@graphty/algorithms 1.2.0 → 1.4.2

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

@@ -23,6 +23,17 @@ export interface SpectralClusteringResult {
 }
 /**
  * Perform spectral clustering on a graph
+ *
+ * Note: 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.
+ * @param graph - The input graph to cluster
+ * @param options - Spectral clustering options (k, laplacianType, etc.)
+ * @returns Spectral clustering result with communities and cluster assignments
  */
 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,EAAE,KAAK,EAAE,MAAM,kBAAkB,CAAC;AAC9C,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAGhD;;;;;;;;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;;;;;;;;;;;;;GAaG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,OAAO,EAAE,yBAAyB,GAAG,wBAAwB,CA0F7G"}

package/dist/src/clustering/spectral.js

@@ -1,8 +1,24 @@
+import { euclideanDistance } from "../utils/math-utilities.js";
 /**
  * Perform spectral clustering on a graph
+ *
+ * Note: 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.
+ * @param graph - The input graph to cluster
+ * @param options - Spectral clustering options (k, laplacianType, etc.)
+ * @returns Spectral clustering result with communities and cluster assignments
  */
 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;
@@ -37,7 +53,7 @@ export function spectralClustering(graph, options) {
     if (laplacianType === "normalized") {
         normalizeRows(dataPoints);
     }
-    const kmeans = kMeansClustering(dataPoints, k, maxIterations);
+    const kmeans = kMeansClustering(dataPoints, k, maxIterations, tolerance);
     // Build communities
     const communities = Array.from({ length: k }, () => []);
     const clusterAssignments = new Map();
@@ -75,6 +91,9 @@ export function spectralClustering(graph, options) {
 }
 /**
  * Build adjacency matrix from graph
+ * @param graph - The input graph
+ * @param nodeIds - Array of node IDs defining matrix index order
+ * @returns Square adjacency matrix with edge weights
  */
 function buildAdjacencyMatrix(graph, nodeIds) {
     const n = nodeIds.length;
@@ -109,6 +128,9 @@ function buildAdjacencyMatrix(graph, nodeIds) {
 }
 /**
  * Build Laplacian matrix from adjacency matrix
+ * @param adjacency - Square adjacency matrix
+ * @param type - Type of Laplacian (unnormalized, normalized, or randomWalk)
+ * @returns The computed Laplacian matrix
  */
 function buildLaplacianMatrix(adjacency, type) {
     const n = adjacency.length;
@@ -168,7 +190,12 @@ function buildLaplacianMatrix(adjacency, type) {
                     const adjacencyVal = adjacencyRow[j];
                     const di = degrees[i];
                     const dj = degrees[j];
-                    if (adjacencyVal !== undefined && adjacencyVal > 0 && di !== undefined && dj !== undefined && di > 0 && dj > 0) {
+                    if (adjacencyVal !== undefined &&
+                        adjacencyVal > 0 &&
+                        di !== undefined &&
+                        dj !== undefined &&
+                        di > 0 &&
+                        dj > 0) {
                         const laplacianRow = laplacian[i];
                         if (laplacianRow) {
                             laplacianRow[j] = -adjacencyVal / Math.sqrt(di * dj);
@@ -211,6 +238,9 @@ function buildLaplacianMatrix(adjacency, type) {
 /**
  * Find k smallest eigenvectors using simplified eigendecomposition
  * This is a simplified implementation - in practice, you'd use LAPACK or similar
+ * @param matrix - The Laplacian matrix for eigendecomposition
+ * @param k - Number of smallest eigenvectors to find
+ * @returns Object containing eigenvalues and corresponding eigenvectors
  */
 function findSmallestEigenvectors(matrix, k) {
     const n = matrix.length;
@@ -234,9 +264,11 @@ function findSmallestEigenvectors(matrix, k) {
     const maxIterations = 100;
     for (let eigIdx = 0; eigIdx < k; eigIdx++) {
         // Initialize random vector
-        let vector = Array(n).fill(0).map(() => Math.random() - 0.5);
+        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));
+        const initNorm = Math.sqrt(vector.reduce((sum, val) => sum + val * val, 0));
         if (initNorm > 0) {
             vector = vector.map((val) => val / initNorm);
         }
@@ -246,8 +278,8 @@ function findSmallestEigenvectors(matrix, k) {
             if (!ejVector) {
                 continue;
             }
-            const dot = vector.reduce((sum, val, idx) => sum + (val * (ejVector[idx] ?? 0)), 0);
-            vector = vector.map((val, idx) => val - (dot * (ejVector[idx] ?? 0)));
+            const dot = vector.reduce((sum, val, idx) => sum + val * (ejVector[idx] ?? 0), 0);
+            vector = vector.map((val, idx) => val - dot * (ejVector[idx] ?? 0));
         }
         // Power iteration
         for (let iter = 0; iter < maxIterations; iter++) {
@@ -261,7 +293,7 @@ function findSmallestEigenvectors(matrix, k) {
                     if (matrixVal !== undefined && vecVal !== undefined) {
                         const nvVal = newVector[i];
                         if (nvVal !== undefined) {
-                            newVector[i] = nvVal + (matrixVal * vecVal);
+                            newVector[i] = nvVal + matrixVal * vecVal;
                         }
                     }
                 }
@@ -272,19 +304,19 @@ function findSmallestEigenvectors(matrix, k) {
                 if (!ejVector) {
                     continue;
                 }
-                const dot = newVector.reduce((sum, val, idx) => sum + (val * (ejVector[idx] ?? 0)), 0);
+                const dot = newVector.reduce((sum, val, idx) => sum + val * (ejVector[idx] ?? 0), 0);
                 for (let i = 0; i < n; i++) {
                     const ejVal = ejVector[i];
                     if (ejVal !== undefined) {
                         const nvVal = newVector[i];
                         if (nvVal !== undefined) {
-                            newVector[i] = nvVal - (dot * ejVal);
+                            newVector[i] = nvVal - dot * ejVal;
                         }
                     }
                 }
             }
             // Normalize
-            const norm = Math.sqrt(newVector.reduce((sum, val) => sum + ((val * val)), 0));
+            const norm = Math.sqrt(newVector.reduce((sum, val) => sum + val * val, 0));
             if (norm > 1e-10) {
                 vector = newVector.map((val) => val / norm);
             }
@@ -303,14 +335,14 @@ function findSmallestEigenvectors(matrix, k) {
                 if (matrixVal !== undefined && vecVal !== undefined) {
                     const avVal = Av[i];
                     if (avVal !== undefined) {
-                        Av[i] = avVal + (matrixVal * vecVal);
+                        Av[i] = avVal + matrixVal * vecVal;
                     }
                 }
             }
         }
         eigenvalue = vector.reduce((sum, val, idx) => {
             const avVal = Av[idx];
-            return sum + (val * (avVal ?? 0));
+            return sum + val * (avVal ?? 0);
         }, 0);
         eigenvectors.push(vector);
         eigenvalues.push(eigenvalue);
@@ -319,10 +351,11 @@ function findSmallestEigenvectors(matrix, k) {
 }
 /**
  * Normalize matrix rows to unit length
+ * @param matrix - Matrix to normalize in place
  */
 function normalizeRows(matrix) {
     for (const row of matrix) {
-        const norm = Math.sqrt(row.reduce((sum, val) => sum + (val * val), 0));
+        const norm = Math.sqrt(row.reduce((sum, val) => sum + val * val, 0));
         if (norm > 0) {
             for (let j = 0; j < row.length; j++) {
                 const val = row[j];
@@ -335,8 +368,13 @@ function normalizeRows(matrix) {
 }
 /**
  * K-means clustering algorithm
+ * @param data - Array of data points, each point is an array of coordinates
+ * @param k - Number of clusters to form
+ * @param maxIterations - Maximum number of iterations
+ * @param tolerance - Convergence tolerance for centroid movement
+ * @returns Object containing cluster assignments and final centroids
  */
-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
@@ -389,18 +427,20 @@ 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));
@@ -436,31 +476,39 @@ 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
- */
-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;
-    }
-    return Math.sqrt(sum);
-}
 /**
  * Compute smallest eigenvectors for small k (optimized for k=2, k=3)
+ * @param matrix - The Laplacian matrix
+ * @param k - Number of eigenvectors to compute (1-3)
+ * @param n - Size of the matrix
+ * @returns Object containing eigenvalues and eigenvectors
  */
 function computeSmallestEigenvectorsSimple(matrix, k, n) {
     const eigenvectors = [];
@@ -473,10 +521,12 @@ function computeSmallestEigenvectorsSimple(matrix, k, n) {
     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);
+        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)));
+        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
@@ -490,16 +540,16 @@ function computeSmallestEigenvectorsSimple(matrix, k, n) {
                 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);
+                    newVector[i] = (newVector[i] ?? 0) - (matrixVal * vecVal) / maxEig;
                 }
             }
             // Orthogonalize against first eigenvector
-            const dot = newVector.reduce((sum, val) => sum + (val / Math.sqrt(n)), 0);
+            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));
+                newVector[i] = (newVector[i] ?? 0) - dot / Math.sqrt(n);
             }
             // Normalize
-            const norm = Math.sqrt(newVector.reduce((sum, val) => sum + (val * val), 0));
+            const norm = Math.sqrt(newVector.reduce((sum, val) => sum + val * val, 0));
             if (norm > 1e-10) {
                 vector = newVector.map((val) => val / norm);
             }
@@ -509,11 +559,13 @@ function computeSmallestEigenvectorsSimple(matrix, k, n) {
     }
     // For k = 3, add another eigenvector
     if (k >= 3) {
-        let vector = Array(n).fill(0).map(() => Math.random() - 0.5);
+        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)));
+            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++) {
@@ -527,18 +579,18 @@ function computeSmallestEigenvectorsSimple(matrix, k, n) {
                 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);
+                    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);
+                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));
+                    newVector[i] = (newVector[i] ?? 0) - dot * (prev[i] ?? 0);
                 }
             }
             // Normalize
-            const norm = Math.sqrt(newVector.reduce((sum, val) => sum + (val * val), 0));
+            const norm = Math.sqrt(newVector.reduce((sum, val) => sum + val * val, 0));
             if (norm > 1e-10) {
                 vector = newVector.map((val) => val / norm);
             }

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

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

@@ -11,89 +11,133 @@ export declare class Graph {
     private incomingEdges;
     private config;
     private edgeCount;
+    /**
+     * Creates a new Graph instance.
+     * @param config - Configuration options for the graph
+     */
     constructor(config?: Partial<GraphConfig>);
     /**
      * Add a node to the graph
+     * @param id - The unique identifier for the node
+     * @param data - Optional key-value data to attach to the node
      */
     addNode(id: NodeId, data?: Record<string, unknown>): void;
     /**
      * Remove a node from the graph
+     * @param id - The unique identifier of the node to remove
+     * @returns True if the node was removed, false if it did not exist
      */
     removeNode(id: NodeId): boolean;
     /**
      * Add an edge to the graph
+     * @param source - The source node identifier
+     * @param target - The target node identifier
+     * @param weight - The weight of the edge (defaults to 1)
+     * @param data - Optional key-value data to attach to the edge
      */
     addEdge(source: NodeId, target: NodeId, weight?: number, data?: Record<string, unknown>): void;
     /**
      * Remove an edge from the graph
+     * @param source - The source node identifier
+     * @param target - The target node identifier
+     * @returns True if the edge was removed, false if it did not exist
      */
     removeEdge(source: NodeId, target: NodeId): boolean;
     /**
      * Check if a node exists in the graph
+     * @param id - The unique identifier of the node to check
+     * @returns True if the node exists, false otherwise
      */
     hasNode(id: NodeId): boolean;
     /**
      * Check if an edge exists in the graph
+     * @param source - The source node identifier
+     * @param target - The target node identifier
+     * @returns True if the edge exists, false otherwise
      */
     hasEdge(source: NodeId, target: NodeId): boolean;
     /**
      * Get a node by ID
+     * @param id - The unique identifier of the node to retrieve
+     * @returns The node if found, undefined otherwise
      */
     getNode(id: NodeId): Node | undefined;
     /**
      * Get an edge by source and target
+     * @param source - The source node identifier
+     * @param target - The target node identifier
+     * @returns The edge if found, undefined otherwise
      */
     getEdge(source: NodeId, target: NodeId): Edge | undefined;
     /**
      * Get the number of nodes in the graph
+     * @returns The total count of nodes
      */
     get nodeCount(): number;
     /**
      * Get the number of edges in the graph
+     * @returns The total count of edges
      */
     get totalEdgeCount(): number;
     /**
      * Check if the graph is directed
+     * @returns True if the graph is directed, false otherwise
      */
     get isDirected(): boolean;
     /**
      * Get all nodes in the graph
+     * @returns An iterator over all nodes
      */
     nodes(): IterableIterator<Node>;
     /**
      * Get all edges in the graph
+     * @yields Each unique edge in the graph
      */
     edges(): IterableIterator<Edge>;
     /**
      * Get neighbors of a node (outgoing edges)
+     * @param nodeId - The node identifier to get neighbors for
+     * @returns An iterator over the neighbor node identifiers
      */
     neighbors(nodeId: NodeId): IterableIterator<NodeId>;
     /**
      * Get incoming neighbors of a node (directed graphs only)
+     * @param nodeId - The node identifier to get incoming neighbors for
+     * @returns An iterator over the incoming neighbor node identifiers
      */
     inNeighbors(nodeId: NodeId): IterableIterator<NodeId>;
     /**
      * Get outgoing neighbors of a node
+     * @param nodeId - The node identifier to get outgoing neighbors for
+     * @returns An iterator over the outgoing neighbor node identifiers
      */
     outNeighbors(nodeId: NodeId): IterableIterator<NodeId>;
     /**
      * Get the degree of a node
+     * @param nodeId - The node identifier to get the degree for
+     * @returns The total degree of the node
      */
     degree(nodeId: NodeId): number;
     /**
      * Get the in-degree of a node
+     * @param nodeId - The node identifier to get the in-degree for
+     * @returns The number of incoming edges to the node
      */
     inDegree(nodeId: NodeId): number;
     /**
      * Get the out-degree of a node
+     * @param nodeId - The node identifier to get the out-degree for
+     * @returns The number of outgoing edges from the node
      */
     outDegree(nodeId: NodeId): number;
     /**
      * Create a copy of the graph
+     * @returns A new Graph instance with the same nodes and edges
      */
     clone(): Graph;
     /**
      * Get graph configuration
+     * @returns A copy of the graph configuration object
      */
     getConfig(): GraphConfig;
     /**
@@ -103,6 +147,7 @@ export declare class Graph {
     /**
      * Get the number of unique edges in the graph
      * For undirected graphs, each edge is counted once
+     * @returns The count of unique edges
      */
     get uniqueEdgeCount(): number;
 }

package/dist/src/core/graph.d.ts.map

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