Given an undirected graph, I want to generate all subgraphs which are trees of size N, where size refers to the number of edges in the tree.
I am aware that there are a lot of them (exponentially many at least for graphs with constant connectivity) - but that's fine, as I believe the number of nodes and edges makes this tractable for at least smallish values of N (say 10 or less).
The algorithm should be memory-efficient - that is, it shouldn't need to have all graphs or some large subset of them in memory at once, since this is likely to exceed available memory even for relatively small graphs. So something like DFS is desirable.
Here's what I'm thinking, in pseudo-code, given the starting graph graph and desired length N:
Pick any arbitrary node, root as a starting point and call alltrees(graph, N, root)
alltrees(graph, N, root)
given that node root has degree M, find all M-tuples with integer, non-negative values whose values sum to N (for example, for 3 children and N=2, you have (0,0,2), (0,2,0), (2,0,0), (0,1,1), (1,0,1), (1,1,0), I think)
for each tuple (X1, X2, ... XM) above
create a subgraph "current" initially empty
for each integer Xi in X1...XM (the current tuple)
if Xi is nonzero
add edge i incident on root to the current tree
add alltrees(graph with root removed, N-1, node adjacent to root along edge i)
add the current tree to the set of all trees
return the set of all trees
This finds only trees containing the chosen initial root, so now remove this node and call alltrees(graph with root removed, N, new arbitrarily chosen root), and repeat until the size of the remaining graph < N (since no trees of the required size will exist).
I forgot also that each visited node (each root for some call of alltrees) needs to be marked, and the set of children considered above should only be the adjacent unmarked children. I guess we need to account for the case where no unmarked children exist, yet depth > 0, this means that this "branch" failed to reach the required depth, and cannot form part of the solution set (so the whole inner loop associated with that tuple can be aborted).
So will this work? Any major flaws? Any simpler/known/canonical way to do this?
One issue with the algorithm outlined above is that it doesn't satisfy the memory-efficient requirement, as the recursion will hold large sets of trees in memory.
This needs an amount of memory that is proportional to what is required to store the graph. It will return every subgraph that is a tree of the desired size exactly once.
Keep in mind that I just typed it into here. There could be bugs. But the idea is that you walk the nodes one at a time, for each node searching for all trees that include that node, but none of the nodes that were searched previously. (Because those have already been exhausted.) That inner search is done recursively by listing edges to nodes in the tree, and for each edge deciding whether or not to include it in your tree. (If it would make a cycle, or add an exhausted node, then you can't include that edge.) If you include it your tree then the used nodes grow, and you have new possible edges to add to your search.
To reduce memory use, the edges that are left to look at is manipulated in place by all of the levels of the recursive call rather than the more obvious approach of duplicating that data at each level. If that list was copied, your total memory usage would get up to the size of the tree times the number of edges in the graph.
def find_all_trees(graph, tree_length):
exhausted_node = set([])
used_node = set([])
used_edge = set([])
current_edge_groups = []
def finish_all_trees(remaining_length, edge_group, edge_position):
while edge_group < len(current_edge_groups):
edges = current_edge_groups[edge_group]
while edge_position < len(edges):
edge = edges[edge_position]
edge_position += 1
(node1, node2) = nodes(edge)
if node1 in exhausted_node or node2 in exhausted_node:
continue
node = node1
if node1 in used_node:
if node2 in used_node:
continue
else:
node = node2
used_node.add(node)
used_edge.add(edge)
edge_groups.append(neighbors(graph, node))
if 1 == remaining_length:
yield build_tree(graph, used_node, used_edge)
else:
for tree in finish_all_trees(remaining_length -1
, edge_group, edge_position):
yield tree
edge_groups.pop()
used_edge.delete(edge)
used_node.delete(node)
edge_position = 0
edge_group += 1
for node in all_nodes(graph):
used_node.add(node)
edge_groups.append(neighbors(graph, node))
for tree in finish_all_trees(tree_length, 0, 0):
yield tree
edge_groups.pop()
used_node.delete(node)
exhausted_node.add(node)
Assuming you can destroy the original graph or make a destroyable copy I came up to something that could work but could be utter sadomaso because I did not calculate its O-Ntiness. It probably would work for small subtrees.
do it in steps, at each step:
sort the graph nodes so you get a list of nodes sorted by number of adjacent edges ASC
process all nodes with the same number of edges of the first one
remove those nodes
For an example for a graph of 6 nodes finding all size 2 subgraphs (sorry for my total lack of artistic expression):
Well the same would go for a bigger graph, but it should be done in more steps.
Assuming:
Z number of edges of most ramificated node
M desired subtree size
S number of steps
Ns number of nodes in step
assuming quicksort for sorting nodes
Worst case:
S*(Ns^2 + MNsZ)
Average case:
S*(NslogNs + MNs(Z/2))
Problem is: cannot calculate the real omicron because the nodes in each step will decrease depending how is the graph...
Solving the whole thing with this approach could be very time consuming on a graph with very connected nodes, however it could be paralelized, and you could do one or two steps, to remove dislocated nodes, extract all subgraphs, and then choose another approach on the remainder, but you would have removed a lot of nodes from the graph so it could decrease the remaining run time...
Unfortunately this approach would benefit the GPU not the CPU, since a LOT of nodes with the same number of edges would go in each step.... and if parallelization is not used this approach is probably bad...
Maybe an inverse would go better with the CPU, sort and proceed with nodes with the maximum number of edges... those will be probably less at start, but you will have more subgraphs to extract from each node...
Another possibility is to calculate the least occuring egde count in the graph and start with nodes that have it, that would alleviate the memory usage and iteration count for extracting subgraphs...
Unless I'm reading the question wrong people seem to be overcomplicating it.
This is just "all possible paths within N edges" and you're allowing cycles.
This, for two nodes: A, B and one edge your result would be:
AA, AB, BA, BB
For two nodes, two edges your result would be:
AAA, AAB, ABA, ABB, BAA, BAB, BBA, BBB
I would recurse into a for each and pass in a "template" tuple
N=edge count
TempTuple = Tuple_of_N_Items ' (01,02,03,...0n) (Could also be an ordered list!)
ListOfTuple_of_N_Items ' Paths (could also be an ordered list!)
edgeDepth = N
Method (Nodes, edgeDepth, TupleTemplate, ListOfTuples, EdgeTotal)
edgeDepth -=1
For Each Node In Nodes
if edgeDepth = 0 'Last Edge
ListOfTuples.Add New Tuple from TupleTemplate + Node ' (x,y,z,...,Node)
else
NewTupleTemplate = TupleTemplate + Node ' (x,y,z,Node,...,0n)
Method(Nodes, edgeDepth, NewTupleTemplate, ListOfTuples, EdgeTotal
next
This will create every possible combination of vertices for a given edge count
What's missing is the factory to generate tuples given an edge count.
You end up with a list of possible paths and the operation is Nodes^(N+1)
If you use ordered lists instead of tuples then you don't need to worry about a factory to create the objects.
If memory is the biggest problem you can use a NP-ish solution using tools from formal verification. I.e., guess a subset of nodes of size N and check whether it's a graph or not. To save space you can use a BDD (http://en.wikipedia.org/wiki/Binary_decision_diagram) to represent the original graph's nodes and edges. Plus you can use a symbolic algorithm to check if the graph you guessed is really a graph - so you don't need to construct the original graph (nor the N-sized graphs) at any point. Your memory consumption should be (in big-O) log(n) (where n is the size of the original graph) to store the original graph, and another log(N) to store every "small graph" you want.
Another tool (which is supposed to be even better) is to use a SAT solver. I.e., construct a SAT formula that is true iff the sub-graph is a graph and supply it to a SAT solver.
For a graph of Kn there are approximately n! paths between any two pairs of vertices. I haven't gone through your code but here is what I would do.
Select a pair of vertices.
Start from a vertex and try to reach the destination vertex recursively (something like dfs but not exactly). I think this would output all the paths between the chosen vertices.
You could do the above for all possible pairs of vertices to get all simple paths.
It seems that the following solution will work.
Go over all partitions into two parts of the set of all vertices. Then count the number of edges which endings lie in different parts (k); these edges correspond to the edge of the tree, they connect subtrees for the first and the second parts. Calculate the answer for both parts recursively (p1, p2). Then the answer for the entire graph can be calculated as sum over all such partitions of k*p1*p2. But all trees will be considered N times: once for each edge. So, the sum must be divided by N to get the answer.
Your solution as is doesn't work I think, although it can be made to work. The main problem is that the subproblems may produce overlapping trees so when you take the union of them you don't end up with a tree of size n. You can reject all solutions where there is an overlap, but you may end up doing a lot more work than needed.
Since you are ok with exponential runtime, and potentially writing 2^n trees out, having V.2^V algorithms is not not bad at all. So the simplest way of doing it would be to generate all possible subsets n nodes, and then test each one if it forms a tree. Since testing whether a subset of nodes form a tree can take O(E.V) time, we are potentially talking about V^2.V^n time, unless you have a graph with O(1) degree. This can be improved slightly by enumerating subsets in a way that two successive subsets differ in exactly one node being swapped. In that case, you just have to check if the new node is connected to any of the existing nodes, which can be done in time proportional to number of outgoing edges of new node by keeping a hash table of all existing nodes.
The next question is how do you enumerate all the subsets of a given size
such that no more than one element is swapped between succesive subsets. I'll leave that as an exercise for you to figure out :)
I think there is a good algorithm (with Perl implementation) at this site (look for TGE), but if you want to use it commercially you'll need to contact the author. The algorithm is similar to yours in the question but avoids the recursion explosion by making the procedure include a current working subtree as a parameter (rather than a single node). That way each edge emanating from the subtree can be selectively included/excluded, and recurse on the expanded tree (with the new edge) and/or reduced graph (without the edge).
This sort of approach is typical of graph enumeration algorithms -- you usually need to keep track of a handful of building blocks that are themselves graphs; if you try to only deal with nodes and edges it becomes intractable.
This algorithm is big and not easy one to post here. But here is link to reservation search algorithm using which you can do what you want. This pdf file contains both algorithms. Also if you understand russian you can take a look to this.
So you have a graph with with edges e_1, e_2, ..., e_E.
If I understand correctly, you are looking to enumerate all subgraphs which are trees and contain N edges.
A simple solution is to generate each of the E choose N subgraphs and check if they are trees.
Have you considered this approach? Of course if E is too large then this is not viable.
EDIT:
We can also use the fact that a tree is a combination of trees, i.e. that each tree of size N can be "grown" by adding an edge to a tree of size N-1. Let E be the set of edges in the graph. An algorithm could then go something like this.
T = E
n = 1
while n<N
newT = empty set
for each tree t in T
for each edge e in E
if t+e is a tree of size n+1 which is not yet in newT
add t+e to newT
T = newT
n = n+1
At the end of this algorithm, T is the set of all subtrees of size N. If space is an issue, don't keep a full list of the trees, but use a compact representation, for instance implement T as a decision tree using ID3.
I think problem is under-specified. You mentioned that graph is undirected and that subgraph you are trying to find is of size N. What is missing is number of edges and whenever trees you are looking for binary or you allowed to have multi-trees. Also - are you interested in mirrored reflections of same tree, or in other words does order in which siblings are listed matters at all?
If single node in a tree you trying to find allowed to have more than 2 siblings which should be allowed given that you don't specify any restriction on initial graph and you mentioned that resulting subgraph should contain all nodes.
You can enumerate all subgraphs that have form of tree by performing depth-first traversal. You need to repeat traversal of the graph for every sibling during traversal. When you'll need to repeat operation for every node as a root.
Discarding symmetric trees you will end up with
N^(N-2)
trees if your graph is fully connected mesh or you need to apply Kirchhoff's Matrix-tree theorem
Related
Given a network of a binary tree of nodes with edge capacities c_e. There are data at the leaf nodes and each has data size s_v. L_e is the set of all leaves in the subtree below edge e. Our aim is to find subset S of leaves such that the number of data size transmitted to the root r is maximized, but for all the edges that the data passes through the capacity constraint must hold. It is assumed that c_e and s_v are non negative integers and let m be their maximum. Using dynamic programming on trees it should run in O(nm^2) time.
I have working on this for hours but haven't really come up woth a working solution. Any hints would be appreciated.
edit:
The data must be transmitted as a whole or not at all. for example if a leaf has 10 the algorithm can only take 10 or 0 at all.
for example,
v4=1, v5=3, v6=2, v7=2.
e1=(v1,r), e2=(v2,v1) and e3=(v3,v1) and so on.
assume that the capacity for e4, e5,e6 and e7 satisfied. But c1=5, c2=3 and c3=4
if we focused on finding the maximum of each subtree, we will end up taking v5 and v6+v7 which is not optimal. how to make dynamic programming rule that can tackle this problem and find the correct optimal solution?
Similar to the dynamic programming solution for subset sum...
For each node, calculate the set of attainable sums for subsets of the leaves, and for each attainable sum, remember the last contributing child and the previous sum. You can use this information to reconstruct the set that produces the sum.
While doing a postorder traversal of the tree, you can calculate this set for each node using only the information on its children.
When you get to the root, pick the maximum attainable sum and reconstruct the leaves that produce it.
I'd like to construct a binary tree from a quite unusual input. The input contains:
Total number of nodes.
The integer label of the root.
A list of all edges (vertices/nodes that are connected to each
other). The edges in the list are UNSORTED, there is only one rule for
determining left/right children - the child in the edge that appears
first in list is always on the left. The order of child/parent in the vertices pair is also random.
I've come up with some straighforward solutions but they require multiple searches through the list of all edges (I'd basically find the 2 edges that have the labeled root in them and repeat this process for all the subtrees.)
I imagine this straightforward approach would be VERY inefficient for trees with a big amount of nodes, but I can't come up with anything else.
Any ideas for more efficient algorithms to solve this?
Here's an example for better visualization:
INPUT: 5 NODES, ROOT LABELED 2, LIST OF EDGES: [(1,0),(1,2),(2,3),(1,4)]
The tree would look like this:
2
1 3
0 4
It is important to clarify whether the given edge list is stated to be directed or not.
If edges are given in a directed fashion (i.e. it is stated that any given edge A-B also includes the information that A is a parent of B) storing the edges in an adjacency list while recording number of incoming edges for each vertex in an array should be sufficient. Once you go through the array for the incoming edges, the vertex with 0 incoming edges(i.e. parents) should be the root. Then you can run a DFS in linear time complexity to traverse the graph and put it in any data structure that is best for your needs.
If the edges given are stated to be undirected, the scheme changes a bit. In that case, you don't have the concept of incoming and outgoing edge. In that case, as no structure for the array is specified(e.g. BST, etc.) you can basically consider any node with less than 3 edges as root and run DFS as mentioned above. (all the leaves and intermediary nodes with single child nodes)
A simple solution is: "Link all the edges in the tree that it!"
Start preparing a dictionary. If nodes don't exist by the start and end point, create them nodes. As it is random in nature, you can set their left and right pointers to NULL initially.
You have rule - " the child in the edge that appears first in list is always on the left.". So create child accordingly.
Also, you already know the root of the tree so you can iterate across the nodes you have constructed so far.
Through this you can generate tree in one shot.
Hope this helps!
How could I get from set of nodes and edges get tree with a root?
(I'm working with connectivity-matrix, each edge has weight: graph[i][j], without any negative edges). Later I need to do DFS and find LCA's in that tree, so it would be good for optimize.
I suppose that your matrix represents the child relationship (i.e. M[i][j] tells that j is the child of i), for a directed graph G(V,E).
You have 2 different strategies:
use a bit vector, go through each cell of your matrix, and mark the child index in the vector if the cell's weight is not null): the root is the vertex not set in the vector,
look for the columns (or rows, if your matrix is column first) whose cells are all null (no ancestors),
The second solution is better for dense matrices. Its worst running time would be when the root is the last entry (O(V²)). In this case you can stop at the first hit, or run til the end to get all the roots, if your graph has many.
The first one is better suited for sparse matrices, since you have to go through all the cells. It's running time is in O(E). You also get all the roots with this algorithm.
If you are certain that your graph has only one root, you can use the walk the edges up technique, as described in other answers.
Here is a computationally MUCH SLOWER version that is also much easier to code. For small graphs, it is just fine.
Find the node with in-degree zero!
You have to compute all node degrees, O(n), but depending on the setting, this is often much easier to code and thus less prone to error.
Pick one node in the tree and walk up, that is, against the orientation of the edges. When you find a node without an ancestor you have the root.
If you need to do something like this often, just remember the parent node for each node.
a DFS search from any graph gives you a tree (assuming the graph is connected, of course).
you can iterate it, and start from each node as a possible root, you will get a spanning tree eventually this way, if there is one. complexity will be O(V^2+VE)
EDIT: it works because for any finite graph, if there is a root form node a to node b, there will be a path from a to b in the tree DFS creates. so, assuming there is a possible spanning tree, there is a root r, which you can get from to each v in V. when iterating when r chosen as root, there is a path from r to each v in V, so there will be a path from r to it in the spanning tree.
I have a huge directed graph with about a million nodes and more than ten million edges. The edges are not weighted. The graph is a small-world like graph. In fact I see that every node is (on average) connected to another node over three intermediate nodes.
Given this graph can you think of a fast algorithm that returns all paths (without cycles) between a start and a destination node, but only up to a given maximum number N of intermediate nodes (and in my case N most of the time will be between 0 and 3)?
If your graph was undirected, you would certainly want to do a bidirectional breadth first search. For length 2 paths, enumerate edges from the start node and the end node and see where they intersect. For the length 3 paths, go 2 deep from the end point with smaller degree, and one deep on the node with greater degree.
Since your graph is directed, you might want to also keep reverse edges so you can do the same trick.
Perhaps breath-first from both directions at once? Take neighbours of A, and neighbours of B. if you haven't found a link yet, add A to "neighbours of a" and B to "neighbours of B", then find any link between the two sets.
To extend it a bit further than three links, the "neighbours of A/B" lists need to contain a bit more. You will not be able to do it in-memory - you'll need a scratch table with
whatever TRANSACTION_ID; (or use an ORACLE 1-per-session temp table)
boolean MY_BFS_WAS_ROOTED_AT_A;
int NODE_ID;
int previous_node_id;
(you don't need to track depth if you check for loops in your insert statement)
you have found a path when there exists any
select from pathfinder a, pathfinder b
where a.taxn_id = foo and b.tnx_id=foo
and a.MY_BFS_WAS_ROOTED_AT_A = false
and b.MY_BFS_WAS_ROOTED_AT_A = true
and a.node_id = b.node_id
Don't forget to clean out the table when you are done! Doing it all as one transaction and rolling it back might be the easiest way.
There is a directed graph (not necessarily connected) of which one or more nodes are distinguished as sources. Any node accessible from any one of the sources is considered 'lit'.
Now suppose one of the edges is removed. The problem is to determine the nodes that were previously lit and are not lit anymore.
An analogy like city electricity system may be considered, I presume.
This is a "dynamic graph reachability" problem. The following paper should be useful:
A fully dynamic reachability algorithm for directed graphs with an almost linear update time. Liam Roditty, Uri Zwick. Theory of Computing, 2002.
This gives an algorithm with O(m * sqrt(n))-time updates (amortized) and O(sqrt(n))-time queries on a possibly-cyclic graph (where m is the number of edges and n the number of nodes). If the graph is acyclic, this can be improved to O(m)-time updates (amortized) and O(n/log n)-time queries.
It's always possible you could do better than this given the specific structure of your problem, or by trading space for time.
If instead of just "lit" or "unlit" you would keep a set of nodes from which a node is powered or lit, and consider a node with an empty set as "unlit" and a node with a non-empty set as "lit", then removing an edge would simply involve removing the source node from the target node's set.
EDIT: Forgot this:
And if you remove the last lit-from-node in the set, traverse the edges and remove the node you just "unlit" from their set (and possibly traverse from there too, and so on)
EDIT2 (rephrase for tafa):
Firstly: I misread the original question and thought that it stated that for each node it was already known to be lit or unlit, which as I re-read it now, was not mentioned.
However, if for each node in your network you store a set containing the nodes it was lit through, you can easily traverse the graph from the removed edge and fix up any lit/unlit references.
So for example if we have nodes A,B,C,D like this: (lame attempt at ascii art)
A -> B >- D
\-> C >-/
Then at node A you would store that it was a source (and thus lit by itself), and in both B and C you would store they were lit by A, and in D you would store that it was lit by both A and C.
Then say we remove the edge from B to D: In D we remove B from the lit-source-list, but it remains lit as it is still lit by A. Next say we remove the edge from A to C after that: A is removed from C's set, and thus C is no longer lit. We then go on to traverse the edges that originated at C, and remove C from D's set which is now also unlit. In this case we are done, but if the set was bigger, we'd just go on from D.
This algorithm will only ever visit the nodes that are directly affected by a removal or addition of an edge, and as such (apart from the extra storage needed at each node) should be close to optimal.
Is this your homework?
The simplest solution is to do a DFS (http://en.wikipedia.org/wiki/Depth-first_search) or a BFS (http://en.wikipedia.org/wiki/Breadth-first_search) on the original graph starting from the source nodes. This will get you all the original lit nodes.
Now remove the edge in question. Do again the DFS. You can the nodes which still remain lit.
Output the nodes that appear in the first set but not the second.
This is an asymptotically optimal algorithm, since you do two DFSs (or BFSs) which take O(n + m) times and space (where n = number of nodes, m = number of edges), which dominate the complexity. You need at least o(n + m) time and space to read the input, therefore the algorithm is optimal.
Now if you want to remove several edges, that would be interesting. In this case, we would be talking about dynamic data structures. Is this what you intended?
EDIT: Taking into account the comments:
not connected is not a problem, since nodes in unreachable connected components will not be reached during the search
there is a smart way to do the DFS or BFS from all nodes at once (I will describe BFS). You just have to put them all at the beginning on the stack/queue.
Pseudo code for a BFS which searches for all nodes reachable from any of the starting nodes:
Queue q = [all starting nodes]
while (q not empty)
{
x = q.pop()
forall (y neighbour of x) {
if (y was not visited) {
visited[y] = true
q.push(y)
}
}
}
Replace Queue with a Stack and you get a sort of DFS.
How big and how connected are the graphs? You could store all paths from the source nodes to all other nodes and look for nodes where all paths to that node contain one of the remove edges.
EDIT: Extend this description a bit
Do a DFS from each source node. Keep track of all paths generated to each node (as edges, not vertices, so then we only need to know the edges involved, not their order, and so we can use a bitmap). Keep a count for each node of the number of paths from source to node.
Now iterate over the paths. Remove any path that contains the removed edge(s) and decrement the counter for that node. If a node counter is decremented to zero, it was lit and now isn't.
I would keep the information of connected source nodes on the edges while building the graph.(such as if edge has connectivity to the sources S1 and S2, its source list contains S1 and S2 ) And create the Nodes with the information of input edges and output edges. When an edge is removed, update the output edges of the target node of that edge by considering the input edges of the node. And traverse thru all the target nodes of the updated edges by using DFS or BFS. (In case of a cycle graph, consider marking). While updating the graph, it is also possible to find nodes without any edge that has source connection (lit->unlit nodes). However, it might not be a good solution, if you'd like to remove multiple edges at the same time since that may cause to traverse over same edges again and again.