@graphty/algorithms 2.1.1 → 2.2.0

package/dist/src/indexed/leiden.js

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+import { renumberPartition } from "@graphty/graph-format";
+import { withGroups } from "./components.js";
+import { exactEdgeWeights, mulberry32 } from "./label-propagation.js";
+import { modularity } from "./modularity.js";
+/** The randomness of refinement: 0.01 as in the paper and leidenalg. */
+const THETA = 0.01;
+/**
+ * Passes in a row that may fail to improve modularity by more than the threshold before the run
+ * stops. A failed pass is discarded, but the next one draws fresh visit orders and can still find a
+ * move the last one missed: on the shared random fixtures, stopping at the first failure leaves the
+ * mean modularity over 40 seeds below the legacy function's, and three restores it.
+ */
+const PATIENCE = 3;
+/**
+ * Per-arc weights and weighted degrees of a level.
+ * @param s - An undirected snapshot
+ * @param edgeW - Exact weight per logical edge
+ * @returns The level
+ */
+function levelOf(s, edgeW) {
+    const { nodeCount: n, rowPtr, colIdx, arcToEdge } = s;
+    const arcW = new Float64Array(s.arcCount);
+    const deg = new Float64Array(n);
+    for (let u = 0; u < n; u++) {
+        for (let a = rowPtr[u], end = rowPtr[u + 1]; a < end; a++) {
+            const w = edgeW[arcToEdge[a]];
+            arcW[a] = w;
+            // An undirected self-loop is one arc; it adds to the degree twice.
+            deg[u] += colIdx[a] === u ? 2 * w : w;
+        }
+    }
+    return { s, edgeW, arcW, deg };
+}
+/**
+ * Shuffle `0..n-1` with the generator.
+ * @param n - Length
+ * @param rand - Generator
+ * @returns The permutation
+ */
+function shuffled(n, rand) {
+    const order = new Uint32Array(n);
+    for (let i = 0; i < n; i++) {
+        order[i] = i;
+    }
+    for (let i = n - 1; i >= 1; i--) {
+        const j = Math.floor(rand() * (i + 1));
+        const t = order[i];
+        order[i] = order[j];
+        order[j] = t;
+    }
+    return order;
+}
+/**
+ * Leiden's fast local moving: nodes wait in a queue started as a seeded shuffle; a visited node
+ * moves to the neighbouring community (or an empty one) with the largest modularity gain, and when
+ * it moves, its neighbours outside its new community are queued again. Ends when the queue empties.
+ * @param level - The level
+ * @param comm - Community of every node, below the node count; moved in place
+ * @param rand - Generator
+ * @param resolution - Resolution gamma
+ * @param m2 - Twice the total edge weight
+ */
+function moveNodesFast(level, comm, rand, resolution, m2) {
+    const { s, arcW, deg } = level;
+    const { nodeCount: n, rowPtr, colIdx } = s;
+    const tot = new Float64Array(n);
+    const size = new Uint32Array(n);
+    for (let u = 0; u < n; u++) {
+        tot[comm[u]] += deg[u];
+        size[comm[u]]++;
+    }
+    const empty = [];
+    for (let c = n - 1; c >= 0; c--) {
+        if (size[c] === 0) {
+            empty.push(c);
+        }
+    }
+    const acc = new Float64Array(n);
+    const stamp = new Int32Array(n).fill(-1);
+    const touched = new Uint32Array(n);
+    const capacity = n + 1;
+    const queue = new Uint32Array(capacity);
+    queue.set(shuffled(n, rand));
+    const queued = new Uint8Array(n).fill(1);
+    let head = 0;
+    let tail = n;
+    let visit = 0;
+    while (head !== tail) {
+        const u = queue[head];
+        head = head + 1 === capacity ? 0 : head + 1;
+        queued[u] = 0;
+        visit++;
+        const cu = comm[u];
+        const ku = deg[u];
+        tot[cu] -= ku;
+        size[cu]--;
+        let cnt = 0;
+        for (let a = rowPtr[u], end = rowPtr[u + 1]; a < end; a++) {
+            const v = colIdx[a];
+            if (v === u) {
+                continue;
+            }
+            const c = comm[v];
+            if (stamp[c] !== visit) {
+                stamp[c] = visit;
+                acc[c] = 0;
+                touched[cnt++] = c;
+            }
+            acc[c] += arcW[a];
+        }
+        let best = cu;
+        let bestGain = (stamp[cu] === visit ? acc[cu] : 0) - (resolution * ku * tot[cu]) / m2;
+        for (let i = 0; i < cnt; i++) {
+            const c = touched[i];
+            const gain = acc[c] - (resolution * ku * tot[c]) / m2;
+            if (c !== cu && gain > bestGain) {
+                bestGain = gain;
+                best = c;
+            }
+        }
+        // An empty community gains 0; when u's own is empty now, staying already is that choice.
+        if (size[cu] > 0 && bestGain < 0) {
+            best = empty[empty.length - 1];
+        }
+        if (best !== cu && size[best] === 0) {
+            empty.pop();
+        }
+        tot[best] += ku;
+        size[best]++;
+        if (best === cu) {
+            continue;
+        }
+        comm[u] = best;
+        if (size[cu] === 0) {
+            empty.push(cu);
+        }
+        for (let a = rowPtr[u], end = rowPtr[u + 1]; a < end; a++) {
+            const v = colIdx[a];
+            if (queued[v] === 0 && comm[v] !== best) {
+                queued[v] = 1;
+                queue[tail] = v;
+                tail = tail + 1 === capacity ? 0 : tail + 1;
+            }
+        }
+    }
+}
+/**
+ * Leiden's refinement: inside every community, nodes start alone and, visited in a seeded order,
+ * a node still alone and well connected to its community merges into the well-connected
+ * sub-community of that community, drawn at random weighted by its modularity gain. Every
+ * sub-community is connected, which is the guarantee Leiden adds over Louvain.
+ *
+ * The target is drawn at random among the candidates with a non-negative gain, with probability
+ * proportional to exp(gain / theta) where the gain is in modularity units, as the paper does
+ * (theta 0.01, leidenalg's default).
+ * @param level - The level
+ * @param comm - Community of every node
+ * @param rand - Generator
+ * @param resolution - Resolution gamma
+ * @param m2 - Twice the total edge weight
+ * @returns The sub-community of every node, labelled by a member's index (not dense)
+ */
+function refine(level, comm, rand, resolution, m2) {
+    const { s, arcW, deg } = level;
+    const { nodeCount: n, rowPtr, colIdx } = s;
+    const commTot = new Float64Array(n);
+    for (let u = 0; u < n; u++) {
+        commTot[comm[u]] += deg[u];
+    }
+    const ref = new Uint32Array(n);
+    const refTot = new Float64Array(n);
+    const refSize = new Uint32Array(n);
+    // Weight from each sub-community to the rest of its community.
+    const ext = new Float64Array(n);
+    for (let u = 0; u < n; u++) {
+        ref[u] = u;
+        refTot[u] = deg[u];
+        refSize[u] = 1;
+        for (let a = rowPtr[u], end = rowPtr[u + 1]; a < end; a++) {
+            const v = colIdx[a];
+            if (v !== u && comm[v] === comm[u]) {
+                ext[u] += arcW[a];
+            }
+        }
+    }
+    const acc = new Float64Array(n);
+    const stamp = new Int32Array(n).fill(-1);
+    const touched = new Uint32Array(n);
+    const order = shuffled(n, rand);
+    for (let i = 0; i < n; i++) {
+        const v = order[i];
+        const c = comm[v];
+        const kv = deg[v];
+        if (refSize[v] !== 1 || ext[v] < (resolution * kv * (commTot[c] - kv)) / m2) {
+            continue;
+        }
+        let cnt = 0;
+        for (let a = rowPtr[v], end = rowPtr[v + 1]; a < end; a++) {
+            const x = colIdx[a];
+            if (x === v || comm[x] !== c) {
+                continue;
+            }
+            const r = ref[x];
+            if (stamp[r] !== v) {
+                stamp[r] = v;
+                acc[r] = 0;
+                touched[cnt++] = r;
+            }
+            acc[r] += arcW[a];
+        }
+        // Candidates: well-connected sub-communities with a non-negative gain, drawn with probability
+        // exp(gain in modularity units / theta), shifted by the best gain so exp never overflows.
+        const gainOf = (r) => acc[r] - (resolution * kv * refTot[r]) / m2;
+        let maxGain = -Infinity;
+        let kept = 0;
+        for (let j = 0; j < cnt; j++) {
+            const r = touched[j];
+            const gain = gainOf(r);
+            if (gain >= 0 && ext[r] >= (resolution * refTot[r] * (commTot[c] - refTot[r])) / m2) {
+                touched[kept++] = r;
+                maxGain = Math.max(maxGain, gain);
+            }
+        }
+        if (kept === 0) {
+            continue;
+        }
+        const weight = (r) => Math.exp(((gainOf(r) - maxGain) * 2) / m2 / THETA);
+        let total = 0;
+        for (let j = 0; j < kept; j++) {
+            total += weight(touched[j]);
+        }
+        let draw = rand() * total;
+        let best = touched[kept - 1];
+        for (let j = 0; j < kept - 1; j++) {
+            draw -= weight(touched[j]);
+            if (draw < 0) {
+                best = touched[j];
+                break;
+            }
+        }
+        ref[v] = best;
+        refSize[v] = 0;
+        refSize[best]++;
+        refTot[best] += kv;
+        // The edges between v and its new sub-community are now inside it.
+        ext[best] += ext[v] - 2 * acc[best];
+    }
+    return ref;
+}
+/**
+ * One pass of Leiden from a starting partition of the original graph: local moving, refinement,
+ * aggregation by the refined partition with each aggregate node starting in its community, repeated
+ * until local moving leaves every community a single node of its level.
+ * @param base - Level 0, the original graph
+ * @param start - Dense community of every original node
+ * @param rand - Generator
+ * @param resolution - Resolution gamma
+ * @param m2 - Twice the total edge weight
+ * @returns The partition of the original nodes (not dense) and the levels processed
+ */
+function pass(base, start, rand, resolution, m2) {
+    const n0 = base.s.nodeCount;
+    // Which node of the current level holds each original node.
+    const top = new Uint32Array(n0);
+    for (let u = 0; u < n0; u++) {
+        top[u] = u;
+    }
+    let level = base;
+    let comm = start.slice();
+    let levels = 0;
+    for (;;) {
+        moveNodesFast(level, comm, rand, resolution, m2);
+        levels++;
+        const dense = renumberPartition(comm);
+        if (dense.count === level.s.nodeCount) {
+            break;
+        }
+        let blocks = refine(level, dense.labels, rand, resolution, m2);
+        if (renumberPartition(blocks).count === level.s.nodeCount) {
+            // No sub-community merged: aggregate by the communities themselves, as Louvain does, so
+            // the next level is smaller.
+            blocks = dense.labels;
+        }
+        const d = level.s.contract(blocks);
+        const { nodeRemap, edgeRemap } = d;
+        const next = d.snapshot;
+        const edgeW = new Float64Array(next.edgeCount);
+        for (let e = 0; e < level.edgeW.length; e++) {
+            edgeW[edgeRemap === null ? e : edgeRemap[e]] += level.edgeW[e];
+        }
+        const nextComm = new Uint32Array(next.nodeCount);
+        for (let u = 0; u < level.s.nodeCount; u++) {
+            nextComm[nodeRemap === null ? u : nodeRemap[u]] = dense.labels[u];
+        }
+        if (nodeRemap !== null) {
+            for (let u = 0; u < n0; u++) {
+                top[u] = nodeRemap[top[u]];
+            }
+        }
+        comm = renumberPartition(nextComm).labels;
+        level = levelOf(next, edgeW);
+    }
+    const out = new Uint32Array(n0);
+    for (let u = 0; u < n0; u++) {
+        out[u] = comm[top[u]];
+    }
+    return { comm: out, levels };
+}
+/**
+ * Leiden community detection (Traag, Waltman and van Eck, Sci. Rep. 9:5233, 2019) over an
+ * undirected snapshot: fast local moving, refinement into well-connected sub-communities, and
+ * aggregation by `contract()` once per level. Whole passes repeat from the previous answer, keeping
+ * a pass only when it raises modularity, until three passes in a row improve it by no more than
+ * `threshold` or `maxIterations` passes have run; every pass starts by moving single original
+ * nodes, so the answer is also a local optimum of those moves.
+ *
+ * Modularity follows graph-format's `weightedDegree()` convention (a self-loop counts twice), which
+ * on a graph without self-loops equals the legacy `leiden`'s. Weights are the exact f64 ones when
+ * the snapshot keeps them. The partition is not the legacy function's move for move: the legacy
+ * `leiden` splits disconnected communities rather than refining them, and visits nodes in another
+ * order; what this guarantees is connected communities. Both are randomised heuristics, so for one
+ * seed either can come out ahead; on the shared fixtures this one's modularity is at least the
+ * legacy's at the default seed and on average over seeds.
+ * @param s - An undirected snapshot
+ * @param options - Resolution, seed, pass cap and stopping threshold
+ * @returns The partition, its modularity, and the levels processed
+ * @throws Error on a directed snapshot; RangeError for a negative, NaN or infinite weight or a
+ *   fractional seed
+ * @public
+ */
+export function leiden(s, options = {}) {
+    if (s.directed) {
+        throw new Error("Leiden requires an undirected graph. Pass s.toUndirected().snapshot.");
+    }
+    const resolution = options.resolution ?? 1;
+    const randomSeed = options.randomSeed ?? 42;
+    const maxIterations = options.maxIterations ?? 100;
+    const threshold = options.threshold ?? 1e-7;
+    if (!Number.isInteger(randomSeed)) {
+        throw new RangeError(`randomSeed must be a finite integer, got ${randomSeed}`);
+    }
+    const n = s.nodeCount;
+    const given = exactEdgeWeights(s) ?? s.edgeList().weights;
+    const edgeW = given === null ? new Float64Array(s.edgeCount).fill(1) : Float64Array.from(given);
+    for (let e = 0; e < edgeW.length; e++) {
+        const w = edgeW[e];
+        if (!(w >= 0) || w === Infinity) {
+            throw new RangeError(`edge ${e} has weight ${w}; Leiden needs finite, non-negative weights`);
+        }
+    }
+    const base = levelOf(s, edgeW);
+    let m2 = 0;
+    for (let u = 0; u < n; u++) {
+        m2 += base.deg[u];
+    }
+    let labels = new Uint32Array(n);
+    for (let u = 0; u < n; u++) {
+        labels[u] = u;
+    }
+    if (m2 === 0) {
+        return { ...withGroups(labels, n), modularity: 0, iterations: 0 };
+    }
+    const quality = (partition) => modularity(s, partition, { resolution, weights: base.arcW });
+    const rand = mulberry32(randomSeed);
+    let q = quality(labels);
+    let iterations = 0;
+    let idle = 0;
+    for (let i = 0; i < maxIterations && idle < PATIENCE; i++) {
+        const { comm, levels } = pass(base, labels, rand, resolution, m2);
+        iterations += levels;
+        const candidate = renumberPartition(comm).labels;
+        const qNext = quality(candidate);
+        if (qNext > q) {
+            idle = qNext - q <= threshold ? idle + 1 : 0;
+            labels = candidate;
+            q = qNext;
+        }
+        else {
+            idle++;
+        }
+    }
+    return { ...withGroups(labels, renumberPartition(labels).count), modularity: q, iterations };
+}
+//# sourceMappingURL=leiden.js.map

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

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package/dist/src/indexed/link-prediction.d.ts

@@ -0,0 +1,147 @@
+/**
+ * Link prediction over a snapshot: common-neighbour and Adamic-Adar scores for one pair, a list of
+ * pairs, every pair, or one node's candidates, and the ranking metrics of a held-out evaluation.
+ *
+ * Every score is a merge of two sorted rows with simple-graph semantics: a neighbour reached by
+ * parallel arcs counts once, and a self-loop makes a node its own neighbour. With
+ * `{ directed: true }` a pair (u, v) intersects out(u) with in(v) -- the nodes on a path u -> z -> v
+ * -- and otherwise the two out rows (the two rows of an undirected snapshot).
+ *
+ * A node index at or beyond `nodeCount`, `INVALID_INDEX` included, is an absent node: its pairs
+ * score 0 and it has no candidates.
+ * @module
+ */
+import type { F64, GraphSnapshot, U32 } from "@graphty/graph-format";
+import { type CommonNeighborsOptions } from "./common-neighbors.js";
+/** Options of the link prediction functions. @public */
+export interface LinkPredictionOptions extends CommonNeighborsOptions {
+    /** Also score pairs already joined by an arc u -> v. Default false. */
+    readonly includeExisting?: boolean | undefined;
+    /**
+     * Keep only the first `topK` ranked pairs. For the whole-graph predictions a value that is not
+     * positive keeps them all; for a node's candidates the default is 10 and the value is a slice
+     * end, so 0 keeps none and -2 drops the last two.
+     */
+    readonly topK?: number | undefined;
+}
+/** Options of the per-node candidate functions. @public */
+export interface CandidateOptions extends LinkPredictionOptions {
+    /** The node indices to consider, in this order; default every node in index order. */
+    readonly candidates?: ArrayLike<number> | undefined;
+}
+/** Node pairs as two parallel index lists: pair k is (sources[k], targets[k]). @public */
+export interface NodePairs {
+    readonly sources: ArrayLike<number>;
+    readonly targets: ArrayLike<number>;
+}
+/** Ranked pairs, highest score first, ties in enumeration order. @public */
+export interface LinkPredictionResult extends NodePairs {
+    readonly sources: U32;
+    readonly targets: U32;
+    readonly scores: F64;
+}
+/** The best-F1 threshold's precision and recall, that F1, and the ranking AUC. @public */
+export interface LinkPredictionMetrics {
+    readonly precision: number;
+    readonly recall: number;
+    readonly f1Score: number;
+    readonly auc: number;
+}
+/**
+ * Common-neighbour scores of every pair not already joined, ranked.
+ * @param s - The snapshot
+ * @param o - Options
+ * @returns The pairs with a positive score, highest first
+ * @public
+ */
+export declare function commonNeighborsPrediction(s: GraphSnapshot, o?: LinkPredictionOptions): LinkPredictionResult;
+/**
+ * Common-neighbour scores of the given pairs, in order.
+ * @param s - The snapshot
+ * @param pairs - The pairs
+ * @param o - Options
+ * @returns One score per pair
+ * @public
+ */
+export declare function commonNeighborsForPairs(s: GraphSnapshot, pairs: NodePairs, o?: CommonNeighborsOptions): F64;
+/**
+ * One node's best common-neighbour candidates, ranked.
+ * @param s - The snapshot
+ * @param u - The node index
+ * @param o - Options
+ * @returns (u, v) pairs with a positive score, highest first
+ * @public
+ */
+export declare function getTopCandidatesForNode(s: GraphSnapshot, u: number, o?: CandidateOptions): LinkPredictionResult;
+/**
+ * Ranking metrics of the common-neighbour score on held-out edges against non-edges.
+ * @param s - The training snapshot
+ * @param edges - The held-out edges
+ * @param nonEdges - The non-edges
+ * @param o - Options
+ * @returns The metrics
+ * @public
+ */
+export declare function evaluateCommonNeighbors(s: GraphSnapshot, edges: NodePairs, nonEdges: NodePairs, o?: CommonNeighborsOptions): LinkPredictionMetrics;
+/**
+ * The Adamic-Adar index of two nodes: the sum over distinct common neighbours z of 1 / ln(degree(z)).
+ * @param s - The snapshot
+ * @param u - A node index
+ * @param v - A node index
+ * @param o - Options
+ * @returns The score
+ * @public
+ */
+export declare function adamicAdarScore(s: GraphSnapshot, u: number, v: number, o?: CommonNeighborsOptions): number;
+/**
+ * Adamic-Adar scores of every pair not already joined, ranked.
+ * @param s - The snapshot
+ * @param o - Options
+ * @returns The pairs with a positive score, highest first
+ * @public
+ */
+export declare function adamicAdarPrediction(s: GraphSnapshot, o?: LinkPredictionOptions): LinkPredictionResult;
+/**
+ * Adamic-Adar scores of the given pairs, in order.
+ * @param s - The snapshot
+ * @param pairs - The pairs
+ * @param o - Options
+ * @returns One score per pair
+ * @public
+ */
+export declare function adamicAdarForPairs(s: GraphSnapshot, pairs: NodePairs, o?: CommonNeighborsOptions): F64;
+/**
+ * One node's best Adamic-Adar candidates, ranked.
+ * @param s - The snapshot
+ * @param u - The node index
+ * @param o - Options
+ * @returns (u, v) pairs with a positive score, highest first
+ * @public
+ */
+export declare function getTopAdamicAdarCandidatesForNode(s: GraphSnapshot, u: number, o?: CandidateOptions): LinkPredictionResult;
+/**
+ * Ranking metrics of the Adamic-Adar score on held-out edges against non-edges.
+ * @param s - The training snapshot
+ * @param edges - The held-out edges
+ * @param nonEdges - The non-edges
+ * @param o - Options
+ * @returns The metrics
+ * @public
+ */
+export declare function evaluateAdamicAdar(s: GraphSnapshot, edges: NodePairs, nonEdges: NodePairs, o?: CommonNeighborsOptions): LinkPredictionMetrics;
+/**
+ * Both evaluations on the same held-out sets. The common-neighbour side always intersects the two
+ * OUT rows, whatever `directed` says, as the legacy function of this name does; the Adamic-Adar side
+ * honours `directed`.
+ * @param s - The training snapshot
+ * @param edges - The held-out edges
+ * @param nonEdges - The non-edges
+ * @param o - Options
+ * @returns The two sets of metrics
+ * @public
+ */
+export declare function compareAdamicAdarWithCommonNeighbors(s: GraphSnapshot, edges: NodePairs, nonEdges: NodePairs, o?: CommonNeighborsOptions): {
+    adamicAdar: LinkPredictionMetrics;
+    commonNeighbors: LinkPredictionMetrics;
+};
+//# sourceMappingURL=link-prediction.d.ts.map

package/dist/src/indexed/link-prediction.d.ts.map

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