@graphty/graph-samples 0.0.1 → 0.1.2

package/dist/src/generators/preferential-attachment.js

@@ -0,0 +1,157 @@
+/**
+ * Growth models: Barabasi-Albert preferential attachment with the Holme-Kim triad-formation step,
+ * and the Watts-Strogatz small world.
+ */
+import { RandomStream, resolveSeed } from "../random/stream.js";
+import { checkEdgeCount, checkInt, checkProbability, EdgeBuffer, toGraph } from "./util.js";
+import { applyWeights } from "./weights.js";
+/**
+ * Barabasi-Albert preferential attachment (A.-L. Barabasi and R. Albert, "Emergence of scaling in
+ * random networks", Science 286, 509-512, 1999), optionally with triad formation (P. Holme and
+ * B. J. Kim, "Growing scale-free networks with tunable clustering", Phys. Rev. E 65, 026107, 2002),
+ * in O(n m) with the repeated-endpoint list of Batagelj and Brandes (2005).
+ *
+ * The algorithm is networkx's `powerlaw_cluster_graph`, which is `barabasi_albert_graph` when the
+ * triad probability is 0: start from m isolated nodes 0 .. m - 1 whose repeated list holds each
+ * once; each new node s = m .. n - 1 draws m distinct targets uniformly from the repeated list
+ * (in draw order), then adds m edges (s, t): the first to the first target; each further one, with
+ * probability `triadProbability`, to a uniformly chosen neighbour of the previous target that s is
+ * not yet joined to, otherwise to the next unused target. Every endpoint is appended to the
+ * repeated list, s itself m times. All draws come from the single stream (seed,
+ * "barabasi-albert", 0): the process is sequential. Edges are listed by new node, in the order
+ * added. (n - m) m edges, no self-loops, no repeats.
+ * @param options - n, m, triadProbability and seed
+ * @returns the undirected graph
+ */
+export function barabasiAlbertGraph(options) {
+    const { n, m } = options;
+    const triad = options.triadProbability ?? 0;
+    checkInt("m", m, 1);
+    checkInt("n", n, m + 1);
+    checkProbability("triadProbability", triad);
+    const seed = resolveSeed(options.seed);
+    const edgeCount = (n - m) * m;
+    checkEdgeCount(edgeCount);
+    const stream = new RandomStream(seed, "barabasi-albert", 0);
+    const out = new EdgeBuffer(edgeCount);
+    const repeated = new Uint32Array(m + 2 * edgeCount);
+    let length = 0;
+    for (let i = 0; i < m; i++) {
+        repeated[length++] = i;
+    }
+    // neighbour lists, only for the triad step
+    // ponytail: number[][] per node; a CSR-like growable adjacency if HK at 1M+ nodes matters
+    const adjacency = triad > 0 ? Array.from({ length: n }, () => []) : null;
+    const targets = new Array(m);
+    const link = (s, t) => {
+        out.push(s, t);
+        repeated[length++] = t;
+        if (adjacency !== null) {
+            adjacency[s].push(t);
+            adjacency[t].push(s);
+        }
+    };
+    for (let s = m; s < n; s++) {
+        // m distinct targets from the repeated list, in draw order
+        let found = 0;
+        while (found < m) {
+            const t = repeated[stream.nextBelow(length)];
+            let fresh = true;
+            for (let i = 0; i < found; i++) {
+                fresh && (fresh = targets[i] !== t);
+            }
+            if (fresh) {
+                targets[found++] = t;
+            }
+        }
+        let next = 0;
+        let target = targets[next++];
+        link(s, target);
+        for (let count = 1; count < m; count++) {
+            if (adjacency !== null && stream.nextFloat() < triad) {
+                const mine = adjacency[s];
+                const candidates = adjacency[target].filter((x) => x !== s && !mine.includes(x));
+                if (candidates.length > 0) {
+                    link(s, candidates[stream.nextBelow(candidates.length)]);
+                    continue;
+                }
+            }
+            // the next unused target (a triad step may already have joined s to it)
+            do {
+                target = targets[next++];
+            } while (adjacency !== null && adjacency[s].includes(target) && next < m);
+            if (adjacency !== null && adjacency[s].includes(target)) {
+                // every planned target is taken: fall back to a fresh preferential draw
+                do {
+                    target = repeated[stream.nextBelow(length)];
+                } while (target === s || adjacency[s].includes(target));
+            }
+            link(s, target);
+        }
+        for (let i = 0; i < m; i++) {
+            repeated[length++] = s;
+        }
+    }
+    return applyWeights(toGraph(n, out, false), options);
+}
+/**
+ * The Watts-Strogatz small world (D. J. Watts and S. H. Strogatz, "Collective dynamics of
+ * 'small-world' networks", Nature 393, 440-442, 1998), as networkx's `watts_strogatz_graph`
+ * builds it, in O(n k).
+ *
+ * Start from the ring lattice: edge slot u k/2 + (j - 1) holds (u, (u + j) mod n) for j = 1 .. k/2.
+ * Then for j = 1 .. k/2 and u = 0 .. n - 1 in that order: draw a float; if it is below beta and u is
+ * not already joined to every other node, redraw w = nextBelow(n) until w is neither u nor a
+ * neighbour of u, and rewire the slot to (u, w). All draws come from the single stream (seed,
+ * "watts-strogatz", 0). Edges are listed in slot order.
+ * @param options - n, k, beta and seed
+ * @returns the undirected graph
+ */
+export function wattsStrogatzGraph(options) {
+    const { n, k, beta } = options;
+    checkInt("k", k, 2);
+    if (k % 2 !== 0) {
+        throw new RangeError(`k must be even, got ${k}`);
+    }
+    checkInt("n", n, k + 1);
+    checkProbability("beta", beta);
+    const seed = resolveSeed(options.seed);
+    const half = k / 2;
+    const m = n * half;
+    checkEdgeCount(m);
+    const src = new Uint32Array(m);
+    const dst = new Uint32Array(m);
+    const degree = new Uint32Array(n).fill(k);
+    // ponytail: a Set of u * n + v keys, fine to a few million edges; a hashed typed table beyond
+    const edges = new Set();
+    const key = (a, b) => (a < b ? a * n + b : b * n + a);
+    for (let u = 0; u < n; u++) {
+        for (let j = 1; j <= half; j++) {
+            const v = (u + j) % n;
+            src[u * half + j - 1] = u;
+            dst[u * half + j - 1] = v;
+            edges.add(key(u, v));
+        }
+    }
+    const stream = new RandomStream(seed, "watts-strogatz", 0);
+    for (let j = 1; j <= half; j++) {
+        for (let u = 0; u < n; u++) {
+            if (stream.nextFloat() >= beta || degree[u] >= n - 1) {
+                continue;
+            }
+            let w = stream.nextBelow(n);
+            while (w === u || edges.has(key(u, w))) {
+                w = stream.nextBelow(n);
+            }
+            const slot = u * half + j - 1;
+            const v = dst[slot];
+            edges.delete(key(u, v));
+            edges.add(key(u, w));
+            degree[v]--;
+            degree[w]++;
+            dst[slot] = w;
+        }
+    }
+    return applyWeights({ directed: false, nodeCount: n, src, dst }, options);
+}
+//# sourceMappingURL=preferential-attachment.js.map

package/dist/src/generators/preferential-attachment.js.map

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package/dist/src/generators/trees-and-dags.d.ts

@@ -0,0 +1,53 @@
+/**
+ * Random trees and random directed acyclic graphs.
+ */
+import { type U32 } from "@graphty/graph-format";
+import { type SampleGraph } from "../types.js";
+import { EdgeBuffer } from "./util.js";
+import { type WeightOptions } from "./weights.js";
+/** Options of {@link randomTreeGraph}. */
+export interface RandomTreeOptions extends WeightOptions {
+    /** The node count, >= 1. */
+    n: number;
+    /** The seed, an integer in [0, 2^53); default 0. */
+    seed?: number | undefined;
+}
+/**
+ * A uniformly random labelled tree: a uniformly random Pruefer sequence (H. Pruefer, Archiv der
+ * Mathematik und Physik 27, 142-144, 1918) of n - 2 draws nextBelow(n) from stream (seed,
+ * "prufer", 0), decoded in O(n). Edge k joins the k-th removed leaf to its neighbour; the last
+ * edge is (leaf, n - 1).
+ * @param options - n and seed
+ * @returns the undirected tree
+ */
+export declare function randomTreeGraph(options: RandomTreeOptions): SampleGraph;
+/** Options of {@link randomDagGraph}. */
+export interface RandomDagOptions extends WeightOptions {
+    /** The width of every layer, top to bottom; layer i holds the next `layers[i]` node indices. */
+    layers: readonly number[];
+    /** The probability of each arc from a node to a node of the next layer. */
+    p: number;
+    /** The seed, an integer in [0, 2^53); default 0. */
+    seed?: number | undefined;
+}
+/**
+ * Rows [start, end) of the layered DAG: node u of layer i < L - 1 draws from stream (seed,
+ * "layered-dag", u) and holds the arcs to the chosen nodes of layer i + 1, ascending.
+ * @param starts - starts[i] = first node of layer i; starts[L] = n
+ * @param layerOf - the layer of every node
+ * @param p - the probability
+ * @param seed - the seed
+ * @param start - the first row
+ * @param end - one past the last row
+ * @param out - receives the arcs
+ */
+export declare function dagRows(starts: readonly number[], layerOf: U32, p: number, seed: number, start: number, end: number, out: EdgeBuffer): void;
+/**
+ * A random layered DAG: arcs only from layer i to layer i + 1, each independently with
+ * probability p, O(n + m). The standard input for layered (Sugiyama) drawing, topological sort
+ * and longest path. Arcs are listed by source node, targets ascending. Node column `layer` (u32).
+ * @param options - layers, p and seed
+ * @returns the directed graph
+ */
+export declare function randomDagGraph(options: RandomDagOptions): SampleGraph;
+//# sourceMappingURL=trees-and-dags.d.ts.map

package/dist/src/generators/trees-and-dags.d.ts.map

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package/dist/src/generators/trees-and-dags.js

@@ -0,0 +1,108 @@
+/**
+ * Random trees and random directed acyclic graphs.
+ */
+import { detLog } from "../random/log.js";
+import { RandomStream, resolveSeed } from "../random/stream.js";
+import { bernoulliSegment, binomialBuffer, checkInt, checkProbability, EdgeBuffer, toGraph } from "./util.js";
+import { applyWeights } from "./weights.js";
+/**
+ * A uniformly random labelled tree: a uniformly random Pruefer sequence (H. Pruefer, Archiv der
+ * Mathematik und Physik 27, 142-144, 1918) of n - 2 draws nextBelow(n) from stream (seed,
+ * "prufer", 0), decoded in O(n). Edge k joins the k-th removed leaf to its neighbour; the last
+ * edge is (leaf, n - 1).
+ * @param options - n and seed
+ * @returns the undirected tree
+ */
+export function randomTreeGraph(options) {
+    const { n } = options;
+    checkInt("n", n, 1);
+    const seed = resolveSeed(options.seed);
+    const out = new EdgeBuffer(n);
+    if (n === 1) {
+        return applyWeights(toGraph(1, out, false), options);
+    }
+    const stream = new RandomStream(seed, "prufer", 0);
+    const code = new Uint32Array(n - 2);
+    const degree = new Uint32Array(n).fill(1);
+    for (let i = 0; i < n - 2; i++) {
+        code[i] = stream.nextBelow(n);
+        degree[code[i]]++;
+    }
+    let ptr = 0;
+    while (degree[ptr] !== 1) {
+        ptr++;
+    }
+    let leaf = ptr;
+    for (let i = 0; i < n - 2; i++) {
+        const v = code[i];
+        out.push(leaf, v);
+        degree[v]--;
+        if (degree[v] === 1 && v < ptr) {
+            leaf = v;
+        }
+        else {
+            ptr++;
+            while (degree[ptr] !== 1) {
+                ptr++;
+            }
+            leaf = ptr;
+        }
+    }
+    out.push(leaf, n - 1);
+    return applyWeights(toGraph(n, out, false), options);
+}
+/**
+ * Rows [start, end) of the layered DAG: node u of layer i < L - 1 draws from stream (seed,
+ * "layered-dag", u) and holds the arcs to the chosen nodes of layer i + 1, ascending.
+ * @param starts - starts[i] = first node of layer i; starts[L] = n
+ * @param layerOf - the layer of every node
+ * @param p - the probability
+ * @param seed - the seed
+ * @param start - the first row
+ * @param end - one past the last row
+ * @param out - receives the arcs
+ */
+export function dagRows(starts, layerOf, p, seed, start, end, out) {
+    const logQ = detLog(1 - p);
+    const stream = new RandomStream(seed, "layered-dag", 0);
+    const last = starts.length - 2;
+    for (let u = start; u < end; u++) {
+        const layer = layerOf[u];
+        if (layer < last) {
+            stream.reset(u);
+            bernoulliSegment(stream, p, logQ, u, starts[layer + 1], starts[layer + 2], out);
+        }
+    }
+}
+/**
+ * A random layered DAG: arcs only from layer i to layer i + 1, each independently with
+ * probability p, O(n + m). The standard input for layered (Sugiyama) drawing, topological sort
+ * and longest path. Arcs are listed by source node, targets ascending. Node column `layer` (u32).
+ * @param options - layers, p and seed
+ * @returns the directed graph
+ */
+export function randomDagGraph(options) {
+    const { layers, p } = options;
+    checkInt("layers.length", layers.length, 1);
+    checkProbability("p", p);
+    const seed = resolveSeed(options.seed);
+    const starts = [0];
+    let pairs = 0;
+    for (let i = 0; i < layers.length; i++) {
+        checkInt(`layers[${i}]`, layers[i], 0);
+        starts.push(starts[i] + layers[i]);
+        if (i > 0) {
+            pairs += layers[i - 1] * layers[i];
+        }
+    }
+    const n = starts[layers.length];
+    checkInt("the total size", n, 0);
+    const layerOf = new Uint32Array(n);
+    for (let i = 0; i < layers.length; i++) {
+        layerOf.fill(i, starts[i], starts[i + 1]);
+    }
+    const out = binomialBuffer(pairs, p);
+    dagRows(starts, layerOf, p, seed, 0, n, out);
+    return applyWeights(toGraph(n, out, true, { layer: layerOf }), options);
+}
+//# sourceMappingURL=trees-and-dags.js.map

package/dist/src/generators/trees-and-dags.js.map

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package/dist/src/generators/util.d.ts

@@ -0,0 +1,84 @@
+/**
+ * Shared plumbing of the generators: argument checks, the growable edge buffer and the Bernoulli
+ * row sampler every G(n, p)-style generator is built on.
+ */
+import { type U32 } from "@graphty/graph-format";
+import { type RandomStream } from "../random/stream.js";
+import { type SampleGraph } from "../types.js";
+/**
+ * Throw unless `value` is an integer in [min, max].
+ * @param name - the option name, for the message
+ * @param value - the value
+ * @param min - the smallest allowed value
+ * @param max - the largest allowed value
+ */
+export declare function checkInt(name: string, value: number, min: number, max?: number): void;
+/**
+ * Throw unless `value` is a probability in [0, 1].
+ * @param name - the option name, for the message
+ * @param value - the value
+ */
+export declare function checkProbability(name: string, value: number): void;
+/**
+ * Throw unless `count` edges fit a graph-format snapshot.
+ * @param count - the edge count
+ */
+export declare function checkEdgeCount(count: number): void;
+/** A growable pair of Uint32Array edge endpoint arrays. */
+export declare class EdgeBuffer {
+    src: U32;
+    dst: U32;
+    length: number;
+    /**
+     * An empty buffer.
+     * @param capacity - the initial capacity in edges
+     */
+    constructor(capacity: number);
+    /**
+     * Append one edge.
+     * @param u - the source index
+     * @param v - the target index
+     */
+    push(u: number, v: number): void;
+    /**
+     * The edges pushed so far as exactly sized arrays (copies when the buffer has slack).
+     * @returns the endpoint arrays
+     */
+    finish(): {
+        src: U32;
+        dst: U32;
+    };
+    private grow;
+}
+/**
+ * A buffer sized for a binomial number of edges: the mean plus six standard deviations, so it
+ * almost never grows.
+ * @param pairs - the number of candidate pairs
+ * @param p - the edge probability
+ * @returns the buffer
+ */
+export declare function binomialBuffer(pairs: number, p: number): EdgeBuffer;
+/**
+ * Append (row, c) for every column c in [lo, hi) chosen independently with probability p, in
+ * ascending c, by geometric skipping (V. Batagelj and U. Brandes, "Efficient generation of large
+ * random networks", Phys. Rev. E 71, 036113, 2005): O(1 + selected) draws instead of hi - lo.
+ * p = 0 and p = 1 draw nothing.
+ * @param stream - the row's stream
+ * @param p - the probability
+ * @param logQ - detLog(1 - p)
+ * @param row - the row node, written as the source
+ * @param lo - the first candidate column
+ * @param hi - one past the last candidate column
+ * @param out - the buffer
+ */
+export declare function bernoulliSegment(stream: RandomStream, p: number, logQ: number, row: number, lo: number, hi: number, out: EdgeBuffer): void;
+/**
+ * Assemble an undirected or directed SampleGraph from a buffer.
+ * @param nodeCount - the node count
+ * @param edges - the edges
+ * @param directed - whether the graph is directed
+ * @param nodeColumns - ground-truth columns, if any
+ * @returns the graph
+ */
+export declare function toGraph(nodeCount: number, edges: EdgeBuffer, directed: boolean, nodeColumns?: SampleGraph["nodeColumns"]): SampleGraph;
+//# sourceMappingURL=util.d.ts.map

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package/dist/src/generators/util.js

@@ -0,0 +1,138 @@
+/**
+ * Shared plumbing of the generators: argument checks, the growable edge buffer and the Bernoulli
+ * row sampler every G(n, p)-style generator is built on.
+ */
+import { MAX_COUNT } from "@graphty/graph-format";
+/**
+ * Throw unless `value` is an integer in [min, max].
+ * @param name - the option name, for the message
+ * @param value - the value
+ * @param min - the smallest allowed value
+ * @param max - the largest allowed value
+ */
+export function checkInt(name, value, min, max = MAX_COUNT) {
+    if (!Number.isInteger(value) || value < min || value > max) {
+        throw new RangeError(`${name} must be an integer in [${min}, ${max}], got ${String(value)}`);
+    }
+}
+/**
+ * Throw unless `value` is a probability in [0, 1].
+ * @param name - the option name, for the message
+ * @param value - the value
+ */
+export function checkProbability(name, value) {
+    if (!(value >= 0 && value <= 1)) {
+        throw new RangeError(`${name} must be a probability in [0, 1], got ${String(value)}`);
+    }
+}
+/**
+ * Throw unless `count` edges fit a graph-format snapshot.
+ * @param count - the edge count
+ */
+export function checkEdgeCount(count) {
+    if (count > MAX_COUNT) {
+        throw new RangeError(`the graph would have ${count} edges, above the limit of ${MAX_COUNT}`);
+    }
+}
+/** A growable pair of Uint32Array edge endpoint arrays. */
+export class EdgeBuffer {
+    /**
+     * An empty buffer.
+     * @param capacity - the initial capacity in edges
+     */
+    constructor(capacity) {
+        this.length = 0;
+        const size = Math.max(16, Math.min(capacity, MAX_COUNT));
+        this.src = new Uint32Array(size);
+        this.dst = new Uint32Array(size);
+    }
+    /**
+     * Append one edge.
+     * @param u - the source index
+     * @param v - the target index
+     */
+    push(u, v) {
+        if (this.length === this.src.length) {
+            this.grow();
+        }
+        this.src[this.length] = u;
+        this.dst[this.length] = v;
+        this.length++;
+    }
+    /**
+     * The edges pushed so far as exactly sized arrays (copies when the buffer has slack).
+     * @returns the endpoint arrays
+     */
+    finish() {
+        if (this.length === this.src.length) {
+            return { src: this.src, dst: this.dst };
+        }
+        return { src: this.src.slice(0, this.length), dst: this.dst.slice(0, this.length) };
+    }
+    grow() {
+        checkEdgeCount(this.length + 1);
+        const size = Math.min(this.src.length * 2, MAX_COUNT);
+        const src = new Uint32Array(size);
+        const dst = new Uint32Array(size);
+        src.set(this.src);
+        dst.set(this.dst);
+        this.src = src;
+        this.dst = dst;
+    }
+}
+/**
+ * A buffer sized for a binomial number of edges: the mean plus six standard deviations, so it
+ * almost never grows.
+ * @param pairs - the number of candidate pairs
+ * @param p - the edge probability
+ * @returns the buffer
+ */
+export function binomialBuffer(pairs, p) {
+    const mean = pairs * p;
+    checkEdgeCount(mean);
+    return new EdgeBuffer(Math.ceil(mean + 6 * Math.sqrt(mean * (1 - p)) + 16));
+}
+/**
+ * Append (row, c) for every column c in [lo, hi) chosen independently with probability p, in
+ * ascending c, by geometric skipping (V. Batagelj and U. Brandes, "Efficient generation of large
+ * random networks", Phys. Rev. E 71, 036113, 2005): O(1 + selected) draws instead of hi - lo.
+ * p = 0 and p = 1 draw nothing.
+ * @param stream - the row's stream
+ * @param p - the probability
+ * @param logQ - detLog(1 - p)
+ * @param row - the row node, written as the source
+ * @param lo - the first candidate column
+ * @param hi - one past the last candidate column
+ * @param out - the buffer
+ */
+export function bernoulliSegment(stream, p, logQ, row, lo, hi, out) {
+    if (p === 0 || lo >= hi) {
+        return;
+    }
+    if (p === 1) {
+        for (let c = lo; c < hi; c++) {
+            out.push(row, c);
+        }
+        return;
+    }
+    let c = lo + stream.nextSkip(logQ);
+    while (c < hi) {
+        out.push(row, c);
+        c += 1 + stream.nextSkip(logQ);
+    }
+}
+/**
+ * Assemble an undirected or directed SampleGraph from a buffer.
+ * @param nodeCount - the node count
+ * @param edges - the edges
+ * @param directed - whether the graph is directed
+ * @param nodeColumns - ground-truth columns, if any
+ * @returns the graph
+ */
+export function toGraph(nodeCount, edges, directed, nodeColumns) {
+    const { src, dst } = edges.finish();
+    return nodeColumns === undefined
+        ? { directed, nodeCount, src, dst }
+        : { directed, nodeCount, src, dst, nodeColumns };
+}
+//# sourceMappingURL=util.js.map

package/dist/src/generators/util.js.map

@@ -0,0 +1 @@
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