SAGA-optimize 1.0.2

Optimization method for solving boundary-value inverse problem based on a combined simulated annealing and genetic algorithm

SAGA_optimize
=============


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`SAGA_optimize` is a novel type of combined simulated annealing and genetic algorithm
used to find the optimal solutions to a set of parameters based on a given energy
function calculated using the set of parameters.


Citation
~~~~~~~~

Please cite the GitHub repository until our manuscript is accepted for
publications: https://github.com/MoseleyBioinformaticsLab/SAGA_optimize.git


Installation
~~~~~~~~~~~~

`SAGA_optimize` runs under Python 3.6+ and is available through python3-pip.
Install via pip or clone the git repo and install the following dependencies
and you are ready to go!


Install on Linux
----------------

Pip installation
................

.. code:: bash

python3 -m pip install SAGA-optimize


GitHub Package installation
...........................


Make sure you have git_ installed:

.. code:: bash

cd ~/
git clone https://github.com/MoseleyBioinformaticsLab/SAGA_optimize.git


Dependecies
...........

`SAGA_optimize` requires the following Python libraries:

* JSONPickle_ for saving Python objects in a JSON serializable form and outputting to a file.


Quickstart
~~~~~~~~~~

.. code:: python

>>> import SAGA_optimize
>>> saga = SAGA_optimize.SAGA(stepNumber=100000, temperatureStepSize=100, startTemperature=0.5,
alpha=1, direction=-1, energyCalculation=energyCalculation, crossoverRate=0.5,
mutationRate=3, annealMutationRate=1, populationSize=20) # SAGA instance creation.
>>> saga.addElementDescriptions(SAGA_optimize.ElementDescription(low=0, high=10),
SAGA_optimize.ElementDescription(low=0, high=10),
SAGA_optimize.ElementDescription(low=0, high=10),
SAGA_optimize.ElementDescription(low=0, high=10),
SAGA_optimize.ElementDescription(low=0, high=10)) # Add optimized parameters.
>>> optimized_population = saga.optimize() # the population returned after the opitimization.

.. note:: Read the User Guide and the ``SAGA_optimize`` Tutorial on ReadTheDocs_ to learn more and to see code examples on using the ``SAGA_optimize`` as a library.


License
~~~~~~~

.. include:: ../LICENSE

Made available under the terms of The Clear BSD License. See full license in LICENSE_.

Authors
~~~~~~~

* **Huan Jin**
* **Hunter N.B. Moseley**

.. _ReadTheDocs: https://saga-optimize.readthedocs.io/en/latest/
.. _jsonpickle: https://jsonpickle.github.io/
.. _git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git/
.. _LICENSE: