@graphty/algorithms 1.6.0 → 1.7.1

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Files changed (18) hide show
  1. package/README.md +13 -0
  2. package/dist/algorithms.js +46 -35
  3. package/dist/algorithms.js.map +1 -1
  4. package/dist/src/algorithms/community/girvan-newman.d.ts.map +1 -1
  5. package/dist/src/algorithms/community/girvan-newman.js +10 -7
  6. package/dist/src/algorithms/community/girvan-newman.js.map +1 -1
  7. package/dist/src/clustering/mcl.d.ts.map +1 -1
  8. package/dist/src/clustering/mcl.js +33 -21
  9. package/dist/src/clustering/mcl.js.map +1 -1
  10. package/dist/src/clustering/spectral.d.ts +1 -0
  11. package/dist/src/clustering/spectral.d.ts.map +1 -1
  12. package/dist/src/clustering/spectral.js +18 -13
  13. package/dist/src/clustering/spectral.js.map +1 -1
  14. package/dist/tsconfig.tsbuildinfo +1 -1
  15. package/package.json +32 -4
  16. package/src/algorithms/community/girvan-newman.ts +19 -8
  17. package/src/clustering/mcl.ts +38 -24
  18. package/src/clustering/spectral.ts +20 -10
package/dist/src/algorithms/community/girvan-newman.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"girvan-newman.d.ts","sourceRoot":"","sources":["../../../../src/algorithms/community/girvan-newman.ts"],"names":[],"mappings":"AAAA,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,CAqE/F"}
1
+ {"version":3,"file":"girvan-newman.d.ts","sourceRoot":"","sources":["../../../../src/algorithms/community/girvan-newman.ts"],"names":[],"mappings":"AAAA,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.js CHANGED
@@ -33,7 +33,7 @@ export function girvanNewman(graph, options = {}) {
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  while (Array.from(workingGraph.edges()).length > 0 && iterations < maxIterations) {
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  iterations++;
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  // Calculate edge betweenness centrality
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- const edgeBetweenness = calculateEdgeBetweenness(workingGraph);
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+ const { betweenness: edgeBetweenness, edgeEndpoints } = calculateEdgeBetweenness(workingGraph);
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  if (edgeBetweenness.size === 0) {
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  break;
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  }
@@ -42,9 +42,10 @@ export function girvanNewman(graph, options = {}) {
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  const edgesToRemove = [];
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  for (const [edgeKey, centrality] of edgeBetweenness) {
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  if (Math.abs(centrality - maxBetweenness) < 1e-10) {
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- const [source, target] = edgeKey.split("|");
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- if (source && target) {
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- edgesToRemove.push({ source, target });
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+ // Use original edge endpoints to preserve node ID types (number vs string)
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+ const endpoints = edgeEndpoints.get(edgeKey);
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+ if (endpoints) {
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+ edgesToRemove.push(endpoints);
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  }
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  }
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  }
@@ -79,14 +80,16 @@ export function girvanNewman(graph, options = {}) {
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  * Edge betweenness is the fraction of shortest paths that pass through the edge.
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  * We adapt node betweenness centrality calculation to work with edges.
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  * @param graph - The input graph to analyze
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- * @returns Map of edge keys to their betweenness centrality values
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+ * @returns Object with betweenness map and edge endpoints map (preserving original ID types)
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  */
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  function calculateEdgeBetweenness(graph) {
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  const edgeBetweenness = new Map();
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- // Initialize all edges with 0 betweenness
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+ const edgeEndpoints = new Map();
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+ // Initialize all edges with 0 betweenness and store original endpoints
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  for (const edge of graph.edges()) {
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  const edgeKey = getEdgeKey(edge.source, edge.target);
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  edgeBetweenness.set(edgeKey, 0);
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+ edgeEndpoints.set(edgeKey, { source: edge.source, target: edge.target });
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  }
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  // For each node as source, calculate shortest paths and accumulate edge betweenness
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  for (const sourceNode of graph.nodes()) {
@@ -148,7 +151,7 @@ function calculateEdgeBetweenness(graph) {
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  edgeBetweenness.set(edgeKey, betweenness / 2);
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  }
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  }
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- return edgeBetweenness;
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+ return { betweenness: edgeBetweenness, edgeEndpoints };
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  }
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  /**
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  * Find all shortest paths from a source node using optimized BFS
package/dist/src/algorithms/community/girvan-newman.js.map CHANGED
@@ -1 +1 @@
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package/dist/src/clustering/mcl.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"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"}
1
+ {"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;AA8WD;;;;;GAKG;AACH,wBAAgB,sBAAsB,CAAC,KAAK,EAAE,KAAK,EAAE,WAAW,EAAE,MAAM,EAAE,EAAE,GAAG,MAAM,CA+BpF"}
package/dist/src/clustering/mcl.js CHANGED
@@ -59,7 +59,7 @@ function buildTransitionMatrix(graph, nodeIds, selfLoops) {
59
59
  // Fill adjacency values
60
60
  for (let i = 0; i < n; i++) {
61
61
  const nodeId = nodeIds[i];
62
- if (!nodeId) {
62
+ if (nodeId === undefined) {
63
63
  continue;
64
64
  }
65
65
  const neighbors = graph.neighbors(nodeId);
@@ -301,40 +301,52 @@ function extractClusters(matrix, nodeIds) {
301
301
  attractors.add(nodeId);
302
302
  }
303
303
  }
304
- // Assign nodes to clusters based on columns
305
- let clusterIndex = 0;
304
+ // Assign nodes (columns) to clusters based on which attractor (row) they flow to
305
+ // After MCL convergence, matrix[i][j] > 0 means node j belongs to attractor i's cluster
306
+ const attractorToCommunity = new Map();
306
307
  for (let j = 0; j < n; j++) {
307
- // Find nodes that belong to this cluster (column)
308
- const clusterNodes = [];
308
+ // Find the attractor for this column (node j)
309
+ // Look for the row with the highest non-zero value in column j
310
+ let maxVal = 0;
311
+ let attractorRow = -1;
309
312
  for (let i = 0; i < n; i++) {
310
313
  const matrixRow = matrix[i];
311
314
  if (!matrixRow) {
312
315
  continue;
313
316
  }
314
317
  const val = matrixRow[j];
315
- if (val !== undefined && val > 0 && !nodeToCluster.has(i)) {
316
- clusterNodes.push(i);
317
- nodeToCluster.set(i, clusterIndex);
318
+ if (val !== undefined && val > maxVal) {
319
+ maxVal = val;
320
+ attractorRow = i;
318
321
  }
319
322
  }
320
- if (clusterNodes.length > 0) {
321
- communities.push(clusterNodes
322
- .map((idx) => {
323
- const nodeId = nodeIds[idx];
324
- return nodeId;
325
- })
326
- .filter((node) => node !== undefined));
327
- clusterIndex++;
323
+ if (attractorRow >= 0) {
324
+ // Node j belongs to the cluster of attractor at row attractorRow
325
+ let community = attractorToCommunity.get(attractorRow);
326
+ if (!community) {
327
+ community = [];
328
+ attractorToCommunity.set(attractorRow, community);
329
+ }
330
+ community.push(j);
331
+ nodeToCluster.set(j, attractorRow);
328
332
  }
329
333
  }
330
- // Handle isolated nodes
331
- for (let i = 0; i < n; i++) {
332
- if (!nodeToCluster.has(i)) {
333
- const nodeId = nodeIds[i];
334
+ // Convert attractor communities to node ID arrays
335
+ for (const [, memberIndices] of attractorToCommunity) {
336
+ communities.push(memberIndices
337
+ .map((idx) => {
338
+ const nodeId = nodeIds[idx];
339
+ return nodeId;
340
+ })
341
+ .filter((node) => node !== undefined));
342
+ }
343
+ // Handle isolated nodes (nodes with all-zero columns)
344
+ for (let j = 0; j < n; j++) {
345
+ if (!nodeToCluster.has(j)) {
346
+ const nodeId = nodeIds[j];
334
347
  if (nodeId !== undefined) {
335
348
  communities.push([nodeId]);
336
349
  }
337
- nodeToCluster.set(i, clusterIndex++);
338
350
  }
339
351
  }
340
352
  return { communities, attractors };
package/dist/src/clustering/mcl.js.map CHANGED
@@ -1 +1 @@
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package/dist/src/clustering/spectral.d.ts CHANGED
@@ -14,6 +14,7 @@ export interface SpectralClusteringOptions {
14
14
  laplacianType?: "unnormalized" | "normalized" | "randomWalk";
15
15
  maxIterations?: number;
16
16
  tolerance?: number;
17
+ seed?: number;
17
18
  }
18
19
  export interface SpectralClusteringResult {
19
20
  communities: NodeId[][];
package/dist/src/clustering/spectral.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"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"}
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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;IACnB,IAAI,CAAC,EAAE,MAAM,CAAC;CACjB;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,CA6F7G"}
package/dist/src/clustering/spectral.js CHANGED
@@ -1,4 +1,4 @@
1
- import { euclideanDistance } from "../utils/math-utilities.js";
1
+ import { euclideanDistance, SeededRandom } from "../utils/math-utilities.js";
2
2
  /**
3
3
  * Perform spectral clustering on a graph
4
4
  *
@@ -14,7 +14,9 @@ import { euclideanDistance } from "../utils/math-utilities.js";
14
14
  * @returns Spectral clustering result with communities and cluster assignments
15
15
  */
16
16
  export function spectralClustering(graph, options) {
17
- const { k, laplacianType = "normalized", maxIterations = 100, tolerance = 1e-4 } = options;
17
+ const { k, laplacianType = "normalized", maxIterations = 100, tolerance = 1e-4, seed } = options;
18
+ // Create random function - use seeded PRNG if seed provided, otherwise Math.random
19
+ const random = seed !== undefined ? SeededRandom.createGenerator(seed) : Math.random;
18
20
  // Input validation
19
21
  if (k < 1 || !Number.isInteger(k)) {
20
22
  throw new Error("k must be a positive integer");
@@ -34,7 +36,7 @@ export function spectralClustering(graph, options) {
34
36
  // Build Laplacian matrix
35
37
  const laplacianMatrix = buildLaplacianMatrix(adjacencyMatrix, laplacianType);
36
38
  // Find k smallest eigenvectors
37
- const eigenResult = findSmallestEigenvectors(laplacianMatrix, k);
39
+ const eigenResult = findSmallestEigenvectors(laplacianMatrix, k, random);
38
40
  // Perform k-means clustering on the eigenvectors
39
41
  // For spectral clustering, we need to transpose the eigenvector matrix
40
42
  // Each row should be a data point (node) with features from the eigenvectors
@@ -53,7 +55,7 @@ export function spectralClustering(graph, options) {
53
55
  if (laplacianType === "normalized") {
54
56
  normalizeRows(dataPoints);
55
57
  }
56
- const kmeans = kMeansClustering(dataPoints, k, maxIterations, tolerance);
58
+ const kmeans = kMeansClustering(dataPoints, k, maxIterations, tolerance, random);
57
59
  // Build communities
58
60
  const communities = Array.from({ length: k }, () => []);
59
61
  const clusterAssignments = new Map();
@@ -240,9 +242,10 @@ function buildLaplacianMatrix(adjacency, type) {
240
242
  * This is a simplified implementation - in practice, you'd use LAPACK or similar
241
243
  * @param matrix - The Laplacian matrix for eigendecomposition
242
244
  * @param k - Number of smallest eigenvectors to find
245
+ * @param random - Random number generator function
243
246
  * @returns Object containing eigenvalues and corresponding eigenvectors
244
247
  */
245
- function findSmallestEigenvectors(matrix, k) {
248
+ function findSmallestEigenvectors(matrix, k, random) {
246
249
  const n = matrix.length;
247
250
  if (n === 0 || k === 0) {
248
251
  return { eigenvalues: [], eigenvectors: [] };
@@ -256,7 +259,7 @@ function findSmallestEigenvectors(matrix, k) {
256
259
  // For spectral clustering, we need proper eigenvectors
257
260
  // Special handling for small k values which are common in clustering
258
261
  if (k <= 3 && n > k) {
259
- return computeSmallestEigenvectorsSimple(matrix, k, n);
262
+ return computeSmallestEigenvectorsSimple(matrix, k, n, random);
260
263
  }
261
264
  // For larger k, use power iteration
262
265
  const eigenvectors = [];
@@ -266,7 +269,7 @@ function findSmallestEigenvectors(matrix, k) {
266
269
  // Initialize random vector
267
270
  let vector = Array(n)
268
271
  .fill(0)
269
- .map(() => Math.random() - 0.5);
272
+ .map(() => random() - 0.5);
270
273
  // Normalize initial vector
271
274
  const initNorm = Math.sqrt(vector.reduce((sum, val) => sum + val * val, 0));
272
275
  if (initNorm > 0) {
@@ -372,9 +375,10 @@ function normalizeRows(matrix) {
372
375
  * @param k - Number of clusters to form
373
376
  * @param maxIterations - Maximum number of iterations
374
377
  * @param tolerance - Convergence tolerance for centroid movement
378
+ * @param random - Random number generator function
375
379
  * @returns Object containing cluster assignments and final centroids
376
380
  */
377
- function kMeansClustering(data, k, maxIterations, tolerance = 1e-4) {
381
+ function kMeansClustering(data, k, maxIterations, tolerance = 1e-4, random = Math.random) {
378
382
  const n = data.length;
379
383
  const d = data[0]?.length ?? 0;
380
384
  // Handle edge cases
@@ -392,7 +396,7 @@ function kMeansClustering(data, k, maxIterations, tolerance = 1e-4) {
392
396
  const centroids = [];
393
397
  const selectedIndices = new Set();
394
398
  while (centroids.length < k && selectedIndices.size < n) {
395
- const idx = Math.floor(Math.random() * n);
399
+ const idx = Math.floor(random() * n);
396
400
  if (!selectedIndices.has(idx) && data[idx]) {
397
401
  selectedIndices.add(idx);
398
402
  centroids.push([...data[idx]]);
@@ -402,7 +406,7 @@ function kMeansClustering(data, k, maxIterations, tolerance = 1e-4) {
402
406
  while (centroids.length < k) {
403
407
  const centroid = Array(d).fill(0);
404
408
  for (let j = 0; j < d; j++) {
405
- centroid[j] = Math.random() - 0.5;
409
+ centroid[j] = random() - 0.5;
406
410
  }
407
411
  centroids.push(centroid);
408
412
  }
@@ -508,9 +512,10 @@ function kMeansClustering(data, k, maxIterations, tolerance = 1e-4) {
508
512
  * @param matrix - The Laplacian matrix
509
513
  * @param k - Number of eigenvectors to compute (1-3)
510
514
  * @param n - Size of the matrix
515
+ * @param random - Random number generator function
511
516
  * @returns Object containing eigenvalues and eigenvectors
512
517
  */
513
- function computeSmallestEigenvectorsSimple(matrix, k, n) {
518
+ function computeSmallestEigenvectorsSimple(matrix, k, n, random) {
514
519
  const eigenvectors = [];
515
520
  const eigenvalues = [];
516
521
  // First eigenvector is constant (corresponds to eigenvalue 0 for connected graph)
@@ -523,7 +528,7 @@ function computeSmallestEigenvectorsSimple(matrix, k, n) {
523
528
  const maxEig = 2; // For normalized Laplacian, max eigenvalue <= 2
524
529
  let vector = Array(n)
525
530
  .fill(0)
526
- .map(() => Math.random() - 0.5);
531
+ .map(() => random() - 0.5);
527
532
  // Make orthogonal to first eigenvector
528
533
  const dot1 = vector.reduce((sum, val) => sum + val / Math.sqrt(n), 0);
529
534
  vector = vector.map((val) => val - dot1 / Math.sqrt(n));
@@ -561,7 +566,7 @@ function computeSmallestEigenvectorsSimple(matrix, k, n) {
561
566
  if (k >= 3) {
562
567
  let vector = Array(n)
563
568
  .fill(0)
564
- .map(() => Math.random() - 0.5);
569
+ .map(() => random() - 0.5);
565
570
  // Orthogonalize against previous eigenvectors
566
571
  for (const prev of eigenvectors) {
567
572
  const dot = vector.reduce((sum, val, idx) => sum + val * (prev[idx] ?? 0), 0);
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@@ -1 +1 @@
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