Machine Learning Toolkit
Machine Learning in Python
Milk is a machine learning toolkit in Python.
Its focus is on supervised classification with several classifiers available: SVMs (based on libsvm), k-NN, random forests, decision trees. It also performs feature selection. These classifiers can be combined in many ways to form different classification systems.
For unsupervised learning, milk supports k-means clustering and affinity propagation.
Milk is flexible about its inputs. It optimised for numpy arrays, but can often handle anything (for example, for SVMs, you can use any dataype and any kernel and it does the right thing).
There is a strong emphasis on speed and low memory usage. Therefore, most of the performance sensitive code is in C++. This is behind Python-based interfaces for convenience.
To learn more, check the docs at http://packages.python.org/milk/ or the code demos included with the source at milk/demos/.
Here is how to test how well you can classify some features,labels data, measured by cross-validation:
import numpy as np import milk features = np.random.rand(100,10) # 2d array of features: 100 examples of 10 features each labels = np.zeros(100) features[50:] += .5 labels[50:] = 1 confusion_matrix, names = milk.nfoldcrossvalidation(features, labels) print 'Accuracy:', confusion_matrix.trace()/float(confusion_matrix.sum())
If want to use a classifier, you instanciate a learner object and call its train() method:
import numpy as np import milk features = np.random.rand(100,10) labels = np.zeros(100) features[50:] += .5 labels[50:] = 1 learner = milk.defaultclassifier() model = learner.train(features, labels) # Now you can use the model on new examples: example = np.random.rand(10) print model.apply(example) example2 = np.random.rand(10) example2 += .5 print model.apply(example2)
There are several classification methods in the package, but they all use the same interface: train() returns a model object, which has an apply() method to execute on new instances.
Author: Luis Pedro Coelho (with code from LibSVM and scikits.learn)
API Documentation: http://packages.python.org/milk/
Mailing List: http://groups.google.com/group/milk-users
SVMs. Using the libsvm solver with a pythonesque wrapper around it.
K-means using as little memory as possible. It can cluster millions of instances efficiently.
Self organising maps
Stepwise Discriminant Analysis for feature selection.
Non-negative matrix factorisation
The ChangeLog file contains a more complete history.
New in 0.5.1 (11 Jan 2013)
Add subspace projection kNN
Export pdist in milk namespace
Add Eigen to source distribution
Add mds_dists function
Add verbose argument to milk.tests.run
New in 0.5 (05 Nov 2012)
Add coordinate-descent based LASSO
Add unsupervised.center function
Make zscore work with NaNs (by ignoring them)
Propagate apply_many calls through transformers
Much faster SVM classification with means a much faster defaultlearner() [measured 2.5x speedup on yeast dataset!]
New in 0.4.3 (17 Sept 2012)
Add select_n_best & rank_corr to featureselection
Add Euclidean MDS
Add tree multi-class strategy
Fix adaboost with boolean weak learners (issue #6, reported by audy (Austin Richardson))
Add axis arguments to zscore()
New in 0.4.2 (16 Jan 2012)
Make defaultlearner able to take extra arguments
Make ctransforms_model a supervised_model (adds apply_many)
Add expanded argument to defaultlearner
Fix corner case in SDA
Fix parallel gridminimise on Windows
Add multi_label argument to normaliselabels
Add multi_label argument to nfoldcrossvalidation.foldgenerator
Do not fork a process in gridminimise if nprocs == 1 (makes for easier debugging, at the cost of slightly more complex code).
Fix ext.jugparallel when features is a Task
New in 0.4.1
Fix important bug in multi-process gridsearch
New in 0.4.0
Use multiprocessing to take advantage of multi core machines (off by default).
Add perceptron learner
Set random seed in random forest learner
Add warning to milk/__init__.py if import fails
Add return value to gridminimise
Set random seed in precluster_learner
Implemented Error-Correcting Output Codes for reduction of multi-class to binary (including probability estimation)
Add multi_strategy argument to defaultlearner()
Make the dot kernel in svm much, much, faster
Make sigmoidal fitting for SVM probability estimates faster
Fix bug in randomforest (patch by Wei on milk-users mailing list)
For older versions, see ChangeLog file
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