Re: [R] any more direct-search optimization method in R
Given that information, I think a genetic algorithm should probably do well with your problem. You may want to try the rgenoud package (R-GENetic Optimization Using Derivatives) which is on CRAN. For more information see: http://sekhon.berkeley.edu/rgenoud/ It works well for these kinds of problems and the package is relatively flexible. For time consuming problems it can be run in parallel if you have multiple cores/cpus or machines. Cheers, JS. === Jasjeet S. Sekhon Associate Professor Survey Research Center UC Berkeley http://sekhon.berkeley.edu/ V: 510-642-9974 F: 617-507-5524 === Given that information, I think a genetic algorithm should probably do well with your problem. Standard derivative-based optimizers are going to get frustrated and give up. I can believe that Nelder-Mead could get confused as well, though I'm not sure that it will. 'genopt' from S Poetry does have box constraints for the parameters. I'm not sure what other genetic algorithms that are in R are like. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) Weijie Cai wrote: Hi All, Thanks for all your replies especially for Graves suggestions. You are right I should give more information about my function. So my responds to your questions are: 1. 2. the function itself is not continuous/smooth. The evaluation at each point is a random number with a non-constant variance. When it approaches the global minimum, the variance is very small. There is some kind of structure from the surface plot of my function but its form is intractable, unfortunately. 3. 4. each evaluation of my function is not slow. The returned results by constrOptim() are just not quite close to true global minimum (error can be as large as 0.2). Of course I can ignore the message of nonconvergence, the precision is really not satisfying. Every time nelder-mead will use up 300 default iterations when doing optimization. I guess the essential reason is the randomness of function surface. 5. Yes I am sure there is a global minimum. I did a lengthy computation at rough grids and global minimum is very close to true minimum. 6. Do you mean I start from a minimum found by grid searching? That's what I did. I never tried using smooth functions to approximate my function though. WC From: Spencer Graves [EMAIL PROTECTED] To: Ingmar Visser [EMAIL PROTECTED] CC: Weijie Cai [EMAIL PROTECTED], r-help@stat.math.ethz.ch Subject: Re: [R] any more direct-search optimization method in R Date: Tue, 28 Feb 2006 09:33:35 -0800 WC: What do you mean by noisy in this context? 1. You say, gradient, hessian not available. Is it continuous with perhaps discontinuities in the first derivative? 2. Or is it something you can compute only to, say, 5 significant digits, and some numerical optimizers get lost trying to estimate derivatives from so fine a grid that the gradient and hessian are mostly noise? 3. Also, why do you think constrOptim is too slow? Does it call your function too many times or does your function take too long to compute each time it's called? 4. What's not satisfactory about the results of constrOptim? 5. Do you know if only one it has only one local minimum in the region, or might it have more? 6. Regardless of the answers to the above, have you considered using expand.grid to get starting values and narrow the search (with possibly system.time or proc.time to find out how much time is required for each function evaluation)? I haven't tried this, but I would think it would be possible to fit a spline (either exactly or a smoothing spline) to a set of points, then optimize the spline. hope this helps. spencer graves Ingmar Visser wrote: If you have only boundary constraints on parameters you can use method L-BFGS in optim. Hth, ingmar From: Weijie Cai [EMAIL PROTECTED] Date: Tue, 28 Feb 2006 11:48:32 -0500 To: r-help@stat.math.ethz.ch Subject: [R] any more direct-search optimization method in R Hello list, I am dealing with a noisy function (gradient,hessian not available) with simple boundary constraints (x_i0). I've tried constrOptim() using nelder mead to minimize it but it is way too slow and the returned results are not satisfying. simulated annealing is so hard to tune and it always crashes R program in my case. I wonder if there are any packages or functions can do direct search optimization? A rough search in literature shows multidirectional search and DIRECT algorithm may help. Is there any other satisfying algorithm? Thanks, WC
Re: [R] any more direct-search optimization method in R
If you have only boundary constraints on parameters you can use method L-BFGS in optim. Hth, ingmar From: Weijie Cai [EMAIL PROTECTED] Date: Tue, 28 Feb 2006 11:48:32 -0500 To: r-help@stat.math.ethz.ch Subject: [R] any more direct-search optimization method in R Hello list, I am dealing with a noisy function (gradient,hessian not available) with simple boundary constraints (x_i0). I've tried constrOptim() using nelder mead to minimize it but it is way too slow and the returned results are not satisfying. simulated annealing is so hard to tune and it always crashes R program in my case. I wonder if there are any packages or functions can do direct search optimization? A rough search in literature shows multidirectional search and DIRECT algorithm may help. Is there any other satisfying algorithm? Thanks, WC __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] any more direct-search optimization method in R
Ingmar Visser I.Visser at uva.nl writes: If you have only boundary constraints on parameters you can use method L-BFGS in optim. Hth, ingmar From: Weijie Cai wcai11 at hotmail.com I am dealing with a noisy function (gradient,hessian not available) with simple boundary constraints (x_i0). I've tried constrOptim() using nelder mead to minimize it but it is way too slow and the returned results are not satisfying. simulated annealing is so hard to tune and it always crashes R program in my case. I wonder if there are any packages or functions can do direct search optimization? Noisy functions are really challenging to optimize; (1) there is no best method (despite all the papers doing comparisons of stochastic global optimizers on various sets of test functions); (2) the fancier methods are hard to program [and existing implementations tend have more restricted licenses]; (3) they tend to be slow (thousands of function evaluations). Packages on CRAN that *might* be helpful are genalg, DEoptim. A typical poor man's approach to boundary constraints is to add a quadratic penalty (perhaps not even trying to evaluate the objective function -- e.g. substituting the value at the closest boundary point) for parameters outside the constraints into the objective function. With more information (number of parameters, time to compute a single function evaluation, kind of noise) we might be able to help more. Ben Bolker __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] any more direct-search optimization method in R
WC: What do you mean by noisy in this context? 1. You say, gradient, hessian not available. Is it continuous with perhaps discontinuities in the first derivative? 2. Or is it something you can compute only to, say, 5 significant digits, and some numerical optimizers get lost trying to estimate derivatives from so fine a grid that the gradient and hessian are mostly noise? 3. Also, why do you think constrOptim is too slow? Does it call your function too many times or does your function take too long to compute each time it's called? 4. What's not satisfactory about the results of constrOptim? 5. Do you know if only one it has only one local minimum in the region, or might it have more? 6. Regardless of the answers to the above, have you considered using expand.grid to get starting values and narrow the search (with possibly system.time or proc.time to find out how much time is required for each function evaluation)? I haven't tried this, but I would think it would be possible to fit a spline (either exactly or a smoothing spline) to a set of points, then optimize the spline. hope this helps. spencer graves Ingmar Visser wrote: If you have only boundary constraints on parameters you can use method L-BFGS in optim. Hth, ingmar From: Weijie Cai [EMAIL PROTECTED] Date: Tue, 28 Feb 2006 11:48:32 -0500 To: r-help@stat.math.ethz.ch Subject: [R] any more direct-search optimization method in R Hello list, I am dealing with a noisy function (gradient,hessian not available) with simple boundary constraints (x_i0). I've tried constrOptim() using nelder mead to minimize it but it is way too slow and the returned results are not satisfying. simulated annealing is so hard to tune and it always crashes R program in my case. I wonder if there are any packages or functions can do direct search optimization? A rough search in literature shows multidirectional search and DIRECT algorithm may help. Is there any other satisfying algorithm? Thanks, WC __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] any more direct-search optimization method in R
Mathematica may well have good optimization routines; I know MATLAB does (e.g. the optimization toolbox, http://www.mathworks.com/products/optimization/?BB=1 , has a general-constraints nonlinear optimizer) -- I also think more people develop optimization code in MATLAB because of its use in engineering circles. (The DIRECT algorithm is implemented in TOMLAB, a MATLAB add-on package from a third party.) (S+NuOPT is also available from Insightful, although it doesn't look like it does global stochastic stuff; our friends at Otter Research have ADMB, although I don't know how well it handles noisy objective functions.) Drawbacks: (1) switching platforms is a pain, (2) most of these alternatives are expensive [although if you have the money it may well be worth it], (3) Mathematica is notoriously bad about documenting its methods and giving references to the peer-reviewed literature. If I were regularly doing really difficult optimization problems I might switch to MATLAB+add-ons. I would like to see more optimization choices implemented in R, but haven't gotten around to doing so myself yet. For hard optimization problems, however, it is nearly always true that you have to know something about your problem and tune methods accordingly (see Spencer Graves' message in this thread). Ben Original Message Subject: Re: [R] any more direct-search optimization method in R Date: Tue, 28 Feb 2006 09:55:15 -0800 (PST) From: Greg Tarpinian [EMAIL PROTECTED] To: Ben Bolker [EMAIL PROTECTED] This may not be the most helpful advice, but Mathematica is a wonderful platform having many more built-in optimization routines than R. I have found the simulated annealing facility to be robust and much easier to use than R's own facility. This may be a case where switching to another platform would be the easiest solution. Kind regards, Greg --- Ben Bolker [EMAIL PROTECTED] wrote: Ingmar Visser I.Visser at uva.nl writes: If you have only boundary constraints on parameters you can use method L-BFGS in optim. Hth, ingmar From: Weijie Cai wcai11 at hotmail.com I am dealing with a noisy function (gradient,hessian not available) with simple boundary constraints (x_i0). I've tried constrOptim() using nelder mead to minimize it but it is way too slow and the returned results are not satisfying. simulated annealing is so hard to tune and it always crashes R program in my case. I wonder if there are any packages or functions can do direct search optimization? Noisy functions are really challenging to optimize; (1) there is no best method (despite all the papers doing comparisons of stochastic global optimizers on various sets of test functions); (2) the fancier methods are hard to program [and existing implementations tend have more restricted licenses]; (3) they tend to be slow (thousands of function evaluations). Packages on CRAN that *might* be helpful are genalg, DEoptim. A typical poor man's approach to boundary constraints is to add a quadratic penalty (perhaps not even trying to evaluate the objective function -- e.g. substituting the value at the closest boundary point) for parameters outside the constraints into the objective function. With more information (number of parameters, time to compute a single function evaluation, kind of noise) we might be able to help more. Ben Bolker __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ -- 620B Bartram Hall[EMAIL PROTECTED] Zoology Department, University of Floridahttp://www.zoo.ufl.edu/bolker Box 118525 (ph) 352-392-5697 Gainesville, FL 32611-8525 (fax) 352-392-3704 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] any more direct-search optimization method in R
Hi All, Thanks for all your replies especially for Graves suggestions. You are right I should give more information about my function. So my responds to your questions are: 1. 2. the function itself is not continuous/smooth. The evaluation at each point is a random number with a non-constant variance. When it approaches the global minimum, the variance is very small. There is some kind of structure from the surface plot of my function but its form is intractable, unfortunately. 3. 4. each evaluation of my function is not slow. The returned results by constrOptim() are just not quite close to true global minimum (error can be as large as 0.2). Of course I can ignore the message of nonconvergence, the precision is really not satisfying. Every time nelder-mead will use up 300 default iterations when doing optimization. I guess the essential reason is the randomness of function surface. 5. Yes I am sure there is a global minimum. I did a lengthy computation at rough grids and global minimum is very close to true minimum. 6. Do you mean I start from a minimum found by grid searching? That's what I did. I never tried using smooth functions to approximate my function though. WC From: Spencer Graves [EMAIL PROTECTED] To: Ingmar Visser [EMAIL PROTECTED] CC: Weijie Cai [EMAIL PROTECTED], r-help@stat.math.ethz.ch Subject: Re: [R] any more direct-search optimization method in R Date: Tue, 28 Feb 2006 09:33:35 -0800 WC: What do you mean by noisy in this context? 1. You say, gradient, hessian not available. Is it continuous with perhaps discontinuities in the first derivative? 2. Or is it something you can compute only to, say, 5 significant digits, and some numerical optimizers get lost trying to estimate derivatives from so fine a grid that the gradient and hessian are mostly noise? 3. Also, why do you think constrOptim is too slow? Does it call your function too many times or does your function take too long to compute each time it's called? 4. What's not satisfactory about the results of constrOptim? 5. Do you know if only one it has only one local minimum in the region, or might it have more? 6. Regardless of the answers to the above, have you considered using expand.grid to get starting values and narrow the search (with possibly system.time or proc.time to find out how much time is required for each function evaluation)? I haven't tried this, but I would think it would be possible to fit a spline (either exactly or a smoothing spline) to a set of points, then optimize the spline. hope this helps. spencer graves Ingmar Visser wrote: If you have only boundary constraints on parameters you can use method L-BFGS in optim. Hth, ingmar From: Weijie Cai [EMAIL PROTECTED] Date: Tue, 28 Feb 2006 11:48:32 -0500 To: r-help@stat.math.ethz.ch Subject: [R] any more direct-search optimization method in R Hello list, I am dealing with a noisy function (gradient,hessian not available) with simple boundary constraints (x_i0). I've tried constrOptim() using nelder mead to minimize it but it is way too slow and the returned results are not satisfying. simulated annealing is so hard to tune and it always crashes R program in my case. I wonder if there are any packages or functions can do direct search optimization? A rough search in literature shows multidirectional search and DIRECT algorithm may help. Is there any other satisfying algorithm? Thanks, WC __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] any more direct-search optimization method in R
Given that information, I think a genetic algorithm should probably do well with your problem. Standard derivative-based optimizers are going to get frustrated and give up. I can believe that Nelder-Mead could get confused as well, though I'm not sure that it will. 'genopt' from S Poetry does have box constraints for the parameters. I'm not sure what other genetic algorithms that are in R are like. Patrick Burns [EMAIL PROTECTED] +44 (0)20 8525 0696 http://www.burns-stat.com (home of S Poetry and A Guide for the Unwilling S User) Weijie Cai wrote: Hi All, Thanks for all your replies especially for Graves suggestions. You are right I should give more information about my function. So my responds to your questions are: 1. 2. the function itself is not continuous/smooth. The evaluation at each point is a random number with a non-constant variance. When it approaches the global minimum, the variance is very small. There is some kind of structure from the surface plot of my function but its form is intractable, unfortunately. 3. 4. each evaluation of my function is not slow. The returned results by constrOptim() are just not quite close to true global minimum (error can be as large as 0.2). Of course I can ignore the message of nonconvergence, the precision is really not satisfying. Every time nelder-mead will use up 300 default iterations when doing optimization. I guess the essential reason is the randomness of function surface. 5. Yes I am sure there is a global minimum. I did a lengthy computation at rough grids and global minimum is very close to true minimum. 6. Do you mean I start from a minimum found by grid searching? That's what I did. I never tried using smooth functions to approximate my function though. WC From: Spencer Graves [EMAIL PROTECTED] To: Ingmar Visser [EMAIL PROTECTED] CC: Weijie Cai [EMAIL PROTECTED], r-help@stat.math.ethz.ch Subject: Re: [R] any more direct-search optimization method in R Date: Tue, 28 Feb 2006 09:33:35 -0800 WC: What do you mean by noisy in this context? 1. You say, gradient, hessian not available. Is it continuous with perhaps discontinuities in the first derivative? 2. Or is it something you can compute only to, say, 5 significant digits, and some numerical optimizers get lost trying to estimate derivatives from so fine a grid that the gradient and hessian are mostly noise? 3. Also, why do you think constrOptim is too slow? Does it call your function too many times or does your function take too long to compute each time it's called? 4. What's not satisfactory about the results of constrOptim? 5. Do you know if only one it has only one local minimum in the region, or might it have more? 6. Regardless of the answers to the above, have you considered using expand.grid to get starting values and narrow the search (with possibly system.time or proc.time to find out how much time is required for each function evaluation)? I haven't tried this, but I would think it would be possible to fit a spline (either exactly or a smoothing spline) to a set of points, then optimize the spline. hope this helps. spencer graves Ingmar Visser wrote: If you have only boundary constraints on parameters you can use method L-BFGS in optim. Hth, ingmar From: Weijie Cai [EMAIL PROTECTED] Date: Tue, 28 Feb 2006 11:48:32 -0500 To: r-help@stat.math.ethz.ch Subject: [R] any more direct-search optimization method in R Hello list, I am dealing with a noisy function (gradient,hessian not available) with simple boundary constraints (x_i0). I've tried constrOptim() using nelder mead to minimize it but it is way too slow and the returned results are not satisfying. simulated annealing is so hard to tune and it always crashes R program in my case. I wonder if there are any packages or functions can do direct search optimization? A rough search in literature shows multidirectional search and DIRECT algorithm may help. Is there any other satisfying algorithm? Thanks, WC __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
