs(centrality - maxBetweenness) < 1e-10) {
+                // Use original edge endpoints to preserve node ID types (number vs string)
+                const endpoints = edgeEndpoints.get(edgeKey);
+                if (endpoints) {
+                    edgesToRemove.push(endpoints);
+                }
+            }
+        }
+        // Remove edges with highest betweenness
+        for (const { source, target } of edgesToRemove) {
+            workingGraph.removeEdge(source, target);
+        }
+        // Find new connected components (communities)
+        components = getConnectedComponentsResult(workingGraph);
+        // Filter communities by minimum size
+        const validCommunities = components.components.filter((community) => community.length >= minCommunitySize);
+        // Calculate modularity for the new community structure
+        const modularity = calculateModularity(graph, components.componentMap);
+        dendrogram.push({
+            communities: validCommunities,
+            modularity,
+        });
+        // Stop if desired number of communities reached
+        if (maxCommunities && validCommunities.length >= maxCommunities) {
+            break;
+        }
+        // Stop if no more meaningful communities can be formed
+        if (validCommunities.length === workingGraph.nodeCount) {
+            break;
+        }
+    }
+    return dendrogram;
+}
+/**
+ * Calculate edge betweenness centrality for all edges in the graph
+ *
+ * Edge betweenness is the fraction of shortest paths that pass through the edge.
+ * We adapt node betweenness centrality calculation to work with edges.
+ * @param graph - The input graph to analyze
+ * @returns Object with betweenness map and edge endpoints map (preserving original ID types)
+ */
+function calculateEdgeBetweenness(graph) {
+    const edgeBetweenness = new Map();
+    const edgeEndpoints = new Map();
+    // Initialize all edges with 0 betweenness and store original endpoints
+    for (const edge of graph.edges()) {
+        const edgeKey = getEdgeKey(edge.source, edge.target);
+        edgeBetweenness.set(edgeKey, 0);
+        edgeEndpoints.set(edgeKey, { source: edge.source, target: edge.target });
+    }
+    // For each node as source, calculate shortest paths and accumulate edge betweenness
+    for (const sourceNode of graph.nodes()) {
+        const source = sourceNode.id;
+        // Run BFS to find all shortest paths from source
+        const { distances, predecessors, pathCounts } = findAllShortestPaths(graph, source);
+        // Calculate dependency for each node and accumulate edge betweenness
+        const dependency = new Map();
+        // Initialize dependency
+        for (const node of graph.nodes()) {
+            dependency.set(node.id, 0);
+        }
+        // Process nodes in order of decreasing distance
+        const sortedNodes = Array.from(distances.keys())
+            .filter((node) => {
+            const distance = distances.get(node);
+            return distance !== undefined && distance < Infinity;
+        })
+            .sort((a, b) => {
+            const distanceA = distances.get(a);
+            const distanceB = distances.get(b);
+            if (distanceA === undefined || distanceB === undefined) {
+                return 0;
+            }
+            return distanceB - distanceA;
+        });
+        for (const node of sortedNodes) {
+            if (node === source) {
+                continue;
+            }
+            const nodeDependency = dependency.get(node);
+            const nodePathCount = pathCounts.get(node);
+            if (nodeDependency === undefined || nodePathCount === undefined) {
+                continue;
+            }
+            // Distribute dependency to predecessors
+            const nodePredecessors = predecessors.get(node) ?? [];
+            for (const predecessor of nodePredecessors) {
+                const predPathCount = pathCounts.get(predecessor);
+                if (predPathCount === undefined) {
+                    continue;
+                }
+                const edgeDependency = (predPathCount / nodePathCount) * (1 + nodeDependency);
+                // Update predecessor dependency
+                const currentDependency = dependency.get(predecessor);
+                if (currentDependency !== undefined) {
+                    dependency.set(predecessor, currentDependency + edgeDependency);
+                }
+                // Update edge betweenness
+                const edgeKey = getEdgeKey(predecessor, node);
+                const currentBetweenness = edgeBetweenness.get(edgeKey) ?? 0;
+                edgeBetweenness.set(edgeKey, currentBetweenness + edgeDependency);
+            }
+        }
+    }
+    // Normalize: divide by 2 for undirected graphs (each edge counted twice)
+    if (!graph.isDirected) {
+        for (const [edgeKey, betweenness] of edgeBetweenness) {
+            edgeBetweenness.set(edgeKey, betweenness / 2);
+        }
+    }
+    return { betweenness: edgeBetweenness, edgeEndpoints };
+}
+/**
+ * Find all shortest paths from a source node using optimized BFS
+ * @param graph - The input graph to search
+ * @param source - The source node to compute shortest paths from
+ * @returns Object containing distances, predecessors, and path counts
+ */
+function findAllShortestPaths(graph, source) {
+    const distances = new Map();
+    const predecessors = new Map();
+    const pathCounts = new Map();
+    const queue = [];
+    const visited = new Set();
+    // Only initialize for reachable nodes
+    distances.set(source, 0);
+    predecessors.set(source, []);
+    pathCounts.set(source, 1);
+    queue.push(source);
+    // Optimized BFS with early termination
+    let queueIndex = 0;
+    while (queueIndex < queue.length) {
+        const current = queue[queueIndex++];
+        if (current === undefined) {
+            continue;
+        }
+        if (visited.has(current)) {
+            continue;
+        }
+        visited.add(current);
+        const currentDistance = distances.get(current);
+        if (currentDistance === undefined) {
+            continue;
+        }
+        for (const neighbor of graph.neighbors(current)) {
+            // Skip if already processed
+            if (visited.has(neighbor)) {
+                continue;
+            }
+            const edgeWeight = 1; // Unweighted for community detection
+            const newDistance = currentDistance + edgeWeight;
+            const neighborDistance = distances.get(neighbor) ?? Infinity;
+            if (newDistance < neighborDistance) {
+                // Found shorter path
+                distances.set(neighbor, newDistance);
+                predecessors.set(neighbor, [current]);
+                const currentPathCount = pathCounts.get(current);
+                if (currentPathCount !== undefined) {
+                    pathCounts.set(neighbor, currentPathCount);
+                }
+                queue.push(neighbor);
+            }
+            else if (newDistance === neighborDistance) {
+                // Found alternative shortest path
+                const neighborPredecessors = predecessors.get(neighbor);
+                if (neighborPredecessors) {
+                    neighborPredecessors.push(current);
+                    const currentPathCount = pathCounts.get(current);
+                    if (currentPathCount !== undefined) {
+                        pathCounts.set(neighbor, (pathCounts.get(neighbor) ?? 0) + currentPathCount);
+                    }
+                }
+            }
+        }
+    }
+    return { distances, predecessors, pathCounts };
+}
+/**
+ * Generate a consistent edge key for undirected graphs
+ * @param source - The source node ID
+ * @param target - The target node ID
+ * @returns A consistent string key for the edge (ordered alphabetically)
+ */
+function getEdgeKey(source, target) {
+    // For undirected graphs, ensure consistent ordering
+    const sourceStr = String(source);
+    const targetStr = String(target);
+    if (sourceStr <= targetStr) {
+        return `${sourceStr}|${targetStr}`;
+    }
+    return `${targetStr}|${sourceStr}`;
+}
+/**
+ * Calculate modularity for a given community structure
+ *
+ * Newman's Q, written per community:
+ *
+ *     Q = sum over communities c of [ w_in(c) / m - ( K_c / (2m) )^2 ]
+ *
+ * where m is the total edge weight with each undirected edge counted once, w_in(c) is the summed
+ * weight of the edges with both endpoints inside c, and K_c is the summed weighted degree of c's
+ * nodes.
+ *
+ * WHY NOT A SUM OVER EDGES. The textbook double sum runs over every ordered PAIR of nodes inside
+ * a community, not only over the pairs an edge happens to join. Collecting the null-model term
+ * only where an edge exists leaves the penalty far too small, and the shortfall grows with
+ * community size -- so the uncut whole graph, whose modularity is 0 by definition, outscores
+ * every real cut and a caller reading the dendrogram the standard way is handed one community
+ * containing everything. The per-community form above counts every pair exactly once and still
+ * costs one pass over the edges rather than a pass over every pair.
+ * @param graph - The original graph
+ * @param communityMap - Map from node IDs to community indices
+ * @returns The modularity score of the partition
+ */
+function calculateModularity(graph, communityMap) {
+    const totalEdgeWeight = getTotalEdgeWeight(graph);
+    if (totalEdgeWeight === 0) {
+        return 0;
+    }
+    // Summed weighted degree of each community's nodes.
+    const degreeSum = new Map();
+    for (const node of graph.nodes()) {
+        const community = communityMap.get(node.id);
+        if (community === undefined) {
+            continue;
+        }
+        degreeSum.set(community, (degreeSum.get(community) ?? 0) + getNodeDegree(graph, node.id));
+    }
+    // Summed weight of the edges that stay inside a community.
+    const internalWeight = new Map();
+    for (const edge of graph.edges()) {
+        const communityI = communityMap.get(edge.source);
+        const communityJ = communityMap.get(edge.target);
+        if (communityI === undefined || communityI !== communityJ) {
+            continue;
+        }
+        internalWeight.set(communityI, (internalWeight.get(communityI) ?? 0) + (edge.weight ?? 1));
+    }
+    let modularity = 0;
+    for (const [community, degrees] of degreeSum) {
+        const share = degrees / (2 * totalEdgeWeight);
+        modularity += (internalWeight.get(community) ?? 0) / totalEdgeWeight - share * share;
+    }
+    return modularity;
+}
+/**
+ * Calculate total edge weight in the graph
+ * @param graph - The input graph
+ * @returns Total sum of all edge weights
+ */
+function getTotalEdgeWeight(graph) {
+    let totalWeight = 0;
+    for (const edge of graph.edges()) {
+        totalWeight += edge.weight ?? 1;
+    }
+    return totalWeight;
+}
+/**
+ * Get the total degree (sum of edge weights) for a node
+ * @param graph - The input graph
+ * @param nodeId - The node ID to compute degree for
+ * @returns The weighted degree of the node
+ */
+function getNodeDegree(graph, nodeId) {
+    let degree = 0;
+    for (const neighbor of graph.neighbors(nodeId)) {
+        const edge = graph.getEdge(nodeId, neighbor);
+        degree += edge?.weight ?? 1;
+    }
+    return degree;
+}
+/**
+ * Convert connected components result to ComponentResult format
+ * @param graph - The input graph
+ * @returns Object containing components array and node-to-component map
+ */
+function getConnectedComponentsResult(graph) {
+    const components = connectedComponents(graph);
+    const componentMap = new Map();
+    components.forEach((component, index) => {
+        component.forEach((nodeId) => {
+            componentMap.set(nodeId, index);
+        });
+    });
+    return { components, componentMap };
+}
+//# sourceMappingURL=girvan-newman-legacy.js.map

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package/dist/src/algorithms/community/girvan-newman.d.ts

@@ -1,4 +1,4 @@
-import { Graph } from "../../core/graph.js";
+import type { Graph } from "../../core/graph.js";
 import type { CommunityResult, GirvanNewmanOptions } from "../../types/index.js";
 /**
  * Girvan-Newman community detection algorithm
@@ -8,15 +8,17 @@ import type { CommunityResult, GirvanNewmanOptions } from "../../types/index.js"
  * splits into disconnected components.
  *
  * This is a divisive hierarchical clustering algorithm that produces a
- * dendrogram of community structures.
+ * dendrogram of community structures. It delegates to `indexed.girvanNewman`; the result equals
+ * the pre-migration implementation in `girvan-newman-legacy.ts`.
  *
  * References:
  * - Girvan, M., & Newman, M. E. J. (2002). Community structure in social
  * and biological networks. Proceedings of the National Academy of Sciences,
  * 99(12), 7821-7826.
- * @param graph - The input graph
+ * @param graph - The input graph (must be undirected)
  * @param options - Algorithm options
  * @returns Array of community detection results representing the dendrogram
+ * @throws Error on a directed graph
  */
 export declare function girvanNewman(graph: Graph, options?: GirvanNewmanOptions): CommunityResult[];
 //# sourceMappingURL=girvan-newman.d.ts.map

package/dist/src/algorithms/community/girvan-newman.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"girvan-newman.d.ts","sourceRoot":"","sources":["../../../../src/algorithms/community/girvan-newman.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,qBAAqB,CAAC;AAIjD,OAAO,KAAK,EAAE,eAAe,EAAE,mBAAmB,EAAE,MAAM,sBAAsB,CAAC;AAGjF;;;;;;;;;;;;;;;;;;;GAmBG;AACH,wBAAgB,YAAY,CAAC,KAAK,EAAE,KAAK,EAAE,OAAO,GAAE,mBAAwB,GAAG,eAAe,EAAE,CA8B/F"}