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https://github.com/JasperSnoek/spearmint

Spearmint is a package to perform Bayesian optimization according to the algorithms outlined in the paper: Practical Bayesian Optimization of Machine Learning Algorithms. Jasper Snoek, Hugo Larochelle and Ryan P. Adams. Advances in Neural Information Processing Systems, 2012
https://github.com/JasperSnoek/spearmint

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Spearmint is a package to perform Bayesian optimization according to the algorithms outlined in the paper: Practical Bayesian Optimization of Machine Learning Algorithms. Jasper Snoek, Hugo Larochelle and Ryan P. Adams. Advances in Neural Information Processing Systems, 2012

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README 

        
New code repository!

As you might have noticed, the development of this repository has been limited to maintenance and bug fixes for some time now.  The reason is that there has been a collaborative effort to overhaul Spearmint into a new codebase.  This includes both algorithmic/theoretical and engineering improvements.  Check it out at https://github.com/HIPS/Spearmint.  Note that the new repository is under a non-commercial license with a contributor license agreement.  If you prefer not to agree to the license, you can freely use code here (though it is a bit older).



Spearmint

---------



Spearmint is a package to perform Bayesian optimization according to the

algorithms outlined in the paper:  



**Practical Bayesian Optimization of Machine Learning Algorithms**  

Jasper Snoek, Hugo Larochelle and Ryan P. Adams  

*Advances in Neural Information Processing Systems*, 2012  



This code is designed to automatically run experiments (thus the code

name 'spearmint') in a manner that iteratively adjusts a number of

parameters so as to minimize some objective in as few runs as

possible.



Spearmint is the result of a collaboration primarily between machine learning researchers at [Harvard University](https://hips.seas.harvard.edu/) and the [University of Toronto](http://learning.cs.toronto.edu/).



Dependencies

------------

This package requires:



* Python 2.7



* [Numpy](http://www.numpy.org/) version 1.6.1+

On Ubuntu linux you can install this package using the command:



		apt-get install python-numpy



* [Scipy](http://www.scipy.org/) version 0.9.0+

On Ubuntu linux you can install this package using the command:



		apt-get install python-scipy



* [Google Protocol Buffers](https://developers.google.com/protocol-buffers/) (for the fully automated code).

Note that you should be able to install protocol-buffers from source without requiring administrator privileges.  Otherwise, on Ubuntu linux you can install this package using the command:



		apt-get install python-protobuf

						

	and on Mac (if you use homebrew) with:



		brew install protobuf



	Then from within the spearmint sub-directory run the command:



		bin/make_protobufs



This package has been tested on Ubuntu linux (versions 11.0+) and

Mac-OSX.



The code consists of several parts.  It is designed to be modular to

allow swapping out various 'driver' and 'chooser' modules.  The

'chooser' modules are implementations of acquisition functions such as

expected improvement, UCB or random.  The drivers determine how

experiments are distributed and run on the system.  As the code is

designed to run experiments in parallel (spawning a new experiment as

soon a result comes in), this requires some engineering.  The current

implementations of these are in the 'spearmint' and 'spearmint-lite' subdirectories:



**Spearmint** is designed to automatically manage the launching and associated bookkeeping 

of experiments in either a single machine or cluster environment.  This requires that you provide

a 'wrapper' in a supported language (currently Python or Matlab) and a configuration file detailing parameters

to be tuned and their respective bounds. The wrapper must accept parameter values and then return simply a value which you wish to minimize with respect to the parameters. Spearmint will then iteratively call the wrapper with different 

parameter settings in an order that seeks to find the minimum value in as few evaluations (or cost) as possible.



**Spearmint-lite** is the 'bare-bones' stripped version of the code.

This version is simply driven by a flat-file and does not

automatically run experiments.  Instead, it proposes new experiments

(potentially multiple at a time) and requires that the user fill in

the result.  This is well suited to the case where writing a wrapper

around the code doesn't make sense (e.g. if the experiments don't

involve code at all) or if the user desires full control of the

process.  Also, the dependency on Google protocol buffers is replaced

with JSON.



Running the automated code: Spearmint

--------------------------------------------------------



The simplest way to get to know the code is probably to look at an

example.  In order to start a new experiment, you must create a directory 

that includes a wrapper script and config file.

We have created one simple example for you that optimizes the

'Braninhoo' benchmark in the subdirectory **examples/braninpy**.  Take a look at

**config.pb**.  It contains the specifications of the algorithm in

protocol buffer format.  In order to specify your optimization, you

have to fill in the variables 'language' (e.g. PYTHON or MATLAB) and

'name' (the name of the wrapper function you want to optimize).



Followed by these is a list of 'variables', which specifies the name,

type and size of the variables you wish to optimize over.  Each

variable must be either a FLOAT, INT or ENUM type, corresponding to

continuous real valued parameters, integer sequences and categorical

variables respectively.  MAX and MIN specify the bounds of the

variables over which to optimize and SIZE is the number of variables

of this type with these bounds.  Spearmint will call your wrapper

function with a dictionary type (in python) containing each of your

variables in a vector of size 'size', which you can access using the

name specified.  



Now take a look at branin.py (the wrapper which was

specified in the 'name' variable at the top of config.pb).  You will

see the file has a function 'main(job_id, params)'.  Your wrapper must

include this function, which spearmint will call passing in a job_id

(which is probably not interesting to you) and a dictionary, 'params',

containing the parameter vectors of the next experiment spearmint

wants to run.  The main function should take as input these parameters

and return a single real valued number representing the observed

function value (that is being optimized) at these inputs.



To install spearmint, go into the spearmint subdirectory and type (most likely preceded with 'sudo'):



	python setup.py install



You should add the spearmint subdirectory to your PYTHONPATH directory.  Note that you can often avoid the above step, but may have to add all the relevant modules to your PYTHONPATH and call spearmint directory from the directory using main.py.



To run spearmint, go into the **/bin** subdirectory and type:



	./spearmint ../examples/braninpy/config.pb --driver=local --method=GPEIOptChooser --method-args=noiseless=1



or alternatively in the **/spearmint** subdirectory:



	python main.py --driver=local --method=GPEIOptChooser --method-args=noiseless=1 ../examples/braninpy/config.pb



This will run spearmint according to the GP-EI MCMC strategy.  The code will sequentially spawn

processes that call the wrapper function and it will poll for results.

You will see that the code prints out the current best (i.e. lowest)

observation seen thus far and sequences of numbers corresponding to GP

hyperparameter samples and candidates it is optimizing over.  The

'method' argument specifies the chooser module (acquisition function)

to use and 'method-args' specifies chooser specific arguments.  In

this case, as braninhoo is an analytic function we tell the GP

hyperparameter sampling routine to not try to estimate noise.  This parameter is very important to specify correctly for the optimization to proceed properly.  If your algorithm is entirely deterministic (e.g. analytic) then specifying that it is noiseless will speed up the optimization considerably.  If your algorithm is not deterministic, as we expect for most machine learning algorithms and indeed most expensive experiments, then you should leave this out or set noiseless=0.



If you let it run for a while you will see that the current-best

decreases, eventually reaching the minimum at ~0.39. You can kill the

process (ctrl-c) at any time and you can restart from where it left off simply

by rerunning the spearmint command.



If you go back in to the braninpy directory you will see a number of

new files that spearmint uses to do bookkeeping.  Of particular

interest are **trace.csv** and the **output** directory.  **trace.csv**

contains a record of the experiments run so far and the best result

(and which experiment it came from) as a series over time.  Each line

of trace.csv contains the following in csv format: a timestamp, the

best value observed up to that timestamp, the job-id of the best value

observed, the number of potential candidates left, the number of

pending (currently running) experiments, the number of experiments

completed thus far.  The output directory contains a text file for

each job-id, containing the output of that job.  So if you want to

see, e.g. what the output (i.e. standard out and standard error) was

for the best job (as obtained from trace.csv) you can look up

job-id.txt in the output directory. 



 If you are debugging your code,

or the code is crashing for some reason, it's a good idea to look at

these files. Finally for ease of use, spearmint also prints out at

each iteration a file called 'best_job_and_result.txt' that contains the

best result observed so far, the job-id it came from and a dump of 

the names and values of all of the parameters corresponding to that result.



A script, bin/cleanup, is provided to completely restart an experiment

and delete all the results and intermediate files.  Simply run

`bin/cleanup `



Matlab code can also be optimized using this package. To do so, you

must specify in config.pb "type: Matlab" and use a matlab wrapper with

the "name" specified in config.pb.  The matlab wrapper must have a

function with the same name as the file name of the following form:

"function result = braninhoo(job_id, params)" Above we assume the file

name is "braninhoo.m".  Spearmint will pass in to this wrapper a

job_id and a matlab struct 'params' where the fields are given by the

variables specified in config.pb.  See the subdirectory "braninhoo"

for a matlab example matching that of python 'braninpy' described

above.



To run multiple jobs in parallel, pass to spearmint the argument:

`--max-concurrent=<#jobs>`



Spearmint is designed to be run in parallel either using multiple processors on a single machine or in a cluster environment.  These different environments, however, involve different queuing and fault-checking code and are thus coded as 'driver' modules.  Currently two drivers are available, but one can easily create a driver for a different environment by creating a new driver module (see the driver subdirectory for examples).



Using the `--driver=sge` flag, Spearmint can run on a system with Sun Grid Engine and it uses SGE to distribute experiments on a multi-node cluster in parallel using a queueing system in a fault-tolerant way.  It is particularly

well suited to the Amazon EC2 system.  Using [StarCluster](http://star.mit.edu/cluster/) will allow you to set up a large cluster and start distributing experiments within minutes.



Using the `--driver=local` flag will run Spearmint on a single machine with potentially many cores.  This driver simply spawns a new process on the current machine to run a new experiment.  This does not allow you to distribute across multiple machines, however.



### Web Status Page

Running spearmint with the flag `-w` will spawn a local web server that will display useful info and statistics about your optimization run in a much more interpretable and intuitive interface than the command line.  Spearmint will provide a link to the status page that you can simply paste into a browser window.



Running the basic code: Spearmint-lite 

---------------------------------------



Spearmint-lite is designed to be simple.  To run an experiment in

spearmint-lite, create a subdirectory as explained above.  Again, the

braninpy directory is provided as a demonstration.  In this case, the

experiment specification, which must be provided in config.json, is in

JSON format.  You must specify your problem as a sequence of JSON

objects.  As in the protocol buffer format above, each object must

have a name, a type (float, int or enum), a 'min', a 'max' and a

'size'. Nothing else needs to be specified.  



Go back to the top-level directory and run: 



	python spearmint-lite.py braninpy



Spearmint-lite will run one iteration of Bayesian

optimization and write out to a file named results.dat in the braninpy

subdirectory.  results.dat will contain a white-space delimited line

for each experiment, of the format: 

`  `



Spearmint will propose new experiments and append them to results.dat each 

time it is run. Each proposed experiment will have a 'pending' result and 

time-taken, indicated by the letter P. The user must then run the experiment 

and fill in these values. Note that the time can safely be set to an arbitrary

value if the chooser module does not use it (only GPEIperSecChooser currently 

does). Spearmint will condition on the pending experiments when proposing new 

ones, so any number of experiments can be conducted in parallel.



A script, **cleanup.sh**, is provided to completely clean up all the intermediate

files and results in an experimental directory and restart the

experiment from scratch.



Chooser modules:

--------------- 



The chooser modules implement functions that tell spearmint which next

job to run.  Some correspond to 'acquisition functions' in the

Bayesian optimization literature.  Spearmint takes as an argument

`--method=ChooserModule` which allows one to easy swap out acquisition

functions. Choosers may optionally include parameters that can be

passed to spearmint using the argument

`--method-args=argument1,argument2,etc`.  These include, for example, the

number of GP hyperparameter samples to use. See the comments in

chooser files for chooser dependent arguments.  Below are described

the choosers provided in this package:



* **SequentialChooser:** Chooses the next experiment using a high

discrepancy Sobol sequence.  Experiments are taken sequentially from a

coarse-to-fine grid.



* **RandomChooser**: Experiments are sampled randomly from the unit hypercube.



* **GPEIOptChooser:** The GP EI MCMC algorithm from the paper. Jobs 

are first sampled densely from a dense grid on the unit hypercube

and then the best candidates are optimized 'fine-tuned' according

to EI.



* **GPEIperSecChooser:** The GP EI per Second algorithm from the paper.

Similar to GPEIOptChooser except points are optimized and evaluated

based on the EI per Second criterion, where each job is weighted

by the expected running time of the experiment.



* **GPEIChooser:** Points are densely sampled on the unit hypercube and the

best is returned according to the EI criterion.  This is considerably

faster than the GPEIOptChooser and works well in low-dimensional cases

where the grid covers the search space densely.



**IMPORTANT!**



When estimating noise, the Gaussian process prior over noise assumes

that the noise level is 'low' (e.g. between -1 to 1). If this is not

the case, make sure to rescale your function to make this true

(e.g. to approximately be between -1 and 1).  Otherwise, the algorithm

will find a bad high-noise mode that will result in bad performance.