HNSW

MNIST test
Fix process find of cutoff for bimodal histogram

TestHNSW/HNSWDemo/Program.cs

@@ -7,118 +7,10 @@ namespace HNSWDemo
     {
         static void Main(string[] args)
         {
-            new AutoClusteringTest().Run();
+            new AutoClusteringMNISTTest().Run();
+            //new HistogramTest().Run();
             Console.WriteLine("Completed");
             Console.ReadKey();
         }
-        
-        /*
-        static void TestOnMnist()
-        {
-            int imageCount, rowCount, colCount;
-            var buf = new byte[4];
-            var image = new byte[28 * 28];
-            var vectors = new List<float[]>();
-            using (var fs = new FileStream("t10k-images.idx3-ubyte", FileMode.Open, FileAccess.Read, FileShare.None))
-            {
-                // first 4 bytes is a magic number
-                fs.Read(buf, 0, 4);
-                // second 4 bytes is the number of images
-                fs.Read(buf, 0, 4);
-                imageCount = BitConverter.ToInt32(buf.Reverse().ToArray(), 0);
-                // third 4 bytes is the row count
-                fs.Read(buf, 0, 4);
-                rowCount = BitConverter.ToInt32(buf.Reverse().ToArray(), 0);
-                // fourth 4 bytes is the column count
-                fs.Read(buf, 0, 4);
-                colCount = BitConverter.ToInt32(buf.Reverse().ToArray(), 0);
-
-                for (int i = 0; i < imageCount; i++)
-                {
-                    fs.Read(image, 0, image.Length);
-                    vectors.Add(image.Select(b => (float)b).ToArray());
-                }
-            }
-
-            //var direct = new VectorsDirectCompare(vectors, Metrics.L2Euclidean);
-            
-            var options = NSWOptions<float[]>.Create(8, 16, 200, 200, Metrics.L2Euclidean, selectionHeuristic: NeighbourSelectionHeuristic.SelectSimple);
-            SmallWorld<float[]> world;
-            if (File.Exists("graph.bin"))
-            {
-                using (var fs = new FileStream("graph.bin", FileMode.Open, FileAccess.Read, FileShare.None))
-                {
-                    world = SmallWorld.CreateWorldFrom<float[]>(options, fs);
-                }
-            }
-            else
-            {
-                world = SmallWorld.CreateWorld<float[]>(options);
-                world.AddItems(vectors);
-                using (var fs = new FileStream("graph.bin", FileMode.Create, FileAccess.Write, FileShare.None))
-                {
-                    world.Serialize(fs);
-                }
-            }
-            
-            var clusters = AutomaticGraphClusterer.DetectClusters(world);
-            Console.WriteLine($"Found {clusters.Count} clusters");
-            for (int i = 0; i < clusters.Count; i++)
-            {
-                Console.WriteLine($"Cluster {i + 1} countains {clusters[i].Count} items");
-            }
-        }
-
-        
-         static void FilterTest()
-        {
-            var count = 1000;
-            var testCount = 100;
-            var dimensionality = 128;
-            var samples = Person.GenerateRandom(dimensionality, count);
-
-            var testDict = samples.ToDictionary(s => s.Item2.Number, s => s.Item2);
-
-            var map = new HNSWMap<long>();
-            var world = new SmallWorld<float[]>(NSWOptions<float[]>.Create(6, 15, 200, 200, CosineDistance.ForUnits, true, true, selectionHeuristic: NeighbourSelectionHeuristic.SelectSimple));
-
-            var ids = world.AddItems(samples.Select(i => i.Item1).ToArray());
-            for (int bi = 0; bi < samples.Count; bi++)
-            {
-                map.Append(samples[bi].Item2.Number, ids[bi]);
-            }
-
-            Console.WriteLine("Start test");
-            int K = 200;
-            var vectors = RandomVectors(dimensionality, testCount);
-
-            var context = new SearchContext()
-                .SetActiveNodes(map
-                    .ConvertFeaturesToIds(samples
-                        .Where(p => p.Item2.Age > 20 && p.Item2.Age < 50 && p.Item2.Gender == Gender.Feemale)
-                        .Select(p => p.Item2.Number)));
-
-            var hits = 0;
-            var miss = 0;
-            foreach (var v in vectors)
-            {
-                var numbers = map.ConvertIdsToFeatures(world.Search(v, K, context).Select(r => r.Item1));
-                foreach (var r in numbers)
-                {
-                    var record = testDict[r];
-                    if (record.Gender == Gender.Feemale && record.Age > 20 && record.Age < 50)
-                    {
-                        hits++;
-                    }
-                    else
-                    {
-                        miss++;
-                    }
-                }
-            }
-            Console.WriteLine($"SUCCESS: {hits}");
-            Console.WriteLine($"ERROR: {miss}");
-        }
-        */
     }
 }

TestHNSW/HNSWDemo/Tests/AccuracityTest.cs

@@ -25,8 +25,8 @@ namespace HNSWDemo.Tests
 
             var sw = new Stopwatch();
 
-            var test = new VectorsDirectCompare(samples, CosineDistance.NonOptimized);
-            var world = new SmallWorld<float[]>(NSWOptions<float[]>.Create(8, 12, 100, 100, CosineDistance.NonOptimized));
+            var test = new VectorsDirectCompare(samples, Metrics.Cosine);
+            var world = new SmallWorld<float[]>(NSWOptions<float[]>.Create(8, 12, 100, 100, Metrics.Cosine));
 
             sw.Start();
             var ids = world.AddItems(samples.ToArray());

TestHNSW/HNSWDemo/Tests/AutoClusteringMNISTTest.cs

@@ -0,0 +1,142 @@
+using System;
+using System.Collections.Generic;
+using System.Drawing;
+using System.Drawing.Imaging;
+using System.IO;
+using System.Linq;
+using System.Runtime.InteropServices;
+using ZeroLevel.HNSW;
+using ZeroLevel.HNSW.Services;
+using ZeroLevel.Services.FileSystem;
+
+namespace HNSWDemo.Tests
+{
+    public class AutoClusteringMNISTTest
+        : ITest
+    {
+        private static int Width = 3000;
+        private static int Height = 3000;
+
+        private static byte[] PadLines(byte[] bytes, int rows, int columns)
+        {
+            int currentStride = columns; // 3
+            int newStride = columns;  // 4
+            byte[] newBytes = new byte[newStride * rows];
+            for (int i = 0; i < rows; i++)
+                Buffer.BlockCopy(bytes, currentStride * i, newBytes, newStride * i, currentStride);
+            return newBytes;
+        }
+
+        public void Run()
+        {
+            var folder = @"D:\Mnist";
+            int columns = 28;
+            int rows = 28;
+            int imageCount, rowCount, colCount;
+            var buf = new byte[4];
+            var image = new byte[rows * columns];
+            var vectors = new List<byte[]>();
+            using (var fs = new FileStream("t10k-images.idx3-ubyte", FileMode.Open, FileAccess.Read, FileShare.None))
+            {
+                // first 4 bytes is a magic number
+                fs.Read(buf, 0, 4);
+                // second 4 bytes is the number of images
+                fs.Read(buf, 0, 4);
+                imageCount = BitConverter.ToInt32(buf.Reverse().ToArray(), 0);
+                // third 4 bytes is the row count
+                fs.Read(buf, 0, 4);
+                rowCount = BitConverter.ToInt32(buf.Reverse().ToArray(), 0);
+                // fourth 4 bytes is the column count
+                fs.Read(buf, 0, 4);
+                colCount = BitConverter.ToInt32(buf.Reverse().ToArray(), 0);
+
+                for (int i = 0; i < imageCount; i++)
+                {
+                    fs.Read(image, 0, image.Length);
+                    var v = new byte[image.Length];
+                    Array.Copy(image, v, image.Length);
+                    vectors.Add(v);
+                }
+            }
+            var options = NSWOptions<byte[]>.Create(8, 16, 200, 200, Metrics.L2Euclidean);
+            SmallWorld<byte[]> world;
+            if (File.Exists("graph_mnist.bin"))
+            {
+                using (var fs = new FileStream("graph_mnist.bin", FileMode.Open, FileAccess.Read, FileShare.None))
+                {
+                    world = SmallWorld.CreateWorldFrom<byte[]>(options, fs);
+                }
+            }
+            else
+            {
+                world = SmallWorld.CreateWorld<byte[]>(options);
+                world.AddItems(vectors);
+                using (var fs = new FileStream("graph_mnist.bin", FileMode.Create, FileAccess.Write, FileShare.None))
+                {
+                    world.Serialize(fs);
+                }
+            }
+
+            var distance = new Func<int, int, float>((id1, id2) => Metrics.L2Euclidean(world.GetVector(id1), world.GetVector(id2)));
+            var links = world.GetLinks().SelectMany(pair => pair.Value.Select(p=> distance(pair.Key, p))).ToList();
+            var exists = links.Where(n => n > 0).ToArray();
+            
+            var histogram = new Histogram(HistogramMode.SQRT, links);
+            DrawHistogram(histogram, @"D:\Mnist\histogram.jpg");
+
+            var clusters = AutomaticGraphClusterer.DetectClusters(world);
+            Console.WriteLine($"Found {clusters.Count} clusters");
+            
+            
+            for (int i = 0; i < clusters.Count; i++)
+            {
+                var ouput = Path.Combine(folder, i.ToString("D3"));
+                FSUtils.CleanAndTestFolder(ouput);
+                foreach (var v in clusters[i])
+                {                    
+                    int stride = columns;
+                    byte[] newbytes = PadLines(world.GetVector(v), rows, columns);
+                    using (var im = new Bitmap(columns, rows, stride, PixelFormat.Format8bppIndexed, Marshal.UnsafeAddrOfPinnedArrayElement(newbytes, 0)))
+                    {
+                        im.Save(Path.Combine(ouput, $"{v}.bmp"));
+                    }
+                }
+                Console.WriteLine($"Cluster {i + 1} countains {clusters[i].Count} items");
+            }
+        }
+
+        static void DrawHistogram(Histogram histogram, string filename)
+        {
+            var wb = Width / histogram.Values.Length;
+            var k = ((float)Height) / (float)histogram.Values.Max();
+
+            var maxes = histogram.GetMaximums().ToDictionary(m => m.Index, m => m);
+            int threshold = histogram.CuttOff();
+
+            using (var bmp = new Bitmap(Width, Height))
+            {
+                using (var g = Graphics.FromImage(bmp))
+                {
+                    for (int i = 0; i < histogram.Values.Length; i++)
+                    {
+                        var height = (int)(histogram.Values[i] * k);
+                        if (maxes.ContainsKey(i))
+                        {
+                            g.DrawRectangle(Pens.Red, i * wb, bmp.Height - height, wb, height);
+                            g.DrawRectangle(Pens.Red, i * wb + 1, bmp.Height - height, wb - 1, height);
+                        }
+                        else
+                        {
+                            g.DrawRectangle(Pens.Blue, i * wb, bmp.Height - height, wb, height);
+                        }
+                        if (i == threshold)
+                        {
+                            g.DrawLine(Pens.Green, i * wb + wb / 2, 0, i * wb + wb / 2, bmp.Height);
+                        }
+                    }
+                }
+                bmp.Save(filename);
+            }
+        }
+    }
+}

TestHNSW/HNSWDemo/Tests/FilterTest.cs

@@ -0,0 +1,57 @@
+using HNSWDemo.Model;
+using System;
+using System.Linq;
+using ZeroLevel.HNSW;
+
+namespace HNSWDemo.Tests
+{
+    public class FilterTest
+        : ITest
+    {
+        private const int count = 3000;
+        private const int testCount = 100;
+        private const int dimensionality = 128;
+
+        public void Run()
+        {
+            var map = new HNSWMap<long>();
+            var samples = Person.GenerateRandom(dimensionality, count);
+            var testDict = samples.ToDictionary(s => s.Item2.Number, s => s.Item2);
+            var world = new SmallWorld<float[]>(NSWOptions<float[]>.Create(6, 15, 200, 200, CosineDistance.ForUnits));
+            var ids = world.AddItems(samples.Select(i => i.Item1).ToArray());
+            for (int bi = 0; bi < samples.Count; bi++)
+            {
+                map.Append(samples[bi].Item2.Number, ids[bi]);
+            }
+            Console.WriteLine("Start test");
+            int K = 200;
+            var vectors = VectorUtils.RandomVectors(dimensionality, testCount);
+
+            var context = new SearchContext()
+                .SetActiveNodes(map
+                    .ConvertFeaturesToIds(samples
+                        .Where(p => p.Item2.Age > 20 && p.Item2.Age < 50 && p.Item2.Gender == Gender.Feemale)
+                        .Select(p => p.Item2.Number)));
+            var hits = 0;
+            var miss = 0;
+            foreach (var v in vectors)
+            {
+                var numbers = map.ConvertIdsToFeatures(world.Search(v, K, context).Select(r => r.Item1));
+                foreach (var r in numbers)
+                {
+                    var record = testDict[r];
+                    if (context.NodeCheckMode == Mode.None || (record.Gender == Gender.Feemale && record.Age > 20 && record.Age < 50))
+                    {
+                        hits++;
+                    }
+                    else
+                    {
+                        miss++;
+                    }
+                }
+            }
+            Console.WriteLine($"SUCCESS: {hits}");
+            Console.WriteLine($"ERROR: {miss}");
+        }
+    }
+}

TestHNSW/HNSWDemo/Tests/HistogramTest.cs

@@ -24,7 +24,7 @@ namespace HNSWDemo.Tests
             var histogram = new Histogram(HistogramMode.SQRT, weights);
             histogram.Smooth();
 
-            int threshold = histogram.OTSU();
+            int threshold = histogram.CuttOff();
             var min = histogram.Bounds[threshold - 1];
             var max = histogram.Bounds[threshold];
             var R = (max + min) / 2;
@@ -38,7 +38,7 @@ namespace HNSWDemo.Tests
             var k = ((float)Height) / (float)histogram.Values.Max();
 
             var maxes = histogram.GetMaximums().ToDictionary(m => m.Index, m => m);
-            int threshold = histogram.OTSU();
+            int threshold = histogram.CuttOff();
 
             using (var bmp = new Bitmap(Width, Height))
             {

TestHNSW/HNSWDemo/Tests/InsertTimeExplosionTest.cs

@@ -14,7 +14,7 @@ namespace HNSWDemo.Tests
         public void Run()
         {
             var sw = new Stopwatch();
-            var world = new SmallWorld<float[]>(NSWOptions<float[]>.Create(6, 12, 100, 100, CosineDistance.NonOptimized));
+            var world = new SmallWorld<float[]>(NSWOptions<float[]>.Create(6, 12, 100, 100, Metrics.Cosine));
             for (int i = 0; i < IterationCount; i++)
             {
                 var samples = VectorUtils.RandomVectors(Dimensionality, Count);

TestHNSW/HNSWDemo/Tests/QuantizatorTest.cs

@@ -26,11 +26,11 @@ namespace HNSWDemo.Tests
             {
                 var v1 = samples[i];
                 var v2 = samples[i + 1];
-                var dist = CosineDistance.NonOptimized(v1, v2);
+                var dist = Metrics.Cosine(v1, v2);
 
                 var qv1 = q_samples[i];
                 var qv2 = q_samples[i + 1];
-                var qdist = CosineDistance.NonOptimized(qv1, qv2);
+                var qdist = Metrics.Cosine(qv1, qv2);
 
                 list.Add(Math.Abs(dist - qdist));
             }

TestHNSW/HNSWDemo/Tests/QuantizeAccuracityTest.cs

@@ -28,8 +28,8 @@ namespace HNSWDemo.Tests
 
             var sw = new Stopwatch();
 
-            var test = new VectorsDirectCompare(s, CosineDistance.NonOptimized);
-            var world = new SmallWorld<long[]>(NSWOptions<long[]>.Create(6, 8, 100, 100, CosineDistance.NonOptimized));
+            var test = new VectorsDirectCompare(s, Metrics.Cosine);
+            var world = new SmallWorld<long[]>(NSWOptions<long[]>.Create(6, 8, 100, 100, Metrics.Cosine));
 
             sw.Start();
             var ids = world.AddItems(samples.ToArray());

TestHNSW/HNSWDemo/Tests/QuantizeHistogramTest.cs

@@ -18,15 +18,15 @@ namespace HNSWDemo.Tests
         {
             var vectors = VectorUtils.RandomVectors(Dimensionality, Count);
             var q = new Quantizator(-1f, 1f);
-            var world = SmallWorld.CreateWorld<long[]>(NSWOptions<long[]>.Create(8, 16, 200, 200, CosineDistance.NonOptimized));
+            var world = SmallWorld.CreateWorld<long[]>(NSWOptions<long[]>.Create(8, 16, 200, 200, Metrics.Cosine));
             world.AddItems(vectors.Select(v => q.QuantizeToLong(v)).ToList());
 
-            var distance = new Func<int, int, float>((id1, id2) => CosineDistance.NonOptimized(world.GetVector(id1), world.GetVector(id2)));
+            var distance = new Func<int, int, float>((id1, id2) => Metrics.Cosine(world.GetVector(id1), world.GetVector(id2)));
             var weights = world.GetLinks().SelectMany(pair => pair.Value.Select(id => distance(pair.Key, id)));
             var histogram = new Histogram(HistogramMode.SQRT, weights);
             histogram.Smooth();
 
-            int threshold = histogram.OTSU();
+            int threshold = histogram.CuttOff();
             var min = histogram.Bounds[threshold - 1];
             var max = histogram.Bounds[threshold];
             var R = (max + min) / 2;
@@ -40,7 +40,7 @@ namespace HNSWDemo.Tests
             var k = ((float)Height) / (float)histogram.Values.Max();
 
             var maxes = histogram.GetMaximums().ToDictionary(m => m.Index, m => m);
-            int threshold = histogram.OTSU();
+            int threshold = histogram.CuttOff();
 
             using (var bmp = new Bitmap(Width, Height))
             {

TestHNSW/HNSWDemo/Tests/QuantizeInsertTimeExplosionTest.cs

@@ -16,7 +16,7 @@ namespace HNSWDemo.Tests
         public void Run()
         {            
             var sw = new Stopwatch();
-            var world = new SmallWorld<long[]>(NSWOptions<long[]>.Create(6, 12, 100, 100, CosineDistance.NonOptimized));
+            var world = new SmallWorld<long[]>(NSWOptions<long[]>.Create(6, 12, 100, 100, Metrics.Cosine));
             var q = new Quantizator(-1f, 1f);
             for (int i = 0; i < IterationCount; i++)
             {

TestHNSW/HNSWDemo/Utils/QLVectorsDirectCompare.cs

@@ -42,7 +42,7 @@ namespace HNSWDemo.Utils
 
             // 1. Find R - bound between intra-cluster distances and out-of-cluster distances
             var histogram = new Histogram(HistogramMode.SQRT, links.Values);
-            int threshold = histogram.OTSU();
+            int threshold = histogram.CuttOff();
             var min = histogram.Bounds[threshold - 1];
             var max = histogram.Bounds[threshold];
             var R = (max + min) / 2;

TestHNSW/HNSWDemo/Utils/QVectorsDirectCompare.cs

@@ -42,7 +42,7 @@ namespace HNSWDemo.Utils
 
             // 1. Find R - bound between intra-cluster distances and out-of-cluster distances
             var histogram = new Histogram(HistogramMode.SQRT, links.Values);
-            int threshold = histogram.OTSU();
+            int threshold = histogram.CuttOff();
             var min = histogram.Bounds[threshold - 1];
             var max = histogram.Bounds[threshold];
             var R = (max + min) / 2;

TestHNSW/HNSWDemo/Utils/VectorsDirectCompare.cs

@@ -42,7 +42,7 @@ namespace HNSWDemo.Utils
 
             // 1. Find R - bound between intra-cluster distances and out-of-cluster distances
             var histogram = new Histogram(HistogramMode.SQRT, links.Values);
-            int threshold = histogram.OTSU();
+            int threshold = histogram.CuttOff();
             var min = histogram.Bounds[threshold - 1];
             var max = histogram.Bounds[threshold];
             var R = (max + min) / 2;

ZeroLevel.HNSW/Model/Histogram.cs

@@ -150,7 +150,7 @@ namespace ZeroLevel.HNSW
 
             return (float)sum;
         }
-
+        /*
         public int OTSU()
         {
             float p1, p2, p12;
@@ -172,15 +172,108 @@ namespace ZeroLevel.HNSW
                     threshold = k;
                 }
             }
-            /*
-            var local_max = Values[threshold];
-            for (int i = threshold + 1; i < Values.Length; i++)
+            return threshold;
+        }
+    */
+        /*
+1. Градиент V[I] - V[i-1]
+2. Походы окнами от 1 и выше, пока не сойдется к бимодальности
+3. Найти cutoff как минимум между пиками
+
+Modes =  0
+W = 1
+D = [V.count1]
+Maxes = []
+For I in [1..V.count] 
+    D= V[I] - V[i-1]
+do
+
+Modes =  0
+S = +1
+do
+    for wnd in D
+        if wnd.sum > 0 & S < 0
+            S = +1
+        Elif wnd.sum < 0 & S > 0
+            Maxes.push(wnd.maxindex)
+            Modes ++
+            S = -1
+W++
+while Modes > 2
+If Modes == 2
+Cutoff = Maxes[0]
+Min = V[I]
+For I=Maxes[0] to Maxes[1]
+    if V[I] < Min   
+        Min = V[I]
+        Cutoff = i         
+         */
+
+        public int CuttOff()
+        {
+            var grad = new int[Values.Length];
+            grad[0] = 0;
+            grad[1] = 0;
+            for (int k = 2; k < Values.Length; k++)
             {
-                
+                grad[k - 1] = Values[k] - Values[k - 1];
             }
-            */
-            return threshold;
+            var modes = 0;
+            var window = 0;
+            var sign = 1;
+            var sum = 0;
+            var max = 0;
+            var maxInd = 0;
+            var maxes = new List<int>();
+            do
+            {
+                maxes.Clear();
+                window++;
+                modes = 0;
+                sum = 0;
+                for (int i = 0; i < grad.Length; i += window)
+                {
+                    sum = grad[i];
+                    max = Values[i];
+                    maxInd = i;
+                    for (var w = 1; w < window && (i + w) < grad.Length; w++)
+                    {
+                        sum += grad[i + w];
+                        if (Values[i + w] > max)
+                        {
+                            max = Values[i + w];
+                            maxInd = i + w;
+                        }
+                    }
+                    if (sum > 0 && sign < 0)
+                    {
+                        sign = 1;
+                    }
+                    else if (sum < 0 && sign > 0)
+                    {
+                        modes++;
+                        maxes.Add(maxInd);
+                        sign = -1;
+                    }
+                }
+            } while (modes > 2);
+            if (modes == 2)
+            {
+                var cutoff = maxes[0];
+                var min = Values[cutoff];
+                for (int i = maxes[0] + 1; i < maxes[1]; i++)
+                {
+                    if (Values[i] < min)
+                    {
+                        cutoff = i;
+                        min = Values[i];
+                    }
+                }
+                return cutoff;
+            }
+            return -1;
         }
+
         #endregion
 
         static bool NumbersHasSameSign(int left, int right)

ZeroLevel.HNSW/Model/SearchContext.cs

@@ -5,20 +5,22 @@ using System.Runtime.CompilerServices;
 
 namespace ZeroLevel.HNSW
 {
-    public sealed class SearchContext
+    public enum Mode
     {
-        enum Mode
-        {
-            None,
-            ActiveCheck,
-            InactiveCheck,
-            ActiveInactiveCheck
-        }
+        None,
+        ActiveCheck,
+        InactiveCheck,
+        ActiveInactiveCheck
+    }
 
+    public sealed class SearchContext
+    {
         private HashSet<int> _activeNodes;
         private HashSet<int> _entryNodes;
         private Mode _mode;
 
+        public Mode NodeCheckMode => _mode;
+
         public SearchContext()
         {
             _mode = Mode.None;

ZeroLevel.HNSW/Services/AutomaticGraphClusterer.cs

@@ -22,7 +22,7 @@ namespace ZeroLevel.HNSW.Services
 
             // 1. Find R - bound between intra-cluster distances and out-of-cluster distances
             var histogram = new Histogram(HistogramMode.SQRT, links.Select(l => l.Distance));
-            int threshold = histogram.OTSU();
+            int threshold = histogram.CuttOff();
             var min = histogram.Bounds[threshold - 1];
             var max = histogram.Bounds[threshold];
             var R = (max + min) / 2;

ZeroLevel.HNSW/Services/Layer.cs

@@ -256,14 +256,80 @@ namespace ZeroLevel.HNSW
             return W;
         }
 
+        internal IEnumerable<(int, float)> KNearestAtLayer(int entryPointId, Func<int, float> targetCosts, int ef, SearchContext context)
+        {
+            int farthestId;
+            float farthestDistance;
+            var d = targetCosts(entryPointId);
+
+            var v = new VisitedBitSet(_vectors.Count, _options.M);
+            // * v ← ep // set of visited elements
+            v.Add(entryPointId);
+            // * C ← ep // set of candidates
+            var C = new MinHeap(ef);
+            C.Push((entryPointId, d));
+            // * W ← ep // dynamic list of found nearest neighbors
+            var W = new MaxHeap(ef + 1);
+            if (context.IsActiveNode(entryPointId))
+            {
+                W.Push((entryPointId, d));
+            }
+
+            // * while │C│ > 0
+            while (C.Count > 0)
+            {
+                // * c ← extract nearest element from C to q
+                var c = C.Pop();
+                // * f ← get furthest element from W to q
+                // * if distance(c, q) > distance(f, q)
+                if (W.TryPeek(out _, out farthestDistance) && c.Item2 > farthestDistance)
+                {
+                    // * break // all elements in W are evaluated
+                    break;
+                }
+
+                // * for each e ∈ neighbourhood(c) at layer lc // update C and W
+                foreach (var e in GetNeighbors(c.Item1))
+                {
+                    // * if e ∉ v
+                    if (!v.Contains(e))
+                    {
+                        // * v ← v ⋃ e
+                        v.Add(e);
+                        // * f ← get furthest element from W to q
+                        W.TryPeek(out farthestId, out farthestDistance);
+
+                        var eDistance = targetCosts(e);
+                        // * if distance(e, q) < distance(f, q) or │W│ < ef
+                        if (W.Count < ef || (farthestId >= 0 && eDistance < farthestDistance))
+                        {
+                            // * C ← C ⋃ e
+                            C.Push((e, eDistance));
+                            // * W ← W ⋃ e
+                            if (context.IsActiveNode(e))
+                            {
+                                W.Push((e, eDistance));
+                                if (W.Count > ef)
+                                {
+                                    W.Pop();
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+            C.Clear();
+            v.Clear();
+            return W;
+        }
+
         /// <summary>
         /// Algorithm 2
         /// </summary>
         /// <param name="q">query element</param>
         /// <param name="ep">enter points ep</param>
         /// <returns>Output: ef closest neighbors to q</returns>
-        /*
-        internal IEnumerable<(int, float)> KNearestAtLayer(int entryPointId, Func<int, float> targetCosts, int ef, SearchContext context)
+        internal IEnumerable<(int, float)> KNearestAвtLayer(int entryPointId, Func<int, float> targetCosts, int ef, SearchContext context)
         {
             int farthestId;
             float farthestDistance;
@@ -326,7 +392,6 @@ namespace ZeroLevel.HNSW
             v.Clear();
             return W;
         }
-        */
 
         /// <summary>
         /// Algorithm 2, modified for LookAlike

ZeroLevel.HNSW/Services/LinksSet.cs

@@ -75,7 +75,8 @@ namespace ZeroLevel.HNSW
         public void Serialize(IBinaryWriter writer)
         {
             writer.WriteBoolean(false); // true - set with weights
-            writer.WriteInt32(_set.Sum(pair => pair.Value.Count));
+            var count = _set.Sum(pair => pair.Value.Count);
+            writer.WriteInt32(count);
             foreach (var record in _set)
             {
                 var id = record.Key;
@@ -89,9 +90,9 @@ namespace ZeroLevel.HNSW
 
         public void Deserialize(IBinaryReader reader)
         {
-            if (reader.ReadBoolean() == false)
+            if (reader.ReadBoolean() != false)
             {
-                throw new InvalidOperationException("Incompatible data format. The set does not contain weights.");
+                throw new InvalidOperationException("Incompatible format");
             }
             _set.Clear();
             _set = null;

ZeroLevel.HNSW/SmallWorld.cs

@@ -40,6 +40,8 @@ namespace ZeroLevel.HNSW
         public SmallWorld(NSWOptions<TItem> options, Stream stream)
         {
             _options = options;
+            _layerLevelGenerator = new ProbabilityLayerNumberGenerator(_options.LayersCount, _options.M);
+            DistanceFunction = new Func<int, int, float>((id1, id2) => _options.Distance(_vectors[id1], _vectors[id2]));
             Deserialize(stream);
         }
 
@@ -57,7 +59,7 @@ namespace ZeroLevel.HNSW
                 yield return (pair.Item1, _vectors[pair.Item1], pair.Item2);
             }
         }
-        /*
+
         public IEnumerable<(int, TItem, float)> Search(TItem vector, int k, SearchContext context)
         {
             if (context == null)
@@ -76,6 +78,7 @@ namespace ZeroLevel.HNSW
             }
         }
 
+        /*
         public IEnumerable<(int, TItem, float)> Search(int k, SearchContext context)
         {
             if (context == null)
@@ -261,7 +264,7 @@ namespace ZeroLevel.HNSW
                 _lockGraph.ExitReadLock();
             }
         }
-        /*
+        
         private IEnumerable<(int, float)> KNearest(TItem q, int k, SearchContext context)
         {
             _lockGraph.EnterReadLock();
@@ -271,6 +274,7 @@ namespace ZeroLevel.HNSW
                 {
                     return Enumerable.Empty<(int, float)>();
                 }
+
                 int id;
                 float value;
                 var distance = new Func<int, float>(candidate => _options.Distance(q, _vectors[candidate]));
@@ -309,7 +313,7 @@ namespace ZeroLevel.HNSW
                 _lockGraph.ExitReadLock();
             }
         }
-        */
+        
 
         /*
         private IEnumerable<(int, float)> KNearest(int k, SearchContext context)

ZeroLevel.HNSW/Utils/CosineDistance.cs

@@ -27,141 +27,7 @@ namespace ZeroLevel.HNSW
         /// <param name="u">Left vector.</param>
         /// <param name="v">Right vector.</param>
         /// <returns>Cosine distance between u and v.</returns>
-        public static float NonOptimized(float[] u, float[] v)
-        {
-            if (u.Length != v.Length)
-            {
-                throw new ArgumentException("Vectors have non-matching dimensions");
-            }
-
-            float dot = 0.0f;
-            float nru = 0.0f;
-            float nrv = 0.0f;
-            for (int i = 0; i < u.Length; ++i)
-            {
-                dot += u[i] * v[i];
-                nru += u[i] * u[i];
-                nrv += v[i] * v[i];
-            }
-
-            var similarity = dot / (float)(Math.Sqrt(nru) * Math.Sqrt(nrv));
-            return 1 - similarity;
-        }
-
-        public static float NonOptimized(byte[] u, byte[] v)
-        {
-            if (u.Length != v.Length)
-            {
-                throw new ArgumentException("Vectors have non-matching dimensions");
-            }
-
-            float dot = 0.0f;
-            float nru = 0.0f;
-            float nrv = 0.0f;
-            for (int i = 0; i < u.Length; ++i)
-            {
-                dot += (float)(u[i] * v[i]);
-                nru += (float)(u[i] * u[i]);
-                nrv += (float)(v[i] * v[i]);
-            }
-
-            var similarity = dot / (float)(Math.Sqrt(nru) * Math.Sqrt(nrv));
-            return 1 - similarity;
-        }
-
-        public static float NonOptimized(int[] u, int[] v)
-        {
-            if (u.Length != v.Length)
-            {
-                throw new ArgumentException("Vectors have non-matching dimensions");
-            }
-
-            float dot = 0.0f;
-            float nru = 0.0f;
-            float nrv = 0.0f;
-            byte[] bu;
-            byte[] bv;
-
-            for (int i = 0; i < u.Length; ++i)
-            {
-                bu = BitConverter.GetBytes(u[i]);
-                bv = BitConverter.GetBytes(v[i]);
-
-                dot += (float)(bu[0] * bv[0]);
-                nru += (float)(bu[0] * bu[0]);
-                nrv += (float)(bv[0] * bv[0]);
-
-                dot += (float)(bu[1] * bv[1]);
-                nru += (float)(bu[1] * bu[1]);
-                nrv += (float)(bv[1] * bv[1]);
-
-                dot += (float)(bu[2] * bv[2]);
-                nru += (float)(bu[2] * bu[2]);
-                nrv += (float)(bv[2] * bv[2]);
-
-                dot += (float)(bu[3] * bv[3]);
-                nru += (float)(bu[3] * bu[3]);
-                nrv += (float)(bv[3] * bv[3]);
-            }
-
-            var similarity = dot / (float)(Math.Sqrt(nru) * Math.Sqrt(nrv));
-            return 1 - similarity;
-        }
-
-        public static float NonOptimized(long[] u, long[] v)
-        {
-            if (u.Length != v.Length)
-            {
-                throw new ArgumentException("Vectors have non-matching dimensions");
-            }
-
-            float dot = 0.0f;
-            float nru = 0.0f;
-            float nrv = 0.0f;
-            byte[] bu;
-            byte[] bv;
-
-            for (int i = 0; i < u.Length; ++i)
-            {
-                bu = BitConverter.GetBytes(u[i]);
-                bv = BitConverter.GetBytes(v[i]);
-
-                dot += (float)(bu[0] * bv[0]);
-                nru += (float)(bu[0] * bu[0]);
-                nrv += (float)(bv[0] * bv[0]);
-
-                dot += (float)(bu[1] * bv[1]);
-                nru += (float)(bu[1] * bu[1]);
-                nrv += (float)(bv[1] * bv[1]);
-
-                dot += (float)(bu[2] * bv[2]);
-                nru += (float)(bu[2] * bu[2]);
-                nrv += (float)(bv[2] * bv[2]);
-
-                dot += (float)(bu[3] * bv[3]);
-                nru += (float)(bu[3] * bu[3]);
-                nrv += (float)(bv[3] * bv[3]);
-
-                dot += (float)(bu[4] * bv[4]);
-                nru += (float)(bu[4] * bu[4]);
-                nrv += (float)(bv[4] * bv[4]);
-
-                dot += (float)(bu[5] * bv[5]);
-                nru += (float)(bu[5] * bu[5]);
-                nrv += (float)(bv[5] * bv[5]);
-
-                dot += (float)(bu[6] * bv[6]);
-                nru += (float)(bu[6] * bu[6]);
-                nrv += (float)(bv[6] * bv[6]);
-
-                dot += (float)(bu[7] * bv[7]);
-                nru += (float)(bu[7] * bu[7]);
-                nrv += (float)(bv[7] * bv[7]);
-            }
-
-            var similarity = dot / (float)(Math.Sqrt(nru) * Math.Sqrt(nrv));
-            return 1 - similarity;
-        }
+        
 
         /// <summary>
         /// Calculates cosine distance with assumption that u and v are unit vectors.

ZeroLevel.HNSW/Utils/EuclidDistance.cs

@@ -1,83 +0,0 @@
-using System;
-
-namespace ZeroLevel.HNSW
-{
-    public static class Metrics
-    {
-        /// <summary>
-        /// The taxicab metric is also known as rectilinear distance, 
-        /// L1 distance or L1 norm, city block distance, Manhattan distance, 
-        /// or Manhattan length, with the corresponding variations in the name of the geometry. 
-        /// It represents the distance between points in a city road grid. 
-        /// It examines the absolute differences between the coordinates of a pair of objects.
-        /// </summary>
-        public static float L1Manhattan(float[] v1, float[] v2)
-        {
-            float res = 0;
-            for (int i = 0; i < v1.Length; i++)
-            {
-                float t = v1[i] - v2[i];
-                res += t * t;
-            }
-            return (res);
-        }
-
-        /// <summary>
-        /// Euclidean distance is the most common use of distance. 
-        /// Euclidean distance, or simply 'distance', 
-        /// examines the root of square differences between the coordinates of a pair of objects. 
-        /// This is most generally known as the Pythagorean theorem.
-        /// </summary>
-        public static float L2Euclidean(float[] v1, float[] v2)
-        {
-            float res = 0;
-            for (int i = 0; i < v1.Length; i++)
-            {
-                float t = v1[i] - v2[i];
-                res += t * t;
-            }
-            return (float)Math.Sqrt(res);
-        }
-
-        /// <summary>
-        /// The general metric for distance is the Minkowski distance. 
-        /// When lambda is equal to 1, it becomes the city block distance (L1), 
-        /// and when lambda is equal to 2, it becomes the Euclidean distance (L2). 
-        /// The special case is when lambda is equal to infinity (taking a limit), 
-        /// where it is considered as the Chebyshev distance.
-        /// </summary>
-        public static float MinkowskiDistance(float[] v1, float[] v2, int order)
-        {
-            int count = v1.Length;
-            double sum = 0.0;
-            for (int i = 0; i < count; i++)
-            {
-                sum = sum + Math.Pow(Math.Abs(v1[i] - v2[i]), order);
-            }
-            return (float)Math.Pow(sum, (1 / order));
-        }
-
-        /// <summary>
-        /// Chebyshev distance is also called the Maximum value distance, 
-        /// defined on a vector space where the distance between two vectors is 
-        /// the greatest of their differences along any coordinate dimension. 
-        /// In other words, it examines the absolute magnitude of the differences 
-        /// between the coordinates of a pair of objects.
-        /// </summary>
-        public static double ChebyshevDistance(float[] v1, float[] v2)
-        {
-            int count = v1.Length;
-            float max = float.MinValue;
-            float c;
-            for (int i = 0; i < count; i++)
-            {
-                c = Math.Abs(v1[i] - v2[i]);
-                if (c > max)
-                {
-                    max = c;
-                }
-            }
-            return max;
-        }
-    }
-}

ZeroLevel.HNSW/Utils/Metrics.cs

@@ -0,0 +1,367 @@
+using System;
+using System.Linq;
+
+namespace ZeroLevel.HNSW
+{
+    public static class Metrics
+    {
+        /// <summary>
+        /// The taxicab metric is also known as rectilinear distance, 
+        /// L1 distance or L1 norm, city block distance, Manhattan distance, 
+        /// or Manhattan length, with the corresponding variations in the name of the geometry. 
+        /// It represents the distance between points in a city road grid. 
+        /// It examines the absolute differences between the coordinates of a pair of objects.
+        /// </summary>
+        public static float L1Manhattan(float[] v1, float[] v2)
+        {
+            float res = 0;
+            for (int i = 0; i < v1.Length; i++)
+            {
+                float t = v1[i] - v2[i];
+                res += t * t;
+            }
+            return (res);
+        }
+
+        public static float L1Manhattan(byte[] v1, byte[] v2)
+        {
+            float res = 0;
+            for (int i = 0; i < v1.Length; i++)
+            {
+                float t = v1[i] - v2[i];
+                res += t * t;
+            }
+            return (res);
+        }
+
+        public static float L1Manhattan(int[] v1, int[] v2)
+        {
+            float res = 0;
+            for (int i = 0; i < v1.Length; i++)
+            {
+                float t = v1[i] - v2[i];
+                res += t * t;
+            }
+            return (res);
+        }
+
+        public static float L1Manhattan(long[] v1, long[] v2)
+        {
+            float res = 0;
+            for (int i = 0; i < v1.Length; i++)
+            {
+                float t = v1[i] - v2[i];
+                res += t * t;
+            }
+            return (res);
+        }
+
+        /// <summary>
+        /// Euclidean distance is the most common use of distance. 
+        /// Euclidean distance, or simply 'distance', 
+        /// examines the root of square differences between the coordinates of a pair of objects. 
+        /// This is most generally known as the Pythagorean theorem.
+        /// </summary>
+        public static float L2Euclidean(float[] v1, float[] v2)
+        {
+            float res = 0;
+            for (int i = 0; i < v1.Length; i++)
+            {
+                float t = v1[i] - v2[i];
+                res += t * t;
+            }
+            return (float)Math.Sqrt(res);
+        }
+
+        public static float L2Euclidean(byte[] v1, byte[] v2)
+        {
+            float res = 0;
+            for (int i = 0; i < v1.Length; i++)
+            {
+                float t = v1[i] - v2[i];
+                res += t * t;
+            }
+            return (float)Math.Sqrt(res);
+        }
+
+        public static float L2Euclidean(int[] v1, int[] v2)
+        {
+            float res = 0;
+            for (int i = 0; i < v1.Length; i++)
+            {
+                float t = v1[i] - v2[i];
+                res += t * t;
+            }
+            return (float)Math.Sqrt(res);
+        }
+
+        public static float L2Euclidean(long[] v1, long[] v2)
+        {
+            float res = 0;
+            for (int i = 0; i < v1.Length; i++)
+            {
+                float t = v1[i] - v2[i];
+                res += t * t;
+            }
+            return (float)Math.Sqrt(res);
+        }
+
+        /// <summary>
+        /// The general metric for distance is the Minkowski distance. 
+        /// When lambda is equal to 1, it becomes the city block distance (L1), 
+        /// and when lambda is equal to 2, it becomes the Euclidean distance (L2). 
+        /// The special case is when lambda is equal to infinity (taking a limit), 
+        /// where it is considered as the Chebyshev distance.
+        /// </summary>
+        public static float MinkowskiDistance(float[] v1, float[] v2, int order)
+        {
+            int count = v1.Length;
+            double sum = 0.0;
+            for (int i = 0; i < count; i++)
+            {
+                sum = sum + Math.Pow(Math.Abs(v1[i] - v2[i]), order);
+            }
+            return (float)Math.Pow(sum, (1 / order));
+        }
+
+        public static float MinkowskiDistance(byte[] v1, byte[] v2, int order)
+        {
+            int count = v1.Length;
+            double sum = 0.0;
+            for (int i = 0; i < count; i++)
+            {
+                sum = sum + Math.Pow(Math.Abs(v1[i] - v2[i]), order);
+            }
+            return (float)Math.Pow(sum, (1 / order));
+        }
+
+        public static float MinkowskiDistance(int[] v1, int[] v2, int order)
+        {
+            int count = v1.Length;
+            double sum = 0.0;
+            for (int i = 0; i < count; i++)
+            {
+                sum = sum + Math.Pow(Math.Abs(v1[i] - v2[i]), order);
+            }
+            return (float)Math.Pow(sum, (1 / order));
+        }
+
+        public static float MinkowskiDistance(long[] v1, long[] v2, int order)
+        {
+            int count = v1.Length;
+            double sum = 0.0;
+            for (int i = 0; i < count; i++)
+            {
+                sum = sum + Math.Pow(Math.Abs(v1[i] - v2[i]), order);
+            }
+            return (float)Math.Pow(sum, (1 / order));
+        }
+
+        /// <summary>
+        /// Chebyshev distance is also called the Maximum value distance, 
+        /// defined on a vector space where the distance between two vectors is 
+        /// the greatest of their differences along any coordinate dimension. 
+        /// In other words, it examines the absolute magnitude of the differences 
+        /// between the coordinates of a pair of objects.
+        /// </summary>
+        public static double ChebyshevDistance(float[] v1, float[] v2)
+        {
+            int count = v1.Length;
+            float max = float.MinValue;
+            float c;
+            for (int i = 0; i < count; i++)
+            {
+                c = Math.Abs(v1[i] - v2[i]);
+                if (c > max)
+                {
+                    max = c;
+                }
+            }
+            return max;
+        }
+
+        public static double ChebyshevDistance(byte[] v1, byte[] v2)
+        {
+            int count = v1.Length;
+            float max = float.MinValue;
+            float c;
+            for (int i = 0; i < count; i++)
+            {
+                c = Math.Abs(v1[i] - v2[i]);
+                if (c > max)
+                {
+                    max = c;
+                }
+            }
+            return max;
+        }
+
+        public static double ChebyshevDistance(int[] v1, int[] v2)
+        {
+            int count = v1.Length;
+            float max = float.MinValue;
+            float c;
+            for (int i = 0; i < count; i++)
+            {
+                c = Math.Abs(v1[i] - v2[i]);
+                if (c > max)
+                {
+                    max = c;
+                }
+            }
+            return max;
+        }
+
+        public static double ChebyshevDistance(long[] v1, long[] v2)
+        {
+            int count = v1.Length;
+            float max = float.MinValue;
+            float c;
+            for (int i = 0; i < count; i++)
+            {
+                c = Math.Abs(v1[i] - v2[i]);
+                if (c > max)
+                {
+                    max = c;
+                }
+            }
+            return max;
+        }
+
+        public static float Cosine(float[] u, float[] v)
+        {
+            if (u.Length != v.Length)
+            {
+                throw new ArgumentException("Vectors have non-matching dimensions");
+            }
+
+            float dot = 0.0f;
+            float nru = 0.0f;
+            float nrv = 0.0f;
+            for (int i = 0; i < u.Length; ++i)
+            {
+                dot += u[i] * v[i];
+                nru += u[i] * u[i];
+                nrv += v[i] * v[i];
+            }
+
+            var similarity = dot / (float)(Math.Sqrt(nru) * Math.Sqrt(nrv));
+            return 1 - similarity;
+        }
+
+        public static float Cosine(byte[] u, byte[] v)
+        {
+            if (u.Length != v.Length)
+            {
+                throw new ArgumentException("Vectors have non-matching dimensions");
+            }
+
+            float dot = 0.0f;
+            float nru = 0.0f;
+            float nrv = 0.0f;
+            for (int i = 0; i < u.Length; ++i)
+            {
+                dot += (float)(u[i] * v[i]);
+                nru += (float)(u[i] * u[i]);
+                nrv += (float)(v[i] * v[i]);
+            }
+
+            var similarity = dot / (float)(Math.Sqrt(nru) * Math.Sqrt(nrv));
+            return 1 - similarity;
+        }
+
+        public static float Cosine(int[] u, int[] v)
+        {
+            if (u.Length != v.Length)
+            {
+                throw new ArgumentException("Vectors have non-matching dimensions");
+            }
+
+            float dot = 0.0f;
+            float nru = 0.0f;
+            float nrv = 0.0f;
+            byte[] bu;
+            byte[] bv;
+
+            for (int i = 0; i < u.Length; ++i)
+            {
+                bu = BitConverter.GetBytes(u[i]);
+                bv = BitConverter.GetBytes(v[i]);
+
+                dot += (float)(bu[0] * bv[0]);
+                nru += (float)(bu[0] * bu[0]);
+                nrv += (float)(bv[0] * bv[0]);
+
+                dot += (float)(bu[1] * bv[1]);
+                nru += (float)(bu[1] * bu[1]);
+                nrv += (float)(bv[1] * bv[1]);
+
+                dot += (float)(bu[2] * bv[2]);
+                nru += (float)(bu[2] * bu[2]);
+                nrv += (float)(bv[2] * bv[2]);
+
+                dot += (float)(bu[3] * bv[3]);
+                nru += (float)(bu[3] * bu[3]);
+                nrv += (float)(bv[3] * bv[3]);
+            }
+
+            var similarity = dot / (float)(Math.Sqrt(nru) * Math.Sqrt(nrv));
+            return 1 - similarity;
+        }
+
+        public static float Cosine(long[] u, long[] v)
+        {
+            if (u.Length != v.Length)
+            {
+                throw new ArgumentException("Vectors have non-matching dimensions");
+            }
+
+            float dot = 0.0f;
+            float nru = 0.0f;
+            float nrv = 0.0f;
+            byte[] bu;
+            byte[] bv;
+
+            for (int i = 0; i < u.Length; ++i)
+            {
+                bu = BitConverter.GetBytes(u[i]);
+                bv = BitConverter.GetBytes(v[i]);
+
+                dot += (float)(bu[0] * bv[0]);
+                nru += (float)(bu[0] * bu[0]);
+                nrv += (float)(bv[0] * bv[0]);
+
+                dot += (float)(bu[1] * bv[1]);
+                nru += (float)(bu[1] * bu[1]);
+                nrv += (float)(bv[1] * bv[1]);
+
+                dot += (float)(bu[2] * bv[2]);
+                nru += (float)(bu[2] * bu[2]);
+                nrv += (float)(bv[2] * bv[2]);
+
+                dot += (float)(bu[3] * bv[3]);
+                nru += (float)(bu[3] * bu[3]);
+                nrv += (float)(bv[3] * bv[3]);
+
+                dot += (float)(bu[4] * bv[4]);
+                nru += (float)(bu[4] * bu[4]);
+                nrv += (float)(bv[4] * bv[4]);
+
+                dot += (float)(bu[5] * bv[5]);
+                nru += (float)(bu[5] * bu[5]);
+                nrv += (float)(bv[5] * bv[5]);
+
+                dot += (float)(bu[6] * bv[6]);
+                nru += (float)(bu[6] * bu[6]);
+                nrv += (float)(bv[6] * bv[6]);
+
+                dot += (float)(bu[7] * bv[7]);
+                nru += (float)(bu[7] * bu[7]);
+                nrv += (float)(bv[7] * bv[7]);
+            }
+
+            var similarity = dot / (float)(Math.Sqrt(nru) * Math.Sqrt(nrv));
+            return 1 - similarity;
+        }
+    }
+}