I have a question on one of the previous Stack Overflow post # Knight's Shortest Path on Chessboard
I understand the reply on 'ok, it's a graph question, and its sparse matrix is like':
(a1,b3)=1,
(a1,c2)=1,
.....
which describe existing edges. However i still don't know what Data Structure of this Graph should looks like (is it an adjacency matrix? stated as 'sparse matrix' above, or something else?), so that it can be readily used by Dijkstra's algorithm.
http://en.wikipedia.org/wiki/Dijkstra%27s_algorithm.
From the algorithm description, it looks convenient if the graph data structure is a set of vertex, with neighbor vertex information available. But how do we achieve this?
How can I write out a sample data structure for this graph? I am seeking an understanding of how it can be linked conveniently to Dijkstra's algorithm.
The graph is very sparse (64 vertices, each vertex has at most 8 edges) thus an adjacency matrix is a waste IMO.
A better structure for this will be adjacency list:
v1->v2,v3,v4,v5
v2->v1,...
...
The idea is indeed to hold a Set<Vertex>, and for the Vertex type to have a field: List<Vertex> neighbors, which will contain all the vertex's neighboring vertices.
There is no need in this case for some additional weight information - since the graph is unweighted.
Also - Dijkstra's algorithm is redundant in here. Again, the graph is unweighted - so a simpler (to program and understand) and faster (run time) algorithm to find the shortest path is a BFS for unweighted graphs.
Since there are only 64 tiles, you can conveniently put the adjacency matrix in an array of 64 integers of 64 bits each. Sure it's sparse, but it's also tiny, so the waste, if it exists at all (pointers are pretty big compared to single bits), will be small too.
Extracting a list of indices from a bitvector is also especially easy when it's sparse, but you don't even need that - you could let the front be a queue of bitvectors instead, and the "already visited" set could be a single bitvector.
edit: ok actually you may still need it if you use that trick, but then it remains that it just takes a couple of fast operations such as bitscan and x &= x -1.
Related
Problem
I have a list of approximatly 200000 nodes that represent lat/lon position in a city and I have to compute the Minimum Spanning Tree. I know that I need to use Prim algorithm but first of all I need a connected graph. (We can assume that those nodes are in a Euclidian plan)
To build this connected graph I thought firstly to compute the complete graph but (205000*(205000-1)/2 is around 19 billions edges and I can't handle that.
Options
Then I came across to Delaunay triangulation: with the fact that if I build this "Delauney graph", it contains a sub graph that is the Minimum Spanning Tree according and I have a total of around 600000 edges according to Wikipedia [..]it has at most 3n-6 edges. So it may be a good starting point for a Minimum Spanning Tree algorithm.
Another options is to build an approximately connected graph but with that I will maybe miss important edges that will influence my Minimum Spanning Tree.
My question
Is Delaunay a reliable solution in this case? If so, is there any other reliable solution than delaunay triangulation to this problem ?
Further information: this problem has to be solved in C.
The Delaunay triangulation of a point set is always a superset of the EMST of these points. So it is absolutely "reliable"*. And recommended, as it has a size linear in the number of points and can be efficiently built.
*When there are cocircular point quadruples, neither the triangulation nor the EMST are uniquely defined, but this is usually harmless.
There's a big question here of what libraries you have access to and how much you trust yourself as a coder. (I'm assuming the fact that you're new on SO should not be taken as a measure of your overall experience as a programmer - if it is, well, RIP.)
If we assume you don't have access to Delaunay and can't implement it yourself, minimum spanning trees algorithms that pre-suppose a graph aren't necessarily off limits to you. You can have the complete graph conceptually but not actually. Kruskal's algorithm, for instance, assumes you have a sorted list of all edges in your graph; most of your edges will not be near the minimum, and you do not have to compare all n^2 to find the minimum.
You can find minimum edges quickly by estimations that give you a reduced set, then refinement. For instance, if you divide your graph into a 100*100 grid, for any point p in the graph, points in the same grid square as p are guaranteed to be closer than points three or more squares away. This gives a much smaller set of points you have to compare to safely know you've found the closest.
It still won't be easy, but that might be easier than Delaunay.
I understand there are 3 common ways to represent graphs:
Adjacency Matrix
Adjacency List
Edge list
That said, problems I’ve solved on LeetCode often use matrices and the solution requires DFS or BFS. For example, given the matrix below, find if a target string exists when you go left, right, up, and down (but not diagonal).
[
[‘a’,‘p’,’p’],
[‘e’,’a’,’l’],
[‘r’,’t’,’e’]
]
This required a DFS approach. Is this because this matrix represents a graph or does DFS and BFS apply to matrices too and not just trees and graphs?
Are DFS and BFS always/mostly used against matrices (2D arrays) in implementation or are there cases where it’s used against a Graph class?
Graph algorithms are often used to solve problems on data structures that do not explicitly represent a graph, like your matrix. The graph is not in the data. It's in your head when you solve the problem. For example, "If I think of this as a graph, the I can solve the problem with DFS or BFS". Then you write a BFS or DFS algorithm, mapping the traversal operations to whatever is equivalent in the data structure you do have.
This is called operating on the "implicit graph": https://en.wikipedia.org/wiki/Implicit_graph
If you actually made a graph data structure out of your data -- an explicit graph -- then you could write a BFS or DFS on that directly, but it's often unnecessary and in fact wasteful.
As an exercise I have to build a satnav system which plans the shortest and fastest routes from location to location. It has to be as fast as I can possibly make it without using too much memory.
I am having trouble deciding which structure to use to represent the graph. I understand that a matrix is better for dense graphs and that a list would be better for sparse graphs. I'm leaning more towards using a list as I'm assuming that adding vertexes will be the most taxing part of this program.
I just want get some of your guys' opinions. If I were to look at a typical road-map as a graph with various locations being nodes and the roads being edges. Would you consider it to be sparse or dense? Which structure seems better in this scenario?
I would go for lists because its only 1 time investment. The good thing about it is that it is able to iterate over all the adjacent vertices faster than matrix which is an important and most frequent steps in most of the shortest path algorithms.
So where matrix is O(N) adjacency list goes only O(k) where k is number of adjacent vertices.
I have an graph with the following attributes:
Undirected
Not weighted
Each vertex has a minimum of 2 and maximum of 6 edges connected to it.
Vertex count will be < 100
Graph is static and no vertices/edges can be added/removed or edited.
I'm looking for paths between a random subset of the vertices (at least 2). The paths should simple paths that only go through any vertex once.
My end goal is to have a set of routes so that you can start at one of the subset vertices and reach any of the other subset vertices. Its not necessary to pass through all the subset nodes when following a route.
All of the algorithms I've found (Dijkstra,Depth first search etc.) seem to be dealing with paths between two vertices and shortest paths.
Is there a known algorithm that will give me all the paths (I suppose these are subgraphs) that connect these subset of vertices?
edit:
I've created a (warning! programmer art) animated gif to illustrate what i'm trying to achieve: http://imgur.com/mGVlX.gif
There are two stages pre-process and runtime.
pre-process
I have a graph and a subset of the vertices (blue nodes)
I generate all the possible routes that connect all the blue nodes
runtime
I can start at any blue node select any of the generated routes and travel along it to reach my destination blue node.
So my task is more about creating all of the subgraphs (routes) that connect all blue nodes, rather than creating a path from A->B.
There are so many ways to approach this and in order not confuse things, here's a separate answer that's addressing the description of your core problem:
Finding ALL possible subgraphs that connect your blue vertices is probably overkill if you're only going to use one at a time anyway. I would rather use an algorithm that finds a single one, but randomly (so not any shortest path algorithm or such, since it will always be the same).
If you want to save one of these subgraphs, you simply have to save the seed you used for the random number generator and you'll be able to produce the same subgraph again.
Also, if you really want to find a bunch of subgraphs, a randomized algorithm is still a good choice since you can run it several times with different seeds.
The only real downside is that you will never know if you've found every single one of the possible subgraphs, but it doesn't really sound like that's a requirement for your application.
So, on to the algorithm: Depending on the properties of your graph(s), the optimal algorithm might vary, but you could always start of with a simple random walk, starting from one blue node, walking to another blue one (while making sure you're not walking in your own old footsteps). Then choose a random node on that path and start walking to the next blue from there, and so on.
For certain graphs, this has very bad worst-case complexity but might suffice for your case. There are of course more intelligent ways to find random paths, but I'd start out easy and see if it's good enough. As they say, premature optimization is evil ;)
A simple breadth-first search will give you the shortest paths from one source vertex to all other vertices. So you can perform a BFS starting from each vertex in the subset you're interested in, to get the distances to all other vertices.
Note that in some places, BFS will be described as giving the path between a pair of vertices, but this is not necessary: You can keep running it until it has visited all nodes in the graph.
This algorithm is similar to Johnson's algorithm, but greatly simplified thanks to the fact that your graph is unweighted.
Time complexity: Since there is a constant number of edges per vertex, each BFS will take O(n), and the total will take O(kn), where n is the number of vertices and k is the size of the subset. As a comparison, the Floyd-Warshall algorithm will take O(n^3).
What you're searching for is (if I understand it correctly) not really all paths, but rather all spanning trees. Read the wikipedia article about spanning trees here to determine if those are what you're looking for. If it is, there is a paper you would probably want to read:
Gabow, Harold N.; Myers, Eugene W. (1978). "Finding All Spanning Trees of Directed and Undirected Graphs". SIAM J. Comput. 7 (280).
Is there an algorithm or heuristics for graph isomorphism?
Corollary: A graph can be represented in different different drawings.
What s the best approach to find different drawing of a graph?
It is a hell of a problem.
In general, the basic idea is to simplify the graph into a canonical form, and then perform comparison of canonical forms. Spanning trees are generated with this objective, but spanning trees are not unique, so you need to have a canonical way to create them.
After you have canonical forms, you can perform isomorphism comparison (relatively) easy, but that's just the start, since non-isomorphic graphs can have the same spanning tree. (e.g. think about a spanning tree T and a single addition of an edge to it to create T'. These two graphs are not isomorph, but they have the same spanning tree).
Other techniques involve comparing descriptors (e.g. number of nodes, number of edges), which can produce false positive in general.
I suggest you to start with the wiki page about the graph isomorphism problem. I also have a book to suggest: "Graph Theory and its applications". It's a tome, but worth every page.
As from you corollary, every possible spatial distribution of a given graph's vertexes is an isomorph. So two isomorph graphs have the same topology and they are, in the end, the same graph, from the topological point of view. Another matter is, for example, to find those isomorph structures enjoying particular properties (e.g. with non crossing edges, if exists), and that depends on the properties you want.
One of the best algorithms out there for finding graph isomorphisms is VF2.
I've written a high-level overview of VF2 as applied to chemistry - where it is used extensively. The post touches on the differences between VF2 and Ullmann. There is also a from-scratch implementation of VF2 written in Java that might be helpful.
A very similar problem - graph automorphism - can be solved by saucy, which is available in source code. This finds all symmetries of a graph. If you have two graphs, join them into one and any isomorphism can be discovered as an automorphism of the join.
Disclaimer: I am one of co-authors of saucy.
There are algorithms to do this -- however, I have not had cause to seriously investigate them as of yet. I believe Donald Knuth is either writing or has written on this subject in his Art of Computing series during his second pass at (re)writing them.
As for a simple way to do something that might work in practice on small graphs, I would recommend counting degrees, then for each vertex, also note the set of degrees for those vertexes that are adjacent. This will then give you a set of potential vertex isomorphisms for each point. Then just try all those (via brute force, but choosing the vertexes in increasing order of potential vertex isomorphism sets) from this restricted set. Intuitively, most graph isomorphism can be practically computed this way, though clearly there would be degenerate cases that might take a long time.
I recently came across the following paper : http://arxiv.org/abs/0711.2010
This paper proposes "A Polynomial Time Algorithm for Graph Isomorphism"
My project - Griso - at sf.net: http://sourceforge.net/projects/griso/ with this description:
Griso is a graph isomorphism testing utility written in C++. It is based on my own POLYNOMIAL-TIME (in this point the salt of the project) algorithm. See Griso's sample input/output on http://funkybee.narod.ru/graphs.htm page.
nauty and Traces
nauty and Traces are programs for computing automorphism groups of graphs and digraphs [*]. They can also produce a canonical label. They are written in a portable subset of C, and run on a considerable number of different systems.
AutGroupGraph command in GRAPE's package of GAP.
bliss: another symmetry and canonical labeling program.
conauto: a graph ismorphism package.
As for heuristics: i've been fantasising about a modified Ullmann's algorithm, where you don't only use breadth first search but mix it with depth first search the way, that first you use breadth first search intensively, than you set a limit for breadth analysis and go deeper after checking a few neighbours, and you lower the breadh every step at some amount. This is practically how i find my way on a map: first locate myself with breadth first search, then search the route with depth first search - largely, and this is the best evolution of my brain has ever invented. :) On the long term some intelligence may be added for increasing breadth first search neighbour count at critical vertexes - for example where there are a large number of neighbouring vertexes with the same edge count. Like checking your actual route sometimes with the car (without a gps).
I've found out that the algorithm belongs in the category of k-dimension Weisfeiler-Lehman algorithms, and it fails with regular graphs. For more here:
http://dabacon.org/pontiff/?p=4148
Original post follows:
I've worked on the problem to find isomorphic graphs in a database of graphs (containing chemical compositions).
In brief, the algorithm creates a hash of a graph using the power iteration method. There might be false positive hash collisions but the probability of that is exceedingly small (i didn't had any such collisions with tens of thousands of graphs).
The way the algorithm works is this:
Do N (where N is the radius of the graph) iterations. On each iteration and for each node:
Sort the hashes (from the previous step) of the node's neighbors
Hash the concatenated sorted hashes
Replace node's hash with newly computed hash
On the first step, a node's hash is affected by the direct neighbors of it. On the second step, a node's hash is affected by the neighborhood 2-hops away from it. On the Nth step a node's hash will be affected by the neighborhood N-hops around it. So you only need to continue running the Powerhash for N = graph_radius steps. In the end, the graph center node's hash will have been affected by the whole graph.
To produce the final hash, sort the final step's node hashes and concatenate them together. After that, you can compare the final hashes to find if two graphs are isomorphic. If you have labels, then add them (on the first step) in the internal hashes that you calculate for each node.
There is more background here:
https://plus.google.com/114866592715069940152/posts/fmBFhjhQcZF
You can find the source code of it here:
https://github.com/madgik/madis/blob/master/src/functions/aggregate/graph.py