Yeah, I don't think we want to include that in the scope of the GSoC. Using MLE parameters still works, just converges a bit slower.
On 03/09/2015 11:28 AM, Jan Hendrik Metzen wrote: > A combination of emcee with GPs (in this case the GPs from george) is > described here: > http://dan.iel.fm/george/current/user/hyper/#sampling-marginalization > As PR #4270 for sklearn also exposes a method > log_marginal_likelihood(theta) in GaussianProcessRegressor, it should be > straight-forward to adapt this example to the PR. If we would use emcee > for the marginalization of the hyperparameters in Bayesian optimization, > we would of course add an additional dependency. As this is probably not > desirable, hyperparameter marginalization would require implementing a > separate MCMC sampler in sklearn, which could go beyond the scope of the > GSoC topic. > > > On 09.03.2015 15:07, Andreas Mueller wrote: >> Does emcee implement Bayesian optimization? >> What is the distribution you assume? GPs? >> I thought emcee was a sampler. I need to check in with Dan ;) >> >> >> On 03/09/2015 09:27 AM, Sturla Molden wrote: >>> For Bayesian optimization with MCMC (which I believe spearmint also >>> does) I have found that emcee is very nice: >>> >>> http://dan.iel.fm/emcee/current/ >>> >>> It is much faster than naïve MCMC methods and all we need to do is >>> compute a callback that computes the loglikelihood given the parameter >>> set (which can just as well be hyperparameters). >>> >>> To do this computation in parallel one can simply evaluate the walkers >>> in parallel and do a barrier synchronization after each step. The >>> contention due to the barrier can be reduced by increasing the number of >>> walkers as needed. Also one should use something like DCMT for random >>> numbers to make sure there are no contention for the PRNG and to ensure >>> that each thread (or process) gets an independent stream of random numbers. >>> >>> emcee implements this kind of optimization using multiprocessing, but it >>> passes parameter sets around using pickle and is therefore not very >>> efficient compared to just storing the current parameter for each walker >>> in shared memory. So there is a lot of room for improvement here. >>> >>> >>> Sturla >>> >>> >>> >>> On 07/03/15 15:06, Kyle Kastner wrote: >>>> I think finding one method is indeed the goal. Even if it is not the >>>> best every time, a 90% solution for 10% of the complexity would be >>>> awesome. I think GPs with parameter space warping are *probably* the >>>> best solution but only a good implementation will show for sure. >>>> >>>> Spearmint and hyperopt exist and work for more complex stuff but with >>>> far more moving parts and complexity. Having a tool which is easy to use >>>> as the grid search and random search modules currently are would be a >>>> big benefit. >>>> >>>> My .02c >>>> >>>> Kyle >>>> >>>> On Mar 7, 2015 7:48 AM, "Christof Angermueller" >>>> <c.angermuel...@gmail.com >>>> <mailto:c.angermuel...@gmail.com>> wrote: >>>> >>>> Hi Andreas (and others), >>>> >>>> I am a PhD student in Bioinformatics at the University of Cambridge, >>>> (EBI/EMBL), supervised by Oliver Stegle and Zoubin Ghahramani. In my >>>> PhD, I apply and develop different machine learning algorithms for >>>> analyzing biological data. >>>> >>>> There are different approaches for hyperparameter optimization, some >>>> of which you mentioned on the topics page: >>>> * Sequential Model-Based Global Optimization (SMBO) -> >>>> http://www.cs.ubc.ca/labs/beta/Projects/SMAC/ >>>> * Gaussian Processes (GP) -> Spearmint; >>>> https://github.com/JasperSnoek/spearmint >>>> * Tree-structured Parzen Estimator Approach (TPE) -> Hyperopt: >>>> http://hyperopt.github.io/hyperopt/ >>>> >>>> And more recent approaches based on neural networks: >>>> * Deep Networks for Global Optimization (DNGO) -> >>>> http://arxiv.org/abs/1502.05700 >>>> >>>> The idea is to implement ONE of this approaches, right? >>>> >>>> Do you prefer a particular approach due to theoretical or practical >>>> reasons? >>>> >>>> Spearmint also supports distributing jobs on a cluster (SGE). I >>>> imagine that this requires platform specific code, which could be >>>> difficult to maintain. What do you think? >>>> >>>> Spearmint and hyperopt are already established python packages. >>>> Another sklearn implementation might be considered as redundant, are >>>> hard to establish. Do you have a particular new feature in mind? >>>> >>>> >>>> Cheers, >>>> Christof >>>> >>>> -- >>>> Christof Angermueller >>>> cangermuel...@gmail.com <mailto:cangermuel...@gmail.com> >>>> http://cangermueller.com >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Dive into the World of Parallel Programming The Go Parallel Website, >>>> sponsored >>>> by Intel and developed in partnership with Slashdot Media, is your >>>> hub for all >>>> things parallel software development, from weekly thought leadership >>>> blogs to >>>> news, videos, case studies, tutorials and more. Take a look and join >>>> the >>>> conversation now. http://goparallel.sourceforge.net/ >>>> _______________________________________________ >>>> Scikit-learn-general mailing list >>>> Scikit-learn-general@lists.sourceforge.net >>>> <mailto:Scikit-learn-general@lists.sourceforge.net> >>>> https://lists.sourceforge.net/lists/listinfo/scikit-learn-general >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Dive into the World of Parallel Programming The Go Parallel Website, >>>> sponsored >>>> by Intel and developed in partnership with Slashdot Media, is your hub for >>>> all >>>> things parallel software development, from weekly thought leadership blogs >>>> to >>>> news, videos, case studies, tutorials and more. Take a look and join the >>>> conversation now. http://goparallel.sourceforge.net/ >>>> >>>> >>>> >>> ------------------------------------------------------------------------------ >>> Dive into the World of Parallel Programming The Go Parallel Website, >>> sponsored >>> by Intel and developed in partnership with Slashdot Media, is your hub for >>> all >>> things parallel software development, from weekly thought leadership blogs >>> to >>> news, videos, case studies, tutorials and more. Take a look and join the >>> conversation now. http://goparallel.sourceforge.net/ >>> _______________________________________________ >>> Scikit-learn-general mailing list >>> Scikit-learn-general@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/scikit-learn-general >> ------------------------------------------------------------------------------ >> Dive into the World of Parallel Programming The Go Parallel Website, >> sponsored >> by Intel and developed in partnership with Slashdot Media, is your hub for >> all >> things parallel software development, from weekly thought leadership blogs to >> news, videos, case studies, tutorials and more. Take a look and join the >> conversation now. http://goparallel.sourceforge.net/ >> _______________________________________________ >> Scikit-learn-general mailing list >> Scikit-learn-general@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/scikit-learn-general >> >> > ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Scikit-learn-general mailing list Scikit-learn-general@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/scikit-learn-general
