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https://github.com/raamana/neuropredict

Easy and comprehensive assessment of predictive power, with support for neuroimaging features
https://github.com/raamana/neuropredict

anatomical-mri cross-validation easy-to-use functional-connectivity machine-learning neuroimaging nilearn pattern-recognition report resting-state scikit-learn structural-imaging tract-based-statistics tractography

Last synced: 11 days ago
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Easy and comprehensive assessment of predictive power, with support for neuroimaging features

Lists

README 

        

.. image:: docs/logo_neuropredict.png

    :width: 150



.. image:: https://img.shields.io/badge/say-thanks-ff69b4.svg

    :target: https://saythanks.io/to/raamana



**Documentation**: https://raamana.github.io/neuropredict/



News

----



-  As of ``v0.6``, **neuropredict now supports regression applications**

   i.e. predicting continuous targets (in addition to categorical

   classes), as well as allow you to **regress out covariates /

   confounds** within the nested-CV (following all the best practices).

   Utilizing this feature requires the input datasets be specified in

   the ``pyradigm`` data structures: code @ https://github.com/raamana/pyradigm,

   docs @ https://raamana.github.io/pyradigm/. Check the changelog below for more details.



Older news

----------



-  ``neuropredict`` can handle missing data now (that are encoded with

   ``numpy.NaN``). This is done respecting the cross-validation splits

   without any data leakage.



Overview

--------



On a high level,



.. image:: docs/high_level_flow.png

   :alt: roleofneuropredict



On a more detailed level,



.. image:: docs/role.png

   :alt: roleofneuropredict



-  Docs: https://raamana.github.io/neuropredict/

-  Contributors most welcome: `check ideas `__ and the following

   `guidelines `__.

   Thanks.



Long term goals

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



neuropredict, the tool, is part of a broader initiative described below

to develop easy, comprehensive and standardized predictive analysis:



.. image:: docs/neuropredict_long_term_goals.jpg

   :alt: longtermgoals



Citation

--------



If ``neuropredict`` helped you in your research in one way or another,

please consider citing one or more of the following, which were

essential building blocks of neuropredict: 



 - Pradeep Reddy Raamana. (2017). neuropredict: easy machine learning and standardized predictive analysis of biomarkers (Version 0.4.5). Zenodo. http://doi.org/10.5281/zenodo.1058993 

 - Raamana et al, (2017), Python class defining a machine learning dataset ensuring key-based correspondence and maintaining integrity, Journal of Open Source Software, 2(17), 382, doi:10.21105/joss.00382



Change Log - version 0.6

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

- Major feature: Ability to predict continuous variables (regression)

- Major feature: Ability to handle confounds (regress them out, augmenting etc)

- Redesigned the internal structure for easier extensibility

- New ``CVResults`` class for easier management of a wealth of outputs generated in the Classification and Regression workflows

- API access is refreshed and easier



Change Log - version 0.5.2

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



-  Imputation of missing values

-  Additional classifiers such as ``XGBoost``, Decision Trees

-  Better internal code structure

-  Lot more tests

-  More precise tests, as we vary number of classes wildly in test

   suites

-  several bug fixes and enhancements

-  More cmd line options such as ``--print_options`` from a previous run



.. |logo| image:: docs/logo_neuropredict.png

.. |travis| image:: https://travis-ci.org/raamana/neuropredict.svg?branch=master

   :target: https://travis-ci.org/raamana/neuropredict.svg?branch=master

.. |Code Health| image:: https://landscape.io/github/raamana/neuropredict/master/landscape.svg?style=flat

   :target: https://landscape.io/github/raamana/neuropredict/master

.. |Codacy Badge| image:: https://api.codacy.com/project/badge/Grade/501e560b8a424562a1b8f7cd2f3cadfe

   :target: https://www.codacy.com/app/raamana/neuropredict?utm_source=github.com&utm_medium=referral&utm_content=raamana/neuropredict&utm_campaign=Badge_Grade

.. |PyPI version| image:: https://badge.fury.io/py/neuropredict.svg

   :target: https://badge.fury.io/py/neuropredict

.. |Python versions| image:: https://img.shields.io/badge/python-3.5%2C%203.6-blue.svg

.. |saythanks| image:: https://img.shields.io/badge/say-thanks-ff69b4.svg

   :target: https://saythanks.io/to/raamana