sklearn_data_preprocess: README.rst annotate

annotate README.rst @ 28:50b3e080cef0 draft

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

author	bgruening
date	Wed, 02 Oct 2019 03:55:06 -0400
parents	f0f1e5ba6fca
children

rev	line source
0 29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	1 Galaxy wrapper for scikit-learn library
17 f0f1e5ba6fca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	2 ***************************************
0 29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	3
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	4 Contents
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	5 ========
17 f0f1e5ba6fca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	6
0 29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	7 - `What is scikit-learn?`_
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	8 - `Scikit-learn main package groups`_
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	9 - `Tools offered by this wrapper`_
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	10
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	11 - `Machine learning workflows`_
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	12 - `Supervised learning workflows`_
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	13 - `Unsupervised learning workflows`_
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	14
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	15
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	16 ____________________________
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	17
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	18
17 f0f1e5ba6fca 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 29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	20
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	21 What is scikit-learn?
17 f0f1e5ba6fca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	22 =====================
0 29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	23
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 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.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	25
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	26 Scikit-learn source code can be accessed at https://github.com/scikit-learn/scikit-learn.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	27 Detailed installation instructions can be found at http://scikit-learn.org/stable/install.html
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	28
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	29
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	30 .. _Scikit-learn main package groups:
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	31
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	32 Scikit-learn main package groups
17 f0f1e5ba6fca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	33 ================================
0 29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	34
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	35 Scikit-learn provides the users with several main groups of related operations.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	36 These are:
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	37
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	38 - Classification
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	39 - Identifying to which category an object belongs.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	40 - Regression
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	41 - Predicting a continuous-valued attribute associated with an object.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	42 - Clustering
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	43 - Automatic grouping of similar objects into sets.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	44 - Preprocessing
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	45 - Feature extraction and normalization.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	46 - Model selection and evaluation
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	47 - Comparing, validating and choosing parameters and models.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	48 - Dimensionality reduction
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	49 - Reducing the number of random variables to consider.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	50
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 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.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	52
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	53
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	54 .. _Tools offered by this wrapper:
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	55
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	56 Available tools in the current wrapper
17 f0f1e5ba6fca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	57 ======================================
0 29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	58
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	59 The current release of the wrapper offers a subset of the packages from scikit-learn library. You can find:
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	60
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	61 - A subset of classification metric functions
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	62 - Linear and quadratic discriminant classifiers
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	63 - Random forest and Ada boost classifiers and regressors
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	64 - All the clustering methods
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	65 - All support vector machine classifiers
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	66 - A subset of data preprocessing estimator classes
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	67 - Pairwise metric measurement functions
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	68
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 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.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	70
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	71 .. _Machine learning workflows:
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	72
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	73 Machine learning workflows
17 f0f1e5ba6fca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	74 ==========================
0 29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	75
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 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.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	77 Here we discuss supervised and unsupervised learning workflows.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	78
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	79 .. _Supervised learning workflows:
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	80
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	81 Supervised machine learning workflows
17 f0f1e5ba6fca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	82 =====================================
0 29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	83
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	84 What is supervised learning?
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	85
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 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.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 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:
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	88
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	89 1. Preprocess the data::
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	90
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	91 * Change the collected data into the proper format and datatype.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	92 * Adjust the data quality by filling the missing values, performing
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	93 required scaling and normalizations, etc.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	94 * Extract features which are the most meaningfull for the learning task.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	95 * Split the ready dataset into training and test samples.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	96
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	97 2. Choose an algorithm::
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	98
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	99 * These factors help one to choose a learning algorithm:
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	100 - Nature of the data (e.g. linear vs. nonlinear data)
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	101 - Structure of the predicted output (e.g. binary vs. multilabel classification)
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	102 - Memory and time usage of the training
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	103 - Predictive accuracy on new data
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	104 - Interpretability of the predictions
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	105
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	106 3. Choose a validation method
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	107
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	108 Every machine learning model should be evaluated before being put into practicical use.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	109 There are numerous performance metrics to evaluate machine learning models.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	110 For supervised learning, usually classification or regression metrics are used.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	111
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	112 A validation method helps to evaluate the performance metrics of a trained model in order
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	113 to optimize its performance or ultimately switch to a more efficient model.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	114 Cross-validation is a known validation method.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	115
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	116 4. Fit a model
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	117
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	118 Given the learning algorithm, validation method, and performance metric(s)
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	119 repeat the following steps::
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	120
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	121 * Train the model.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	122 * Evaluate based on metrics.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	123 * Optimize unitl satisfied.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	124
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	125 5. Use fitted model for prediction::
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	126
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	127 This is a final evaluation in which, the optimized model is used to make predictions
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	128 on unseen (here test) samples. After this, the model is put into production.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	129
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	130 .. _Unsupervised learning workflows:
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	131
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	132 Unsupervised machine learning workflows
17 f0f1e5ba6fca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit cfc9fe24b7975fc5838bb3e456646202898eb977 bgruening parents: 0 diff changeset	133 =======================================
0 29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	134
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	135 What is unsupervised learning?
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	136
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	137 Unlike supervised learning and more liklely in real life, here the initial data is not labeled.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	138 The task is to extract the structure from the data and group the samples based on their similarities.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	139 Clustering and dimensionality reduction are two famous examples of unsupervised learning tasks.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	140
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	141 In this case, the workflow is as follows::
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	142
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	143 * Preprocess the data (without splitting to train and test).
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	144 * Train a model.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	145 * Evaluate and tune parameters.
29899feb4d44 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9 bgruening parents: diff changeset	146 * Analyse the model and test on real data.

Mercurial > repos > bgruening > sklearn_data_preprocess

annotate README.rst @ 28:50b3e080cef0 draft