w-cluster 1.0.20 → 1.0.21

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Files changed (72) hide show
  1. package/.github/workflows/ci-test.yml +3 -3
  2. package/README.md +4 -6
  3. package/babel.config.js +4 -3
  4. package/dist/w-cluster.umd.js +2 -2
  5. package/dist/w-cluster.umd.js.map +1 -1
  6. package/dist/w-cluster.wk.umd.js +1 -1
  7. package/docs/DenseMatrix.html +202 -0
  8. package/docs/DistancePair.html +202 -0
  9. package/docs/LowerTriangle.html +202 -0
  10. package/docs/Rec.html +202 -0
  11. package/docs/Reco.html +202 -0
  12. package/docs/WCluster.mjs.html +8 -4
  13. package/docs/examples/ex-PCA.html +1 -1
  14. package/docs/examples/ex-cluster-webworker.html +1 -1
  15. package/docs/examples/ex-cluster.html +1 -1
  16. package/docs/global.html +6799 -164
  17. package/docs/index.html +2 -2
  18. package/docs/k-medoids_alternating.mjs.html +144 -0
  19. package/docs/k-medoids_arrayadapter.mjs.html +107 -0
  20. package/docs/k-medoids_dynmsc.mjs.html +255 -0
  21. package/docs/k-medoids_fastermsc.mjs.html +411 -0
  22. package/docs/k-medoids_fasterpam.mjs.html +305 -0
  23. package/docs/k-medoids_fastmsc.mjs.html +166 -0
  24. package/docs/k-medoids_fastpam1.mjs.html +132 -0
  25. package/docs/k-medoids_initialization.mjs.html +107 -0
  26. package/docs/k-medoids_pam.mjs.html +275 -0
  27. package/docs/k-medoids_pammedsil.mjs.html +307 -0
  28. package/docs/k-medoids_pamsil.mjs.html +225 -0
  29. package/docs/k-medoids_par_fasterpam.mjs.html +134 -0
  30. package/docs/k-medoids_par_silhouette.mjs.html +126 -0
  31. package/docs/k-medoids_silhouette.mjs.html +193 -0
  32. package/docs/k-medoids_util.mjs.html +135 -0
  33. package/g-PCA-nodeworker.mjs +1 -1
  34. package/g-PCA.mjs +1 -1
  35. package/g-cluster-kMeans-large.mjs +83 -0
  36. package/g-cluster-kMeans-nodeworker.mjs +181 -0
  37. package/g-cluster-kMeans.mjs +178 -0
  38. package/g-cluster-kMedoids-large-suggest.mjs +95 -0
  39. package/g-cluster-kMedoids-large.mjs +104 -0
  40. package/{g-cluster-nodeworker.mjs → g-cluster-kMedoids-nodeworker.mjs} +1 -2
  41. package/{g-cluster.mjs → g-cluster-kMedoids-simple.mjs} +1 -1
  42. package/package.json +7 -7
  43. package/script.txt +5 -7
  44. package/src/WCluster.mjs +6 -2
  45. package/src/WClusterCore.mjs +30 -21
  46. package/src/WClusterMat.mjs +98 -24
  47. package/src/jaccardBitset.mjs +63 -0
  48. package/src/k-medoids/README.md +124 -0
  49. package/src/k-medoids/alternating.mjs +72 -0
  50. package/src/k-medoids/arrayadapter.mjs +35 -0
  51. package/src/k-medoids/dynmsc.mjs +183 -0
  52. package/src/k-medoids/fastermsc.mjs +339 -0
  53. package/src/k-medoids/fasterpam.mjs +233 -0
  54. package/src/k-medoids/fastmsc.mjs +94 -0
  55. package/src/k-medoids/fastpam1.mjs +60 -0
  56. package/src/k-medoids/index.mjs +37 -0
  57. package/src/k-medoids/initialization.mjs +35 -0
  58. package/src/k-medoids/package.json +8 -0
  59. package/src/k-medoids/pam.mjs +203 -0
  60. package/src/k-medoids/pammedsil.mjs +235 -0
  61. package/src/k-medoids/pamsil.mjs +153 -0
  62. package/src/k-medoids/par_fasterpam.mjs +62 -0
  63. package/src/k-medoids/par_silhouette.mjs +54 -0
  64. package/src/k-medoids/silhouette.mjs +121 -0
  65. package/src/k-medoids/test.mjs +357 -0
  66. package/src/k-medoids/util.mjs +63 -0
  67. package/test/jaccardBitset.test.mjs +141 -0
  68. package/test/kMeans.test.mjs +278 -0
  69. package/test/kMedoids-large-suggest.test.mjs +140 -0
  70. package/test/kMedoids-large.test.mjs +142 -0
  71. package/test/{cluster.test.mjs → kMedoids-simple.test.mjs} +5 -5
  72. package/toolg/gDocsExams.mjs +1 -1
package/docs/k-medoids_par_fasterpam.mjs.html ADDED
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+ <!DOCTYPE html>
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+ <html lang="en">
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+ <head>
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+
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+ <meta charset="utf-8">
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+ <title>k-medoids/par_fasterpam.mjs - Documentation</title>
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+
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+
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+ <script src="scripts/prettify/prettify.js"></script>
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+ <script src="scripts/prettify/lang-css.js"></script>
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+ <!--[if lt IE 9]>
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+ <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
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+ <![endif]-->
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+ <link type="text/css" rel="stylesheet" href="styles/prettify.css">
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+ <link type="text/css" rel="stylesheet" href="styles/jsdoc.css">
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+ <script src="scripts/nav.js" defer></script>
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+
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+ </head>
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+ <body>
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+
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+ <input type="checkbox" id="nav-trigger" class="nav-trigger" />
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+ <label for="nav-trigger" class="navicon-button x">
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+ <div class="navicon"></div>
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+ </label>
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+
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+ <label for="nav-trigger" class="overlay"></label>
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+
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+ <nav >
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+
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+
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+ <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="DenseMatrix.html">DenseMatrix</a></li><li><a href="DistancePair.html">DistancePair</a></li><li><a href="LowerTriangle.html">LowerTriangle</a></li><li><a href="Rec.html">Rec</a></li><li><a href="Reco.html">Reco</a></li></ul><h3>Global</h3><ul><li><a href="global.html#PCA">PCA</a></li><li><a href="global.html#WCluster">WCluster</a></li><li><a href="global.html#alternating">alternating</a></li><li><a href="global.html#arrayAdapter">arrayAdapter</a></li><li><a href="global.html#assign_nearest">assign_nearest</a></li><li><a href="global.html#choose_medoid_within_partition">choose_medoid_within_partition</a></li><li><a href="global.html#cluster">cluster</a></li><li><a href="global.html#do_swap">do_swap</a></li><li><a href="global.html#do_swap_k2">do_swap_k2</a></li><li><a href="global.html#dynmsc">dynmsc</a></li><li><a href="global.html#fastermsc">fastermsc</a></li><li><a href="global.html#fastermsc_k2">fastermsc_k2</a></li><li><a href="global.html#fasterpam">fasterpam</a></li><li><a href="global.html#fastmsc">fastmsc</a></li><li><a href="global.html#fastmsc_k2">fastmsc_k2</a></li><li><a href="global.html#fastpam1">fastpam1</a></li><li><a href="global.html#find_best_swap">find_best_swap</a></li><li><a href="global.html#find_best_swap_k2">find_best_swap_k2</a></li><li><a href="global.html#find_best_swap_pam">find_best_swap_pam</a></li><li><a href="global.html#find_best_swap_pammedsil">find_best_swap_pammedsil</a></li><li><a href="global.html#find_best_swap_pammedsil_k2">find_best_swap_pammedsil_k2</a></li><li><a href="global.html#find_max">find_max</a></li><li><a href="global.html#find_min">find_min</a></li><li><a href="global.html#first_k">first_k</a></li><li><a href="global.html#initial_assignment">initial_assignment</a></li><li><a href="global.html#initial_assignment_k2">initial_assignment_k2</a></li><li><a href="global.html#medoid_silhouette">medoid_silhouette</a></li><li><a href="global.html#pam">pam</a></li><li><a href="global.html#pam_build">pam_build</a></li><li><a href="global.html#pam_build_initialize">pam_build_initialize</a></li><li><a href="global.html#pam_optimize">pam_optimize</a></li><li><a href="global.html#pam_swap">pam_swap</a></li><li><a href="global.html#pammedsil">pammedsil</a></li><li><a href="global.html#pammedsil_build_initialize">pammedsil_build_initialize</a></li><li><a href="global.html#pammedsil_optimize">pammedsil_optimize</a></li><li><a href="global.html#pammedsil_swap">pammedsil_swap</a></li><li><a href="global.html#pamsil">pamsil</a></li><li><a href="global.html#pamsil_build_initialize">pamsil_build_initialize</a></li><li><a href="global.html#pamsil_optimize">pamsil_optimize</a></li><li><a href="global.html#pamsil_swap">pamsil_swap</a></li><li><a href="global.html#par_fasterpam">par_fasterpam</a></li><li><a href="global.html#par_silhouette">par_silhouette</a></li><li><a href="global.html#rand_fasterpam">rand_fasterpam</a></li><li><a href="global.html#random_initialization">random_initialization</a></li><li><a href="global.html#remove_med">remove_med</a></li><li><a href="global.html#sample">sample</a></li><li><a href="global.html#shuffle">shuffle</a></li><li><a href="global.html#silhouette">silhouette</a></li><li><a href="global.html#update_removal_loss">update_removal_loss</a></li><li><a href="global.html#update_second_nearest">update_second_nearest</a></li><li><a href="global.html#update_third_nearest">update_third_nearest</a></li><li><a href="global.html#update_third_nearest_without_new">update_third_nearest_without_new</a></li></ul>
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+
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+ </nav>
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+
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+ <div id="main">
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+
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+ <h1 class="page-title">k-medoids/par_fasterpam.mjs</h1>
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+
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+
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+
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+
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+
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+
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+
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+ <section>
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+ <article>
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+ <pre class="prettyprint source linenums"><code>// Parallel FasterPAM algorithm, ported 1:1 from src/par_fasterpam.rs
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+ // JS is single-threaded; parallelism is collapsed to a sequential equivalent
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+ // by delegating to fasterpam.mjs helpers (result-identical to the Rust parallel internals).
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+ import { arrayAdapter } from './arrayadapter.mjs';
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+ import { choose_medoid_within_partition } from './util.mjs';
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+ import { initial_assignment, find_best_swap, do_swap, update_removal_loss } from './fasterpam.mjs';
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+ import { shuffle } from './initialization.mjs';
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+
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+ /**
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+ * Run the FasterPAM algorithm (parallel version).
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+ *
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+ * For small data sets (n&lt;1000) it is usually faster to use the non-parallel version.
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+ *
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+ * @param mat - a pairwise distance matrix
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+ * @param med - the list of medoids (mutated in place)
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+ * @param maxiter - the maximum number of iterations allowed
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+ * @param rng - random number generator for shuffling the input data
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+ * @returns { loss, assi, nIter, nSwaps }
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+ *
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+ * Panics (throws) when the dissimilarity matrix is not square, or k is 0 or larger than N.
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+ */
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+ export function par_fasterpam(mat, med, maxiter, rng = Math.random) {
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+ mat = arrayAdapter(mat);
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+ const n = mat.len(), k = med.length;
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+ if (k === 1) {
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+ const assi = new Array(n).fill(0);
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+ const [swapped, loss] = choose_medoid_within_partition(mat, assi, med, 0);
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+ return { loss, assi, nIter: 1, nSwaps: swapped ? 1 : 0 };
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+ }
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+ let [loss, data] = initial_assignment(mat, med);
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+
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+ let removal_loss = new Array(k).fill(0);
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+ update_removal_loss(data, removal_loss);
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+ let lastswap = n, n_swaps = 0, iter = 0;
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+ const seq = shuffle(rng, n); // random shuffling
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+ while (iter &lt; maxiter) {
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+ iter += 1;
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+ const swaps_before = n_swaps, lastloss = loss;
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+ for (const j of seq) {
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+ if (j === lastswap) {
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+ break;
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+ }
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+ if (j === med[data[j].near.i]) {
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+ continue; // This already is a medoid
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+ }
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+ const [change, b] = find_best_swap(mat, removal_loss, data, j);
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+ if (change >= 0) {
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+ continue; // No improvement
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+ }
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+ n_swaps += 1;
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+ lastswap = j;
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+ // perform the swap
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+ loss = do_swap(mat, med, data, b, j);
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+ update_removal_loss(data, removal_loss);
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+ }
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+ if (n_swaps === swaps_before || loss >= lastloss) {
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+ break; // converged
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+ }
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+ }
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+ const assi = data.map((x) => x.near.i);
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+ return { loss, assi, nIter: iter, nSwaps: n_swaps };
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+ }
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+ </code></pre>
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+ </article>
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+ </section>
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+
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+
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+ </div>
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+
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+ <br class="clear">
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+
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+ <footer>
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+ Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 4.0.5</a> on Sun Jun 14 2026 10:59:21 GMT+0800 (台北標準時間) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
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+ </footer>
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+
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+ <script>prettyPrint();</script>
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+ <script src="scripts/polyfill.js"></script>
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+ <script src="scripts/linenumber.js"></script>
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+
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+
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+ </body>
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+ </html>
package/docs/k-medoids_par_silhouette.mjs.html ADDED
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+ <!DOCTYPE html>
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+ <html lang="en">
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+ <head>
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+
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+ <meta charset="utf-8">
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+ <title>k-medoids/par_silhouette.mjs - Documentation</title>
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+
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+
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+ <script src="scripts/prettify/prettify.js"></script>
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+ <script src="scripts/prettify/lang-css.js"></script>
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+ <!--[if lt IE 9]>
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+ <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
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+ <![endif]-->
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+ <link type="text/css" rel="stylesheet" href="styles/prettify.css">
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+ <link type="text/css" rel="stylesheet" href="styles/jsdoc.css">
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+ <script src="scripts/nav.js" defer></script>
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+
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+ <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+ </head>
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+ <body>
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+
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+ <input type="checkbox" id="nav-trigger" class="nav-trigger" />
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+ <label for="nav-trigger" class="navicon-button x">
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+ <div class="navicon"></div>
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+ </label>
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+
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+ <label for="nav-trigger" class="overlay"></label>
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+
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+ <nav >
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+
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+
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+ <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="DenseMatrix.html">DenseMatrix</a></li><li><a href="DistancePair.html">DistancePair</a></li><li><a href="LowerTriangle.html">LowerTriangle</a></li><li><a href="Rec.html">Rec</a></li><li><a href="Reco.html">Reco</a></li></ul><h3>Global</h3><ul><li><a href="global.html#PCA">PCA</a></li><li><a href="global.html#WCluster">WCluster</a></li><li><a href="global.html#alternating">alternating</a></li><li><a href="global.html#arrayAdapter">arrayAdapter</a></li><li><a href="global.html#assign_nearest">assign_nearest</a></li><li><a href="global.html#choose_medoid_within_partition">choose_medoid_within_partition</a></li><li><a href="global.html#cluster">cluster</a></li><li><a href="global.html#do_swap">do_swap</a></li><li><a href="global.html#do_swap_k2">do_swap_k2</a></li><li><a href="global.html#dynmsc">dynmsc</a></li><li><a href="global.html#fastermsc">fastermsc</a></li><li><a href="global.html#fastermsc_k2">fastermsc_k2</a></li><li><a href="global.html#fasterpam">fasterpam</a></li><li><a href="global.html#fastmsc">fastmsc</a></li><li><a href="global.html#fastmsc_k2">fastmsc_k2</a></li><li><a href="global.html#fastpam1">fastpam1</a></li><li><a href="global.html#find_best_swap">find_best_swap</a></li><li><a href="global.html#find_best_swap_k2">find_best_swap_k2</a></li><li><a href="global.html#find_best_swap_pam">find_best_swap_pam</a></li><li><a href="global.html#find_best_swap_pammedsil">find_best_swap_pammedsil</a></li><li><a href="global.html#find_best_swap_pammedsil_k2">find_best_swap_pammedsil_k2</a></li><li><a href="global.html#find_max">find_max</a></li><li><a href="global.html#find_min">find_min</a></li><li><a href="global.html#first_k">first_k</a></li><li><a href="global.html#initial_assignment">initial_assignment</a></li><li><a href="global.html#initial_assignment_k2">initial_assignment_k2</a></li><li><a href="global.html#medoid_silhouette">medoid_silhouette</a></li><li><a href="global.html#pam">pam</a></li><li><a href="global.html#pam_build">pam_build</a></li><li><a href="global.html#pam_build_initialize">pam_build_initialize</a></li><li><a href="global.html#pam_optimize">pam_optimize</a></li><li><a href="global.html#pam_swap">pam_swap</a></li><li><a href="global.html#pammedsil">pammedsil</a></li><li><a href="global.html#pammedsil_build_initialize">pammedsil_build_initialize</a></li><li><a href="global.html#pammedsil_optimize">pammedsil_optimize</a></li><li><a href="global.html#pammedsil_swap">pammedsil_swap</a></li><li><a href="global.html#pamsil">pamsil</a></li><li><a href="global.html#pamsil_build_initialize">pamsil_build_initialize</a></li><li><a href="global.html#pamsil_optimize">pamsil_optimize</a></li><li><a href="global.html#pamsil_swap">pamsil_swap</a></li><li><a href="global.html#par_fasterpam">par_fasterpam</a></li><li><a href="global.html#par_silhouette">par_silhouette</a></li><li><a href="global.html#rand_fasterpam">rand_fasterpam</a></li><li><a href="global.html#random_initialization">random_initialization</a></li><li><a href="global.html#remove_med">remove_med</a></li><li><a href="global.html#sample">sample</a></li><li><a href="global.html#shuffle">shuffle</a></li><li><a href="global.html#silhouette">silhouette</a></li><li><a href="global.html#update_removal_loss">update_removal_loss</a></li><li><a href="global.html#update_second_nearest">update_second_nearest</a></li><li><a href="global.html#update_third_nearest">update_third_nearest</a></li><li><a href="global.html#update_third_nearest_without_new">update_third_nearest_without_new</a></li></ul>
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+
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+ </nav>
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+
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+ <div id="main">
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+
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+ <h1 class="page-title">k-medoids/par_silhouette.mjs</h1>
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+
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+
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+
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+
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+
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+
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+
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+ <section>
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+ <article>
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+ <pre class="prettyprint source linenums"><code>// Parallelism (rayon) collapsed to sequential equivalent for JS.
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+ import { arrayAdapter } from './arrayadapter.mjs';
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+ import { checked_div } from './silhouette.mjs';
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+
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+ /**
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+ * Compute the Silhouette of a strict partitional clustering (sequential JS port of parallel Rust impl).
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+ *
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+ * @param {object|Array} mat - pairwise distance matrix (will be wrapped by arrayAdapter)
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+ * @param {number[]} assi - cluster assignment for each point
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+ * @returns {number} the average silhouette value
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+ */
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+ export function par_silhouette(mat, assi) {
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+ mat = arrayAdapter(mat);
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+ if (!mat.isSquare()) throw new Error('Dissimilarity matrix is not square');
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+ let lsum = 0;
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+ for (let i = 0; i &lt; assi.length; i++) {
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+ const ai = assi[i];
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+ // buf[c] = [count, sum] for cluster c
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+ const buf = [];
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+ for (let j = 0; j &lt; assi.length; j++) {
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+ const aj = assi[j];
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+ while (aj >= buf.length) {
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+ buf.push([0, 0]);
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+ }
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+ if (i !== j) {
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+ buf[aj][0] += 1;
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+ buf[aj][1] += mat.get(i, j);
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+ }
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+ }
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+ if (buf[ai][0] > 0) {
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+ const a = checked_div(buf[ai][1], buf[ai][0]);
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+ // find minimum average distance to any other cluster (b)
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+ // mirrors Rust: tmp.next().unwrap_or_else(L::zero) seeds the fold
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+ let tmp2 = 0;
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+ let foundFirst = false;
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+ let b = 0;
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+ for (let c = 0; c &lt; buf.length; c++) {
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+ if (c === ai) continue;
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+ const avg = checked_div(buf[c][1], buf[c][0]);
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+ if (!foundFirst) {
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+ tmp2 = avg;
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+ foundFirst = true;
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+ b = tmp2;
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+ } else {
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+ b = avg &lt; b ? avg : b;
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+ }
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+ }
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+ // if no other cluster exists, foundFirst is false → b = tmp2 = 0
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+ lsum += checked_div(b - a, a > b ? a : b);
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+ }
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+ // else: singleton, contributes 0 (lsum unchanged)
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+ }
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+ return lsum / assi.length;
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+ }
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+ </code></pre>
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+ </article>
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+ </section>
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+
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+
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+ </div>
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+
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+ <br class="clear">
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+
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+ <footer>
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+ Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 4.0.5</a> on Sun Jun 14 2026 10:59:21 GMT+0800 (台北標準時間) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
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+ </footer>
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+ <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="DenseMatrix.html">DenseMatrix</a></li><li><a href="DistancePair.html">DistancePair</a></li><li><a href="LowerTriangle.html">LowerTriangle</a></li><li><a href="Rec.html">Rec</a></li><li><a href="Reco.html">Reco</a></li></ul><h3>Global</h3><ul><li><a href="global.html#PCA">PCA</a></li><li><a href="global.html#WCluster">WCluster</a></li><li><a href="global.html#alternating">alternating</a></li><li><a href="global.html#arrayAdapter">arrayAdapter</a></li><li><a href="global.html#assign_nearest">assign_nearest</a></li><li><a href="global.html#choose_medoid_within_partition">choose_medoid_within_partition</a></li><li><a href="global.html#cluster">cluster</a></li><li><a href="global.html#do_swap">do_swap</a></li><li><a href="global.html#do_swap_k2">do_swap_k2</a></li><li><a href="global.html#dynmsc">dynmsc</a></li><li><a href="global.html#fastermsc">fastermsc</a></li><li><a href="global.html#fastermsc_k2">fastermsc_k2</a></li><li><a href="global.html#fasterpam">fasterpam</a></li><li><a href="global.html#fastmsc">fastmsc</a></li><li><a href="global.html#fastmsc_k2">fastmsc_k2</a></li><li><a href="global.html#fastpam1">fastpam1</a></li><li><a href="global.html#find_best_swap">find_best_swap</a></li><li><a href="global.html#find_best_swap_k2">find_best_swap_k2</a></li><li><a href="global.html#find_best_swap_pam">find_best_swap_pam</a></li><li><a href="global.html#find_best_swap_pammedsil">find_best_swap_pammedsil</a></li><li><a href="global.html#find_best_swap_pammedsil_k2">find_best_swap_pammedsil_k2</a></li><li><a href="global.html#find_max">find_max</a></li><li><a href="global.html#find_min">find_min</a></li><li><a href="global.html#first_k">first_k</a></li><li><a href="global.html#initial_assignment">initial_assignment</a></li><li><a href="global.html#initial_assignment_k2">initial_assignment_k2</a></li><li><a href="global.html#medoid_silhouette">medoid_silhouette</a></li><li><a href="global.html#pam">pam</a></li><li><a href="global.html#pam_build">pam_build</a></li><li><a href="global.html#pam_build_initialize">pam_build_initialize</a></li><li><a href="global.html#pam_optimize">pam_optimize</a></li><li><a href="global.html#pam_swap">pam_swap</a></li><li><a href="global.html#pammedsil">pammedsil</a></li><li><a href="global.html#pammedsil_build_initialize">pammedsil_build_initialize</a></li><li><a href="global.html#pammedsil_optimize">pammedsil_optimize</a></li><li><a href="global.html#pammedsil_swap">pammedsil_swap</a></li><li><a href="global.html#pamsil">pamsil</a></li><li><a href="global.html#pamsil_build_initialize">pamsil_build_initialize</a></li><li><a href="global.html#pamsil_optimize">pamsil_optimize</a></li><li><a href="global.html#pamsil_swap">pamsil_swap</a></li><li><a href="global.html#par_fasterpam">par_fasterpam</a></li><li><a href="global.html#par_silhouette">par_silhouette</a></li><li><a href="global.html#rand_fasterpam">rand_fasterpam</a></li><li><a href="global.html#random_initialization">random_initialization</a></li><li><a href="global.html#remove_med">remove_med</a></li><li><a href="global.html#sample">sample</a></li><li><a href="global.html#shuffle">shuffle</a></li><li><a href="global.html#silhouette">silhouette</a></li><li><a href="global.html#update_removal_loss">update_removal_loss</a></li><li><a href="global.html#update_second_nearest">update_second_nearest</a></li><li><a href="global.html#update_third_nearest">update_third_nearest</a></li><li><a href="global.html#update_third_nearest_without_new">update_third_nearest_without_new</a></li></ul>
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+
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+ </nav>
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+
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+ <div id="main">
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+
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+ <h1 class="page-title">k-medoids/silhouette.mjs</h1>
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+
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+
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+
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+
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+
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+
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+
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+ <section>
47
+ <article>
48
+ <pre class="prettyprint source linenums"><code>// Silhouette evaluation measures, ported from src/silhouette.rs
49
+ import { arrayAdapter } from './arrayadapter.mjs';
50
+
51
+ /**
52
+ * Compute the Silhouette of a strict partitional clustering.
53
+ *
54
+ * The Silhouette, proposed by Peter Rousseeuw in 1987, is a popular internal
55
+ * evaluation measure for clusterings.
56
+ *
57
+ * @param mat - a pairwise distance matrix
58
+ * @param assi - the cluster assignment
59
+ * @param samples - whether to keep the individual samples, or not
60
+ * @returns { sil, samples } where sil is the average silhouette and samples are
61
+ * the individual silhouette values (empty [] if samples = false)
62
+ */
63
+ export function silhouette(mat, assi, samples = false) {
64
+ mat = arrayAdapter(mat);
65
+ if (!mat.isSquare()) throw new Error('Dissimilarity matrix is not square');
66
+ let sil = new Array(samples ? assi.length : 0).fill(0);
67
+ let lsum = 0;
68
+ let buf = []; // array of [count(u32), sum(L)] pairs
69
+ for (let i = 0; i &lt; assi.length; i++) {
70
+ const ai = assi[i];
71
+ buf.length = 0;
72
+ for (let j = 0; j &lt; assi.length; j++) {
73
+ const aj = assi[j];
74
+ while (aj >= buf.length) {
75
+ buf.push([0, 0]);
76
+ }
77
+ if (i !== j) {
78
+ buf[aj][0] += 1;
79
+ buf[aj][1] += mat.get(i, j);
80
+ }
81
+ }
82
+ if (buf.length === 1) {
83
+ return { sil: 0, samples: sil };
84
+ }
85
+ let s;
86
+ if (buf[ai][0] > 0) {
87
+ const a = checked_div(buf[ai][1], buf[ai][0]);
88
+ // Ugly hack to get the min():
89
+ let started = false;
90
+ let b = 0;
91
+ for (let k = 0; k &lt; buf.length; k++) {
92
+ if (k === ai) continue;
93
+ const p = buf[k];
94
+ const y = checked_div(p[1], p[0]);
95
+ if (!started) {
96
+ b = y; // tmp.next().unwrap_or_else(L::zero)
97
+ started = true;
98
+ } else {
99
+ b = y &lt; b ? y : b; // tmp.fold(tmp2, |x, y| if y &lt; x { y } else { x })
100
+ }
101
+ }
102
+ // tmp2 = tmp.next().unwrap_or_else(L::zero): if no element, b stays 0
103
+ s = checked_div(b - a, a > b ? a : b);
104
+ } else {
105
+ s = 0; // singleton
106
+ }
107
+ if (samples) {
108
+ sil[i] = s;
109
+ }
110
+ lsum += s;
111
+ }
112
+ return { sil: lsum / assi.length, samples: sil };
113
+ }
114
+
115
+ /**
116
+ * Compute the Medoid Silhouette of a clustering.
117
+ *
118
+ * The Medoid Silhouette is an approximation to the original Silhouette where the
119
+ * distance to the cluster medoid is used instead of the average distance.
120
+ *
121
+ * @param mat - a pairwise distance matrix
122
+ * @param meds - the medoid list
123
+ * @param samples - whether to keep the individual samples, or not
124
+ * @returns { sil, samples } where sil is the average medoid silhouette and
125
+ * samples are the individual values (empty [] if samples = false)
126
+ */
127
+ export function medoid_silhouette(mat, meds, samples = false) {
128
+ mat = arrayAdapter(mat);
129
+ const n = mat.len(), k = meds.length;
130
+ if (!mat.isSquare()) throw new Error('Dissimilarity matrix is not square');
131
+ if (!(n &lt;= U32_MAX_GUARD)) throw new Error('N is too large');
132
+ let sil = new Array(samples ? n : 0).fill(1);
133
+ if (k === 1) { return { sil: 1, samples: sil }; } // not really well-defined
134
+ if (!(k >= 2 &amp;&amp; k &lt;= n)) throw new Error('invalid k, must be over 1 and at most N');
135
+ let loss = 0;
136
+ for (let i = 0; i &lt; n; i++) {
137
+ const d1 = mat.get(i, meds[0]), d2 = mat.get(i, meds[1]);
138
+ let best = d1 &lt; d2 ? [d1, d2] : [d2, d1];
139
+ for (let s2 = 2; s2 &lt; meds.length; s2++) {
140
+ const m = meds[s2];
141
+ const d = mat.get(i, m);
142
+ if (d &lt; best[0]) {
143
+ best = [d, best[0]];
144
+ } else if (d &lt; best[1]) {
145
+ best = [best[0], d];
146
+ }
147
+ }
148
+ if (best[0] !== 0) {
149
+ const s = best[0] / best[1];
150
+ if (samples) { sil[i] = 1 - s; }
151
+ loss += s;
152
+ }
153
+ }
154
+ loss = 1 - loss / n;
155
+ return { sil: loss, samples: sil };
156
+ }
157
+
158
+ // u32::MAX, used only for the "N is too large" assertion.
159
+ const U32_MAX_GUARD = 4294967295;
160
+
161
+ // helper function, returns 0 on division by 0
162
+ export function checked_div(x, y) {
163
+ if (y > 0) {
164
+ return x / y;
165
+ } else {
166
+ return 0;
167
+ }
168
+ }
169
+ </code></pre>
170
+ </article>
171
+ </section>
172
+
173
+
174
+
175
+
176
+
177
+
178
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179
+
180
+ <br class="clear">
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+
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+ <footer>
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+ Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 4.0.5</a> on Sun Jun 14 2026 10:59:21 GMT+0800 (台北標準時間) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
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package/docs/k-medoids_util.mjs.html ADDED
@@ -0,0 +1,135 @@
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+ <!DOCTYPE html>
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+ <html lang="en">
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+ <head>
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+
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+ <meta charset="utf-8">
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+ <title>k-medoids/util.mjs - Documentation</title>
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+
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+
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+ <script src="scripts/prettify/prettify.js"></script>
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+ </label>
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+
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+ <label for="nav-trigger" class="overlay"></label>
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+
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+ <nav >
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+
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+
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+ <h2><a href="index.html">Home</a></h2><h3>Classes</h3><ul><li><a href="DenseMatrix.html">DenseMatrix</a></li><li><a href="DistancePair.html">DistancePair</a></li><li><a href="LowerTriangle.html">LowerTriangle</a></li><li><a href="Rec.html">Rec</a></li><li><a href="Reco.html">Reco</a></li></ul><h3>Global</h3><ul><li><a href="global.html#PCA">PCA</a></li><li><a href="global.html#WCluster">WCluster</a></li><li><a href="global.html#alternating">alternating</a></li><li><a href="global.html#arrayAdapter">arrayAdapter</a></li><li><a href="global.html#assign_nearest">assign_nearest</a></li><li><a href="global.html#choose_medoid_within_partition">choose_medoid_within_partition</a></li><li><a href="global.html#cluster">cluster</a></li><li><a href="global.html#do_swap">do_swap</a></li><li><a href="global.html#do_swap_k2">do_swap_k2</a></li><li><a href="global.html#dynmsc">dynmsc</a></li><li><a href="global.html#fastermsc">fastermsc</a></li><li><a href="global.html#fastermsc_k2">fastermsc_k2</a></li><li><a href="global.html#fasterpam">fasterpam</a></li><li><a href="global.html#fastmsc">fastmsc</a></li><li><a href="global.html#fastmsc_k2">fastmsc_k2</a></li><li><a href="global.html#fastpam1">fastpam1</a></li><li><a href="global.html#find_best_swap">find_best_swap</a></li><li><a href="global.html#find_best_swap_k2">find_best_swap_k2</a></li><li><a href="global.html#find_best_swap_pam">find_best_swap_pam</a></li><li><a href="global.html#find_best_swap_pammedsil">find_best_swap_pammedsil</a></li><li><a href="global.html#find_best_swap_pammedsil_k2">find_best_swap_pammedsil_k2</a></li><li><a href="global.html#find_max">find_max</a></li><li><a href="global.html#find_min">find_min</a></li><li><a href="global.html#first_k">first_k</a></li><li><a href="global.html#initial_assignment">initial_assignment</a></li><li><a href="global.html#initial_assignment_k2">initial_assignment_k2</a></li><li><a href="global.html#medoid_silhouette">medoid_silhouette</a></li><li><a href="global.html#pam">pam</a></li><li><a href="global.html#pam_build">pam_build</a></li><li><a href="global.html#pam_build_initialize">pam_build_initialize</a></li><li><a href="global.html#pam_optimize">pam_optimize</a></li><li><a href="global.html#pam_swap">pam_swap</a></li><li><a href="global.html#pammedsil">pammedsil</a></li><li><a href="global.html#pammedsil_build_initialize">pammedsil_build_initialize</a></li><li><a href="global.html#pammedsil_optimize">pammedsil_optimize</a></li><li><a href="global.html#pammedsil_swap">pammedsil_swap</a></li><li><a href="global.html#pamsil">pamsil</a></li><li><a href="global.html#pamsil_build_initialize">pamsil_build_initialize</a></li><li><a href="global.html#pamsil_optimize">pamsil_optimize</a></li><li><a href="global.html#pamsil_swap">pamsil_swap</a></li><li><a href="global.html#par_fasterpam">par_fasterpam</a></li><li><a href="global.html#par_silhouette">par_silhouette</a></li><li><a href="global.html#rand_fasterpam">rand_fasterpam</a></li><li><a href="global.html#random_initialization">random_initialization</a></li><li><a href="global.html#remove_med">remove_med</a></li><li><a href="global.html#sample">sample</a></li><li><a href="global.html#shuffle">shuffle</a></li><li><a href="global.html#silhouette">silhouette</a></li><li><a href="global.html#update_removal_loss">update_removal_loss</a></li><li><a href="global.html#update_second_nearest">update_second_nearest</a></li><li><a href="global.html#update_third_nearest">update_third_nearest</a></li><li><a href="global.html#update_third_nearest_without_new">update_third_nearest_without_new</a></li></ul>
33
+
34
+ </nav>
35
+
36
+ <div id="main">
37
+
38
+ <h1 class="page-title">k-medoids/util.mjs</h1>
39
+
40
+
41
+
42
+
43
+
44
+
45
+
46
+ <section>
47
+ <article>
48
+ <pre class="prettyprint source linenums"><code>// Utility types and helpers, ported from src/util.rs
49
+ export const U32_MAX = 4294967295;
50
+ export const USIZE_MAX = Number.MAX_SAFE_INTEGER;
51
+
52
+ /** Object id (i) and distance (d) pair. */
53
+ export class DistancePair {
54
+ constructor(i, d) { this.i = i; this.d = d; }
55
+ clone() { return new DistancePair(this.i, this.d); }
56
+ static empty() { return new DistancePair(U32_MAX, 0); }
57
+ }
58
+
59
+ /** Per-point record: nearest + second nearest medoid. */
60
+ export class Rec {
61
+ constructor(i1, d1, i2, d2) { this.near = new DistancePair(i1, d1); this.seco = new DistancePair(i2, d2); }
62
+ clone() { return new Rec(this.near.i, this.near.d, this.seco.i, this.seco.d); }
63
+ static empty() { return new Rec(U32_MAX, 0, U32_MAX, 0); }
64
+ }
65
+
66
+ /** Per-point record: nearest + second + third nearest medoid. */
67
+ export class Reco {
68
+ constructor(i1, d1, i2, d2, i3, d3) {
69
+ this.near = new DistancePair(i1, d1);
70
+ this.seco = new DistancePair(i2, d2);
71
+ this.third = new DistancePair(i3, d3);
72
+ }
73
+ clone() { return new Reco(this.near.i, this.near.d, this.seco.i, this.seco.d, this.third.i, this.third.d); }
74
+ static empty() { return new Reco(U32_MAX, 0, U32_MAX, 0, U32_MAX, 0); }
75
+ }
76
+
77
+ /** Find the minimum (index and value) over an array of numbers. */
78
+ export function find_min(arr) {
79
+ let bi = 0, bv = arr[0];
80
+ for (let i = 1; i &lt; arr.length; i++) { if (arr[i] &lt; bv) { bi = i; bv = arr[i]; } }
81
+ return [bi, bv];
82
+ }
83
+
84
+ /** Find the maximum (index and value) over an array of numbers. */
85
+ export function find_max(arr) {
86
+ let bi = 0, bv = arr[0];
87
+ for (let i = 1; i &lt; arr.length; i++) { if (arr[i] > bv) { bi = i; bv = arr[i]; } }
88
+ return [bi, bv];
89
+ }
90
+
91
+ /** Choose the best medoid within a partition. Mutates med[m]. Returns [changed, sumb]. */
92
+ export function choose_medoid_within_partition(mat, assi, med, m) {
93
+ const first = med[m];
94
+ let best = first;
95
+ let sumb = 0;
96
+ for (let i = 0; i &lt; assi.length; i++) {
97
+ if (first !== i &amp;&amp; assi[i] === m) sumb += mat.get(first, i);
98
+ }
99
+ for (let j = 0; j &lt; assi.length; j++) {
100
+ if (j !== first &amp;&amp; assi[j] === m) {
101
+ let sumj = 0;
102
+ for (let i = 0; i &lt; assi.length; i++) {
103
+ if (i !== j &amp;&amp; assi[i] === m) sumj += mat.get(j, i);
104
+ }
105
+ if (sumj &lt; sumb) { best = j; sumb = sumj; }
106
+ }
107
+ }
108
+ med[m] = best;
109
+ return [best !== first, sumb];
110
+ }
111
+ </code></pre>
112
+ </article>
113
+ </section>
114
+
115
+
116
+
117
+
118
+
119
+
120
+ </div>
121
+
122
+ <br class="clear">
123
+
124
+ <footer>
125
+ Documentation generated by <a href="https://github.com/jsdoc3/jsdoc">JSDoc 4.0.5</a> on Sun Jun 14 2026 10:59:21 GMT+0800 (台北標準時間) using the <a href="https://github.com/clenemt/docdash">docdash</a> theme.
126
+ </footer>
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+
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+ <script>prettyPrint();</script>
129
+ <script src="scripts/polyfill.js"></script>
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+ <script src="scripts/linenumber.js"></script>
131
+
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+
133
+
134
+ </body>
135
+ </html>
package/g-PCA-nodeworker.mjs CHANGED
@@ -64,4 +64,4 @@ testPCA()
64
64
  console.log(err)
65
65
  })
66
66
 
67
- //node --experimental-modules --es-module-specifier-resolution=node g-PCA-nodeworker.mjs
67
+ //node g-PCA-nodeworker.mjs
package/g-PCA.mjs CHANGED
@@ -63,4 +63,4 @@ testPCA()
63
63
  console.log(err)
64
64
  })
65
65
 
66
- //node --experimental-modules --es-module-specifier-resolution=node g-PCA.mjs
66
+ //node g-PCA.mjs