@graphty/algorithms 1.2.0 → 1.4.2

package/dist/src/link-prediction/common-neighbors.js

@@ -1,28 +1,32 @@
+import { getCommonNeighbors, getIntermediateNodes } from "../utils/graph-utilities.js";
 /**
  * Calculate common neighbors score for a pair of nodes
+ * @param graph - The input graph
+ * @param source - The source node ID
+ * @param target - The target node ID
+ * @param options - Link prediction options
+ * @returns The number of common neighbors
  */
 export function commonNeighborsScore(graph, source, target, options = {}) {
     if (!graph.hasNode(source) || !graph.hasNode(target)) {
         return 0;
     }
     const { directed = false } = options;
-    // Get neighbors
-    const sourceNeighbors = new Set(directed ? Array.from(graph.outNeighbors(source)) : Array.from(graph.neighbors(source)));
-    const targetNeighbors = new Set(directed ? Array.from(graph.inNeighbors(target)) : Array.from(graph.neighbors(target)));
-    // Count common neighbors
-    let commonCount = 0;
-    for (const neighbor of sourceNeighbors) {
-        if (targetNeighbors.has(neighbor)) {
-            commonCount++;
-        }
-    }
-    return commonCount;
+    // Use utility function to get common neighbors
+    // For directed graphs, we want intermediate nodes that form paths source->X->target
+    const commonNeighborsSet = directed
+        ? getIntermediateNodes(graph, source, target)
+        : getCommonNeighbors(graph, source, target, false);
+    return commonNeighborsSet.size;
 }
 /**
  * Calculate common neighbors scores for all possible node pairs
+ * @param graph - The input graph
+ * @param options - Link prediction options
+ * @returns Array of link prediction scores sorted by score descending
  */
 export function commonNeighborsPrediction(graph, options = {}) {
-    const { directed = false, includeExisting = false, topK, } = options;
+    const { directed = false, includeExisting = false, topK } = options;
     const scores = [];
     const nodes = Array.from(graph.nodes()).map((n) => n.id);
     for (let i = 0; i < nodes.length; i++) {
@@ -56,6 +60,10 @@ export function commonNeighborsPrediction(graph, options = {}) {
 }
 /**
  * Calculate common neighbors scores for specific node pairs
+ * @param graph - The input graph
+ * @param pairs - Array of node ID pairs to calculate scores for
+ * @param options - Link prediction options
+ * @returns Array of link prediction scores for the specified pairs
  */
 export function commonNeighborsForPairs(graph, pairs, options = {}) {
     return pairs.map(([source, target]) => ({
@@ -66,12 +74,16 @@ export function commonNeighborsForPairs(graph, pairs, options = {}) {
 }
 /**
  * Get top candidates for link prediction for a specific node
+ * @param graph - The input graph
+ * @param node - The node ID to get candidates for
+ * @param options - Link prediction options with optional candidate list
+ * @returns Array of top link prediction candidates sorted by score descending
  */
 export function getTopCandidatesForNode(graph, node, options = {}) {
     if (!graph.hasNode(node)) {
         return [];
     }
-    const { directed = false, includeExisting = false, topK = 10, candidates, } = options;
+    const { directed = false, includeExisting = false, topK = 10, candidates } = options;
     const scores = [];
     const targetNodes = candidates ?? Array.from(graph.nodes()).map((n) => n.id);
     for (const target of targetNodes) {
@@ -93,6 +105,11 @@ export function getTopCandidatesForNode(graph, node, options = {}) {
 }
 /**
  * Calculate precision and recall for link prediction evaluation
+ * @param trainingGraph - The training graph without test edges
+ * @param testEdges - Array of node pairs that are actual edges
+ * @param nonEdges - Array of node pairs that are not edges
+ * @param options - Link prediction options
+ * @returns Evaluation metrics including precision, recall, F1 score, and AUC
  */
 export function evaluateCommonNeighbors(trainingGraph, testEdges, nonEdges, options = {}) {
     // Get scores for test edges and non-edges
@@ -119,7 +136,7 @@ export function evaluateCommonNeighbors(trainingGraph, testEdges, nonEdges, opti
         }
         const precision = truePositives / (truePositives + falsePositives);
         const recall = truePositives / totalPositives;
-        const f1 = precision + recall > 0 ? 2 * (precision * recall) / (precision + recall) : 0;
+        const f1 = precision + recall > 0 ? (2 * (precision * recall)) / (precision + recall) : 0;
         if (f1 > bestF1) {
             bestF1 = f1;
             bestPrecision = precision;

package/dist/src/link-prediction/common-neighbors.js.map

@@ -1 +1 @@
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package/dist/src/link-prediction/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/link-prediction/index.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EACH,kBAAkB,EAClB,oBAAoB,EACpB,eAAe,EACf,oCAAoC,EACpC,kBAAkB,EAClB,iCAAiC,GACpC,MAAM,kBAAkB,CAAC;AAC1B,YAAY,EAAE,qBAAqB,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AACxF,OAAO,EACH,uBAAuB,EACvB,yBAAyB,EACzB,oBAAoB,EACpB,uBAAuB,EACvB,uBAAuB,GAC1B,MAAM,uBAAuB,CAAC"}

package/dist/src/optimized/bit-packed.d.ts

@@ -0,0 +1,193 @@
+/**
+ * Wrapper around TypedFastBitSet with graph-specific optimizations
+ *
+ * Provides efficient bit-packed set operations optimized for graph algorithms
+ * with 8x memory reduction compared to standard JavaScript Set for boolean values.
+ */
+export declare class GraphBitSet {
+    private bitset;
+    private _cardinality;
+    /**
+     * Creates a new GraphBitSet with optional pre-allocated capacity.
+     * @param capacity - The initial capacity to pre-allocate for the bitset
+     */
+    constructor(capacity?: number);
+    /**
+     * Add a single element to the set.
+     * @param index - The element index to add
+     */
+    add(index: number): void;
+    /**
+     * Remove a single element from the set.
+     * @param index - The element index to remove
+     */
+    remove(index: number): void;
+    /**
+     * Check if an element exists in the set.
+     * @param index - The element index to check
+     * @returns True if the element exists, false otherwise
+     */
+    has(index: number): boolean;
+    /**
+     * Clear all elements
+     */
+    clear(): void;
+    /**
+     * Check if the set is empty.
+     * @returns True if the set contains no elements, false otherwise
+     */
+    isEmpty(): boolean;
+    /**
+     * Optimized for graph algorithms - add a range of indices.
+     * @param start - The starting index (inclusive)
+     * @param end - The ending index (exclusive)
+     */
+    addRange(start: number, end: number): void;
+    /**
+     * Fast cardinality tracking - get the number of elements in the set.
+     * @returns The number of elements in the set
+     */
+    size(): number;
+    /**
+     * Batch operations for frontier management - swap contents with another GraphBitSet.
+     * @param other - The GraphBitSet to swap contents with
+     */
+    swap(other: GraphBitSet): void;
+    /**
+     * Efficient iteration over all elements in the set.
+     * @yields The indices of elements in the set
+     */
+    [Symbol.iterator](): Generator<number>;
+    /**
+     * Perform union operation with another GraphBitSet, updating this set in place.
+     * @param other - The GraphBitSet to union with
+     */
+    union(other: GraphBitSet): void;
+    /**
+     * Perform intersection operation with another GraphBitSet, updating this set in place.
+     * @param other - The GraphBitSet to intersect with
+     */
+    intersection(other: GraphBitSet): void;
+    /**
+     * Perform difference operation with another GraphBitSet, updating this set in place.
+     * @param other - The GraphBitSet to subtract from this set
+     */
+    difference(other: GraphBitSet): void;
+    /**
+     * Clone the bitset.
+     * @returns A new GraphBitSet with the same elements
+     */
+    clone(): GraphBitSet;
+}
+/**
+ * Specialized bit array for visited tracking
+ *
+ * More memory efficient than GraphBitSet for simple boolean arrays
+ * that don't need set operations.
+ */
+export declare class VisitedBitArray {
+    private words;
+    private wordCount;
+    private _size;
+    /**
+     * Creates a new VisitedBitArray with the specified size.
+     * @param size - The number of bits to allocate
+     */
+    constructor(size: number);
+    /**
+     * Set bit at the specified index.
+     * @param index - The bit index to set
+     */
+    set(index: number): void;
+    /**
+     * Get bit value at the specified index.
+     * @param index - The bit index to get
+     * @returns True if the bit is set, false otherwise
+     */
+    get(index: number): boolean;
+    /**
+     * Clear all bits
+     */
+    clear(): void;
+    /**
+     * Toggle bit at the specified index.
+     * @param index - The bit index to toggle
+     */
+    toggle(index: number): void;
+    /**
+     * Population count for statistics - count the number of set bits.
+     * @returns The number of bits set to 1
+     */
+    popcount(): number;
+    /**
+     * Efficient population count for a single word.
+     * Uses bit manipulation tricks for fast counting.
+     * @param n - The 32-bit word to count
+     * @returns The number of bits set to 1 in the word
+     */
+    private popcountWord;
+    /**
+     * Get size of the bit array.
+     * @returns The total number of bits in the array
+     */
+    size(): number;
+    /**
+     * Check if all bits are zero.
+     * @returns True if no bits are set, false otherwise
+     */
+    isEmpty(): boolean;
+    /**
+     * Set multiple bits from an array of indices.
+     * @param indices - Array of bit indices to set
+     */
+    setMultiple(indices: number[]): void;
+    /**
+     * Get indices of all set bits.
+     * @returns Array containing the indices of all bits that are set to 1
+     */
+    getSetIndices(): number[];
+}
+/**
+ * Bit-packed distance array for BFS
+ *
+ * Optimized for storing distances using 16-bit integers (up to 65,535 levels)
+ * Still provides 2x memory savings compared to standard 32-bit numbers
+ */
+export declare class CompactDistanceArray {
+    private data;
+    private _size;
+    private static readonly INFINITY;
+    /**
+     * Creates a new CompactDistanceArray with the specified size.
+     * @param size - The number of distance values to store
+     */
+    constructor(size: number);
+    /**
+     * Set distance at the specified index.
+     * @param index - The node index to set the distance for
+     * @param distance - The distance value to set
+     */
+    set(index: number, distance: number): void;
+    /**
+     * Get distance at the specified index.
+     * @param index - The node index to get the distance for
+     * @returns The distance value, or INFINITY if not set
+     */
+    get(index: number): number;
+    /**
+     * Check if a node has been visited (has a valid distance).
+     * @param index - The node index to check
+     * @returns True if the node has been visited, false otherwise
+     */
+    isVisited(index: number): boolean;
+    /**
+     * Reset all distances to unvisited state.
+     */
+    clear(): void;
+    /**
+     * Get the size of the distance array.
+     * @returns The number of elements in the array
+     */
+    size(): number;
+}
+//# sourceMappingURL=bit-packed.d.ts.map

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package/dist/src/optimized/bit-packed.js

@@ -0,0 +1,342 @@
+import { TypedFastBitSet } from "typedfastbitset";
+/**
+ * Wrapper around TypedFastBitSet with graph-specific optimizations
+ *
+ * Provides efficient bit-packed set operations optimized for graph algorithms
+ * with 8x memory reduction compared to standard JavaScript Set for boolean values.
+ */
+export class GraphBitSet {
+    /**
+     * Creates a new GraphBitSet with optional pre-allocated capacity.
+     * @param capacity - The initial capacity to pre-allocate for the bitset
+     */
+    constructor(capacity) {
+        this._cardinality = 0;
+        this.bitset = new TypedFastBitSet();
+        if (capacity) {
+            // Pre-allocate for known size
+            this.bitset.resize(capacity);
+        }
+    }
+    /**
+     * Add a single element to the set.
+     * @param index - The element index to add
+     */
+    add(index) {
+        if (!this.bitset.has(index)) {
+            this.bitset.add(index);
+            this._cardinality++;
+        }
+    }
+    /**
+     * Remove a single element from the set.
+     * @param index - The element index to remove
+     */
+    remove(index) {
+        if (this.bitset.has(index)) {
+            this.bitset.remove(index);
+            this._cardinality--;
+        }
+    }
+    /**
+     * Check if an element exists in the set.
+     * @param index - The element index to check
+     * @returns True if the element exists, false otherwise
+     */
+    has(index) {
+        return this.bitset.has(index);
+    }
+    /**
+     * Clear all elements
+     */
+    clear() {
+        this.bitset.clear();
+        this._cardinality = 0;
+    }
+    /**
+     * Check if the set is empty.
+     * @returns True if the set contains no elements, false otherwise
+     */
+    isEmpty() {
+        return this._cardinality === 0;
+    }
+    /**
+     * Optimized for graph algorithms - add a range of indices.
+     * @param start - The starting index (inclusive)
+     * @param end - The ending index (exclusive)
+     */
+    addRange(start, end) {
+        for (let i = start; i < end; i++) {
+            if (!this.bitset.has(i)) {
+                this.bitset.add(i);
+                this._cardinality++;
+            }
+        }
+    }
+    /**
+     * Fast cardinality tracking - get the number of elements in the set.
+     * @returns The number of elements in the set
+     */
+    size() {
+        return this._cardinality;
+    }
+    /**
+     * Batch operations for frontier management - swap contents with another GraphBitSet.
+     * @param other - The GraphBitSet to swap contents with
+     */
+    swap(other) {
+        [this.bitset, other.bitset] = [other.bitset, this.bitset];
+        [this._cardinality, other._cardinality] = [other._cardinality, this._cardinality];
+    }
+    /**
+     * Efficient iteration over all elements in the set.
+     * @yields The indices of elements in the set
+     */
+    *[Symbol.iterator]() {
+        // Use TypedFastBitSet's optimized iteration
+        yield* this.bitset;
+    }
+    /**
+     * Perform union operation with another GraphBitSet, updating this set in place.
+     * @param other - The GraphBitSet to union with
+     */
+    union(other) {
+        const result = this.bitset.union(other.bitset);
+        this.bitset = result;
+        const size = this.bitset.size();
+        this._cardinality = size;
+    }
+    /**
+     * Perform intersection operation with another GraphBitSet, updating this set in place.
+     * @param other - The GraphBitSet to intersect with
+     */
+    intersection(other) {
+        const result = this.bitset.intersection(other.bitset);
+        this.bitset = result;
+        const size = this.bitset.size();
+        this._cardinality = size;
+    }
+    /**
+     * Perform difference operation with another GraphBitSet, updating this set in place.
+     * @param other - The GraphBitSet to subtract from this set
+     */
+    difference(other) {
+        const result = this.bitset.difference(other.bitset);
+        this.bitset = result;
+        const size = this.bitset.size();
+        this._cardinality = size;
+    }
+    /**
+     * Clone the bitset.
+     * @returns A new GraphBitSet with the same elements
+     */
+    clone() {
+        const cloned = new GraphBitSet();
+        cloned.bitset = this.bitset.clone();
+        cloned._cardinality = this._cardinality;
+        return cloned;
+    }
+}
+/**
+ * Specialized bit array for visited tracking
+ *
+ * More memory efficient than GraphBitSet for simple boolean arrays
+ * that don't need set operations.
+ */
+export class VisitedBitArray {
+    /**
+     * Creates a new VisitedBitArray with the specified size.
+     * @param size - The number of bits to allocate
+     */
+    constructor(size) {
+        this._size = size;
+        this.wordCount = Math.ceil(size / 32);
+        this.words = new Uint32Array(this.wordCount);
+    }
+    /**
+     * Set bit at the specified index.
+     * @param index - The bit index to set
+     */
+    set(index) {
+        if (index < 0 || index >= this._size) {
+            throw new Error(`Index ${String(index)} out of bounds [0, ${String(this._size)})`);
+        }
+        const wordIndex = index >>> 5; // divide by 32
+        const bitIndex = index & 31; // modulo 32
+        const word = this.words[wordIndex];
+        if (word !== undefined) {
+            this.words[wordIndex] = word | (1 << bitIndex);
+        }
+    }
+    /**
+     * Get bit value at the specified index.
+     * @param index - The bit index to get
+     * @returns True if the bit is set, false otherwise
+     */
+    get(index) {
+        if (index < 0 || index >= this._size) {
+            return false;
+        }
+        const wordIndex = index >>> 5;
+        const bitIndex = index & 31;
+        const word = this.words[wordIndex];
+        return word !== undefined && (word & (1 << bitIndex)) !== 0;
+    }
+    /**
+     * Clear all bits
+     */
+    clear() {
+        this.words.fill(0);
+    }
+    /**
+     * Toggle bit at the specified index.
+     * @param index - The bit index to toggle
+     */
+    toggle(index) {
+        if (index < 0 || index >= this._size) {
+            throw new Error(`Index ${String(index)} out of bounds [0, ${String(this._size)})`);
+        }
+        const wordIndex = index >>> 5;
+        const bitIndex = index & 31;
+        const word = this.words[wordIndex];
+        if (word !== undefined) {
+            this.words[wordIndex] = word ^ (1 << bitIndex);
+        }
+    }
+    /**
+     * Population count for statistics - count the number of set bits.
+     * @returns The number of bits set to 1
+     */
+    popcount() {
+        let count = 0;
+        for (let i = 0; i < this.wordCount; i++) {
+            const word = this.words[i];
+            if (word !== undefined) {
+                count += this.popcountWord(word);
+            }
+        }
+        return count;
+    }
+    /**
+     * Efficient population count for a single word.
+     * Uses bit manipulation tricks for fast counting.
+     * @param n - The 32-bit word to count
+     * @returns The number of bits set to 1 in the word
+     */
+    popcountWord(n) {
+        let x = n;
+        x = x - ((x >>> 1) & 0x55555555);
+        x = (x & 0x33333333) + ((x >>> 2) & 0x33333333);
+        return (((x + (x >>> 4)) & 0xf0f0f0f) * 0x1010101) >>> 24;
+    }
+    /**
+     * Get size of the bit array.
+     * @returns The total number of bits in the array
+     */
+    size() {
+        return this._size;
+    }
+    /**
+     * Check if all bits are zero.
+     * @returns True if no bits are set, false otherwise
+     */
+    isEmpty() {
+        for (let i = 0; i < this.wordCount; i++) {
+            if (this.words[i] !== 0) {
+                return false;
+            }
+        }
+        return true;
+    }
+    /**
+     * Set multiple bits from an array of indices.
+     * @param indices - Array of bit indices to set
+     */
+    setMultiple(indices) {
+        for (const index of indices) {
+            this.set(index);
+        }
+    }
+    /**
+     * Get indices of all set bits.
+     * @returns Array containing the indices of all bits that are set to 1
+     */
+    getSetIndices() {
+        const indices = [];
+        for (let wordIndex = 0; wordIndex < this.wordCount; wordIndex++) {
+            const word = this.words[wordIndex];
+            if (!word || word === 0) {
+                continue;
+            }
+            for (let bitIndex = 0; bitIndex < 32; bitIndex++) {
+                if (word & (1 << bitIndex)) {
+                    const index = (wordIndex << 5) + bitIndex;
+                    if (index < this._size) {
+                        indices.push(index);
+                    }
+                }
+            }
+        }
+        return indices;
+    }
+}
+/**
+ * Bit-packed distance array for BFS
+ *
+ * Optimized for storing distances using 16-bit integers (up to 65,535 levels)
+ * Still provides 2x memory savings compared to standard 32-bit numbers
+ */
+export class CompactDistanceArray {
+    /**
+     * Creates a new CompactDistanceArray with the specified size.
+     * @param size - The number of distance values to store
+     */
+    constructor(size) {
+        this._size = size;
+        this.data = new Uint16Array(size);
+        this.data.fill(CompactDistanceArray.INFINITY); // Initialize with max value (unvisited)
+    }
+    /**
+     * Set distance at the specified index.
+     * @param index - The node index to set the distance for
+     * @param distance - The distance value to set
+     */
+    set(index, distance) {
+        if (distance >= CompactDistanceArray.INFINITY) {
+            throw new Error(`Distance exceeds maximum value (${String(CompactDistanceArray.INFINITY - 1)})`);
+        }
+        this.data[index] = distance;
+    }
+    /**
+     * Get distance at the specified index.
+     * @param index - The node index to get the distance for
+     * @returns The distance value, or INFINITY if not set
+     */
+    get(index) {
+        const value = this.data[index];
+        return value ?? CompactDistanceArray.INFINITY; // Default to unvisited
+    }
+    /**
+     * Check if a node has been visited (has a valid distance).
+     * @param index - The node index to check
+     * @returns True if the node has been visited, false otherwise
+     */
+    isVisited(index) {
+        return this.data[index] !== CompactDistanceArray.INFINITY;
+    }
+    /**
+     * Reset all distances to unvisited state.
+     */
+    clear() {
+        this.data.fill(CompactDistanceArray.INFINITY);
+    }
+    /**
+     * Get the size of the distance array.
+     * @returns The number of elements in the array
+     */
+    size() {
+        return this._size;
+    }
+}
+CompactDistanceArray.INFINITY = 65535;
+//# sourceMappingURL=bit-packed.js.map

package/dist/src/optimized/bit-packed.js.map

@@ -0,0 +1 @@
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