I have a graph-theoretic (which is also related to combinatorics) problem that is illustrated below, and wonder what is the best approach to design an algorithm to solve it.
Given 4 different graphs of 6 nodes (by different, I mean different structures, e.g. STAR, LINE, COMPLETE, etc), and 24 unique objects, design an algorithm to assign these objects to these 4 graphs 4 times, so that the number of repeating neighbors on the graphs over the 4 assignments is minimized. For example, if object A and B are neighbors on 1 of the 4 graphs in one assignment, then in the best case, A and B will not be neighbors again in the other 3 assignments.
Obviously, the degree to which such minimization can go is dependent on the specific graph structures given. But I am more interested in a general solution here so that given any 4 graph structures, such minimization is guaranteed as the result of the algorithm.
Any suggestion/idea of solving this problem is welcome, and some pseudo-code may well be sufficient to illustrate the design. Thank you.
Representation:
You have 24 elements, I will name this elements from A to X (24 first letters).
Each of these elements will have a place in one of the 4 graphs. I will assign a number to the 24 nodes of the 4 graphs from 1 to 24.
I will identify the position of A by a 24-uple =(xA1,xA2...,xA24), and if I want to assign A to the node number 8 for exemple, I will write (xa1,Xa2..xa24) = (0,0,0,0,0,0,0,1,0,0...0), where 1 is on position 8.
We can say that A =(xa1,...xa24)
e1...e24 are the unit vectors (1,0...0) to (0,0...1)
note about the operator '.':
A.e1=xa1
...
X.e24=Xx24
There are some constraints on A,...X with these notations :
Xii is in {0,1}
and
Sum(Xai)=1 ... Sum(Xxi)=1
Sum(Xa1,xb1,...Xx1)=1 ... Sum(Xa24,Xb24,... Xx24)=1
Since one element can be assign to only one node.
I will define a graph by defining the neighbors relation of each node, lets say node 8 has neighbors node 7 and node 10
to check that A and B are neighbors on node 8 for exemple I nedd:
A.e8=1 and B.e7 or B.e10 =1 then I just need A.e8*(B.e7+B.e10)==1
in the function isNeighborInGraphs(A,B) I test that for every nodes and I get one or zero depending on the neighborhood.
Notations:
4 graphs of 6 nodes, the position of each element is defined by an integer from 1 to 24.
(1 to 6 for first graph, etc...)
e1... e24 are the unit vectors (1,0,0...0) to (0,0...1)
Let A, B ...X be the N elements.
A=(0,0...,1,...,0)=(xa1,xa2...xa24)
B=...
...
X=(0,0...,1,...,0)
Graph descriptions:
IsNeigborInGraphs(A,B)=A.e1*B.e2+...
//if 1 and 2 are neigbors in one graph
for exemple
State of the system:
L(A)=[B,B,C,E,G...] // list of
neigbors of A (can repeat)
actualise(L(A)):
for element in [B,X]
if IsNeigbotInGraphs(A,Element)
L(A).append(Element)
endIf
endfor
Objective functions
N(A)=len(L(A))+Sum(IsneigborInGraph(A,i),i in L(A))
...
N(X)= ...
Description of the algorithm
start with an initial position
A=e1... X=e24
Actualize L(A),L(B)... L(X)
Solve this (with a solveur, ampl for
exemple will work I guess since it's
a nonlinear optimization
problem):
Objective function
min(Sum(N(Z),Z=A to X)
Constraints:
Sum(Xai)=1 ... Sum(Xxi)=1
Sum(Xa1,xb1,...Xx1)=1 ...
Sum(Xa24,Xb24,... Xx24)=1
You get the best solution
4.Repeat step 2 and 3, 3 more times.
If all four graphs are K_6, then the best you can do is choose 4 set partitions of your 24 objects into 4 sets each of cardinality 6 so that the pairwise intersection of any two sets has cardinality at most 2. You can do this by choosing set partitions that are maximally far apart in the Hasse diagram of set partitions with partial order given by refinement. The general case is much harder, but perhaps you can still begin with this crude approximation of a solution and then be clever with which vertex is assigned which object in the four assignments.
Assuming you don't want to cycle all combinations and calculate the sum every time and choose the lowest, you can implement a minimum problem (solved depending on your constraints using either a linear programming solver i.e. symplex algorithm engines or a non-linear solver, much harder talking in terms of time) with constraints on your variables (24) depending on the shape of your path. You can also use free software like LINGO/LINDO to create rapidly a decision theory model and test its correctness (you need decision theory notions though)
If this has anything to do with the real world, then it's unlikely that you absolutely must have a solution that is the true minimum. Close to the minimum should be good enough, right? If so, you could repeatedly randomly make the 4 assignments and check the results until you either run out of time or have a good-enough solution or appear to have stopped improving your best solution.
Related
For example, we have a set of formulas as below:
B*2*j
B*3*i
B*3*j
C*2*j
C*3*i
C*3*j
D*2*i
D*2*j
D*3*i
D*3*j
And we could have three Cartesian products to represent the formulas above:
D*(2+3)*(i+j)
(B+c)*3*(i+j)
(B+C)*2*j
So the total number is 3. And we could also have:
3*(B+C+D)*(i+j)
2*(B+C)*D
2*D*(i+j)
which is also 3.
I wanna ask that is there a algorithm to determine the minimum number of Cartesian products from a set of formulas? And also come up with these products?
First, I'll write a set of formulas as terms separated by +, since the transformation you're looking for makes sense algebraically (apart from the fact that you don't want to combine numbers like 2+3 into 5).
The basic operation that you have available is factorising: combining two terms like ABC+ABD into AB(C+D). Based on your comment, you can only generate new factors that consist of a sum of single-factor terms, like C+D in the previous example; you're not allowed to factorise e.g. ABCD+ABDE into AB(CD+DE).
You can factorise 2 k-factor terms if and only if they share exactly k-1 factors. (E.g. k=3 in my ABC+ABD example.) Every such factorisation reduces the number of terms in the set by 1: 2 are removed and 1 is added back in.
Doing this multiple times works when combining 3 or more terms: ABC+ABD+ABE can first be factorised into AB(C+D)+ABE and then those 2 terms factorised again into AB(C+D+E). Notice that it doesn't matter in which order we list terms in a sum or factors in a product, and nor does it matter in which order we perform factorisation steps when building a factor containing 3 or more terms.
We can then frame the problem as a search problem in a graph, in which the start vertex corresponds to the original formula (B*2*j + B*3*i + ... + D*3*j in your example) and from each vertex v there emanate arcs to its child vertices, which each correspond to the result of performing some factorisation on v. v will have a child vertex for each possible factorisation that could be performed on it; if there are m terms in v, then this means it could have up to m(m-1)/2 children in the worst case, because it could be that all m terms share a full complement of k-1 factors, meaning that any pair of them could be combined.
If a vertex has no pair of terms that can be combined via factorisation then it is a "leaf" -- it has no children, and can't be processed further. What we want to find is a leaf vertex that has the fewest number of terms. Since every factorisation, corresponding to an arc in the graph, reduces the number of terms by 1, this is equivalent to searching for a deepest-possible vertex. This can be done using DFS or BFS. Note however that the same expression (vertex) can be generated many times over using this approach, so it will be crucial for performance to maintain a hashtable seen that records all expressions that have already been processed; then if we visit a vertex, try to generate a child for it, and see that this child is already in seen, we avoid visiting this child a second time.
To mitigate against the phenomenon of the same expression being generated via multiple different orderings of the same set of factorisations, you can add a rule: order v's child factorisations somehow, so that if there are n children they correspond to factorisations 1, 2, ..., n in this ordering, and record in a separate "already skipped" field in each child vertex the set of earlier (in the ordering) factorisations that were skipped over to generate this child. Then, when visiting a vertex, avoid generating any of its "already skipped" factorisations as children, since doing so would create a vertex that is identical to some other existing vertex (by performing the same pair of operations in reverse order).
There are probably other speedups available that will reduce the number of duplicate vertices that are generated in the first place, but this should be enough to get results for small problems.
Write down you sum in matrix form. Then what you are asking for is the rank of that matrix, and a corresponding decomposition into dyadic products. This decomposition is far from unique.
[ 3 5 ] [ i ]
[ B C D ] * | 3 5 | * [ j ]
[ 5 5 ]
As one can see, the matrix in the middle has full rank 2
If you intend to use 2 and 3 also as variables, then you are asking to decompose a tensor of order 3 into a minimum number of terms that factorize, i.e., that are tensor products of vectors.
Suppose I have a a graph with 2^N - 1 nodes, numbered 1 to 2^N - 1. Node i "depends on" node j if all the bits in the binary representation of j that are 1, are also 1 in the binary representation of i. So, for instance, if N=3, then node 7 depends on all other nodes. Node 6 depends on nodes 4 and 2.
The problem is eliminating nodes. I can eliminate a node if no other nodes depend on it. No nodes depend on 7; so I can eliminate 7. After eliminating 7, I can eliminate 6, 5, and 3, etc. What I'd like is to find an efficient algorithm for listing all the possible unique elimination paths. (that is, 7-6-5 is the same as 7-5-6, so we only need to list one of the two). I have a dumb algorithm already, but I think there must be a better way.
I have three related questions:
Does this problem have a general name?
What's the best way to solve it?
Is there a general formula for the number of unique elimination paths?
Edit: I should note that a node cannot depend on itself, by definition.
Edit2: Let S = {s_1, s_2, s_3,...,s_m} be the set of all m valid elimination paths. s_i and s_j are "equivalent" (for my purposes) iff the two eliminations s_i and s_j would lead to the same graph after elimination. I suppose to be clearer I could say that what I want is the set of all unique graphs resulting from valid elimination steps.
Edit3: Note that elimination paths may be different lengths. For N=2, the 5 valid elimination paths are (),(3),(3,2),(3,1),(3,2,1). For N=3, there are 19 unique paths.
Edit4: Re: my application - the application is in statistics. Given N factors, there are 2^N - 1 possible terms in statistical model (see http://en.wikipedia.org/wiki/Analysis_of_variance#ANOVA_for_multiple_factors) that can contain the main effects (the factors alone) and various (2,3,... way) interactions between the factors. But an interaction can only be present in a model if all sub-interactions (or main effects) are present. For three factors a, b, and c, for example, the 3 way interaction a:b:c can only be in present if all the constituent two-way interactions (a:b, a:c, b:c) are present (and likewise for the two-ways). Thus, the model a + b + c + a:b + a:b:c would not be allowed. I'm looking for a quick way to generate all valid models.
It seems easier to think about this in terms of sets: you are looking for families of subsets of {1, ..., N} such that for each set in the family also all its subsets are present. Each such family is determined by the inclusion-wise maximal sets, which must be overlapping. Families of pairwise overlapping sets are called Sperner families. So you are looking for Sperner families, plus the union of all the subsets in the family. Possibly known algorithms for enumerating Sperner families or antichains in general are useful; without knowing what you actually want to do with them, it's hard to tell.
Thanks to #FalkHüffner's answer, I saw that what I wanted to do was equivalent to finding monotonic Boolean functions for N arguments. If you look at the figure on the Wikipedia page for Dedekind numbers (http://en.wikipedia.org/wiki/Dedekind_number) the figure expresses the problem graphically. There is an algorithm for generating monotonic Boolean functions (http://www.mathpages.com/home/kmath094.htm) and it is quite simple to construct.
For my purposes, I use the algorithm, then eliminate the first column and last row of the resulting binary arrays. Starting from the top row down, each row has a 1 in the ith column if one can eliminate the ith node.
Thanks!
You can build a "heap", in which at depth X are all the nodes with X zeros in their binary representation.
Then, starting from the bottom layer, connect each item to a random parent at the layer above, until you get a single-component graph.
Note that this graph is a tree, i.e., each node except for the root has exactly one parent.
Then, traverse the tree (starting from the root) and count the total number of paths in it.
UPDATE:
The method above is bad, because you cannot just pick a random parent for a given item - you have a limited number of items from which you can pick a "legal" parent... But I'm leaving this method here for other people to give their opinion (perhaps it is not "that bad").
In any case, why don't you take your graph, extract a spanning-tree (you can use Prim algorithm or Kruskal algorithm for finding a minimal-spanning-tree), and then count the number of paths in it?
The source data for the subject is an m-by-n binary matrix (only 0s and 1s are allowed).
m Rows represent observations, n columns - features. Some observations are marked as targets which need to be separated from the rest.
While it looks like a typical NN, SVM, etc problem, I don't need generalization. What I need is an efficient algorithm to find as many as possible combinations of columns (features) that completely separate targets from other observations, classify, that is.
For example:
f1 f2 f3
o1 1 1 0
t1 1 0 1
o2 0 1 1
Here {f1, f3} is an acceptable combo which separates target t1 from the rest (o1, o2) (btw, {f2} is NOT as by task definition a feature MUST be present in a target). In other words,
t1(f1) & t1(f3) = 1 and o1(f1) & o1(f3) = 0, o2(f1) & o2(f3) = 0
where '&' represents logical conjunction (AND).
The m is about 100,000, n is 1,000. Currently the data is packed into 128bit words along m and the search is optimized with sse4 and whatnot. Yet it takes way too long to obtain those feature combos.
After 2 billion calls to the tree descent routine it has covered about 15% of root nodes. And found about 8,000 combos which is a decent result for my particular application.
I use some empirical criteria to cut off less probable descent paths, not without limited success, but is there something radically better? Im pretty sure there gotta be?.. Any help, in whatever form, reference or suggestion, would be appreciated.
I believe the problem you describe is NP-Hard so you shouldn't expect to find the optimum solution in a reasonable time. I do not understand your current algorithm, but here are some suggestions on the top of my head:
1) Construct a decision tree. Label targets as A and non-targets as B and let the decision tree learn the categorization. At each node select the feature such that a function of P(target | feature) and P(target' | feature') is maximum. (i.e. as many targets as possible fall to positive side and as many non-targets as possible fall to negative side)
2) Use a greedy algorithm. Start from the empty set and at each time step add the feauture that kills the most non-target rows.
3) Use a randomized algorithm. Start from a small subset of positive features of some target, use the set as the seed for the greedy algorithm. Repeat many times. Pick the best solution. Greedy algorithm will be fast so it will be ok.
4) Use a genetic algorithm. Generate random seeds for the greedy algorithm as in 3 to generate good solutions and cross-product them (bitwise-and probably) to generate new candidates seeds. Remember the best solution. Keep good solutions as the current population. Repeat for many generations.
You will need to find the answer "how many of the given rows have the given feature f" fast so probably you'll need specialized data structures, perhaps using a BitArray for each feature.
I have an algorithmic problem in which I have derived a transfer matrix between a lot of states. The next step is to exponentiate it, but it is very large, so I need to do some reductions on it. Specifically it contains a lot of symmetry. Below are some examples on how many nodes can be eliminated by simple observations.
My question is whether there is an algorithm to efficiently eliminate symmetry in digraphs, similarly to the way I've done it manually below.
In all cases the initial vector has the same value for all nodes.
In the first example we see that b, c, d and e all receive values from a and one of each other. Hence they will always contain an identical value, and we can merge them.
In this example we quickly spot, that the graph is identical from the point of view of a, b, c and d. Also for their respective sidenodes, it doesn't matter to which inner node it is attached. Hence we can reduce the graph down to only two states.
Update: Some people were reasonable enough not quite sure what was meant by "State transfer matrix". The idea here is, that you can split a combinatorial problem up into a number of state types for each n in your recurrence. The matrix then tell you how to get from n-1 to n.
Usually you are only interested about the value of one of your states, but you need to calculate the others as well, so you can always get to the next level. In some cases however, multiple states are symmetrical, meaning they will always have the same value. Obviously it's quite a waste to calculate all of these, so we want to reduce the graph until all nodes are "unique".
Below is an example of the transfer matrix for the reduced graph in example 1.
[S_a(n)] [1 1 1] [S_a(n-1)]
[S_f(n)] = [1 0 0]*[S_f(n-1)]
[S_B(n)] [4 0 1] [S_B(n-1)]
Any suggestions or references to papers are appreciated.
Brendan McKay's nauty ( http://cs.anu.edu.au/~bdm/nauty/) is the best tool I know of for computing automorphisms of graphs. It may be too expensive to compute the whole automorphism group of your graph, but you might be able to reuse some of the algorithms described in McKay's paper "Practical Graph Isomorphism" (linked from the nauty page).
I'll just add an extra answer building on what userOVER9000 suggested, if anybody else are interested.
The below is an example of using nauty on Example 2, through the dreadnaut tool.
$ ./dreadnaut
Dreadnaut version 2.4 (64 bits).
> n=8 d g -- Starting a new 8-node digraph
0 : 1 3 4; -- Entering edge data
1 : 0 2 5;
2 : 3 1 6;
3 : 0 2 7;
4 : 0;
5 : 1;
6 : 2;
7 : 3;
> cx -- Calling nauty
(1 3)(5 7)
level 2: 6 orbits; 5 fixed; index 2
(0 1)(2 3)(4 5)(6 7)
level 1: 2 orbits; 4 fixed; index 4
2 orbits; grpsize=8; 2 gens; 6 nodes; maxlev=3
tctotal=8; canupdates=1; cpu time = 0.00 seconds
> o -- Output "orbits"
0:3; 4:7;
Notice it suggests joining nodes 0:3 which are a:d in Example 2 and 4:7 which are e:h.
The nauty algorithm is not well documented, but the authors describe it as exponential worst case, n^2 average.
Computing symmetries seems to be a bit of a second order problem. Taking just a,b,c and d in your second graph, the symmetry would have to be expressed
a(b,c,d) = b(a,d,c)
and all its permutations, or some such. Consider a second subgraph a', b', c', d' added to it. Again, we have the symmetries, but parameterised differently.
For computing people (rather than math people), could we express the problem like so?
Each graph node contains a set of letters. At each iteration, all of the letters in each node are copied to its neighbours by the arrows (some arrows take more than one iteration and can be treated as a pipe of anonymous nodes).
We are trying to find efficient ways of determining things such as
* what letters each set/node contains after N iterations.
* for each node the N after which its set no longer changes.
* what sets of nodes wind up containing the same sets of letters (equivalence class)
?
This is intended to be a more concrete, easily expressable form of my earlier question.
Take a list of words from a dictionary with common letter length.
How to reorder this list tto keep as many letters as possible common between adjacent words?
Example 1:
AGNI, CIVA, DEVA, DEWA, KAMA, RAMA, SIVA, VAYU
reorders to:
AGNI, CIVA, SIVA, DEVA, DEWA, KAMA, RAMA, VAYU
Example 2:
DEVI, KALI, SHRI, VACH
reorders to:
DEVI, SHRI, KALI, VACH
The simplest algorithm seems to be: Pick anything, then search for the shortest distance?
However, DEVI->KALI (1 common) is equivalent to DEVI->SHRI (1 common)
Choosing the first match would result in fewer common pairs in the entire list (4 versus 5).
This seems that it should be simpler than full TSP?
What you're trying to do, is calculate the shortest hamiltonian path in a complete weighted graph, where each word is a vertex, and the weight of each edge is the number of letters that are differenct between those two words.
For your example, the graph would have edges weighted as so:
DEVI KALI SHRI VACH
DEVI X 3 3 4
KALI 3 X 3 3
SHRI 3 3 X 4
VACH 4 3 4 X
Then it's just a simple matter of picking your favorite TSP solving algorithm, and you're good to go.
My pseudo code:
Create a graph of nodes where each node represents a word
Create connections between all the nodes (every node connects to every other node). Each connection has a "value" which is the number of common characters.
Drop connections where the "value" is 0.
Walk the graph by preferring connections with the highest values. If you have two connections with the same value, try both recursively.
Store the output of a walk in a list along with the sum of the distance between the words in this particular result. I'm not 100% sure ATM if you can simply sum the connections you used. See for yourself.
From all outputs, chose the one with the highest value.
This problem is probably NP complete which means that the runtime of the algorithm will become unbearable as the dictionaries grow. Right now, I see only one way to optimize it: Cut the graph into several smaller graphs, run the code on each and then join the lists. The result won't be as perfect as when you try every permutation but the runtime will be much better and the final result might be "good enough".
[EDIT] Since this algorithm doesn't try every possible combination, it's quite possible to miss the perfect result. It's even possible to get caught in a local maximum. Say, you have a pair with a value of 7 but if you chose this pair, all other values drop to 1; if you didn't take this pair, most other values would be 2, giving a much better overall final result.
This algorithm trades perfection for speed. When trying every possible combination would take years, even with the fastest computer in the world, you must find some way to bound the runtime.
If the dictionaries are small, you can simply create every permutation and then select the best result. If they grow beyond a certain bound, you're doomed.
Another solution is to mix the two. Use the greedy algorithm to find "islands" which are probably pretty good and then use the "complete search" to sort the small islands.
This can be done with a recursive approach. Pseudo-code:
Start with one of the words, call it w
FindNext(w, l) // l = list of words without w
Get a list l of the words near to w
If only one word in list
Return that word
Else
For every word w' in l do FindNext(w', l') //l' = l without w'
You can add some score to count common pairs and to prefer "better" lists.
You may want to take a look at BK-Trees, which make finding words with a given distance to each other efficient. Not a total solution, but possibly a component of one.
This problem has a name: n-ary Gray code. Since you're using English letters, n = 26. The Wikipedia article on Gray code describes the problem and includes some sample code.