program.cs

using System;
using System.Collections.Generic;
using System.Diagnostics;
using System.Linq;

namespace Test
{
	class Program
	{
		static Random rand = new Random();
		
		public static int[] GetArray()
		{
			List<int> res = new List<int>();
			for(int i = 0 ; i < rand.Next(1, 4) ; i++)
			{
				res.Add(rand.Next(1, 100));
			}
			
			return res.ToArray();
		}		
		
		public static void Main()
		{
			var items = Enumerable.Range(0, 5000)
				.Select(x => new { Name = x.ToString(), Values = GetArray() })
				.ToList();
			
			Stopwatch sw = Stopwatch.StartNew();
			sw.Start();
			 
			var tuples = items 
				.SelectMany(x => x.Values, (x, y) => new { x.Name, Value = y })
				.ToList();	
			
			var result = tuples.Join(tuples, 
					   x => x.Value, 
					   x => x.Value, 
					   (x, y) => new { NameA = x.Name, NameB = y.Name })
				.Where(x => x.NameA != x.NameB)
				.Distinct()
				.GroupBy(x => x.NameA, x => x.NameB, (x, y) => new { x, y = y.ToList() })
				.ToList();
						
			sw.Stop();
			Console.WriteLine(sw.Elapsed);
			
			sw = Stopwatch.StartNew();
			
			var hashed = items
				.Select(i => new { i.Name, Values = i.Values.ToHashSet() })
				.ToList();
			
			var overlaps = hashed.Select(h1 => new
			{
				h1.Name,
				Overlaps = hashed
					.Where(h2 => h2.Name != h1.Name && h2.Values.Overlaps(h1.Values))
					.Select(h => h.Name)
					.ToList()
			}).ToList();
			
			Console.WriteLine(sw.Elapsed);
			Console.ReadLine();
		}
	}
}