@graphty/algorithms 1.3.1 → 1.4.2

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

@@ -23,21 +23,28 @@ export interface HierarchicalClusteringResult<T> {
 export type LinkageMethod = "single" | "complete" | "average" | "ward";
 /**
  * Cut dendrogram at specific height to get clusters
+ * @param root - Root node of the dendrogram
+ * @param height - Height at which to cut the dendrogram
+ * @returns Array of sets representing clusters at the specified height
  */
 export declare function cutDendrogram<T>(root: ClusterNode<T>, height: number): Set<T>[];
 /**
  * Cut dendrogram to get exactly k clusters
+ * @param root - Root node of the dendrogram
+ * @param k - Target number of clusters
+ * @returns Array of sets representing exactly k clusters
  */
 export declare function cutDendrogramKClusters<T>(root: ClusterNode<T>, k: number): Set<T>[];
 /**
  * Compute modularity-based hierarchical clustering
  * Uses modularity gain to decide merges
+ * @param graph - The input graph to cluster
+ * @returns Hierarchical clustering result with dendrogram and cluster assignments
  */
 export declare function modularityHierarchicalClustering(graph: Graph): HierarchicalClusteringResult<string>;
 /**
  * Agglomerative hierarchical clustering
  * Builds clusters bottom-up by merging closest pairs
- *
  * @param graph - Undirected graph - accepts Graph class or Map<T, Set<T>>
  * @param linkage - Linkage method for cluster distance
  * @returns Hierarchical clustering result

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

@@ -1 +1 @@
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package/dist/src/clustering/hierarchical.js

@@ -7,6 +7,8 @@
  */
 /**
  * Convert Graph to adjacency set representation for clustering
+ * @param graph - The input graph to convert
+ * @returns Map of node IDs to sets of neighbor node IDs
  */
 function graphToAdjacencySet(graph) {
     const adjacency = new Map();
@@ -34,6 +36,8 @@ function graphToAdjacencySet(graph) {
 }
 /**
  * Compute distance between two nodes based on graph structure
+ * @param graph - Adjacency map representation of the graph
+ * @param distances - Map to store computed distances between nodes
  */
 function computeGraphDistance(graph, distances) {
     // Use BFS to compute shortest path distances
@@ -61,6 +65,11 @@ function computeGraphDistance(graph, distances) {
 }
 /**
  * Compute distance between two clusters based on linkage method
+ * @param cluster1 - First cluster node
+ * @param cluster2 - Second cluster node
+ * @param distances - Precomputed distance matrix between nodes
+ * @param linkage - Linkage method to use for computing cluster distance
+ * @returns The distance between the two clusters
  */
 function clusterDistance(cluster1, cluster2, distances, linkage) {
     const allDistances = [];
@@ -99,6 +108,9 @@ function clusterDistance(cluster1, cluster2, distances, linkage) {
 }
 /**
  * Internal implementation of agglomerative hierarchical clustering
+ * @param graph - Adjacency map representation of the graph
+ * @param linkage - Linkage method for cluster distance computation
+ * @returns Hierarchical clustering result with dendrogram and cluster assignments
  */
 function hierarchicalClusteringImpl(graph, linkage = "single") {
     const nodes = Array.from(graph.keys());
@@ -158,9 +170,7 @@ function hierarchicalClusteringImpl(graph, linkage = "single") {
                 if (cluster1.id >= cluster2.id) {
                     continue;
                 }
-                const dist = distMap.get(cluster2.id) ??
-                    clusterDistances.get(cluster2.id)?.get(cluster1.id) ??
-                    Infinity;
+                const dist = distMap.get(cluster2.id) ?? clusterDistances.get(cluster2.id)?.get(cluster1.id) ?? Infinity;
                 if (dist < minDist) {
                     minDist = dist;
                     mergeCluster1 = cluster1;
@@ -242,6 +252,9 @@ function hierarchicalClusteringImpl(graph, linkage = "single") {
 }
 /**
  * Cut dendrogram at specific height to get clusters
+ * @param root - Root node of the dendrogram
+ * @param height - Height at which to cut the dendrogram
+ * @returns Array of sets representing clusters at the specified height
  */
 export function cutDendrogram(root, height) {
     const clusters = [];
@@ -271,6 +284,9 @@ export function cutDendrogram(root, height) {
 }
 /**
  * Cut dendrogram to get exactly k clusters
+ * @param root - Root node of the dendrogram
+ * @param k - Target number of clusters
+ * @returns Array of sets representing exactly k clusters
  */
 export function cutDendrogramKClusters(root, k) {
     if (k <= 0) {
@@ -300,6 +316,8 @@ export function cutDendrogramKClusters(root, k) {
 /**
  * Compute modularity-based hierarchical clustering
  * Uses modularity gain to decide merges
+ * @param graph - The input graph to cluster
+ * @returns Hierarchical clustering result with dendrogram and cluster assignments
  */
 export function modularityHierarchicalClustering(graph) {
     const adjacencySet = graphToAdjacencySet(graph);
@@ -359,8 +377,7 @@ export function modularityHierarchicalClustering(graph) {
                         degreeProduct += degree1 * degree2;
                     }
                 }
-                const gain = (edgesBetween / totalEdges) -
-                    (degreeProduct / (4 * totalEdges * totalEdges));
+                const gain = edgesBetween / totalEdges - degreeProduct / (4 * totalEdges * totalEdges);
                 if (gain > maxGain) {
                     maxGain = gain;
                     mergeCluster1 = cluster1;
@@ -409,7 +426,6 @@ export function modularityHierarchicalClustering(graph) {
 /**
  * Agglomerative hierarchical clustering
  * Builds clusters bottom-up by merging closest pairs
- *
  * @param graph - Undirected graph - accepts Graph class or Map<T, Set<T>>
  * @param linkage - Linkage method for cluster distance
  * @returns Hierarchical clustering result

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

@@ -1 +1 @@
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package/dist/src/clustering/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/clustering/index.ts"],"names":[],"mappings":"AAAA,YAAY,EAAE,WAAW,EAAE,4BAA4B,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAClG,OAAO,EAAE,sBAAsB,EAAE,MAAM,mBAAmB,CAAC;AAC3D,YAAY,EAAE,WAAW,EAAE,MAAM,aAAa,CAAC;AAC/C,OAAO,EAAE,QAAQ,EAAE,kBAAkB,EAAE,MAAM,aAAa,CAAC;AAC3D,YAAY,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,UAAU,CAAC;AACtD,OAAO,EAAE,sBAAsB,EAAE,gBAAgB,EAAE,MAAM,UAAU,CAAC;AACpE,YAAY,EAAE,yBAAyB,EAAE,wBAAwB,EAAE,MAAM,eAAe,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,eAAe,CAAC"}

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

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/clustering/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,sBAAsB,EAAE,MAAM,mBAAmB,CAAC;AAE3D,OAAO,EAAE,QAAQ,EAAE,kBAAkB,EAAE,MAAM,aAAa,CAAC;AAE3D,OAAO,EAAE,sBAAsB,EAAE,gBAAgB,EAAE,MAAM,UAAU,CAAC;AAEpE,OAAO,EAAE,kBAAkB,EAAE,MAAM,eAAe,CAAC"}

package/dist/src/clustering/k-core.d.ts

@@ -14,7 +14,6 @@ export interface KCoreResult<T> {
 /**
  * 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
@@ -23,7 +22,6 @@ export declare function getKCore(graph: Graph, k: number): Set<string>;
 /**
  * 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
@@ -32,7 +30,6 @@ export declare function getKCoreSubgraph(graph: Graph, k: number): Map<string, S
 /**
  * Degeneracy ordering of the graph
  * Orders nodes by their coreness values
- *
  * @param graph - Undirected graph
  * @returns Array of nodes ordered by degeneracy
  */
@@ -40,7 +37,6 @@ export declare function degeneracyOrdering(graph: Graph): string[];
 /**
  * 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
@@ -48,12 +44,13 @@ export declare function degeneracyOrdering(graph: Graph): string[];
 export declare function kTruss(graph: Graph, k: number): Set<string>;
 /**
  * Convert directed graph to undirected for k-core analysis
+ * @param directedGraph - Directed graph represented as adjacency map with edge weights
+ * @returns Undirected graph represented as adjacency map with neighbor sets
  */
 export declare function toUndirected<T>(directedGraph: Map<T, Map<T, number>>): Map<T, Set<T>>;
 /**
  * K-Core decomposition algorithm
  * Finds all k-cores in the graph and assigns coreness values to nodes
- *
  * @param graph - Undirected graph - accepts Graph class or Map<T, Set<T>>
  * @returns K-core decomposition results
  *

package/dist/src/clustering/k-core.d.ts.map

@@ -1 +1 @@
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package/dist/src/clustering/k-core.js

@@ -7,6 +7,8 @@
  */
 /**
  * Convert Graph to adjacency set representation
+ * @param graph - The input graph to convert
+ * @returns Map of node IDs to sets of neighbor node IDs
  */
 function graphToAdjacencySet(graph) {
     const adjacency = new Map();
@@ -34,6 +36,8 @@ function graphToAdjacencySet(graph) {
 }
 /**
  * Internal implementation of K-Core decomposition algorithm
+ * @param graph - Adjacency map representation of the graph
+ * @returns K-core decomposition result with cores, coreness values, and maximum core number
  */
 function kCoreDecompositionImpl(graph) {
     if (graph.size === 0) {
@@ -173,7 +177,6 @@ function kCoreDecompositionImpl(graph) {
 /**
  * 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
@@ -191,7 +194,6 @@ export function getKCore(graph, k) {
 /**
  * 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
@@ -217,7 +219,6 @@ export function getKCoreSubgraph(graph, k) {
 /**
  * Degeneracy ordering of the graph
  * Orders nodes by their coreness values
- *
  * @param graph - Undirected graph
  * @returns Array of nodes ordered by degeneracy
  */
@@ -263,7 +264,6 @@ export function degeneracyOrdering(graph) {
 /**
  * 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
@@ -279,8 +279,9 @@ export function kTruss(graph, k) {
     // Initialize edges
     for (const [u, neighbors] of adjacencySet) {
         for (const v of neighbors) {
-            if (u < v) { // Avoid duplicates
-                const edge = `${String(u)},${String(v)}`;
+            if (u < v) {
+                // Avoid duplicates
+                const edge = `${u},${v}`;
                 edges.add(edge);
                 edgeTriangles.set(edge, 0);
             }
@@ -296,9 +297,9 @@ export function kTruss(graph, k) {
                     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 edge1 = `${u},${v}`;
+                            const edge2 = `${u},${w}`;
+                            const edge3 = `${v},${w}`;
                             const edge1Count = edgeTriangles.get(edge1);
                             const edge2Count = edgeTriangles.get(edge2);
                             const edge3Count = edgeTriangles.get(edge3);
@@ -347,8 +348,8 @@ export function kTruss(graph, k) {
             if (uNeighbors && vNeighbors) {
                 for (const w of uNeighbors) {
                     if (vNeighbors.has(w)) {
-                        const edge1 = u < w ? `${String(u)},${String(w)}` : `${String(w)},${String(u)}`;
-                        const edge2 = v < w ? `${String(v)},${String(w)}` : `${String(w)},${String(v)}`;
+                        const edge1 = u < w ? `${u},${w}` : `${w},${u}`;
+                        const edge2 = v < w ? `${v},${w}` : `${w},${v}`;
                         if (kTrussEdges.has(edge1)) {
                             const edge1Count = edgeTriangles.get(edge1);
                             if (edge1Count !== undefined) {
@@ -370,6 +371,8 @@ export function kTruss(graph, k) {
 }
 /**
  * Convert directed graph to undirected for k-core analysis
+ * @param directedGraph - Directed graph represented as adjacency map with edge weights
+ * @returns Undirected graph represented as adjacency map with neighbor sets
  */
 export function toUndirected(directedGraph) {
     const undirected = new Map();
@@ -398,7 +401,6 @@ export function toUndirected(directedGraph) {
 /**
  * K-Core decomposition algorithm
  * Finds all k-cores in the graph and assigns coreness values to nodes
- *
  * @param graph - Undirected graph - accepts Graph class or Map<T, Set<T>>
  * @returns K-core decomposition results
  *

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

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

@@ -27,10 +27,16 @@ export interface MCLResult {
 }
 /**
  * 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 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

@@ -1 +1 @@
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+{"version":3,"file":"mcl.d.ts","sourceRoot":"","sources":["../../../src/clustering/mcl.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAC9C,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAEhD;;;;;;;;;;GAUG;AAEH,MAAM,WAAW,UAAU;IACvB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,SAAS,CAAC,EAAE,OAAO,CAAC;CACvB;AAED,MAAM,WAAW,SAAS;IACtB,WAAW,EAAE,MAAM,EAAE,EAAE,CAAC;IACxB,UAAU,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACxB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,OAAO,CAAC;CACtB;AAED;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,KAAK,EAAE,OAAO,GAAE,UAAe,GAAG,SAAS,CAyDlF;AAgWD;;;;;GAKG;AACH,wBAAgB,sBAAsB,CAAC,KAAK,EAAE,KAAK,EAAE,WAAW,EAAE,MAAM,EAAE,EAAE,GAAG,MAAM,CA+BpF"}

package/dist/src/clustering/mcl.js

@@ -1,5 +1,8 @@
 /**
  * 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;
@@ -43,6 +46,10 @@ export function markovClustering(graph, options = {}) {
 }
 /**
  * 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;
@@ -103,6 +110,9 @@ function buildTransitionMatrix(graph, nodeIds, selfLoops) {
 }
 /**
  * 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) {
@@ -119,6 +129,9 @@ function matrixPower(matrix, power) {
 }
 /**
  * Multiply two matrices
+ * @param a - First matrix
+ * @param b - Second matrix
+ * @returns Product matrix a * b
  */
 function matrixMultiply(a, b) {
     const n = a.length;
@@ -136,7 +149,7 @@ function matrixMultiply(a, b) {
                 }
                 const prevVal = resultRow[j];
                 if (prevVal !== undefined) {
-                    resultRow[j] = prevVal + (aVal * bVal);
+                    resultRow[j] = prevVal + aVal * bVal;
                 }
             }
         }
@@ -145,6 +158,9 @@ function matrixMultiply(a, b) {
 }
 /**
  * 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;
@@ -187,6 +203,9 @@ function inflate(matrix, inflation) {
 }
 /**
  * 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;
@@ -236,6 +255,10 @@ function prune(matrix, threshold) {
 }
 /**
  * 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;
@@ -257,6 +280,9 @@ function hasConverged(oldMatrix, newMatrix, tolerance) {
 }
 /**
  * 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;
@@ -292,10 +318,12 @@ function extractClusters(matrix, nodeIds) {
             }
         }
         if (clusterNodes.length > 0) {
-            communities.push(clusterNodes.map((idx) => {
+            communities.push(clusterNodes
+                .map((idx) => {
                 const nodeId = nodeIds[idx];
                 return nodeId;
-            }).filter((node) => node !== undefined));
+            })
+                .filter((node) => node !== undefined));
             clusterIndex++;
         }
     }
@@ -313,6 +341,9 @@ function extractClusters(matrix, nodeIds) {
 }
 /**
  * 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;

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

@@ -1 +1 @@
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