@graphty/algorithms 1.1.0 → 1.3.1

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

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

@@ -1,5 +1,5 @@
-export * from "./hierarchical.js";
-export * from "./k-core.js";
+export { hierarchicalClustering } from "./hierarchical.js";
+export { getKCore, kCoreDecomposition } from "./k-core.js";
 export { calculateMCLModularity, markovClustering } from "./mcl.js";
 export { spectralClustering } from "./spectral.js";
 //# sourceMappingURL=index.js.map

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

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

@@ -5,22 +5,12 @@
  * within the subgraph. Used for identifying cohesive groups and
  * understanding graph structure.
  */
+import type { Graph } from "../core/graph.js";
 export interface KCoreResult<T> {
     cores: Map<number, Set<T>>;
     coreness: Map<T, number>;
     maxCore: number;
 }
-/**
- * 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 declare function kCoreDecomposition<T>(graph: Map<T, Set<T>>): KCoreResult<T>;
 /**
  * Extract the k-core subgraph
  * Returns nodes that belong to k-core or higher
@@ -29,7 +19,7 @@ export declare function kCoreDecomposition<T>(graph: Map<T, Set<T>>): KCoreResul
  * @param k - Core number
  * @returns Set of nodes in k-core or higher
  */
-export declare function getKCore<T>(graph: Map<T, Set<T>>, k: number): Set<T>;
+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
@@ -38,7 +28,7 @@ export declare function getKCore<T>(graph: Map<T, Set<T>>, k: number): Set<T>;
  * @param k - Core number
  * @returns K-core subgraph
  */
-export declare function getKCoreSubgraph<T>(graph: Map<T, Set<T>>, k: number): Map<T, Set<T>>;
+export declare function getKCoreSubgraph(graph: Graph, k: number): Map<string, Set<string>>;
 /**
  * Degeneracy ordering of the graph
  * Orders nodes by their coreness values
@@ -46,7 +36,7 @@ export declare function getKCoreSubgraph<T>(graph: Map<T, Set<T>>, k: number): M
  * @param graph - Undirected graph
  * @returns Array of nodes ordered by degeneracy
  */
-export declare function degeneracyOrdering<T>(graph: Map<T, Set<T>>): T[];
+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
@@ -55,9 +45,20 @@ export declare function degeneracyOrdering<T>(graph: Map<T, Set<T>>): T[];
  * @param k - Truss number (k >= 2)
  * @returns Edges in k-truss
  */
-export declare function kTruss<T>(graph: Map<T, Set<T>>, k: number): Set<string>;
+export declare function kTruss(graph: Graph, k: number): Set<string>;
 /**
  * Convert directed graph to undirected for k-core analysis
  */
 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
+ *
+ * Time Complexity: O(V + E)
+ * Space Complexity: O(V)
+ */
+export declare function kCoreDecomposition(graph: Graph): KCoreResult<string>;
 //# sourceMappingURL=k-core.d.ts.map

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

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

@@ -6,16 +6,36 @@
  * 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)
+ * Convert Graph to adjacency set representation
  */
-export function kCoreDecomposition(graph) {
+function graphToAdjacencySet(graph) {
+    const adjacency = new Map();
+    // Initialize all nodes
+    for (const node of graph.nodes()) {
+        adjacency.set(String(node.id), new Set());
+    }
+    // Add edges
+    for (const edge of graph.edges()) {
+        const source = String(edge.source);
+        const target = String(edge.target);
+        const sourceSet = adjacency.get(source);
+        if (sourceSet) {
+            sourceSet.add(target);
+        }
+        // For undirected graphs, add reverse edge
+        if (!graph.isDirected) {
+            const targetSet = adjacency.get(target);
+            if (targetSet) {
+                targetSet.add(source);
+            }
+        }
+    }
+    return adjacency;
+}
+/**
+ * Internal implementation of K-Core decomposition algorithm
+ */
+function kCoreDecompositionImpl(graph) {
     if (graph.size === 0) {
         return { cores: new Map(), coreness: new Map(), maxCore: 0 };
     }
@@ -178,9 +198,10 @@ export function getKCore(graph, k) {
  */
 export function getKCoreSubgraph(graph, k) {
     const kCoreNodes = getKCore(graph, k);
+    const adjacencySet = graphToAdjacencySet(graph);
     const subgraph = new Map();
     for (const node of kCoreNodes) {
-        const neighbors = graph.get(node);
+        const neighbors = adjacencySet.get(node);
         if (neighbors) {
             const coreNeighbors = new Set();
             for (const neighbor of neighbors) {
@@ -201,16 +222,17 @@ export function getKCoreSubgraph(graph, k) {
  * @returns Array of nodes ordered by degeneracy
  */
 export function degeneracyOrdering(graph) {
+    const adjacencySet = graphToAdjacencySet(graph);
     const degree = new Map();
     const remaining = new Map();
     const ordering = [];
     // Initialize
-    for (const [node, neighbors] of graph) {
+    for (const [node, neighbors] of adjacencySet) {
         degree.set(node, neighbors.size);
         remaining.set(node, new Set(neighbors));
     }
     // Build ordering
-    while (ordering.length < graph.size) {
+    while (ordering.length < adjacencySet.size) {
         // Find minimum degree node
         let minDegree = Infinity;
         let minNode;
@@ -250,11 +272,12 @@ export function kTruss(graph, k) {
     if (k < 2) {
         throw new Error("k must be at least 2 for k-truss");
     }
+    const adjacencySet = graphToAdjacencySet(graph);
     // Count triangles for each edge
     const edgeTriangles = new Map();
     const edges = new Set();
     // Initialize edges
-    for (const [u, neighbors] of graph) {
+    for (const [u, neighbors] of adjacencySet) {
         for (const v of neighbors) {
             if (u < v) { // Avoid duplicates
                 const edge = `${String(u)},${String(v)}`;
@@ -264,10 +287,10 @@ export function kTruss(graph, k) {
         }
     }
     // Count triangles
-    for (const [u, uNeighbors] of graph) {
+    for (const [u, uNeighbors] of adjacencySet) {
         for (const v of uNeighbors) {
             if (u < v) {
-                const vNeighbors = graph.get(v);
+                const vNeighbors = adjacencySet.get(v);
                 if (vNeighbors) {
                     // Find common neighbors (triangles)
                     for (const w of uNeighbors) {
@@ -319,15 +342,13 @@ export function kTruss(graph, k) {
                 continue;
             }
             // Update triangle counts for affected edges
-            const uNode = u;
-            const vNode = v;
-            const uNeighbors = graph.get(uNode);
-            const vNeighbors = graph.get(vNode);
+            const uNeighbors = adjacencySet.get(u);
+            const vNeighbors = adjacencySet.get(v);
             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)}`;
+                        const edge1 = u < w ? `${String(u)},${String(w)}` : `${String(w)},${String(u)}`;
+                        const edge2 = v < w ? `${String(v)},${String(w)}` : `${String(w)},${String(v)}`;
                         if (kTrussEdges.has(edge1)) {
                             const edge1Count = edgeTriangles.get(edge1);
                             if (edge1Count !== undefined) {
@@ -374,4 +395,19 @@ export function toUndirected(directedGraph) {
     }
     return undirected;
 }
+/**
+ * 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
+ *
+ * Time Complexity: O(V + E)
+ * Space Complexity: O(V)
+ */
+export function kCoreDecomposition(graph) {
+    // Convert Graph to adjacency set representation
+    const adjacencySet = graphToAdjacencySet(graph);
+    return kCoreDecompositionImpl(adjacencySet);
+}
 //# sourceMappingURL=k-core.js.map

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

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

@@ -23,6 +23,14 @@ export interface SpectralClusteringResult {
 }
 /**
  * Perform spectral clustering on a graph
+ *
+ * @warning This implementation uses simplified power iteration for eigenvector
+ * computation with approximate eigenvalues. For production use cases requiring
+ * precise clustering, consider using a proper linear algebra library like ml-matrix.
+ *
+ * The approximate eigenvalues (0.1, 0.2 for second and third eigenvectors) work
+ * well for most graph structures but may produce suboptimal results for graphs
+ * with unusual spectral properties.
  */
 export declare function spectralClustering(graph: Graph, options: SpectralClusteringOptions): SpectralClusteringResult;
 //# sourceMappingURL=spectral.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"spectral.d.ts","sourceRoot":"","sources":["../../../src/clustering/spectral.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAC,KAAK,EAAC,MAAM,kBAAkB,CAAC;AAC5C,OAAO,KAAK,EAAC,MAAM,EAAC,MAAM,mBAAmB,CAAC;AAG9C;;;;;;;;GAQG;AAEH,MAAM,WAAW,yBAAyB;IACtC,CAAC,EAAE,MAAM,CAAC;IACV,aAAa,CAAC,EAAE,cAAc,GAAG,YAAY,GAAG,YAAY,CAAC;IAC7D,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,SAAS,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,wBAAwB;IACrC,WAAW,EAAE,MAAM,EAAE,EAAE,CAAC;IACxB,kBAAkB,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACxC,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB,YAAY,CAAC,EAAE,MAAM,EAAE,EAAE,CAAC;CAC7B;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,kBAAkB,CAC9B,KAAK,EAAE,KAAK,EACZ,OAAO,EAAE,yBAAyB,GACnC,wBAAwB,CA+F1B"}

package/dist/src/clustering/spectral.js

@@ -1,8 +1,21 @@
+import { euclideanDistance } from "../utils/math-utilities.js";
 /**
  * Perform spectral clustering on a graph
+ *
+ * @warning This implementation uses simplified power iteration for eigenvector
+ * computation with approximate eigenvalues. For production use cases requiring
+ * precise clustering, consider using a proper linear algebra library like ml-matrix.
+ *
+ * The approximate eigenvalues (0.1, 0.2 for second and third eigenvectors) work
+ * well for most graph structures but may produce suboptimal results for graphs
+ * with unusual spectral properties.
  */
 export function spectralClustering(graph, options) {
-    const { k, laplacianType = "normalized", maxIterations = 100, } = options;
+    const { k, laplacianType = "normalized", maxIterations = 100, tolerance = 1e-4, } = options;
+    // Input validation
+    if (k < 1 || !Number.isInteger(k)) {
+        throw new Error("k must be a positive integer");
+    }
     const nodes = Array.from(graph.nodes());
     const nodeIds = nodes.map((node) => node.id);
     const n = nodeIds.length;
@@ -19,12 +32,25 @@ export function spectralClustering(graph, options) {
     const laplacianMatrix = buildLaplacianMatrix(adjacencyMatrix, laplacianType);
     // Find k smallest eigenvectors
     const eigenResult = findSmallestEigenvectors(laplacianMatrix, k);
-    // Normalize the eigenvector matrix row-wise (for normalized spectral clustering)
+    // Perform k-means clustering on the eigenvectors
+    // For spectral clustering, we need to transpose the eigenvector matrix
+    // Each row should be a data point (node) with features from the eigenvectors
+    const dataPoints = [];
+    for (let i = 0; i < nodeIds.length; i++) {
+        const point = [];
+        for (let j = 0; j < k; j++) {
+            const eigenvector = eigenResult.eigenvectors[j];
+            if (eigenvector) {
+                point.push(eigenvector[i] ?? 0);
+            }
+        }
+        dataPoints.push(point);
+    }
+    // Normalize the data points row-wise (for normalized spectral clustering)
     if (laplacianType === "normalized") {
-        normalizeRows(eigenResult.eigenvectors);
+        normalizeRows(dataPoints);
     }
-    // Perform k-means clustering on the eigenvectors
-    const kmeans = kMeansClustering(eigenResult.eigenvectors, k, maxIterations);
+    const kmeans = kMeansClustering(dataPoints, k, maxIterations, tolerance);
     // Build communities
     const communities = Array.from({ length: k }, () => []);
     const clusterAssignments = new Map();
@@ -204,27 +230,29 @@ function findSmallestEigenvectors(matrix, k) {
     if (n === 0 || k === 0) {
         return { eigenvalues: [], eigenvectors: [] };
     }
-    // For small matrices or when k >= n, use a simplified approach
-    if (n <= 3 || k >= n) {
-        // Create identity-like eigenvectors for simplicity
-        const eigenvectors = [];
-        const eigenvalues = [];
-        for (let i = 0; i < Math.min(k, n); i++) {
-            const vector = Array(n).fill(0);
-            vector[i] = 1;
-            eigenvectors.push(vector);
-            eigenvalues.push(i);
-        }
-        return { eigenvalues, eigenvectors };
+    // For very small matrices, use the full power iteration approach
+    // Remove the simplified approach that was causing issues
+    if (k >= n) {
+        // If k >= n, we still need proper eigenvectors, not identity
+        // Fall through to the power iteration below
     }
-    // For larger matrices, use power iteration to find dominant eigenvectors
-    // This is still simplified but better than random
+    // For spectral clustering, we need proper eigenvectors
+    // Special handling for small k values which are common in clustering
+    if (k <= 3 && n > k) {
+        return computeSmallestEigenvectorsSimple(matrix, k, n);
+    }
+    // For larger k, use power iteration
     const eigenvectors = [];
     const eigenvalues = [];
-    const maxIterations = 50;
+    const maxIterations = 100;
     for (let eigIdx = 0; eigIdx < k; eigIdx++) {
         // Initialize random vector
         let vector = Array(n).fill(0).map(() => Math.random() - 0.5);
+        // Normalize initial vector
+        const initNorm = Math.sqrt(vector.reduce((sum, val) => sum + (val * val), 0));
+        if (initNorm > 0) {
+            vector = vector.map((val) => val / initNorm);
+        }
         // Orthogonalize against previous eigenvectors
         for (let j = 0; j < eigIdx; j++) {
             const ejVector = eigenvectors[j];
@@ -321,7 +349,7 @@ function normalizeRows(matrix) {
 /**
  * K-means clustering algorithm
  */
-function kMeansClustering(data, k, maxIterations) {
+function kMeansClustering(data, k, maxIterations, tolerance = 1e-4) {
     const n = data.length;
     const d = data[0]?.length ?? 0;
     // Handle edge cases
@@ -374,18 +402,20 @@ function kMeansClustering(data, k, maxIterations) {
             }
             assignments[i] = bestCluster;
         }
-        // Check for convergence
-        let changed = false;
+        // Check for convergence based on assignment changes
+        let assignmentsChanged = false;
         for (let i = 0; i < n; i++) {
             if (assignments[i] !== oldAssignments[i]) {
-                changed = true;
+                assignmentsChanged = true;
                 break;
             }
         }
-        if (!changed) {
+        if (!assignmentsChanged) {
             break;
         }
         oldAssignments = [...assignments];
+        // Store old centroids for tolerance-based convergence check
+        const oldCentroids = centroids.map((c) => [...c]);
         // Update centroids
         const counts = Array(k).fill(0);
         const sums = Array.from({ length: k }, () => Array(d).fill(0));
@@ -421,27 +451,120 @@ function kMeansClustering(data, k, maxIterations) {
                     for (let j = 0; j < d; j++) {
                         const sumVal = sumsRow[j];
                         if (sumVal !== undefined) {
-                            const countVal = counts[i];
-                            if (countVal !== undefined) {
-                                centroidsRow[j] = sumVal / countVal;
+                            const countValInner = counts[i];
+                            if (countValInner !== undefined) {
+                                centroidsRow[j] = sumVal / countValInner;
                             }
                         }
                     }
                 }
             }
         }
+        // Check for tolerance-based convergence (centroid movement)
+        let maxCentroidShift = 0;
+        for (let i = 0; i < k; i++) {
+            const oldCentroid = oldCentroids[i];
+            const newCentroid = centroids[i];
+            if (oldCentroid && newCentroid) {
+                const shift = euclideanDistance(oldCentroid, newCentroid);
+                if (shift > maxCentroidShift) {
+                    maxCentroidShift = shift;
+                }
+            }
+        }
+        if (maxCentroidShift < tolerance) {
+            break;
+        }
     }
     return { assignments, centroids };
 }
 /**
- * Calculate Euclidean distance between two vectors
+ * Compute smallest eigenvectors for small k (optimized for k=2, k=3)
  */
-function euclideanDistance(a, b) {
-    let sum = 0;
-    for (let i = 0; i < a.length; i++) {
-        const diff = (a[i] ?? 0) - (b[i] ?? 0);
-        sum += diff * diff;
+function computeSmallestEigenvectorsSimple(matrix, k, n) {
+    const eigenvectors = [];
+    const eigenvalues = [];
+    // First eigenvector is constant (corresponds to eigenvalue 0 for connected graph)
+    const firstVector = Array(n).fill(1 / Math.sqrt(n));
+    eigenvectors.push(firstVector);
+    eigenvalues.push(0);
+    // For k >= 2, compute the Fiedler vector (second smallest eigenvector)
+    if (k >= 2) {
+        // Use power iteration on I - L/lambda_max to find second smallest
+        const maxEig = 2; // For normalized Laplacian, max eigenvalue <= 2
+        let vector = Array(n).fill(0).map(() => Math.random() - 0.5);
+        // Make orthogonal to first eigenvector
+        const dot1 = vector.reduce((sum, val) => sum + (val / Math.sqrt(n)), 0);
+        vector = vector.map((val) => val - (dot1 / Math.sqrt(n)));
+        // Power iteration on shifted matrix
+        for (let iter = 0; iter < 100; iter++) {
+            // Compute (I - L/maxEig) * v
+            const newVector = Array(n).fill(0);
+            // Identity part
+            for (let i = 0; i < n; i++) {
+                newVector[i] = vector[i] ?? 0;
+            }
+            // Subtract L * v / maxEig
+            for (let i = 0; i < n; i++) {
+                for (let j = 0; j < n; j++) {
+                    const matrixVal = matrix[i]?.[j] ?? 0;
+                    const vecVal = vector[j] ?? 0;
+                    newVector[i] = (newVector[i] ?? 0) - ((matrixVal * vecVal) / maxEig);
+                }
+            }
+            // Orthogonalize against first eigenvector
+            const dot = newVector.reduce((sum, val) => sum + (val / Math.sqrt(n)), 0);
+            for (let i = 0; i < n; i++) {
+                newVector[i] = (newVector[i] ?? 0) - (dot / Math.sqrt(n));
+            }
+            // Normalize
+            const norm = Math.sqrt(newVector.reduce((sum, val) => sum + (val * val), 0));
+            if (norm > 1e-10) {
+                vector = newVector.map((val) => val / norm);
+            }
+        }
+        eigenvectors.push(vector);
+        eigenvalues.push(0.1); // Approximate
+    }
+    // For k = 3, add another eigenvector
+    if (k >= 3) {
+        let vector = Array(n).fill(0).map(() => Math.random() - 0.5);
+        // Orthogonalize against previous eigenvectors
+        for (const prev of eigenvectors) {
+            const dot = vector.reduce((sum, val, idx) => sum + (val * (prev[idx] ?? 0)), 0);
+            vector = vector.map((val, idx) => val - (dot * (prev[idx] ?? 0)));
+        }
+        // Similar power iteration
+        for (let iter = 0; iter < 50; iter++) {
+            const newVector = Array(n).fill(0);
+            // Identity part
+            for (let i = 0; i < n; i++) {
+                newVector[i] = vector[i] ?? 0;
+            }
+            // Subtract L * v / 2
+            for (let i = 0; i < n; i++) {
+                for (let j = 0; j < n; j++) {
+                    const matrixVal = matrix[i]?.[j] ?? 0;
+                    const vecVal = vector[j] ?? 0;
+                    newVector[i] = (newVector[i] ?? 0) - ((matrixVal * vecVal) / 2);
+                }
+            }
+            // Orthogonalize
+            for (const prev of eigenvectors) {
+                const dot = newVector.reduce((sum, val, idx) => sum + (val * (prev[idx] ?? 0)), 0);
+                for (let i = 0; i < n; i++) {
+                    newVector[i] = (newVector[i] ?? 0) - (dot * (prev[i] ?? 0));
+                }
+            }
+            // Normalize
+            const norm = Math.sqrt(newVector.reduce((sum, val) => sum + (val * val), 0));
+            if (norm > 1e-10) {
+                vector = newVector.map((val) => val / norm);
+            }
+        }
+        eigenvectors.push(vector);
+        eigenvalues.push(0.2); // Approximate
     }
-    return Math.sqrt(sum);
+    return { eigenvalues: eigenvalues.slice(0, k), eigenvectors: eigenvectors.slice(0, k) };
 }
 //# sourceMappingURL=spectral.js.map