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README.md

ProjectB

ProjectB Logo

ProjectB is a graphical user interface, which allows untrained users to optimize any model that can be invoked through a command line. The GUI is built on top of a modular Bayesian Optimization library, pybo, which includes most common acquisition functions and kernels and more.

Installation

The easiest way to install this package is by running

pip install -r https://github.com/udoniyor/projectb/raw/master/requirements.txt
pip install git+https://github.com/udoniyor/projectb.git

The first line installs any dependencies of the package and the second line installs the package itself. Alternatively the repository can be cloned directly in order to make any local modifications to the code. In this case the dependencies can easily be installed by running

pip install -r requirements.txt

from the main directory.

Tips

If you are having trouble installing via pip, try installing scipy and numpy with package manager on UNIX based systems. For more details on how to install SciPy stack on your machine look here

If you are on Windows and having troubles with pip, try Anaconda. It includes numpy and scipy, therefore reducing the chances of running into an error.

Usage (GUI)

To invoke the Graphical User Interface, you need to type in following command into the command line:

	python -m projectb.start

This will launch the GUI of the framework. You may also specify the settings file to prefill the fields in the UI.

	python -m projectb.start /home/user/settingsfile.projectb

Your settings file can have any extension name, but for clarity purposes keep it simple and relevant.

Usage (Command Line)

The framework can be executed via commandline, but you must specify a settings file. Settings file format is a CSV file, with one parameters per line. You will find the specification for the settings file in the next section. Alternatively, you may create a settings file via the GUI by exporting the settings defined in the UI. To invoke the command line, you simply add -cli to the command.

	python -m projectb.start /home/user/settingsfile.projectb -cli

Optionally, you can specify the output directory during the invokation.

	python -m projectb.start /home/user/settingsfile.projectb /home/user/outputhere/ -cli

It is adviced to provide an output directory, otherwise the framework will write to the directory called from.

File Format Specification

The Framework defines a simple CSV (Comma Separated Values) as a file format which specifies the parameters of the Bayesian Optimization and model details; such as the input file, command and the output directory.

The file structure follows a simple pattern, each line stores only one parameter. First value is the parameter key, for example “policies”; followed by the value of the parameter, separated by a comma such as “ei” (expected improvement policy). The structure allows having multiple values for each parameter, but this is limited only to the kernel and policy parameters. The limitation is imposed by the graphical user interface, where only multiple kernel and policies can be selected.

Another exception is the bounds parameter. The bounds can be described by stating the key "bounds", followed by a comma, lower bound, comma and upper bound. The key can be defined multiple times to specify many bounds. For example if function has three inputs with bounds between 0 and 100, it should be specified as follows:

	...
	bounds,0,100
	bounds,0,100
	bounds,0,100
	...

In addition, to the parameters, the file format stores the data gathered during optimization or user pre-processed data. The order of the parameters does not matter, except for the data parameter. The data parameter must be defined last followed by the data where the second column is y values and starting from the 4th column are the x inputs. The purpose of the strict data column layout is to match the output of the framework. The framework, output is structured in a following way: time per iteration in seconds, objective value achieved at the iteration, mean calculated from the posterior for the point prior evaluation, variance calculated from the posterior for the point prior evaluation, followed by the input values separated via commas.

You do not need to specify all the kays and parameters for the framework, most have reasonable default values. Only following are required for the framework: command, modelinput, modeloutput, and bounds. By default, the framework maximizes with EI policy and SE kernel for 150 iterations with sobol initialzer.

Basic Settings Spefication:

Keys	|	Parameters
command |	command line string to invoke the function
modelinput | input file for the function. One parameter per line
modeloutput | output file for the function.
bounds | lowerbound,upperbound
outputdir | directory to output the results to
policies | ei,pi,ucb,thompson
kernels | matern1,matern3,matern5,se
iter | number of iterations
objective | min/max
solver | direct*/lbfgs 
initializer | sobol/middle/uniform
initializernum | number of samples to sample by the initializer
recommender | latent/incumbent/observed
normalize | True/False **
  • Requires nlopt python library ** Normalize the bounds between 0 and 1. Experiments have shown normalizing the input helps with performence of the lbfgs solver. Preferably, use direct solver without normalization. *** Dimension Scheduler is a technique to improve the performence of the Bayesian Optimization.

Advanced Settings Specification:

dims | If dimension scheduler enabled, number of dimensions per permutation
dimscheudler | True/False ***
mcmcburn | Burn number
mcmcn | Number of GPs
eixi | Exploration parameter for the EI policy
pixi | Exploration parameter for the PI policy
ucbxi | Exploration parameter for the UCB policy
ucbdelta | Probability of that the upper bound holds
thompsonn | number of Fourier components
thompsonrng | Random seed

Following keys have python code snippets as parameters:

Gaussian Process Settings:
gpsf, gpmu, gpell, gpsn

Hyper-prior Settings
priorsnscale, priorsnmin, priorsfmu
priorsfsigma, priorsfmin 
priorella, priorellb
priormumu, priormuvar