@graphty/graph-samples 0.0.1 → 0.1.2

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

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package/dist/src/generators/block-model.d.ts

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+/**
+ * Stochastic block models (P. W. Holland, K. B. Laskey and S. Leinhardt, "Stochastic blockmodels:
+ * first steps", Social Networks 5, 109-137, 1983) and the planted partition model (A. Condon and
+ * R. M. Karp, Random Structures and Algorithms 18, 116-140, 2001), with the planted blocks emitted
+ * as ground truth.
+ */
+import { type U32 } from "@graphty/graph-format";
+import { type SampleGraph } from "../types.js";
+import { type EdgeBuffer } from "./util.js";
+import { type WeightOptions } from "./weights.js";
+/** Options of {@link stochasticBlockModelGraph}. */
+export interface StochasticBlockModelOptions extends WeightOptions {
+    /** The size of every block; block b holds the next `sizes[b]` node indices. */
+    sizes: readonly number[];
+    /** The symmetric B x B matrix of edge probabilities between blocks. */
+    probabilities: readonly (readonly number[])[];
+    /** The seed, an integer in [0, 2^53); default 0. */
+    seed?: number | undefined;
+}
+/** The checked and precomputed form of the options. */
+interface BlockPlan {
+    readonly n: number;
+    readonly seed: number;
+    /** starts[b] = first node of block b; starts[B] = n. */
+    readonly starts: readonly number[];
+    readonly block: U32;
+    readonly p: readonly (readonly number[])[];
+    readonly logQ: readonly (readonly number[])[];
+}
+/**
+ * Check the options and precompute block boundaries and detLog(1 - p).
+ * @param options - the options
+ * @returns the plan
+ */
+export declare function planBlocks(options: StochasticBlockModelOptions): BlockPlan;
+/**
+ * Rows [start, end) of the block model: row u (in block b) draws from stream (seed, "sbm", u) and
+ * walks blocks c = b .. B - 1 in order, holding the pairs (u, v) for v > u in block c with
+ * probability p[b][c], ascending v. Concatenating consecutive row ranges gives the whole graph.
+ * @param plan - the checked options
+ * @param start - the first row
+ * @param end - one past the last row
+ * @param out - receives the edges
+ */
+export declare function blockModelRows(plan: BlockPlan, start: number, end: number, out: EdgeBuffer): void;
+/**
+ * The stochastic block model in O(n B + m): node pairs are joined independently with the
+ * probability of their blocks, by geometric skipping inside each row's block segments. Edges are
+ * the pairs (u, v), u < v, row-major. Node column `community` (u32): the block.
+ * @param options - sizes, probabilities and seed
+ * @returns the undirected graph
+ */
+export declare function stochasticBlockModelGraph(options: StochasticBlockModelOptions): SampleGraph;
+/** Options of {@link plantedPartitionGraph}. */
+export interface PlantedPartitionOptions extends WeightOptions {
+    /** The number of groups, >= 1. */
+    groups: number;
+    /** The size of every group, >= 1. */
+    groupSize: number;
+    /** The edge probability inside a group. */
+    pIn: number;
+    /** The edge probability between groups. */
+    pOut: number;
+    /** The seed, an integer in [0, 2^53); default 0. */
+    seed?: number | undefined;
+}
+/**
+ * The planted partition model: `groups` equal blocks, `pIn` inside, `pOut` between. Exactly the
+ * stochastic block model with that matrix (same seed, same graph). Node column `community` (u32).
+ * @param options - groups, groupSize, pIn, pOut and seed
+ * @returns the undirected graph
+ */
+export declare function plantedPartitionGraph(options: PlantedPartitionOptions): SampleGraph;
+export {};
+//# sourceMappingURL=block-model.d.ts.map

package/dist/src/generators/block-model.d.ts.map

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package/dist/src/generators/block-model.js

@@ -0,0 +1,116 @@
+/**
+ * Stochastic block models (P. W. Holland, K. B. Laskey and S. Leinhardt, "Stochastic blockmodels:
+ * first steps", Social Networks 5, 109-137, 1983) and the planted partition model (A. Condon and
+ * R. M. Karp, Random Structures and Algorithms 18, 116-140, 2001), with the planted blocks emitted
+ * as ground truth.
+ */
+import { detLog } from "../random/log.js";
+import { RandomStream, resolveSeed } from "../random/stream.js";
+import { bernoulliSegment, binomialBuffer, checkInt, checkProbability, toGraph } from "./util.js";
+import { applyWeights } from "./weights.js";
+/**
+ * Check the options and precompute block boundaries and detLog(1 - p).
+ * @param options - the options
+ * @returns the plan
+ */
+export function planBlocks(options) {
+    const { sizes, probabilities } = options;
+    const seed = resolveSeed(options.seed);
+    const count = sizes.length;
+    checkInt("sizes.length", count, 1);
+    if (probabilities.length !== count) {
+        throw new RangeError(`probabilities must be ${count} x ${count}`);
+    }
+    const starts = [0];
+    for (let b = 0; b < count; b++) {
+        checkInt(`sizes[${b}]`, sizes[b], 0);
+        starts.push(starts[b] + sizes[b]);
+        if (probabilities[b].length !== count) {
+            throw new RangeError(`probabilities must be ${count} x ${count}`);
+        }
+        for (let c = 0; c < count; c++) {
+            checkProbability(`probabilities[${b}][${c}]`, probabilities[b][c]);
+            if (probabilities[b][c] !== probabilities[c][b]) {
+                throw new RangeError(`probabilities must be symmetric: [${b}][${c}] differs from [${c}][${b}]`);
+            }
+        }
+    }
+    const n = starts[count];
+    checkInt("the total size", n, 0);
+    const block = new Uint32Array(n);
+    for (let b = 0; b < count; b++) {
+        block.fill(b, starts[b], starts[b + 1]);
+    }
+    return {
+        n,
+        seed,
+        starts,
+        block,
+        p: probabilities,
+        logQ: probabilities.map((row) => row.map((p) => detLog(1 - p))),
+    };
+}
+/**
+ * Rows [start, end) of the block model: row u (in block b) draws from stream (seed, "sbm", u) and
+ * walks blocks c = b .. B - 1 in order, holding the pairs (u, v) for v > u in block c with
+ * probability p[b][c], ascending v. Concatenating consecutive row ranges gives the whole graph.
+ * @param plan - the checked options
+ * @param start - the first row
+ * @param end - one past the last row
+ * @param out - receives the edges
+ */
+export function blockModelRows(plan, start, end, out) {
+    const { starts, block, p, logQ } = plan;
+    const stream = new RandomStream(plan.seed, "sbm", 0);
+    const count = starts.length - 1;
+    for (let u = start; u < end; u++) {
+        stream.reset(u);
+        const b = block[u];
+        // ponytail: O(B) per row, fine to n * B ~ 1e8; iterate only non-zero blocks if B grows large
+        for (let c = b; c < count; c++) {
+            bernoulliSegment(stream, p[b][c], logQ[b][c], u, c === b ? u + 1 : starts[c], starts[c + 1], out);
+        }
+    }
+}
+/**
+ * The stochastic block model in O(n B + m): node pairs are joined independently with the
+ * probability of their blocks, by geometric skipping inside each row's block segments. Edges are
+ * the pairs (u, v), u < v, row-major. Node column `community` (u32): the block.
+ * @param options - sizes, probabilities and seed
+ * @returns the undirected graph
+ */
+export function stochasticBlockModelGraph(options) {
+    const plan = planBlocks(options);
+    let expected = 0;
+    let pairs = 0;
+    for (let b = 0; b < plan.starts.length - 1; b++) {
+        for (let c = b; c < plan.starts.length - 1; c++) {
+            const sb = plan.starts[b + 1] - plan.starts[b];
+            const sc = plan.starts[c + 1] - plan.starts[c];
+            const blockPairs = b === c ? (sb * (sb - 1)) / 2 : sb * sc;
+            expected += blockPairs * plan.p[b][c];
+            pairs += blockPairs;
+        }
+    }
+    const out = binomialBuffer(pairs, pairs === 0 ? 0 : expected / pairs);
+    blockModelRows(plan, 0, plan.n, out);
+    return applyWeights(toGraph(plan.n, out, false, { community: plan.block }), options);
+}
+/**
+ * The planted partition model: `groups` equal blocks, `pIn` inside, `pOut` between. Exactly the
+ * stochastic block model with that matrix (same seed, same graph). Node column `community` (u32).
+ * @param options - groups, groupSize, pIn, pOut and seed
+ * @returns the undirected graph
+ */
+export function plantedPartitionGraph(options) {
+    const { groups, groupSize, pIn, pOut, seed } = options;
+    checkInt("groups", groups, 1);
+    checkInt("groupSize", groupSize, 1);
+    return stochasticBlockModelGraph({
+        sizes: new Array(groups).fill(groupSize),
+        probabilities: Array.from({ length: groups }, (_, b) => Array.from({ length: groups }, (_2, c) => (b === c ? pIn : pOut))),
+        seed,
+        weights: options.weights,
+    });
+}
+//# sourceMappingURL=block-model.js.map

package/dist/src/generators/block-model.js.map

@@ -0,0 +1 @@
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package/dist/src/generators/classic.d.ts

@@ -0,0 +1,208 @@
+/**
+ * The deterministic families: no seed, closed-form structure, O(n + m). Every function returns an
+ * undirected simple graph whose node order and edge order are part of its contract (stated in each
+ * JSDoc), so an index means the same node in every version.
+ */
+import { type SampleGraph } from "../types.js";
+import { type WeightOptions } from "./weights.js";
+/**
+ * The path P_n: edges (i, i + 1) for i = 0 .. n - 2.
+ * @param options - the options
+ * @param options.n - the node count, >= 0
+ * @returns the graph
+ */
+export declare function pathGraph(options: {
+    n: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The cycle C_n: the path P_n plus the edge (n - 1, 0).
+ * @param options - the options
+ * @param options.n - the node count, >= 3
+ * @returns the graph
+ */
+export declare function cycleGraph(options: {
+    n: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The star: hub 0 joined to every other node, edges (0, i) for i = 1 .. n - 1.
+ * @param options - the options
+ * @param options.n - the node count including the hub, >= 1
+ * @returns the graph
+ */
+export declare function starGraph(options: {
+    n: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The wheel W_n: the star's spokes (0, i), then the rim (i, i + 1) for i = 1 .. n - 2, then
+ * (n - 1, 1).
+ * @param options - the options
+ * @param options.n - the node count including the hub, >= 4
+ * @returns the graph
+ */
+export declare function wheelGraph(options: {
+    n: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The complete graph K_n: every pair (i, j), i < j, row-major.
+ * @param options - the options
+ * @param options.n - the node count, >= 0
+ * @returns the graph
+ */
+export declare function completeGraph(options: {
+    n: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The complete bipartite graph K_{a,b}: left nodes 0 .. a - 1, right nodes a .. a + b - 1, every
+ * pair (i, a + j), row-major. Node column `side` (u8): 0 left, 1 right.
+ * @param options - the options
+ * @param options.a - the left side's size, >= 0
+ * @param options.b - the right side's size, >= 0
+ * @returns the graph
+ */
+export declare function completeBipartiteGraph(options: {
+    a: number;
+    b: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The hypercube Q_d: nodes are the d-bit integers, edges join integers one bit apart; for each node
+ * i in order and each bit b ascending that is 0 in i, the edge (i, i | 2^b).
+ * @param options - the options
+ * @param options.dimension - d, in [0, 26]
+ * @returns the graph
+ */
+export declare function hypercubeGraph(options: {
+    dimension: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The ladder L_n: two paths 0 .. n - 1 and n .. 2n - 1, then the rungs (i, n + i).
+ * @param options - the options
+ * @param options.n - the number of rungs, >= 1
+ * @returns the graph
+ */
+export declare function ladderGraph(options: {
+    n: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The barbell: a clique on 0 .. m1 - 1, the path m1 - 1, m1, .., m1 + m2 (m2 path nodes plus the
+ * two joining edges' ends), and a clique on m1 + m2 .. 2 m1 + m2 - 1. Edge order: left clique, path,
+ * right clique.
+ * @param options - the options
+ * @param options.cliqueSize - m1, each bell's size, >= 2
+ * @param options.pathLength - m2, the number of nodes on the bar, >= 0
+ * @returns the graph
+ */
+export declare function barbellGraph(options: {
+    cliqueSize: number;
+    pathLength: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The lollipop: a clique on 0 .. m - 1 and a tail path m - 1, m, .., m + n - 1.
+ * @param options - the options
+ * @param options.cliqueSize - m, >= 2
+ * @param options.pathLength - n, the number of tail nodes, >= 0
+ * @returns the graph
+ */
+export declare function lollipopGraph(options: {
+    cliqueSize: number;
+    pathLength: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The caveman graph (Watts 1999): `cliques` disjoint cliques of `size` nodes, clique g on
+ * g * size .. (g + 1) * size - 1. Node column `community` (u32): the clique.
+ * @param options - the options
+ * @param options.cliques - the number of cliques, >= 1
+ * @param options.size - the clique size, >= 1
+ * @returns the graph
+ */
+export declare function cavemanGraph(options: {
+    cliques: number;
+    size: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The connected caveman graph (Watts 1999, as networkx builds it): the caveman graph with, in each
+ * clique starting at s, the edge (s, s + 1) replaced in place by (s, s - 1 mod n), which joins the
+ * cliques into a ring. Node column `community` (u32): the clique.
+ * @param options - the options
+ * @param options.cliques - the number of cliques, >= 2
+ * @param options.size - the clique size, >= 2
+ * @returns the graph
+ */
+export declare function connectedCavemanGraph(options: {
+    cliques: number;
+    size: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The balanced r-ary tree of height h, numbered breadth first: node i's children are
+ * r i + 1 .. r i + r; edges (parent(c), c) for c = 1 .. n - 1.
+ * @param options - the options
+ * @param options.branching - r, >= 1
+ * @param options.height - h, >= 0 (a single root at 0)
+ * @returns the graph
+ */
+export declare function balancedTreeGraph(options: {
+    branching: number;
+    height: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The Petersen graph: outer cycle 0 .. 4, spokes (i, i + 5), inner pentagram (5 + i, 5 + (i + 2) mod 5).
+ * 3-regular, girth 5, non-planar.
+ * @param options - the common weight options
+ * @returns the graph
+ */
+export declare function petersenGraph(options?: WeightOptions): SampleGraph;
+/**
+ * The empty graph: n isolated nodes, no edges.
+ * @param options - the options
+ * @param options.n - the node count, >= 0
+ * @returns the graph
+ */
+export declare function emptyGraph(options: {
+    n: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The complete multipartite graph K_{s0, s1, ...}: part p holds the next `sizes[p]` node indices,
+ * and every pair of nodes in different parts is joined; for each node in index order, the edges to
+ * every later node of a later part, ascending. Node column `part` (u32).
+ * @param options - the options
+ * @param options.sizes - the part sizes, each >= 0
+ * @returns the graph
+ */
+export declare function completeMultipartiteGraph(options: {
+    sizes: readonly number[];
+} & WeightOptions): SampleGraph;
+/**
+ * The circular ladder CL_n (the n-prism): the ladder's rails 0 .. n - 1 and n .. 2n - 1 and rungs
+ * (i, n + i), as {@link ladderGraph} lists them, then the closing edges (n - 1, 0) and
+ * (2n - 1, n). 3-regular and planar.
+ * @param options - the options
+ * @param options.n - the number of rungs, >= 3
+ * @returns the graph
+ */
+export declare function circularLadderGraph(options: {
+    n: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The Moebius ladder M_{2n}: the cycle 0 .. 2n - 1 (edges (i, i + 1), then (2n - 1, 0)) and the n
+ * chords (i, i + n). 3-regular and, unlike the circular ladder, not planar for n >= 3.
+ * @param options - the options
+ * @param options.n - the number of rungs, >= 3
+ * @returns the graph
+ */
+export declare function mobiusLadderGraph(options: {
+    n: number;
+} & WeightOptions): SampleGraph;
+/**
+ * The ring of cliques, as networkx's `ring_of_cliques`: for each clique i in order, its edges
+ * (row-major), then the ring edge (i size + 1, (i + 1) size mod n). The standard example of
+ * modularity's resolution limit (Fortunato and Barthelemy, PNAS 104:36-41, 2007,
+ * doi:10.1073/pnas.0605965104). Node column `community` (u32): the clique.
+ * @param options - the options
+ * @param options.cliques - the number of cliques, >= 2
+ * @param options.size - the clique size, >= 2
+ * @returns the graph
+ */
+export declare function ringOfCliquesGraph(options: {
+    cliques: number;
+    size: number;
+} & WeightOptions): SampleGraph;
+//# sourceMappingURL=classic.d.ts.map

package/dist/src/generators/classic.d.ts.map

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