sklearn_searchcv: README.rst annotate

annotate README.rst @ 12:dfdf0b54ef4a draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"

author	bgruening
date	Wed, 02 Oct 2019 03:20:36 -0400
parents	1eb6f9e2e30b
children

rev	line source
0 f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	1 Galaxy wrapper for scikit-learn library
1 1eb6f9e2e30b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	2 ***************************************
0 f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	3
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	4 Contents
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	5 ========
1 1eb6f9e2e30b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	6
0 f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	7 - `What is scikit-learn?`_
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	8 - `Scikit-learn main package groups`_
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	9 - `Tools offered by this wrapper`_
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	10
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	11 - `Machine learning workflows`_
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	12 - `Supervised learning workflows`_
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	13 - `Unsupervised learning workflows`_
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	14
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	15
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	16 ____________________________
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	17
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	18
1 1eb6f9e2e30b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	19 .. _What is scikit-learn?:
0 f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	20
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	21 What is scikit-learn?
1 1eb6f9e2e30b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	22 =====================
0 f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	23
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	24 Scikit-learn is an open-source machine learning library for the Python programming language. It offers various algorithms for performing supervised and unsupervised learning as well as data preprocessing and transformation, model selection and evaluation, and dataset utilities. It is built upon SciPy (Scientific Python) library.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	25
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	26 Scikit-learn source code can be accessed at https://github.com/scikit-learn/scikit-learn.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	27 Detailed installation instructions can be found at http://scikit-learn.org/stable/install.html
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	28
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	29
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	30 .. _Scikit-learn main package groups:
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	31
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	32 Scikit-learn main package groups
1 1eb6f9e2e30b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	33 ================================
0 f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	34
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	35 Scikit-learn provides the users with several main groups of related operations.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	36 These are:
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	37
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	38 - Classification
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	39 - Identifying to which category an object belongs.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	40 - Regression
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	41 - Predicting a continuous-valued attribute associated with an object.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	42 - Clustering
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	43 - Automatic grouping of similar objects into sets.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	44 - Preprocessing
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	45 - Feature extraction and normalization.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	46 - Model selection and evaluation
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	47 - Comparing, validating and choosing parameters and models.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	48 - Dimensionality reduction
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	49 - Reducing the number of random variables to consider.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	50
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	51 Each group consists of a number of well-known algorithms from the category. For example, one can find hierarchical, spectral, kmeans, and other clustering methods in sklearn.cluster package.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	52
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	53
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	54 .. _Tools offered by this wrapper:
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	55
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	56 Available tools in the current wrapper
1 1eb6f9e2e30b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	57 ======================================
0 f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	58
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	59 The current release of the wrapper offers a subset of the packages from scikit-learn library. You can find:
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	60
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	61 - A subset of classification metric functions
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	62 - Linear and quadratic discriminant classifiers
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	63 - Random forest and Ada boost classifiers and regressors
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	64 - All the clustering methods
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	65 - All support vector machine classifiers
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	66 - A subset of data preprocessing estimator classes
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	67 - Pairwise metric measurement functions
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	68
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	69 In addition, several tools for performing matrix operations, generating problem-specific datasets, and encoding text and extracting features have been prepared to help the user with more advanced operations.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	70
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	71 .. _Machine learning workflows:
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	72
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	73 Machine learning workflows
1 1eb6f9e2e30b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	74 ==========================
0 f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	75
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	76 Machine learning is about processes. No matter what machine learning algorithm we use, we can apply typical workflows and dataflows to produce more robust models and better predictions.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	77 Here we discuss supervised and unsupervised learning workflows.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	78
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	79 .. _Supervised learning workflows:
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	80
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	81 Supervised machine learning workflows
1 1eb6f9e2e30b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	82 =====================================
0 f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	83
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	84 What is supervised learning?
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	85
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	86 In this machine learning task, given sample data which are labeled, the aim is to build a model which can predict the labels for new observations.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	87 In practice, there are five steps which we can go through to start from raw input data and end up getting reasonable predictions for new samples:
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	88
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	89 1. Preprocess the data::
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	90
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	91 * Change the collected data into the proper format and datatype.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	92 * Adjust the data quality by filling the missing values, performing
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	93 required scaling and normalizations, etc.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	94 * Extract features which are the most meaningfull for the learning task.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	95 * Split the ready dataset into training and test samples.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	96
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	97 2. Choose an algorithm::
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	98
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	99 * These factors help one to choose a learning algorithm:
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	100 - Nature of the data (e.g. linear vs. nonlinear data)
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	101 - Structure of the predicted output (e.g. binary vs. multilabel classification)
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	102 - Memory and time usage of the training
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	103 - Predictive accuracy on new data
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	104 - Interpretability of the predictions
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	105
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	106 3. Choose a validation method
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	107
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	108 Every machine learning model should be evaluated before being put into practicical use.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	109 There are numerous performance metrics to evaluate machine learning models.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	110 For supervised learning, usually classification or regression metrics are used.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	111
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	112 A validation method helps to evaluate the performance metrics of a trained model in order
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	113 to optimize its performance or ultimately switch to a more efficient model.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	114 Cross-validation is a known validation method.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	115
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	116 4. Fit a model
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	117
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	118 Given the learning algorithm, validation method, and performance metric(s)
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	119 repeat the following steps::
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	120
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	121 * Train the model.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	122 * Evaluate based on metrics.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	123 * Optimize unitl satisfied.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	124
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	125 5. Use fitted model for prediction::
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	126
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	127 This is a final evaluation in which, the optimized model is used to make predictions
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	128 on unseen (here test) samples. After this, the model is put into production.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	129
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	130 .. _Unsupervised learning workflows:
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	131
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	132 Unsupervised machine learning workflows
1 1eb6f9e2e30b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	133 =======================================
0 f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	134
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	135 What is unsupervised learning?
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	136
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	137 Unlike supervised learning and more liklely in real life, here the initial data is not labeled.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	138 The task is to extract the structure from the data and group the samples based on their similarities.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	139 Clustering and dimensionality reduction are two famous examples of unsupervised learning tasks.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	140
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	141 In this case, the workflow is as follows::
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	142
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	143 * Preprocess the data (without splitting to train and test).
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	144 * Train a model.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	145 * Evaluate and tune parameters.
f6802e2b5bc7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 76583c1fcd9d06a4679cc46ffaee44117b9e22cd bgruening parents: diff changeset	146 * Analyse the model and test on real data.

Mercurial > repos > bgruening > sklearn_searchcv

annotate README.rst @ 12:dfdf0b54ef4a draft