npm - w-cluster - Versions diffs - 1.0.20 → 1.0.21 - Mend

w-cluster 1.0.20 → 1.0.21

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Files changed (72) hide show

package/.github/workflows/ci-test.yml +3 -3
package/README.md +4 -6
package/babel.config.js +4 -3
package/dist/w-cluster.umd.js +2 -2
package/dist/w-cluster.umd.js.map +1 -1
package/dist/w-cluster.wk.umd.js +1 -1
package/docs/DenseMatrix.html +202 -0
package/docs/DistancePair.html +202 -0
package/docs/LowerTriangle.html +202 -0
package/docs/Rec.html +202 -0
package/docs/Reco.html +202 -0
package/docs/WCluster.mjs.html +8 -4
package/docs/examples/ex-PCA.html +1 -1
package/docs/examples/ex-cluster-webworker.html +1 -1
package/docs/examples/ex-cluster.html +1 -1
package/docs/global.html +6799 -164
package/docs/index.html +2 -2
package/docs/k-medoids_alternating.mjs.html +144 -0
package/docs/k-medoids_arrayadapter.mjs.html +107 -0
package/docs/k-medoids_dynmsc.mjs.html +255 -0
package/docs/k-medoids_fastermsc.mjs.html +411 -0
package/docs/k-medoids_fasterpam.mjs.html +305 -0
package/docs/k-medoids_fastmsc.mjs.html +166 -0
package/docs/k-medoids_fastpam1.mjs.html +132 -0
package/docs/k-medoids_initialization.mjs.html +107 -0
package/docs/k-medoids_pam.mjs.html +275 -0
package/docs/k-medoids_pammedsil.mjs.html +307 -0
package/docs/k-medoids_pamsil.mjs.html +225 -0
package/docs/k-medoids_par_fasterpam.mjs.html +134 -0
package/docs/k-medoids_par_silhouette.mjs.html +126 -0
package/docs/k-medoids_silhouette.mjs.html +193 -0
package/docs/k-medoids_util.mjs.html +135 -0
package/g-PCA-nodeworker.mjs +1 -1
package/g-PCA.mjs +1 -1
package/g-cluster-kMeans-large.mjs +83 -0
package/g-cluster-kMeans-nodeworker.mjs +181 -0
package/g-cluster-kMeans.mjs +178 -0
package/g-cluster-kMedoids-large-suggest.mjs +95 -0
package/g-cluster-kMedoids-large.mjs +104 -0
package/{g-cluster-nodeworker.mjs → g-cluster-kMedoids-nodeworker.mjs} +1 -2
package/{g-cluster.mjs → g-cluster-kMedoids-simple.mjs} +1 -1
package/package.json +7 -7
package/script.txt +5 -7
package/src/WCluster.mjs +6 -2
package/src/WClusterCore.mjs +30 -21
package/src/WClusterMat.mjs +98 -24
package/src/jaccardBitset.mjs +63 -0
package/src/k-medoids/README.md +124 -0
package/src/k-medoids/alternating.mjs +72 -0
package/src/k-medoids/arrayadapter.mjs +35 -0
package/src/k-medoids/dynmsc.mjs +183 -0
package/src/k-medoids/fastermsc.mjs +339 -0
package/src/k-medoids/fasterpam.mjs +233 -0
package/src/k-medoids/fastmsc.mjs +94 -0
package/src/k-medoids/fastpam1.mjs +60 -0
package/src/k-medoids/index.mjs +37 -0
package/src/k-medoids/initialization.mjs +35 -0
package/src/k-medoids/package.json +8 -0
package/src/k-medoids/pam.mjs +203 -0
package/src/k-medoids/pammedsil.mjs +235 -0
package/src/k-medoids/pamsil.mjs +153 -0
package/src/k-medoids/par_fasterpam.mjs +62 -0
package/src/k-medoids/par_silhouette.mjs +54 -0
package/src/k-medoids/silhouette.mjs +121 -0
package/src/k-medoids/test.mjs +357 -0
package/src/k-medoids/util.mjs +63 -0
package/test/jaccardBitset.test.mjs +141 -0
package/test/kMeans.test.mjs +278 -0
package/test/kMedoids-large-suggest.test.mjs +140 -0
package/test/kMedoids-large.test.mjs +142 -0
package/test/{cluster.test.mjs → kMedoids-simple.test.mjs} +5 -5
package/toolg/gDocsExams.mjs +1 -1

package/docs/k-medoids_initialization.mjs.html ADDED Viewed

@@ -0,0 +1,107 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="utf-8">
+    <title>k-medoids/initialization.mjs - Documentation</title>
+    <script src="scripts/prettify/prettify.js"></script>
+    <script src="scripts/prettify/lang-css.js"></script>
+    <!--[if lt IE 9]>
+      <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
+    <![endif]-->
+    <link type="text/css" rel="stylesheet" href="styles/prettify.css">
+    <link type="text/css" rel="stylesheet" href="styles/jsdoc.css">
+    <script src="scripts/nav.js" defer></script>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+</head>
+<body>
+<input type="checkbox" id="nav-trigger" class="nav-trigger" />
+<label for="nav-trigger" class="navicon-button x">
+  <div class="navicon"></div>
+</label>
+<label for="nav-trigger" class="overlay"></label>
+<nav >
+    <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>
+</nav>
+<div id="main">
+    <h1 class="page-title">k-medoids/initialization.mjs</h1>
+    <section>
+        <article>
+            <pre class="prettyprint source linenums"><code>// Initialization helpers, ported from src/initialization.rs (RNG approximated for JS)
+/** Use the first k objects (0..k-1) as initial medoids. */
+export function first_k(k) {
+  return Array.from({ length: k }, (_, i) => i);
+}
+/** Sample k DISTINCT indices from [0, n) using Floyd's algorithm. rng: () => float in [0,1). */
+export function sample(rng, n, k) {
+  if (k > n) throw new Error('`amount` of samples must be less than or equal to `length`');
+  const chosen = new Set();
+  const res = [];
+  for (let j = n - k; j &lt; n; j++) {
+    const t = Math.floor(rng() * (j + 1)); // 0..j inclusive
+    const v = chosen.has(t) ? j : t;
+    chosen.add(v);
+    res.push(v);
+  }
+  return res;
+}
+/** Random initialization: k distinct medoid indices in [0, n). */
+export function random_initialization(n, k, rng = Math.random) {
+  return sample(rng, n, k);
+}
+/** Fisher-Yates shuffle of [0, n). Used by rand_fasterpam / par_fasterpam. */
+export function shuffle(rng, n) {
+  const a = Array.from({ length: n }, (_, i) => i);
+  for (let i = n - 1; i > 0; i--) {
+    const j = Math.floor(rng() * (i + 1));
+    const tmp = a[i]; a[i] = a[j]; a[j] = tmp;
+  }
+  return a;
+}
+</code></pre>
+        </article>
+    </section>
+</div>
+<br class="clear">
+<footer>
+    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.
+</footer>
+<script>prettyPrint();</script>
+<script src="scripts/polyfill.js"></script>
+<script src="scripts/linenumber.js"></script>
+</body>
+</html>

package/docs/k-medoids_pam.mjs.html ADDED Viewed

@@ -0,0 +1,275 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="utf-8">
+    <title>k-medoids/pam.mjs - Documentation</title>
+    <script src="scripts/prettify/prettify.js"></script>
+    <script src="scripts/prettify/lang-css.js"></script>
+    <!--[if lt IE 9]>
+      <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
+    <![endif]-->
+    <link type="text/css" rel="stylesheet" href="styles/prettify.css">
+    <link type="text/css" rel="stylesheet" href="styles/jsdoc.css">
+    <script src="scripts/nav.js" defer></script>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+</head>
+<body>
+<input type="checkbox" id="nav-trigger" class="nav-trigger" />
+<label for="nav-trigger" class="navicon-button x">
+  <div class="navicon"></div>
+</label>
+<label for="nav-trigger" class="overlay"></label>
+<nav >
+    <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>
+</nav>
+<div id="main">
+    <h1 class="page-title">k-medoids/pam.mjs</h1>
+    <section>
+        <article>
+            <pre class="prettyprint source linenums"><code>// PAM (BUILD and SWAP) algorithm, ported 1:1 from src/pam.rs
+import { arrayAdapter } from './arrayadapter.mjs';
+import { Rec, DistancePair, U32_MAX, USIZE_MAX, choose_medoid_within_partition } from './util.mjs';
+import { initial_assignment, do_swap } from './fasterpam.mjs';
+/**
+ * Run the original PAM SWAP algorithm (no BUILD, but given initial medoids).
+ *
+ * Provided for academic reasons to see the performance difference.
+ *
+ * @param mat - a pairwise distance matrix
+ * @param med - the list of medoids (mutated in place)
+ * @param maxiter - the maximum number of iterations allowed
+ * @returns { loss, assi, nIter, nSwaps }
+ */
+export function pam_swap(mat, med, maxiter) {
+  mat = arrayAdapter(mat);
+  const [loss, data] = initial_assignment(mat, med);
+  const [nloss, assi, nIter, nSwaps] = pam_optimize(mat, med, data, maxiter, loss);
+  return { loss: nloss, assi, nIter, nSwaps };
+}
+/**
+ * Run the original PAM BUILD algorithm.
+ *
+ * Provided for academic reasons to see the performance difference.
+ *
+ * @param mat - a pairwise distance matrix
+ * @param k - the number of medoids to pick
+ * @returns { loss, assi, meds }
+ */
+export function pam_build(mat, k) {
+  mat = arrayAdapter(mat);
+  const n = mat.len();
+  if (!mat.isSquare()) throw new Error('Dissimilarity matrix is not square');
+  if (!(n &lt;= U32_MAX)) throw new Error('N is too large');
+  if (!(k > 0 &amp;&amp; k &lt; U32_MAX)) throw new Error('invalid N');
+  if (!(k &lt;= n)) throw new Error('k must be at most N');
+  const meds = [];
+  const data = [];
+  const loss = pam_build_initialize(mat, meds, data, k);
+  const assi = data.map((x) => x.near.i);
+  return { loss, assi, meds };
+}
+/**
+ * Run the original PAM algorithm (BUILD and SWAP).
+ *
+ * Provided for academic reasons to see the performance difference.
+ *
+ * @param mat - a pairwise distance matrix
+ * @param k - the number of medoids to pick
+ * @param maxiter - the maximum number of iterations allowed
+ * @returns { loss, assi, meds, nIter, nSwaps }
+ */
+export function pam(mat, k, maxiter) {
+  mat = arrayAdapter(mat);
+  const n = mat.len();
+  if (!mat.isSquare()) throw new Error('Dissimilarity matrix is not square');
+  if (!(n &lt;= U32_MAX)) throw new Error('N is too large');
+  if (!(k > 0 &amp;&amp; k &lt; U32_MAX)) throw new Error('invalid N');
+  if (!(k &lt;= n)) throw new Error('k must be at most N');
+  const meds = [];
+  const data = [];
+  const loss = pam_build_initialize(mat, meds, data, k);
+  const [nloss, assi, nIter, nSwaps] = pam_optimize(mat, meds, data, maxiter, loss);
+  return { loss: nloss, assi, meds, nIter, nSwaps }; // also return medoids
+}
+/** Main optimization function of PAM, not exposed (use pam_swap or pam). Returns [loss, assi, nIter, nSwaps]. */
+function pam_optimize(mat, med, data, maxiter, loss) {
+  const n = mat.len(), k = med.length;
+  if (k === 1) {
+    const assi = new Array(n).fill(0);
+    const [swapped, sloss] = choose_medoid_within_partition(mat, assi, med, 0);
+    return [sloss, assi, 1, swapped ? 1 : 0];
+  }
+  let n_swaps = 0, iter = 0;
+  while (iter &lt; maxiter) {
+    iter += 1;
+    let best = [0, k, USIZE_MAX];
+    for (let j = 0; j &lt; n; j++) {
+      if (j === med[data[j].near.i]) {
+        continue; // This already is a medoid
+      }
+      const [change, b] = find_best_swap_pam(mat, med, data, j);
+      if (change >= best[0]) {
+        continue; // No improvement
+      }
+      best = [change, b, j];
+    }
+    if (best[0] &lt; 0) {
+      n_swaps += 1;
+      // perform the swap
+      const newloss = do_swap(mat, med, data, best[1], best[2]);
+      if (newloss >= loss) {
+        break; // Probably numerically unstable now.
+      }
+      loss = newloss;
+    } else {
+      break; // No improvement, or NaN.
+    }
+  }
+  const assi = data.map((x) => x.near.i);
+  return [loss, assi, iter, n_swaps];
+}
+/** Find the best swap for object j - slower PAM version. Returns [acc_best, m_best]. */
+function find_best_swap_pam(mat, med, data, j) {
+  const recj = data[j];
+  let best = [0, USIZE_MAX];
+  for (let m = 0; m &lt; med.length; m++) {
+    let acc = -recj.near.d; // j becomes medoid
+    for (let o = 0; o &lt; data.length; o++) {
+      const reco = data[o];
+      if (o === j) {
+        continue;
+      }
+      const doj = mat.get(o, j);
+      // Current medoid is being replaced:
+      if (reco.near.i === m) {
+        if (doj &lt; reco.seco.d) {
+          // Assign to new medoid:
+          acc += doj - reco.near.d;
+        } else {
+          // Assign to second nearest instead:
+          acc += reco.seco.d - reco.near.d;
+        }
+      } else if (doj &lt; reco.near.d) {
+        // new mediod is closer:
+        acc += doj - reco.near.d;
+      } // else no change
+    }
+    if (acc &lt; best[0]) {
+      best = [acc, m];
+    }
+  }
+  return best;
+}
+/** Not exposed. Use pam_build or pam. Pushes into medsArr (numbers) and dataArr (Rec). Returns loss. */
+export function pam_build_initialize(mat, meds, data, k) {
+  const n = mat.len();
+  if (!mat.isSquare()) throw new Error('Dissimilarity matrix is not square');
+  // choose first medoid
+  let best = [0, k];
+  for (let i = 0; i &lt; n; i++) {
+    let sum = 0;
+    for (let j = 0; j &lt; n; j++) {
+      if (j !== i) {
+        sum += mat.get(j, i);
+      }
+    }
+    if (i === 0 || sum &lt; best[0]) {
+      best = [sum, i];
+    }
+  }
+  let loss = best[0];
+  meds.push(best[1]);
+  for (let j = 0; j &lt; n; j++) {
+    data.push(new Rec(0, mat.get(j, best[1]), U32_MAX, 0));
+  }
+  // choose remaining medoids
+  for (let l = 1; l &lt; k; l++) {
+    best = [0, k];
+    for (let i = 0; i &lt; data.length; i++) {
+      let sum = -data[i].near.d;
+      for (let j = 0; j &lt; data.length; j++) {
+        const dj = data[j];
+        if (j !== i) {
+          const d = mat.get(j, i);
+          if (d &lt; dj.near.d) {
+            sum += d - dj.near.d;
+          }
+        }
+      }
+      if (i === 0 || sum &lt; best[0]) {
+        best = [sum, i];
+      }
+    }
+    if (best[0] >= 0) { break; } // No further improvements - duplicates etc.
+    // Update assignments:
+    loss = 0;
+    for (let j = 0; j &lt; data.length; j++) {
+      const recj = data[j];
+      if (j === best[1]) {
+        recj.seco = recj.near.clone();
+        recj.near = new DistancePair(l, 0);
+        continue;
+      }
+      const dj = mat.get(j, best[1]);
+      if (dj &lt; recj.near.d) {
+        recj.seco = recj.near.clone();
+        recj.near = new DistancePair(l, dj);
+      } else if (recj.seco.i === U32_MAX || dj &lt; recj.seco.d) {
+        recj.seco = new DistancePair(l, dj);
+      }
+      loss += recj.near.d;
+    }
+    meds.push(best[1]);
+  }
+  return loss;
+}
+</code></pre>
+        </article>
+    </section>
+</div>
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