@graphty/algorithms 2.1.2 → 2.2.0

package/dist/src/indexed/girvan-newman.js.map

@@ -0,0 +1 @@
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package/dist/src/indexed/grsbm.d.ts

@@ -0,0 +1,85 @@
+import { type F64, type GraphSnapshot, type U32 } from "@graphty/graph-format";
+import { type LabelResult } from "./components.js";
+/** Options of the index-based GRSBM, matching the legacy `grsbm`. @public */
+export interface GrsbmOptions {
+    /** Clusters at this depth are not split; default 10. */
+    readonly maxDepth?: number | undefined;
+    /** A cluster is split only when it has at least twice this many members; default 2. */
+    readonly minClusterSize?: number | undefined;
+    /** Convergence tolerance of the Fiedler-vector iteration; default 1e-6. */
+    readonly tolerance?: number | undefined;
+    /** Iteration cap of the Fiedler-vector iteration; default 100. */
+    readonly maxIterations?: number | undefined;
+    /** Seed of the iteration's start vectors; default 42. */
+    readonly seed?: number | undefined;
+    /**
+     * Use arc weights in the Laplacian and the modularity (true, the default), or count arcs
+     * (false, which is what the legacy `grsbm` does). A parallel arc counts once per arc.
+     */
+    readonly weighted?: boolean | undefined;
+}
+/** Why a cluster was split: the legacy `ClusterExplanation`, over node indices. @public */
+export interface GrsbmSplit {
+    /** The split's modularity minus the parent's. */
+    readonly improvement: number;
+    /** Modularity of the chosen split point (the legacy explanation text prints it to 3 places). */
+    readonly bisectionModularity: number;
+    /** Up to five members with the largest-magnitude Fiedler values, in member order. */
+    readonly keyNodes: U32;
+    /** The Fiedler vector, one value per member in member order. */
+    readonly spectralValues: F64;
+}
+/** One cluster of the hierarchy. @public */
+export interface GrsbmCluster {
+    /**
+     * 0 for the root, k for the k-th cluster a bisection proposed, counting the proposals that were
+     * rejected: the number in the legacy id `cluster_k`.
+     */
+    readonly serial: number;
+    /** Member node indices, in the legacy member order. */
+    readonly members: U32;
+    /** Depth below the root. */
+    readonly depth: number;
+    /** Modularity of the split that made this cluster (the root: of the whole graph as one cluster). */
+    readonly modularity: number;
+    /** Spread of the Fiedler values of the split that made this cluster; 0 for the root. */
+    readonly spectralScore: number;
+    /** Index in `clusters` of the left child, or `INVALID_INDEX` for a leaf. */
+    readonly left: number;
+    /** Index in `clusters` of the right child, or `INVALID_INDEX` for a leaf. */
+    readonly right: number;
+    /** Why this cluster was split; null for a leaf. */
+    readonly split: GrsbmSplit | null;
+}
+/**
+ * Result of the index-based GRSBM: the leaves as a partition, plus the hierarchy. `clusters[0]` is
+ * the root; the others follow in the order they were made, children in pairs.
+ * @public
+ */
+export interface GrsbmResult extends LabelResult {
+    /** Every cluster of the hierarchy. */
+    readonly clusters: readonly GrsbmCluster[];
+    /** The root's modularity, then each accepted split's, in split order. */
+    readonly modularityScores: F64;
+}
+/**
+ * GRSBM over a snapshot: recursive spectral bisection. Each cluster's Laplacian (over the arcs
+ * between its members, self-loops left out) gives an approximate Fiedler vector; members are sorted
+ * by it and cut at the point between 20% and 80% that maximises modularity; the split is kept when
+ * modularity drops by no more than 0.01. The arithmetic and the random draws are the legacy
+ * `grsbm`'s, so with `weighted: false` the result equals legacy's exactly on a graph without
+ * self-loops; the port draws from its own generator instead of replacing `Math.random`.
+ *
+ * Modularity uses `weightedDegree()` (a self-loop counts twice) against `totalWeight()`, or
+ * `degree()` against the edge count when unweighted. Like legacy's, a split's modularity sums only
+ * the two halves of the cluster being split. A self-loop follows the standard convention (left out
+ * of the Laplacian, twice in the degree), so on a graph with self-loops the result differs from
+ * legacy's, which scores the whole graph as one community above 0. On a directed graph the
+ * unweighted path keeps legacy's halving of internal arcs; the weighted path does not, so there the
+ * whole graph as one community scores 0. Weights must be finite and non-negative (RangeError).
+ * @param s - The snapshot
+ * @param options - {@link GrsbmOptions}
+ * @returns The leaf partition and the hierarchy
+ */
+export declare function grsbm(s: GraphSnapshot, options?: GrsbmOptions): GrsbmResult;
+//# sourceMappingURL=grsbm.d.ts.map

package/dist/src/indexed/grsbm.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/indexed/grsbm.js

@@ -0,0 +1,287 @@
+import { INVALID_INDEX, renumberPartition } from "@graphty/graph-format";
+import { SeededRandom } from "../utils/math-utilities.js";
+import { withGroups } from "./components.js";
+/**
+ * GRSBM over a snapshot: recursive spectral bisection. Each cluster's Laplacian (over the arcs
+ * between its members, self-loops left out) gives an approximate Fiedler vector; members are sorted
+ * by it and cut at the point between 20% and 80% that maximises modularity; the split is kept when
+ * modularity drops by no more than 0.01. The arithmetic and the random draws are the legacy
+ * `grsbm`'s, so with `weighted: false` the result equals legacy's exactly on a graph without
+ * self-loops; the port draws from its own generator instead of replacing `Math.random`.
+ *
+ * Modularity uses `weightedDegree()` (a self-loop counts twice) against `totalWeight()`, or
+ * `degree()` against the edge count when unweighted. Like legacy's, a split's modularity sums only
+ * the two halves of the cluster being split. A self-loop follows the standard convention (left out
+ * of the Laplacian, twice in the degree), so on a graph with self-loops the result differs from
+ * legacy's, which scores the whole graph as one community above 0. On a directed graph the
+ * unweighted path keeps legacy's halving of internal arcs; the weighted path does not, so there the
+ * whole graph as one community scores 0. Weights must be finite and non-negative (RangeError).
+ * @param s - The snapshot
+ * @param options - {@link GrsbmOptions}
+ * @returns The leaf partition and the hierarchy
+ */
+export function grsbm(s, options = {}) {
+    const { maxDepth = 10, minClusterSize = 2, tolerance = 1e-6, maxIterations = 100, seed = 42, weighted = true, } = options;
+    const n = s.nodeCount;
+    if (n === 0) {
+        throw new Error("Cannot cluster empty graph");
+    }
+    const random = SeededRandom.createGenerator(seed);
+    const arcWeights = weighted ? s.weights : null;
+    if (arcWeights !== null) {
+        for (let a = 0; a < arcWeights.length; a++) {
+            const w = arcWeights[a];
+            if (!(w >= 0) || w === Infinity) {
+                throw new RangeError(`arc ${String(a)} has weight ${String(w)}; grsbm needs finite, non-negative weights`);
+            }
+        }
+    }
+    const degree = weighted ? s.weightedDegree() : s.degree();
+    const m = weighted ? s.totalWeight() : s.edgeCount;
+    const loopFactor = s.directed ? 1 : 2;
+    // An undirected edge is stored as two arcs, so the internal sum counts it twice. A directed arc is
+    // stored once; legacy halves it anyway (the whole graph as one community scores -0.5), and the
+    // unweighted path keeps that for parity.
+    const halveInternal = !s.directed || !weighted;
+    const { rowPtr, colIdx } = s;
+    // side[u]: the community of u in the split being scored, -1 outside the cluster.
+    const side = new Int32Array(n).fill(-1);
+    const communityTerm = (group) => {
+        let internal = 0;
+        let total = 0;
+        for (let p = 0; p < group.length; p++) {
+            const u = group[p];
+            total += degree[u];
+            for (let a = rowPtr[u]; a < rowPtr[u + 1]; a++) {
+                const v = colIdx[a];
+                if (side[v] === side[u]) {
+                    const w = arcWeights === null ? 1 : arcWeights[a];
+                    internal += v === u ? loopFactor * w : w;
+                }
+            }
+        }
+        if (halveInternal) {
+            internal /= 2;
+        }
+        return (internal - (total * total) / (4 * m)) / m;
+    };
+    const modularity = (groups) => {
+        if (m === 0) {
+            return 0;
+        }
+        let q = 0;
+        groups.forEach((group, c) => {
+            for (let p = 0; p < group.length; p++) {
+                side[group[p]] = c;
+            }
+        });
+        for (const group of groups) {
+            if (group.length > 0) {
+                q += communityTerm(group);
+            }
+        }
+        for (const group of groups) {
+            for (let p = 0; p < group.length; p++) {
+                side[group[p]] = -1;
+            }
+        }
+        return q;
+    };
+    const everyone = new Uint32Array(n);
+    for (let i = 0; i < n; i++) {
+        everyone[i] = i;
+    }
+    const initial = modularity([everyone]);
+    const clusters = [
+        {
+            serial: 0,
+            members: everyone,
+            depth: 0,
+            modularity: initial,
+            spectralScore: 0,
+            left: INVALID_INDEX,
+            right: INVALID_INDEX,
+            split: null,
+        },
+    ];
+    const scores = [initial];
+    const position = new Int32Array(n).fill(-1);
+    let nextSerial = 1;
+    // The clusters array doubles as the breadth-first work queue: children are appended as made.
+    for (let head = 0; head < clusters.length; head++) {
+        const cluster = clusters[head];
+        const { members } = cluster;
+        const size = members.length;
+        if (cluster.depth >= maxDepth || size < minClusterSize * 2 || size < 4) {
+            continue;
+        }
+        const fiedler = fiedlerVector(members, position, s, arcWeights, random, tolerance, maxIterations);
+        const order = Array.from({ length: size }, (_, p) => p).sort((a, b) => fiedler[a] - fiedler[b]);
+        const sorted = Uint32Array.from(order, (p) => members[p]);
+        let bestSplit = Math.floor(size / 2);
+        let best = -Infinity;
+        for (let cut = Math.floor(size * 0.2); cut <= Math.floor(size * 0.8); cut++) {
+            const q = modularity([sorted.subarray(0, cut), sorted.subarray(cut)]);
+            if (q > best) {
+                best = q;
+                bestSplit = cut;
+            }
+        }
+        const leftMembers = sorted.slice(0, bestSplit);
+        const rightMembers = sorted.slice(bestSplit);
+        const byMagnitude = Array.from(fiedler).sort((a, b) => Math.abs(b) - Math.abs(a));
+        const threshold = Math.abs(byMagnitude[Math.floor(size * 0.1)]);
+        const keyNodes = [];
+        for (let p = 0; p < size && keyNodes.length < 5; p++) {
+            if (Math.abs(fiedler[p]) >= threshold) {
+                keyNodes.push(members[p]);
+            }
+        }
+        const spectralScore = Math.abs(byMagnitude[0] - byMagnitude[size - 1]);
+        const leftSerial = nextSerial++;
+        const rightSerial = nextSerial++;
+        const improvement = best - cluster.modularity;
+        if (improvement < -0.01) {
+            continue;
+        }
+        const child = (serial, childMembers) => ({
+            serial,
+            members: childMembers,
+            depth: cluster.depth + 1,
+            modularity: best,
+            spectralScore,
+            left: INVALID_INDEX,
+            right: INVALID_INDEX,
+            split: null,
+        });
+        cluster.left = clusters.length;
+        cluster.right = clusters.length + 1;
+        cluster.split = {
+            improvement,
+            bisectionModularity: best,
+            keyNodes: Uint32Array.from(keyNodes),
+            spectralValues: fiedler,
+        };
+        clusters.push(child(leftSerial, leftMembers), child(rightSerial, rightMembers));
+        scores.push(best);
+    }
+    // One label per leaf, renumbered by each leaf's lowest node index.
+    const leafOf = new Uint32Array(n);
+    let leaves = 0;
+    const stack = [0];
+    while (stack.length > 0) {
+        const c = clusters[stack.pop() ?? 0];
+        if (c.left === INVALID_INDEX) {
+            for (const u of c.members) {
+                leafOf[u] = leaves;
+            }
+            leaves++;
+        }
+        else {
+            stack.push(c.right, c.left);
+        }
+    }
+    const { labels, count } = renumberPartition(leafOf);
+    return { ...withGroups(labels, count), clusters, modularityScores: Float64Array.from(scores) };
+}
+/**
+ * Legacy's approximate Fiedler vector of a cluster's Laplacian: a seeded random start orthogonal to
+ * the all-ones vector, then repeated multiplication by -L, re-centred and normalised, until it stops
+ * moving. Each row is summed in member order, the order legacy's dense matrix product uses, so the
+ * vector matches legacy's to the last bit.
+ * @param members - The cluster's node indices
+ * @param position - Scratch, -1 everywhere on entry and exit
+ * @param s - The snapshot
+ * @param arcWeights - Arc weights, or null to count arcs
+ * @param random - The generator
+ * @param tolerance - Convergence tolerance
+ * @param maxIterations - Iteration cap
+ * @returns One value per member
+ */
+function fiedlerVector(members, position, s, arcWeights, random, tolerance, maxIterations) {
+    const size = members.length;
+    for (let p = 0; p < size; p++) {
+        position[members[p]] = p;
+    }
+    // The Laplacian as sorted sparse rows: off-diagonal -w per member neighbour, diagonal their sum.
+    const rowStart = new Uint32Array(size + 1);
+    const cols = [];
+    const vals = [];
+    const row = new Map();
+    for (let p = 0; p < size; p++) {
+        const u = members[p];
+        row.clear();
+        let diagonal = 0;
+        for (let a = s.rowPtr[u]; a < s.rowPtr[u + 1]; a++) {
+            const q = position[s.colIdx[a]];
+            if (q >= 0 && q !== p) {
+                const w = arcWeights === null ? 1 : arcWeights[a];
+                row.set(q, (row.get(q) ?? 0) - w);
+                diagonal += w;
+            }
+        }
+        row.set(p, diagonal);
+        for (const q of [...row.keys()].sort((a, b) => a - b)) {
+            cols.push(q);
+            vals.push(row.get(q) ?? 0);
+        }
+        rowStart[p + 1] = cols.length;
+    }
+    for (let p = 0; p < size; p++) {
+        position[members[p]] = -1;
+    }
+    let vector = new Float64Array(size);
+    for (let p = 0; p < size; p++) {
+        vector[p] = random() - 0.5;
+    }
+    const recentre = (v) => {
+        let sum = 0;
+        for (const x of v) {
+            sum += x;
+        }
+        const mean = sum / size;
+        for (let p = 0; p < size; p++) {
+            v[p] -= mean;
+        }
+    };
+    const norm = (v) => {
+        let sum = 0;
+        for (const x of v) {
+            sum += x * x;
+        }
+        return Math.sqrt(sum);
+    };
+    recentre(vector);
+    const start = norm(vector);
+    if (start > 0) {
+        for (let p = 0; p < size; p++) {
+            vector[p] /= start;
+        }
+    }
+    for (let iteration = 0; iteration < maxIterations; iteration++) {
+        const next = new Float64Array(size);
+        for (let p = 0; p < size; p++) {
+            let sum = 0;
+            for (let k = rowStart[p]; k < rowStart[p + 1]; k++) {
+                sum += vals[k] * vector[cols[k]];
+            }
+            next[p] = -sum;
+        }
+        recentre(next);
+        const length = norm(next);
+        if (length < tolerance) {
+            break;
+        }
+        let moved = 0;
+        for (let p = 0; p < size; p++) {
+            next[p] /= length;
+            moved += Math.abs(next[p] - vector[p]);
+        }
+        vector = next;
+        if (moved < tolerance) {
+            break;
+        }
+    }
+    return vector;
+}
+//# sourceMappingURL=grsbm.js.map

package/dist/src/indexed/grsbm.js.map

@@ -0,0 +1 @@
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package/dist/src/indexed/hierarchical.d.ts

@@ -0,0 +1,69 @@
+import { type AdjacencyView } from "@graphty/graph-format";
+/** How the distance between two clusters is taken from their members' hop distances. @public */
+export type Linkage = "single" | "complete" | "average" | "ward";
+/** Options of the index-based hierarchical clustering. @public */
+export interface HierarchicalOptions {
+    /** Cluster distance: the minimum, maximum or mean member distance, or Ward's scaled mean; default single. */
+    readonly linkage?: Linkage | undefined;
+}
+/**
+ * The dendrogram of an agglomerative clustering. Clusters `0 .. nodeCount - 1` are the nodes
+ * themselves; merge `k` creates cluster `nodeCount + k` from `left[k]` and `right[k]`.
+ * @public
+ */
+export interface HierarchicalResult {
+    /** The node count the clustering ran over. */
+    readonly nodeCount: number;
+    /** First cluster of every merge. */
+    readonly left: Uint32Array;
+    /** Second cluster of every merge. */
+    readonly right: Uint32Array;
+    /** Linkage distance of every merge. */
+    readonly distance: Float64Array;
+    /** Height of every cluster: 0 for a node, one more than its taller child for a merge. */
+    readonly height: Uint32Array;
+    /**
+     * The clusters left unmerged, in the order the legacy function lists its forest's trees: one
+     * entry (the last merge) when every pair of nodes could be linked, one per disconnected part
+     * otherwise, and none for an empty snapshot.
+     */
+    readonly roots: Uint32Array;
+    /**
+     * The node indices of a cluster, left subtree first -- the order the legacy function's member
+     * Sets iterate in.
+     * @param cluster - A cluster index
+     */
+    members(cluster: number): Uint32Array;
+    /**
+     * Cut every root at `height`: a cluster no taller than `height` is kept whole, a taller one is
+     * replaced by its two children. The clusters come in left-to-right order, root by root.
+     * @param height - The cut height
+     */
+    cut(height: number): Uint32Array[];
+}
+/**
+ * Agglomerative hierarchical clustering over hop distances, the index-based port of the legacy
+ * `hierarchicalClustering`: every node starts as its own cluster and the closest pair is merged
+ * until one cluster remains or no remaining pair is linked by a path.
+ *
+ * The distance between two nodes is the BFS hop count over out-arcs (weights are ignored, as the
+ * legacy function ignores them); an unreachable pair has none and is left out of every linkage.
+ * The distance between two clusters over the member pairs that have one is their minimum
+ * (`single`), maximum (`complete`), mean (`average`), or mean times `|A| |B| / (|A| + |B|)`
+ * (`ward`). A pair with no connected member pair is never merged. On a directed snapshot the
+ * distance is taken in one direction, and which one follows the legacy function exactly, as do the
+ * tie-breaks: the merges, their order and their distances equal the legacy function's.
+ *
+ * One difference in what the result offers: `cut` descends into every root of a disconnected
+ * snapshot, where the legacy `clusters` map lists all nodes as one cluster at every height (its
+ * forest node has no children, so its cut never splits it).
+ *
+ * O(n^2) memory for the distance aggregates and O(n^3) time for the pair search; the legacy
+ * function is the same order with Map and Set per step.
+ * @param s - Any snapshot or adjacency view
+ * @param options - The linkage
+ * @returns The dendrogram
+ * @public
+ */
+export declare function hierarchicalClustering(s: AdjacencyView, options?: HierarchicalOptions): HierarchicalResult;
+//# sourceMappingURL=hierarchical.d.ts.map

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