I had a brief exposure to CP and MiniZinc but I'm no expert.
I have a CP model, which I cannot post here ATM, implemented in MiniZinc.
I need to generate all the feasible solution for the problem. We expect to have just a "few" ones, say less than 1000, more than 100.
I tried to solve the model with the -a flag passed to minizinc ver. 1.6 but I notice a lot of solutions being printed are identical.
Here they refer to "projection". In another paper I read they used some "backtracking mechanism".
It's still not clear to me.
My questions then are:
what is the best way to generate only unique solutions from a CP model?
Is there a standard mechanism implemented in CP libraries like SCIP or Gecode? Does it have a common name?
Is it computationally efficient?
does minizinc support that? How do I access that feature?
Normally, CP systems give you just distinct solutions. I suspect that you have decision variables that are not printed (not in the output section) and you don't see that if these values are included in the solution it would be unique solutions.
In the question you linked to (this recent discussion), it is mentioned that Gecode's FlatZinc solver (at least the SVN version) now generates distinct solutions given a subset of decision variables in the output section. Other FlatZinc solver don't seem to have this feature.
If that doesn't answer your questions, please give more details of the model and example of the output (including the output section).
Related
I am concerned whether torch.solve() examine the condition of the coefficient matrix for a linear system and employ desirable preconditionings; thus I am curious about its implementation details. I have read through several answers trying to track down the source file but in vain. I hope somebody can help me to locate its definition in the ATen library.
I think it just uses LAPACK for CPU and CUBLAS for GPU, since torch.solve is listed under "BLAS and LAPACK Operations" on the official docs.
Then we're looking for wrapper code, which I believe is this part.
I wanted to see how the conv1d module is implemented
https://pytorch.org/docs/stable/_modules/torch/nn/modules/conv.html#Conv1d. So I looked at functional.py but still couldn’t find the looping and cross-correlation computation.
Then I searched Github by keyword ‘conv1d’, checked conv.cpp https://github.com/pytorch/pytorch/blob/eb5d28ecefb9d78d4fff5fac099e70e5eb3fbe2e/torch/csrc/api/src/nn/modules/conv.cpp 1 but still couldn’t locate where the computation is happening.
My question is two-fold.
Where is the source code that "conv1d” is implemented?
In general, if I want to check how the modules are implemented, where is the best place to find? Any pointer to the documentation will be appreciated. Thank you.
It depends on the backend (GPU, CPU, distributed etc) but in the most interesting case of GPU it's pulled from cuDNN which is released in binary format and thus you can't inspect its source code. It's a similar story for CPU MKLDNN. I am not aware of any place where PyTorch would "handroll" it's own convolution kernels, but I may be wrong. EDIT: indeed, I was wrong as pointed out in an answer below.
It's difficult without knowing how PyTorch is structured. A lot of code is actually being autogenerated based on various markup files, as explained here. Figuring this out requires a lot of jumping around. For instance, the conv.cpp file you're linking uses torch::conv1d, which is defined here and uses at::convolution which in turn uses at::_convolution, which dispatches to multiple variants, for instance at::cudnn_convolution. at::cudnn_convolution is, I believe, created here via a markup file and just plugs in directly to cuDNN implementation (though I cannot pinpoint the exact point in code when that happens).
Below is an answer that I got from pytorch discussion board:
I believe the “handroll”-ed convolution is defined here: https://github.com/pytorch/pytorch/blob/master/aten/src/THNN/generic/SpatialConvolutionMM.c 3
The NN module implementations are here: https://github.com/pytorch/pytorch/tree/master/aten/src
The GPU version is in THCUNN and the CPU version in THNN
I have a Gurobi licence and I am after a good MILP/LP modelling language, which should be
free/open source
intuitive, i.e. something that looks like (taken from MiniZinc)
var int: x;
constraint x >= 0.5;
solve minimize x;
fast: the time to build the model and send it to Gurobi should be of similar order to the best ones (AMPL GAMS etc.)
flexible/powerful (ability to deal with 3D+ arrays, activate/deactivate constraints easily, provide initial solutions to the solver, etc.)
Of course, and correct me if I'm wrong, AMPL GAMS fail at 1), Python and R fail at 2) (and perhaps at 3)?).
How about GLPK, Minizinc, ZIMPL etc.? They satisfy 1) and 2) but what about 3) and 4)? Are they as good as AMPL in this regard? If not, is there a modelling language satisfying 1-4?
I've used AMPL with Gurobi for mid-sized MIPs (~ 100k-1m variables?) and MiniZinc, mostly with Gecode, for smaller combinatorial problems. I've seen some Gurobi work done with R and Python, but haven't used it that way myself.
I'm less familiar with the other options. My understanding is that GAMS is quite similar to AMPL and much of what I have to say about AMPL may also be valid for GAMS, but I can't vouch for it.
Of course, and correct me if I'm wrong, AMPL GAMS fail at 1),
Yes, generally. There is an exception which probably isn't helpful for your specific requirements but might be useful to others: you can get free use of AMPL, Gurobi, and many other optimisation products, by using the NEOS web service. This is restricted to academic non-commercial purposes and you have to grant NEOS certain rights in relation to the problems you send them; definitely read those terms of service before using it. It also requires waiting for an available server, so if speed is a high priority this probably isn't the solution for you.
Python and R fail at 2) (and perhaps at 3)?).
In my limited experience, yes for (2). AMPL, GAMS, and MiniZinc are designed specifically for defining optimisation problems, so it's unsurprising that their syntax is more user-friendly for that purpose than languages like Python and R.
The flip-side to this is that if you want to do just about anything other than defining an optimisation problem with these languages, Python/R/etc. will probably be better for that purpose.
On speed: for the problems I usually work with, AMPL takes maybe a couple of seconds to build and presolve a MIP model which takes Gurobi a couple of minutes to solve. Obviously this is going to vary somewhat with hardware and details of the problem, but in general I would expect build time to be small compared to solve time for any of the solutions under discussion. Even with a good solver like Gurobi, big MIPs are hard. Many of the serious optimisation programmers I've met do use Python, so I presume the performance side is good enough.
However, that doesn't mean the choice of language/platform is irrelevant to speed. One of the nice features of AMPL (and also GAMS) is presolve, which attempts to reduce the problem size before sending it to the solver. My standard problems have a lot of redundant variables and constraints; AMPL identifies and eliminates many of these, reducing the problem size by about 80% and giving a noticeable improvement in solver time (as compared to runs where I switch off presolve, which I sometimes do for debugging-related reasons). This might be a consideration if you expect a lot of redundancy.
flexible/powerful (ability to deal with 3D+ arrays, activate/deactivate constraints easily, provide initial solutions to the solver, etc.)
MiniZinc handles up to 6D arrays, which may or may not be enough depending on your applications.
It's more flexible than AMPL in some areas and less so in others. AMPL has a lot of set-based functionality that I find useful (e.g. I can define a variable whose index set is something like "pairs of non-identical cities separated by no more than 500 km") and MiniZinc doesn't have this. OTOH, MiniZinc seems to be better than AMPL for solver-hopping, e.g. if I write a MZ model with a combinatorial constraint like "alldifferent" but then try to run it on a solver that doesn't recognise such constraints, MZ will translate it into something the solver can deal with.
I haven't tried deactivating constraints in MZ other than by commenting them out, so I can't help there, and similarly on providing initial solutions.
Overall, MiniZinc is a good choice to consider. Some pluses and minuses relative to AMPL ("free" being a big plus!) but it fills a similar niche.
IMHO, there is no such system if you consider the Python interfaces/modeling environments to SCIP or Gurobi too complicated:
x = model.addVar()
y = model.addVar(vtype="INTEGER")
model.setObjective(x + y)
model.addCons(2*x - y*y >= 0)
model.optimize()
To me this looks quite natural and straight forward. The immense benefit of using an actual programming language instead of modeling language is that you can do anything in there, while there will always be boundaries in the latter.
If you are a looking for a modeling GUI, you should check out LITIC. It can be used almost entirely with drag-and-drop operations: https://litic.com/showcase.html
I've used a lot of the options mentioned, and some not yet mentioned
GAMS
GAMS' Python API
GAMS' MATLAB API
AMPL
FICO Xpress Mosel
FICO Xpress Model's Python API
IBM ILOG OPL
Gurobi's Python API
PuLP (Python)
Pyomo (Python)
Python-MIP
JuMP (Julia)
MATLAB Optimization Toolbox
Google OR-Tools
Based on your requirements, I'd suggest trying Python-MIP, PuLP or JuMP. They are free and have easy syntax with no limit on array dimensionality.
Take a look at Google or-tools. I’m not sure if getting initial solution to the solver is available in all of its interfaces, but if you use it in python, it should probably satisfy all 1-4.
Today I read that there is a software called WinCalibra (scroll a bit down) which can take a text file with properties as input.
This program can then optimize the input properties based on the output values of your algorithm. See this paper or the user documentation for more information (see link above; sadly doc is a zipped exe).
Do you know other software which can do the same which runs under Linux? (preferable Open Source)
EDIT: Since I need this for a java application: should I invest my research in java libraries like gaul or watchmaker? The problem is that I don't want to roll out my own solution nor I have time to do so. Do you have pointers to an out-of-the-box applications like Calibra? (internet searches weren't successfull; I only found libraries)
I decided to give away the bounty (otherwise no one would have a benefit) although I didn't found a satisfactory solution :-( (out-of-the-box application)
Some kind of (Metropolis algorithm-like) probability selected random walk is a possibility in this instance. Perhaps with simulated annealing to improve the final selection. Though the timing parameters you've supplied are not optimal for getting a really great result this way.
It works like this:
You start at some point. Use your existing data to pick one that look promising (like the highest value you've got). Set o to the output value at this point.
You propose a randomly selected step in the input space, assign the output value there to n.
Accept the step (that is update the working position) if 1) n>o or 2) the new value is lower, but a random number on [0,1) is less than f(n/o) for some monotonically increasing f() with range and domain on [0,1).
Repeat steps 2 and 3 as long as you can afford, collecting statistics at each step.
Finally compute the result. In your case an average of all points is probably sufficient.
Important frill: This approach has trouble if the space has many local maxima with deep dips between them unless the step size is big enough to get past the dips; but big steps makes the whole thing slow to converge. To fix this you do two things:
Do simulated annealing (start with a large step size and gradually reduce it, thus allowing the walker to move between local maxima early on, but trapping it in one region later to accumulate precision results.
Use several (many if you can afford it) independent walkers so that they can get trapped in different local maxima. The more you use, and the bigger the difference in output values, the more likely you are to get the best maxima.
This is not necessary if you know that you only have one, big, broad, nicely behaved local extreme.
Finally, the selection of f(). You can just use f(x) = x, but you'll get optimal convergence if you use f(x) = exp(-(1/x)).
Again, you don't have enough time for a great many steps (though if you have multiple computers, you can run separate instances to get the multiple walkers effect, which will help), so you might be better off with some kind of deterministic approach. But that is not a subject I know enough about to offer any advice.
There are a lot of genetic algorithm based software that can do exactly that. Wrote a PHD about it a decade or two ago.
A google for Genetic Algorithms Linux shows a load of starting points.
Intrigued by the question, I did a bit of poking around, trying to get a better understanding of the nature of CALIBRA, its standing in academic circles and the existence of similar software of projects, in the Open Source and Linux world.
Please be kind (and, please, edit directly, or suggest editing) for the likely instances where my assertions are incomplete, inexact and even flat-out incorrect. While working in related fields, I'm by no mean an Operational Research (OR) authority!
[Algorithm] Parameter tuning problem is a relatively well defined problem, typically framed as one of a solution search problem whereby, the combination of all possible parameter values constitute a solution space and the parameter tuning logic's aim is to "navigate" [portions of] this space in search of an optimal (or locally optimal) set of parameters.
The optimality of a given solution is measured in various ways and such metrics help direct the search. In the case of the Parameter Tuning problem, the validity of a given solution is measured, directly or through a function, from the output of the algorithm [i.e. the algorithm being tuned not the algorithm of the tuning logic!].
Framed as a search problem, the discipline of Algorithm Parameter Tuning doesn't differ significantly from other other Solution Search problems where the solution space is defined by something else than the parameters to a given algorithm. But because it works on algorithms which are in themselves solutions of sorts, this discipline is sometimes referred as Metaheuristics or Metasearch. (A metaheuristics approach can be applied to various algorihms)
Certainly there are many specific features of the parameter tuning problem as compared to the other optimization applications but with regard to the solution searching per-se, the approaches and problems are generally the same.
Indeed, while well defined, the search problem is generally still broadly unsolved, and is the object of active research in very many different directions, for many different domains. Various approaches offer mixed success depending on the specific conditions and requirements of the domain, and this vibrant and diverse mix of academic research and practical applications is a common trait to Metaheuristics and to Optimization at large.
So... back to CALIBRA...
From its own authors' admission, Calibra has several limitations
Limit of 5 parameters, maximum
Requirement of a range of values for [some of ?] the parameters
Works better when the parameters are relatively independent (but... wait, when that is the case, isn't the whole search problem much easier ;-) )
CALIBRA is based on a combination of approaches, which are repeated in a sequence. A mix of guided search and local optimization.
The paper where CALIBRA was presented is dated 2006. Since then, there's been relatively few references to this paper and to CALIBRA at large. Its two authors have since published several other papers in various disciplines related to Operational Research (OR).
This may be indicative that CALIBRA hasn't been perceived as a breakthrough.
State of the art in that area ("parameter tuning", "algorithm configuration") is the SPOT package in R. You can connect external fitness functions using a language of your choice. It is really powerful.
I am working on adapters for e.g. C++ and Java that simplify the experimental setup, which requires some getting used to in SPOT. The project goes under name InPUT, and a first version of the tuning part will be up soon.
I'm writing an app to help facilitate some research, and part of this involves doing some statistical calculations. Right now, the researchers are using a program called SPSS. Part of the output that they care about looks like this:
They're really only concerned about the F and Sig. values. My problem is that I have no background in statistics, and I can't figure out what the tests are called, or how to calculate them.
I thought the F value might be the result of the F-test, but after following the steps given on Wikipedia, I got a result that was different from what SPSS gives.
This website might help you out a bit more. Also this one.
I'm working from a fairly rusty memory of a statistics course, but here goes nothing:
When you're doing analysis of variance (ANOVA), you actually calculate the F statistic as the ratio from the mean-square variances "between the groups" and the mean-square variances "within the groups". The second link above seems pretty good for this calculation.
This makes the F statistic measure exactly how powerful your model is, because the "between the groups" variance is explanatory power, and "within the groups" variance is random error. High F implies a highly significant model.
As in many statistical operations, you back-determine Sig. using the F statistic. Here's where your Wikipedia information comes in slightly handy. What you want to do is - using the degrees of freedom given to you by SPSS - find the proper P value at which an F table will give you the F statistic you calculated. The P value where this happens [F(table) = F(calculated)] is the significance.
Conceptually, a lower significance value shows a very strong ability to reject the null hypothesis (which for these purposes means to determine your model has explanatory power).
Sorry to any math folks if any of this is wrong. I'll be checking back to make edits!!!
Good luck to you. Stats is fun, just maybe not this part. =)
I assume from your question that your research colleagues want to automate the process by which certain statistical analyses are performed (i.e., they want to batch process data sets). You have two options:
1) SPSS is now scriptable through python (as of version 15) - go to spss.com and search for python. You can write python scripts to automate data analyses and extract key values from pivot tables, and then process the answers any way you like. This has the virtue of allowing an exact comparison between the results from your python script and the hand-calculated efforts in SPSS of your collaborators. Thus you won't have to really know any statistics to do this work (which is a key advantage)
2) You could do this in R, a free statistics environment, which could probably be scripted. This has the disadvantage that you will have to learn statistics to ensure that you are doing it correctly.
Statistics is hard :-). After a year of reading and re-reading books and papers and can only say with confidence that I understand the very basics of it.
You might wish to investigate ready-made libraries for whichever programming language you are using, because they are many gotcha's in math in general and statistics in particular (rounding errors being an obvious example).
As an example you could take a look at the R project, which is both an interactive environment and a library which you can use from your C++ code, distributed under the GPL (ie if you are using it only internally and publishing only the results, you don't need to open your code).
In short: don't do this by hand, link/use existing software. And sain_grocen's answer is incorrect. :(
These are all tests for significance of parameter estimates that are typically used in Multivariate response Multiple Regressions. These would not be simple things to do outside of a statistical programming environment. I would suggest either getting the output from a pre-existing statistical program, or using one that you can link to and use that code.
I'm afraid that the first answer (sain_grocen's) will lead you down the wrong path. His explanation is likely of a special case of what you are actually dealing with. The anova explained in his links is for a single variate response, in a balanced design. These aren't the F statistics you are seeing. The names in your output (Pillai's Trace, Hotelling's Trace,...) are some of the available multivariate versions. They have F distributions under certain assumptions. I can't explain a text books worth of material here, I would advise you to start by looking at
"Applied Multivariate Statistical Analysis" by Johnson and Wichern
Can you explain more why SPSS itself isn't a fine solution to the problem? Is it that it generates pivot tables as output that are hard to manipulate? Is it the cost of the program?
F-statistics can arise from any number of particular tests. The F is just a distribution (loosely: a description of the "frequencies" of groups of values), like a Normal (Gaussian), or Uniform. In general they arise from ratios of variances. Opinion: many statisticians (myself included), find F-based tests to be unstable (jargon: non-robust).
The particular output statistics (Pillai's trace, etc.) suggest that the original analysis is a MANOVA example, which as other posters describe is a complicated, and hard to get right procedure.
I'm guess also that, based on the MANOVA, and the use of SPSS, this is a psychology or sociology project... if not please enlighten. It might be that other, simpler models might actually be easier to understand and more repeatable. Consult your local university statistical consulting group, if you have one.
Good luck!
Here's an explanation of MANOVA ouptput, from a very good site on statistics and on SPSS:
Output with explanation:
http://faculty.chass.ncsu.edu/garson/PA765/manospss.htm
How and why to do MANOVA or multivariate GLM:
(same path as above, but terminating in '/manova.htm')
Writing software from scratch to calculate these outputs would be both lengthy and difficult;
there's lots of numerical problems and matrix inversions to do.
As Henry said, use Python scripts, or R. I'd suggest working with somebody who knows SPSS if scripting.
In addition, SPSS itself is capable of exporting the output tables to files using something called OMS.
A script within SPSS can do this.
Find out who in your research group knows SPSS and work with them.