causantic 0.2.0

package/dist/clusters/hdbscan/mst.js

@@ -0,0 +1,77 @@
+/**
+ * Minimum Spanning Tree construction using Prim's algorithm.
+ * Uses mutual reachability distance for HDBSCAN.
+ */
+import { MinHeap } from './min-heap.js';
+import { euclideanDistance, angularDistance } from './kd-tree.js';
+/**
+ * Build a minimum spanning tree using Prim's algorithm.
+ * Uses mutual reachability distance: MRD(a, b) = max(core(a), core(b), dist(a, b))
+ *
+ * @param points All points (embeddings).
+ * @param coreDistances Core distance for each point.
+ * @param metric Distance metric.
+ * @returns MST edges sorted by weight (ascending).
+ */
+export function buildMST(points, coreDistances, metric = 'euclidean') {
+    const n = points.length;
+    if (n <= 1) {
+        return [];
+    }
+    const distFn = metric === 'euclidean' ? euclideanDistance : angularDistance;
+    const edges = [];
+    const inMST = new Set();
+    const heap = new MinHeap();
+    // Start from vertex 0
+    inMST.add(0);
+    // Add all edges from vertex 0 to the heap
+    for (let i = 1; i < n; i++) {
+        const dist = distFn(points[0], points[i]);
+        const mrd = Math.max(coreDistances[0], coreDistances[i], dist);
+        heap.insert(mrd, i);
+    }
+    // Track the closest MST vertex for each non-MST vertex
+    const closestMSTVertex = new Array(n).fill(0);
+    while (edges.length < n - 1 && !heap.isEmpty()) {
+        const entry = heap.extractMin();
+        const v = entry.value;
+        const weight = entry.key;
+        if (inMST.has(v)) {
+            continue;
+        }
+        // Add edge to MST
+        const from = closestMSTVertex[v];
+        edges.push({ from, to: v, weight });
+        inMST.add(v);
+        // Update heap with edges from new vertex
+        for (let u = 0; u < n; u++) {
+            if (!inMST.has(u)) {
+                const dist = distFn(points[v], points[u]);
+                const mrd = Math.max(coreDistances[v], coreDistances[u], dist);
+                const currentKey = heap.getKey(u);
+                if (currentKey !== undefined) {
+                    if (mrd < currentKey) {
+                        heap.decreaseKey(u, mrd);
+                        closestMSTVertex[u] = v;
+                    }
+                }
+                else {
+                    heap.insert(mrd, u);
+                    closestMSTVertex[u] = v;
+                }
+            }
+        }
+    }
+    // Sort edges by weight for hierarchy construction
+    edges.sort((a, b) => a.weight - b.weight);
+    return edges;
+}
+/**
+ * Compute mutual reachability distance between two points.
+ */
+export function mutualReachabilityDistance(pointA, pointB, coreDistA, coreDistB, metric = 'euclidean') {
+    const distFn = metric === 'euclidean' ? euclideanDistance : angularDistance;
+    const rawDist = distFn(pointA, pointB);
+    return Math.max(coreDistA, coreDistB, rawDist);
+}
+//# sourceMappingURL=mst.js.map

package/dist/clusters/hdbscan/mst.js.map

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package/dist/clusters/hdbscan/probabilities.d.ts

@@ -0,0 +1,37 @@
+/**
+ * Membership probabilities and outlier scores for HDBSCAN.
+ */
+import type { CondensedTree } from './types.js';
+/**
+ * Compute membership probabilities for each point.
+ * Probability indicates how "core" a point is to its cluster.
+ *
+ * probability[i] = (lambda[i] - lambda_birth) / (lambda_max - lambda_birth)
+ *
+ * @param tree Condensed cluster tree.
+ * @param labels Cluster labels for each point.
+ * @param selectedClusters Selected cluster IDs.
+ * @returns Probability for each point (0.0-1.0).
+ */
+export declare function computeProbabilities(tree: CondensedTree, labels: number[], selectedClusters: number[]): number[];
+/**
+ * Compute outlier scores (GLOSH) for each point.
+ * Higher scores indicate more outlier-ish points.
+ *
+ * outlierScore[i] = 1 - (lambda[i] / lambda_max_in_cluster)
+ *
+ * @param tree Condensed cluster tree.
+ * @param labels Cluster labels for each point.
+ * @param selectedClusters Selected cluster IDs.
+ * @returns Outlier score for each point (0.0-1.0).
+ */
+export declare function computeOutlierScores(tree: CondensedTree, labels: number[], selectedClusters: number[]): number[];
+/**
+ * Get lambda values for all points.
+ */
+export declare function getLambdaValues(tree: CondensedTree): number[];
+/**
+ * Get maximum lambda for each cluster.
+ */
+export declare function getClusterMaxLambda(tree: CondensedTree, labels: number[]): Map<number, number>;
+//# sourceMappingURL=probabilities.d.ts.map

package/dist/clusters/hdbscan/probabilities.d.ts.map

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package/dist/clusters/hdbscan/probabilities.js

@@ -0,0 +1,149 @@
+/**
+ * Membership probabilities and outlier scores for HDBSCAN.
+ */
+/**
+ * Compute membership probabilities for each point.
+ * Probability indicates how "core" a point is to its cluster.
+ *
+ * probability[i] = (lambda[i] - lambda_birth) / (lambda_max - lambda_birth)
+ *
+ * @param tree Condensed cluster tree.
+ * @param labels Cluster labels for each point.
+ * @param selectedClusters Selected cluster IDs.
+ * @returns Probability for each point (0.0-1.0).
+ */
+export function computeProbabilities(tree, labels, selectedClusters) {
+    const probabilities = new Array(tree.numPoints).fill(0);
+    // Compute max lambda for each cluster
+    const clusterMaxLambda = new Map();
+    for (let i = 0; i < labels.length; i++) {
+        const label = labels[i];
+        if (label < 0)
+            continue;
+        const pointNode = tree.nodes.get(i);
+        if (!pointNode)
+            continue;
+        const lambda = pointNode.lambdaDeath;
+        if (isFinite(lambda)) {
+            const current = clusterMaxLambda.get(label) ?? 0;
+            clusterMaxLambda.set(label, Math.max(current, lambda));
+        }
+    }
+    // Compute probabilities
+    for (let i = 0; i < labels.length; i++) {
+        const label = labels[i];
+        if (label < 0) {
+            probabilities[i] = 0;
+            continue;
+        }
+        const pointNode = tree.nodes.get(i);
+        if (!pointNode) {
+            probabilities[i] = 0;
+            continue;
+        }
+        const clusterId = selectedClusters[label];
+        const clusterNode = tree.nodes.get(clusterId);
+        if (!clusterNode) {
+            probabilities[i] = 0;
+            continue;
+        }
+        const lambdaBirth = clusterNode.lambdaBirth;
+        const lambdaMax = clusterMaxLambda.get(label) ?? pointNode.lambdaDeath;
+        const lambdaPoint = pointNode.lambdaDeath;
+        if (lambdaMax === lambdaBirth || !isFinite(lambdaMax)) {
+            probabilities[i] = 1;
+        }
+        else {
+            const prob = (lambdaPoint - lambdaBirth) / (lambdaMax - lambdaBirth);
+            probabilities[i] = Math.max(0, Math.min(1, prob));
+        }
+    }
+    return probabilities;
+}
+/**
+ * Compute outlier scores (GLOSH) for each point.
+ * Higher scores indicate more outlier-ish points.
+ *
+ * outlierScore[i] = 1 - (lambda[i] / lambda_max_in_cluster)
+ *
+ * @param tree Condensed cluster tree.
+ * @param labels Cluster labels for each point.
+ * @param selectedClusters Selected cluster IDs.
+ * @returns Outlier score for each point (0.0-1.0).
+ */
+export function computeOutlierScores(tree, labels, selectedClusters) {
+    const scores = new Array(tree.numPoints).fill(1);
+    // Compute max lambda for each cluster
+    const clusterMaxLambda = new Map();
+    for (let i = 0; i < labels.length; i++) {
+        const label = labels[i];
+        if (label < 0)
+            continue;
+        const pointNode = tree.nodes.get(i);
+        if (!pointNode)
+            continue;
+        const lambda = pointNode.lambdaDeath;
+        if (isFinite(lambda)) {
+            const current = clusterMaxLambda.get(label) ?? 0;
+            clusterMaxLambda.set(label, Math.max(current, lambda));
+        }
+    }
+    // Compute outlier scores
+    for (let i = 0; i < labels.length; i++) {
+        const label = labels[i];
+        if (label < 0) {
+            // Noise points have maximum outlier score
+            scores[i] = 1;
+            continue;
+        }
+        const pointNode = tree.nodes.get(i);
+        if (!pointNode) {
+            scores[i] = 1;
+            continue;
+        }
+        const lambdaMax = clusterMaxLambda.get(label);
+        const lambdaPoint = pointNode.lambdaDeath;
+        if (!lambdaMax || lambdaMax === 0 || !isFinite(lambdaPoint)) {
+            scores[i] = 0;
+        }
+        else {
+            const score = 1 - lambdaPoint / lambdaMax;
+            scores[i] = Math.max(0, Math.min(1, score));
+        }
+    }
+    return scores;
+}
+/**
+ * Get lambda values for all points.
+ */
+export function getLambdaValues(tree) {
+    const lambdas = new Array(tree.numPoints).fill(0);
+    for (let i = 0; i < tree.numPoints; i++) {
+        const node = tree.nodes.get(i);
+        if (node && isFinite(node.lambdaDeath)) {
+            lambdas[i] = node.lambdaDeath;
+        }
+    }
+    return lambdas;
+}
+/**
+ * Get maximum lambda for each cluster.
+ */
+export function getClusterMaxLambda(tree, labels) {
+    const maxLambda = new Map();
+    for (let i = 0; i < labels.length; i++) {
+        const label = labels[i];
+        if (label < 0)
+            continue;
+        const node = tree.nodes.get(i);
+        if (!node)
+            continue;
+        const lambda = node.lambdaDeath;
+        if (isFinite(lambda)) {
+            const current = maxLambda.get(label) ?? 0;
+            maxLambda.set(label, Math.max(current, lambda));
+        }
+    }
+    return maxLambda;
+}
+//# sourceMappingURL=probabilities.js.map

package/dist/clusters/hdbscan/probabilities.js.map

@@ -0,0 +1 @@
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package/dist/clusters/hdbscan/types.d.ts

@@ -0,0 +1,123 @@
+/**
+ * Type definitions for native HDBSCAN implementation.
+ */
+/**
+ * Options for HDBSCAN clustering.
+ */
+export interface HDBSCANOptions {
+    /** Minimum cluster size. Clusters smaller than this are considered noise. */
+    minClusterSize: number;
+    /** Minimum samples for core point. Defaults to minClusterSize. */
+    minSamples?: number;
+    /** Distance metric. Default: 'euclidean'. */
+    metric?: 'euclidean' | 'angular';
+    /** Cluster selection method. Default: 'eom' (Excess of Mass). */
+    clusterSelectionMethod?: 'eom' | 'leaf';
+    /** Use KD-tree for approximate k-NN. Default: false. */
+    approximateKNN?: boolean;
+    /** Use worker_threads for parallel core distance. Default: true. */
+    parallel?: boolean;
+}
+/**
+ * Full result from HDBSCAN clustering.
+ */
+export interface HDBSCANResult {
+    /** Cluster labels. -1 = noise, 0+ = cluster ID. */
+    labels: number[];
+    /** Membership probability (0.0-1.0) for each point. */
+    probabilities: number[];
+    /** Outlier scores (0.0-1.0) for each point. Higher = more outlier-ish. */
+    outlierScores: number[];
+    /** Number of clusters found. */
+    numClusters: number;
+    /** Number of noise points. */
+    noiseCount: number;
+}
+/**
+ * Model state for persistence and incremental assignment.
+ */
+export interface HDBSCANModel {
+    /** Original embeddings used for fitting. */
+    embeddings: number[][];
+    /** Core distances for each point. */
+    coreDistances: number[];
+    /** Cluster labels. */
+    labels: number[];
+    /** Cluster centroids for incremental assignment. */
+    centroids: Map<number, number[]>;
+    /** Exemplar indices per cluster (closest to centroid). */
+    exemplars: Map<number, number[]>;
+    /** Lambda values for probability computation. */
+    lambdaValues: number[];
+    /** Maximum lambda per cluster. */
+    clusterMaxLambda: Map<number, number>;
+}
+/**
+ * MST edge representation.
+ */
+export interface MSTEdge {
+    /** Source point index. */
+    from: number;
+    /** Destination point index. */
+    to: number;
+    /** Mutual reachability distance. */
+    weight: number;
+}
+/**
+ * Node in condensed cluster tree.
+ */
+export interface CondensedTreeNode {
+    /** Node ID (cluster or point). */
+    id: number;
+    /** Parent node ID. */
+    parent: number;
+    /** Lambda value (1/distance) when this node was created. */
+    lambdaBirth: number;
+    /** Lambda value when this node died (merged or became noise). */
+    lambdaDeath: number;
+    /** Number of points in this node. */
+    size: number;
+    /** Whether this is a cluster (vs single point). */
+    isCluster: boolean;
+    /** Child nodes. */
+    children: number[];
+    /** Stability score for cluster selection. */
+    stability: number;
+    /** Whether this cluster is selected in final result. */
+    selected: boolean;
+}
+/**
+ * Condensed cluster tree.
+ */
+export interface CondensedTree {
+    /** All nodes indexed by ID. */
+    nodes: Map<number, CondensedTreeNode>;
+    /** Root node ID. */
+    root: number;
+    /** Number of original data points. */
+    numPoints: number;
+}
+/**
+ * Worker message for parallel core distance computation.
+ */
+export interface CoreDistanceWorkerData {
+    /** Indices to process in this chunk. */
+    indices: number[];
+    /** All points (for distance computation). */
+    allPoints: number[][];
+    /** k value for k-th nearest neighbor. */
+    k: number;
+    /** Distance metric. */
+    metric: 'euclidean' | 'angular';
+}
+/**
+ * Worker result for parallel core distance computation.
+ */
+export interface CoreDistanceWorkerResult {
+    /** Core distances for processed indices. */
+    coreDistances: Array<{
+        index: number;
+        coreDistance: number;
+    }>;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/clusters/hdbscan/types.d.ts.map

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package/dist/clusters/hdbscan/types.js

@@ -0,0 +1,5 @@
+/**
+ * Type definitions for native HDBSCAN implementation.
+ */
+export {};
+//# sourceMappingURL=types.js.map

package/dist/clusters/hdbscan/types.js.map

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package/dist/clusters/hdbscan/union-find.d.ts

@@ -0,0 +1,51 @@
+/**
+ * Union-Find (Disjoint Set) with path compression and union by rank.
+ * Used for efficient component tracking during MST processing.
+ */
+/**
+ * Union-Find data structure with path compression and union by rank.
+ * Provides near-constant time operations for union and find.
+ */
+export declare class UnionFind {
+    private parent;
+    private rank;
+    private componentSize;
+    private numComponents;
+    /**
+     * Create a new Union-Find structure.
+     * @param n Number of elements (0 to n-1).
+     */
+    constructor(n: number);
+    /**
+     * Find the root of the set containing element x.
+     * Uses path compression for efficiency.
+     */
+    find(x: number): number;
+    /**
+     * Union the sets containing elements x and y.
+     * Uses union by rank for balanced trees.
+     * Returns the root of the merged set, or -1 if already in same set.
+     */
+    union(x: number, y: number): number;
+    /**
+     * Check if two elements are in the same set.
+     */
+    connected(x: number, y: number): boolean;
+    /**
+     * Get the size of the component containing element x.
+     */
+    getSize(x: number): number;
+    /**
+     * Get the number of disjoint components.
+     */
+    getNumComponents(): number;
+    /**
+     * Get all components as a map from root to member indices.
+     */
+    getComponents(): Map<number, number[]>;
+    /**
+     * Get all elements in the component containing x.
+     */
+    getComponentMembers(x: number): number[];
+}
+//# sourceMappingURL=union-find.d.ts.map

package/dist/clusters/hdbscan/union-find.d.ts.map

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package/dist/clusters/hdbscan/union-find.js

@@ -0,0 +1,115 @@
+/**
+ * Union-Find (Disjoint Set) with path compression and union by rank.
+ * Used for efficient component tracking during MST processing.
+ */
+/**
+ * Union-Find data structure with path compression and union by rank.
+ * Provides near-constant time operations for union and find.
+ */
+export class UnionFind {
+    parent;
+    rank;
+    componentSize;
+    numComponents;
+    /**
+     * Create a new Union-Find structure.
+     * @param n Number of elements (0 to n-1).
+     */
+    constructor(n) {
+        this.parent = new Array(n);
+        this.rank = new Array(n);
+        this.componentSize = new Array(n);
+        this.numComponents = n;
+        for (let i = 0; i < n; i++) {
+            this.parent[i] = i;
+            this.rank[i] = 0;
+            this.componentSize[i] = 1;
+        }
+    }
+    /**
+     * Find the root of the set containing element x.
+     * Uses path compression for efficiency.
+     */
+    find(x) {
+        if (this.parent[x] !== x) {
+            this.parent[x] = this.find(this.parent[x]); // Path compression
+        }
+        return this.parent[x];
+    }
+    /**
+     * Union the sets containing elements x and y.
+     * Uses union by rank for balanced trees.
+     * Returns the root of the merged set, or -1 if already in same set.
+     */
+    union(x, y) {
+        const rootX = this.find(x);
+        const rootY = this.find(y);
+        if (rootX === rootY) {
+            return -1; // Already in same set
+        }
+        this.numComponents--;
+        // Union by rank
+        if (this.rank[rootX] < this.rank[rootY]) {
+            this.parent[rootX] = rootY;
+            this.componentSize[rootY] += this.componentSize[rootX];
+            return rootY;
+        }
+        else if (this.rank[rootX] > this.rank[rootY]) {
+            this.parent[rootY] = rootX;
+            this.componentSize[rootX] += this.componentSize[rootY];
+            return rootX;
+        }
+        else {
+            this.parent[rootY] = rootX;
+            this.componentSize[rootX] += this.componentSize[rootY];
+            this.rank[rootX]++;
+            return rootX;
+        }
+    }
+    /**
+     * Check if two elements are in the same set.
+     */
+    connected(x, y) {
+        return this.find(x) === this.find(y);
+    }
+    /**
+     * Get the size of the component containing element x.
+     */
+    getSize(x) {
+        return this.componentSize[this.find(x)];
+    }
+    /**
+     * Get the number of disjoint components.
+     */
+    getNumComponents() {
+        return this.numComponents;
+    }
+    /**
+     * Get all components as a map from root to member indices.
+     */
+    getComponents() {
+        const components = new Map();
+        for (let i = 0; i < this.parent.length; i++) {
+            const root = this.find(i);
+            if (!components.has(root)) {
+                components.set(root, []);
+            }
+            components.get(root).push(i);
+        }
+        return components;
+    }
+    /**
+     * Get all elements in the component containing x.
+     */
+    getComponentMembers(x) {
+        const root = this.find(x);
+        const members = [];
+        for (let i = 0; i < this.parent.length; i++) {
+            if (this.find(i) === root) {
+                members.push(i);
+            }
+        }
+        return members;
+    }
+}
+//# sourceMappingURL=union-find.js.map

package/dist/clusters/hdbscan/union-find.js.map

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package/dist/clusters/hdbscan.d.ts

@@ -0,0 +1,71 @@
+/**
+ * Native TypeScript HDBSCAN implementation.
+ * Replaces hdbscan-ts library with optimized implementation.
+ *
+ * Features:
+ * - Efficient data structures (Set, MinHeap, UnionFind)
+ * - Optional parallel core distance computation (worker_threads)
+ * - Both EOM and Leaf cluster extraction methods
+ * - Membership probabilities and outlier scores
+ * - Incremental point assignment (predict)
+ * - Optional KD-tree for approximate k-NN
+ */
+import type { HDBSCANOptions, HDBSCANResult, HDBSCANModel } from './hdbscan/types.js';
+/**
+ * HDBSCAN clustering algorithm.
+ *
+ * Usage:
+ * ```typescript
+ * const hdbscan = new HDBSCAN({ minClusterSize: 5 });
+ * const result = hdbscan.fit(embeddings);
+ * console.log(result.labels, result.numClusters);
+ * ```
+ */
+export declare class HDBSCAN {
+    private options;
+    private model;
+    constructor(options: HDBSCANOptions);
+    /**
+     * Fit HDBSCAN and return full result with probabilities and outlier scores.
+     */
+    fit(embeddings: number[][]): Promise<HDBSCANResult>;
+    /**
+     * Simple interface - just returns labels (drop-in for hdbscan-ts).
+     * This is synchronous for compatibility.
+     */
+    fitSync(embeddings: number[][]): number[];
+    /**
+     * Internal fit method.
+     */
+    private fitInternal;
+    /**
+     * Extract clusters and assign labels.
+     */
+    private extractClustersAndLabels;
+    /**
+     * Compute membership probabilities.
+     */
+    private computeProbabilities;
+    /**
+     * Compute outlier scores.
+     */
+    private computeOutlierScores;
+    /**
+     * Assign new points to existing clusters without reclustering.
+     */
+    predict(newEmbeddings: number[][]): number[];
+    /**
+     * Compute average distance from points to their cluster centroids.
+     */
+    private computeAverageCentroidDistance;
+    /**
+     * Get the fitted model for persistence.
+     */
+    getModel(): HDBSCANModel | null;
+    /**
+     * Build model from clustering result.
+     */
+    private buildModel;
+}
+export type { HDBSCANOptions, HDBSCANResult, HDBSCANModel } from './hdbscan/types.js';
+//# sourceMappingURL=hdbscan.d.ts.map