Here is what I want to do:
keep a reference curve unchanged (only shift and stretch a query curve)
constrain how many elements are duplicated
keep both start and end open
I tried:
dtw(ref_curve,query_curve,step_pattern=asymmetric,open_end=True,open_begin=True)
but I cannot constrain how the query curve is stretched
dtw(ref_curve,query_curve,step_pattern=mvmStepPattern(10))
it didn’t do anything to the curves!
dtw(ref_curve,query_curve,step_pattern=rabinerJuangStepPattern(4, "c"),open_end=True, open_begin=True)
I liked this one the most but in some cases it shifts the query curve more than needed...
I read the paper (https://www.jstatsoft.org/article/view/v031i07) and the API but still don't quite understand how to achieve what I want. Any other options to constrain number of elements that are duplicated? I would appreciate your help!
to clarify: we are talking about functions provided by the DTW suite packages at dynamictimewarping.github.io. The question is in fact language-independent (and may be more suited to the Cross-validated Stack Exchange).
The pattern rabinerJuangStepPattern(4, "c") you have found does in fact satisfy your requirements:
it's asymmetric, and each step advances the reference by exactly one step
it's slope-limited between 1/2 and 2
it's type "c", so can be normalized in a way that allows open-begin and open-end
If you haven't already, check out dtw.rabinerJuangStepPattern(4, "c").plot().
It goes without saying that in all cases you are getting is the optimal alignment, i.e. the one with the least accumulated distance among all allowed paths.
As an alternative, you may consider the simpler asymmetric recursion -- as your first attempt above -- constrained with a global warping window: see dtw.window and the window_type argument. This provides constraints of a different shape (and flexible size), which might suit your specific case.
PS: edited to add that the asymmetricP2 recursion is also similar to RJ-4c, but with a more constrained slope.
I try to use the z3 solver for a minimization problem. I was trying to get a timeout, and return the best solution so far. I use the python API, and the timeout option "smt.timeout" with
set_option("smt.timeout", 1000) # 1s timeout
This actually times out after about 1 second. However a larger timeout does not provide a smaller objective. I ended up turning on the verbosity with
set_option("verbose", 2)
And I think that z3 successively evaluates larger values of my objective, until the problem is satisfiable:
(opt.maxres [0:6117664])
(opt.maxres [175560:6117664])
(opt.maxres [236460:6117664])
(opt.maxres [297360:6117664])
...
(opt.maxres [940415:6117664])
(opt.maxres [945805:6117664])
...
I thus have the two questions:
Can I on contrary tell z3 to start with the upper bound, and successively return models with a smaller value for my objective function (just like for instance Minizinc annotations indomain_max http://www.minizinc.org/2.0/doc-lib/doc-annotations-search.html)
It still looks like the solver returns a satisfiable instance of my problem. How is it found? If it's trying to evaluates larger values of my objective successively, it should not have found a satisfiable instance yet when the timeout occurs...
edit: In the opt.maxres log, the upper bound never shrinks.
For the record, I found a more verbose description of the options in the source here opt_params.pyg
Edit Sorry to bother, I've beed diving into this recently once again. Anyway I think this might be usefull to others. I've been finding that I actually have to call the Optimize.upper method in order to get the upper bound, and the model is still not the one that corresponds to this upper bound. I've been able to add it as a new constraint, and call a solver (without optimization, just SAT), but that's probably not the best idea. By reading this I feel like I should call Optimize.update_upper after the solver times out, but the python interface has no such method (?). At least I can get the upper bound, and the corresponding model now (at the cost of unneccessary computations I guess).
Z3 finds solutions for the hard constraints and records the current values for the objectives and soft constraints. The last model that was found (the last model with the so-far best value for the objectives) is returned if you ask for a model. The maxres strategy mainly improves the lower bounds on the soft constraints (e.g., any solution must have cost at least xx) and whenever possible improves the upper bound (the optional solution has cost at most yy). The lower bounds don't tell you too much other than narrowing the range of possible optimal values. The upper bounds are available when you timeout.
You could try one of the other strategies, such as the one called "wmax", which
performs a branch-and-prune. Typically maxres does significantly better, but you may have better experience (depending on the problems) with wmax for improving upper bounds.
I don't have a mode where you get a stream of models. It is in principle possible, but it would require some (non-trivial) reorganization. For Pareto fronts you make successive invocations to Optimize.check() to get the successive fronts.
I successfully amended the nice CloudBalancing example to include the fact that I may only have a limited number of computers open at any given time (thanx optaplanner team - easy to do). I believe this is referred to as a bounded-space problem. It works dandy.
The processes come in groupwise, say 20 processes in a given order per group. I would like to amend the example to have optaplanner also change the order of these groups (not the processes within one group). I have therefore added a class ProcessGroup in the domain with a member List<Process>, the instances of ProcessGroup being stored in a List<ProcessGroup>. The desired optimisation would shuffle the members of this List, causing the instances of ProcessGroup to be placed at different indices of the List List<ProcessGroup>. The index of ProcessGroup should be ProcessGroup.index.
The documentation states that "if in doubt, the planning entity is the many side of the many-to-one relationsship." This would mean that ProcessGroup is the planning entity, the member index being a planning variable, getting assigned to (hopefully) different integers. After every new assignment of indices, I would have to resort the list List<ProcessGroup in ascending order of ProcessGroup.index. This seems very odd and cumbersome. Any better ideas?
Thank you in advance!
Philip.
The current design has a few disadvantages:
It requires 2 (genuine) entity classes (each with 1 planning variable): probably increases search space (= longer to solve, more difficult to find a good or even feasible solution) + it increases configuration complexity. Don't use multiple genuine entity classes if you can avoid it reasonably.
That Integer variable of GroupProcess need to be all different and somehow sequential. That smelled like a chained planning variable (see docs about chained variables and Vehicle Routing example), in which case the entire problem could be represented as a simple VRP with just 1 variable, but does that really apply here?
Train of thought: there's something off in this model:
ProcessGroup has in Integer variable: What does that Integer represent? Shouldn't that Integer variable be on Process instead? Are you ordering Processes or ProcessGroups? If it should be on Process instead, then both Process's variables can be replaced by a chained variable (like VRP) which will be far more efficient.
ProcessGroup has a list of Processes, but that a problem property: which means it doesn't change during planning. I suspect that's correct for your use case, but do assert it.
If none of the reasoning above applies (which would surprise me) than the original model might be valid nonetheless :)
I am building a pymc model which must evaluate a very cpu expensive function (up to 1 sec per call on a very decent hardware). I am trying to limit the explored parameter space to meaningful solutions by means of a potential (the sum of a list of my variables has to stay within a given range). This works but I noticed that even when my potential returns an infinite value and forbids the parameters choice, this function gets evaluated. Is there a way to prevent that? Can one force the sampler to use a given evaluation sequence (pick up the necessary variables, check if the potential is ok and proceed if allowed)
I thought of using the potential inside the function itself and use it to determine whether it must proceed or immediately return, but is there a better way?
Jean-François
I am not aware of a way of ordering the evaluation of the potentials. This might not be the best way of doing so, but you might be able to check if the parameters are within reasonable at the beginning of the simulation. If the parameters are not within reasonable bounds you can return a value that will create your posterior to be zero.
Another option is to create a function for your likelihood. At the beginning of this function you could check if the parameters are within reasonable limits. If they are not you can return -inf without running your simulation. If they are reasonable you can run your model and calculate the log(p).
This is definitely not an elegant solution but it should work.
Full disclosure - I am not by any means a pymc expert.
Question after BIG edition :
I need to built a ranking using genetic algorithm, I have data like this :
P(a>b)=0.9
P(b>c)=0.7
P(c>d)=0.8
P(b>d)=0.3
now, lets interpret a,b,c,d as names of football teams, and P(x>y) is probability that x wins with y. We want to build ranking of teams, we lack some observations P(a>d),P(a>c) are missing due to lack of matches between a vs d and a vs c.
Goal is to find ordering of team names, which the best describes current situation in that four team league.
If we have only 4 teams than solution is straightforward, first we compute probabilities for all 4!=24 orderings of four teams, while ignoring missing values we have :
P(abcd)=P(a>b)P(b>c)P(c>d)P(b>d)
P(abdc)=P(a>b)P(b>c)(1-P(c>d))P(b>d)
...
P(dcba)=(1-P(a>b))(1-P(b>c))(1-P(c>d))(1-P(b>d))
and we choose the ranking with highest probability. I don't want to use any other fitness function.
My question :
As numbers of permutations of n elements is n! calculation of probabilities for all
orderings is impossible for large n (my n is about 40). I want to use genetic algorithm for that problem.
Mutation operator is simple switching of places of two (or more) elements of ranking.
But how to make crossover of two orderings ?
Could P(abcd) be interpreted as cost function of path 'abcd' in assymetric TSP problem but cost of travelling from x to y is different than cost of travelling from y to x, P(x>y)=1-P(y<x) ? There are so many crossover operators for TSP problem, but I think I have to design my own crossover operator, because my problem is slightly different from TSP. Do you have any ideas for solution or frame for conceptual analysis ?
The easiest way, on conceptual and implementation level, is to use crossover operator which make exchange of suborderings between two solutions :
CrossOver(ABcD,AcDB) = AcBD
for random subset of elements (in this case 'a,b,d' in capital letters) we copy and paste first subordering - sequence of elements 'a,b,d' to second ordering.
Edition : asymetric TSP could be turned into symmetric TSP, but with forbidden suborderings, which make GA approach unsuitable.
It's definitely an interesting problem, and it seems most of the answers and comments have focused on the semantic aspects of the problem (i.e., the meaning of the fitness function, etc.).
I'll chip in some information about the syntactic elements -- how do you do crossover and/or mutation in ways that make sense. Obviously, as you noted with the parallel to the TSP, you have a permutation problem. So if you want to use a GA, the natural representation of candidate solutions is simply an ordered list of your points, careful to avoid repitition -- that is, a permutation.
TSP is one such permutation problem, and there are a number of crossover operators (e.g., Edge Assembly Crossover) that you can take from TSP algorithms and use directly. However, I think you'll have problems with that approach. Basically, the problem is this: in TSP, the important quality of solutions is adjacency. That is, abcd has the same fitness as cdab, because it's the same tour, just starting and ending at a different city. In your example, absolute position is much more important that this notion of relative position. abcd means in a sense that a is the best point -- it's important that it came first in the list.
The key thing you have to do to get an effective crossover operator is to account for what the properties are in the parents that make them good, and try to extract and combine exactly those properties. Nick Radcliffe called this "respectful recombination" (note that paper is quite old, and the theory is now understood a bit differently, but the principle is sound). Taking a TSP-designed operator and applying it to your problem will end up producing offspring that try to conserve irrelevant information from the parents.
You ideally need an operator that attempts to preserve absolute position in the string. The best one I know of offhand is known as Cycle Crossover (CX). I'm missing a good reference off the top of my head, but I can point you to some code where I implemented it as part of my graduate work. The basic idea of CX is fairly complicated to describe, and much easier to see in action. Take the following two points:
abcdefgh
cfhgedba
Pick a starting point in parent 1 at random. For simplicity, I'll just start at position 0 with the "a".
Now drop straight down into parent 2, and observe the value there (in this case, "c").
Now search for "c" in parent 1. We find it at position 2.
Now drop straight down again, and observe the "h" in parent 2, position 2.
Again, search for this "h" in parent 1, found at position 7.
Drop straight down and observe the "a" in parent 2.
At this point note that if we search for "a" in parent one, we reach a position where we've already been. Continuing past that will just cycle. In fact, we call the sequence of positions we visited (0, 2, 7) a "cycle". Note that we can simply exchange the values at these positions between the parents as a group and both parents will retain the permutation property, because we have the same three values at each position in the cycle for both parents, just in different orders.
Make the swap of the positions included in the cycle.
Note that this is only one cycle. You then repeat this process starting from a new (unvisited) position each time until all positions have been included in a cycle. After the one iteration described in the above steps, you get the following strings (where an "X" denotes a position in the cycle where the values were swapped between the parents.
cbhdefga
afcgedbh
X X X
Just keep finding and swapping cycles until you're done.
The code I linked from my github account is going to be tightly bound to my own metaheuristics framework, but I think it's a reasonably easy task to pull the basic algorithm out from the code and adapt it for your own system.
Note that you can potentially gain quite a lot from doing something more customized to your particular domain. I think something like CX will make a better black box algorithm than something based on a TSP operator, but black boxes are usually a last resort. Other people's suggestions might lead you to a better overall algorithm.
I've worked on a somewhat similar ranking problem and followed a technique similar to what I describe below. Does this work for you:
Assume the unknown value of an object diverges from your estimate via some distribution, say, the normal distribution. Interpret your ranking statements such as a > b, 0.9 as the statement "The value a lies at the 90% percentile of the distribution centered on b".
For every statement:
def realArrival = calculate a's location on a distribution centered on b
def arrivalGap = | realArrival - expectedArrival |
def fitness = Σ arrivalGap
Fitness function is MIN(fitness)
FWIW, my problem was actually a bin-packing problem, where the equivalent of your "rank" statements were user-provided rankings (1, 2, 3, etc.). So not quite TSP, but NP-Hard. OTOH, bin-packing has a pseudo-polynomial solution proportional to accepted error, which is what I eventually used. I'm not quite sure that would work with your probabilistic ranking statements.
What an interesting problem! If I understand it, what you're really asking is:
"Given a weighted, directed graph, with each edge-weight in the graph representing the probability that the arc is drawn in the correct direction, return the complete sequence of nodes with maximum probability of being a topological sort of the graph."
So if your graph has N edges, there are 2^N graphs of varying likelihood, with some orderings appearing in more than one graph.
I don't know if this will help (very brief Google searches did not enlighten me, but maybe you'll have more success with more perseverance) but my thoughts are that looking for "topological sort" in conjunction with any of "probabilistic", "random", "noise," or "error" (because the edge weights can be considered as a reliability factor) might be helpful.
I strongly question your assertion, in your example, that P(a>c) is not needed, though. You know your application space best, but it seems to me that specifying P(a>c) = 0.99 will give a different fitness for f(abc) than specifying P(a>c) = 0.01.
You might want to throw in "Bayesian" as well, since you might be able to start to infer values for (in your example) P(a>c) given your conditions and hypothetical solutions. The problem is, "topological sort" and "bayesian" is going to give you a whole bunch of hits related to markov chains and markov decision problems, which may or may not be helpful.