Frequently Asked Questions¶

Here we try to give some answers to questions that regularly pop up on the mailing list.

What is the project name (a lot of people get it wrong)?¶

scikit-learn, but not scikit or SciKit nor sci-kit learn. Also not scikits.learn or scikits-learn, which where previously used.

How do you pronounce the project name?¶

sy-kit learn. sci stands for science!

Why scikit?¶

There are multiple scikits, which are scientific toolboxes build around SciPy. You can find a list at https://scikits.appspot.com/scikits. Apart from scikit-learn, another popular one is scikit-image.

How can I contribute to scikit-learn?¶

See Contributing. Before wanting to add a new algorithm, which is usually a major and lengthy undertaking, it is recommended to start with known issues.

How can I create a bunch object?¶

Don’t make a bunch object! They are not part of the scikit-learn API. Bunch objects are just a way to package some numpy arrays. As a scikit-learn user you only ever need numpy arrays to feed your model with data.

For instance to train a classifier, all you need is a 2D array X for the input variables and a 1D array y for the target variables. The array X holds the features as columns and samples as rows . The array y contains integer values to encode the class membership of each sample in X.

To load data as numpy arrays you can use different libraries depending on the original data format:

numpy.loadtxt to load text files (such as CSV) assuming that all the columns have an homogeneous data type (e.g. all numeric values).
scipy.io for common binary formats often used in scientific computing context.
scipy.misc.imread (requires the Pillow package) to load pixel intensities data from various image file formats.
pandas.io to load heterogeneously typed data from various file formats and database protocols that can slice and dice before conversion to numerical features in a numpy array.

Note: if you manage your own numerical data it is recommended to use an optimized file format such as HDF5 to reduce data load times. Various libraries such as H5Py, PyTables and pandas provides a Python interface for reading and writing data in that format.

Can I add this new algorithm that I (or someone else) just published?¶

No. As a rule we only add well-established algorithms. A rule of thumb is at least 3 years since publications, 200+ citations and wide use and usefullness. A technique that provides a clear-cut improvement (e.g. an enhanced data structure or efficient approximation) on a widely-used method will also be considered for inclusion. Your implementation doesn’t need to be in scikit-learn to be used together with scikit-learn tools, though. Implement your favorite algorithm in a scikit-learn compatible way, upload it to github and we will list it under Related Projects. Also see selectiveness.

Can I add this classical algorithm from the 80s?¶

Depends. If there is a common usecase within the scope of scikit-learn, such as classification, regression or clustering, where it outperforms methods that are already implemented in scikit-learn, we will consider it.

Why are you so selective on what algorithms you include in scikit-learn?¶

Code is maintenance cost, and we need to balance the amount of code we have with the size of the team (and add to this the fact that complexity scales non linearly with the number of features). The package relies on core developers using their free time to fix bugs, maintain code and review contributions. Any algorithm that is added needs future attention by the developers, at which point the original author might long have lost interest. Also see this thread on the mailing list.

Why did you remove HMMs from scikit-learn?¶

See Will you add graphical models or sequence prediction to scikit-learn?.

Will you add graphical models or sequence prediction to scikit-learn?¶

Not in the foreseeable future. scikit-learn tries to provide a unified API for the basic tasks in machine learning, with pipelines and meta-algorithms like grid search to tie everything together. The required concepts, APIs, algorithms and expertise required for structured learning are different from what scikit-learn has to offer. If we started doing arbitrary structured learning, we’d need to redesign the whole package and the project would likely collapse under its own weight.

There are two project with API similar to scikit-learn that do structured prediction:

pystruct handles general structured learning (focuses on SSVMs on arbitrary graph structures with approximate inference; defines the notion of sample as an instance of the graph structure)
seqlearn handles sequences only (focuses on exact inference; has HMMs, but mostly for the sake of completeness; treats a feature vector as a sample and uses an offset encoding for the dependencies between feature vectors)

Will you add GPU support?¶

No, or at least not in the near future. The main reason is that GPU support will introduce many software dependencies and introduce platform specific issues. scikit-learn is designed to be easy to install on a wide variety of platforms. Outside of neural networks, GPUs don’t play a large role in machine learning today, and much larger gains in speed can often be achieved by a careful choice of algorithms.

Do you support PyPy?¶

In case you didn’t know, PyPy is the new, fast, just-in-time compiling Python implementation. We don’t support it. When the NumPy support in PyPy is complete or near-complete, and SciPy is ported over as well, we can start thinking of a port. We use too much of NumPy to work with a partial implementation.

How do I deal with string data (or trees, graphs...)?¶

scikit-learn estimators assume you’ll feed them real-valued feature vectors. This assumption is hard-coded in pretty much all of the library. However, you can feed non-numerical inputs to estimators in several ways.

If you have text documents, you can use a term frequency features; see Text feature extraction for the built-in text vectorizers. For more general feature extraction from any kind of data, see Loading features from dicts and Feature hashing.

Another common case is when you have non-numerical data and a custom distance (or similarity) metric on these data. Examples include strings with edit distance (aka. Levenshtein distance; e.g., DNA or RNA sequences). These can be encoded as numbers, but doing so is painful and error-prone. Working with distance metrics on arbitrary data can be done in two ways.

Firstly, many estimators take precomputed distance/similarity matrices, so if the dataset is not too large, you can compute distances for all pairs of inputs. If the dataset is large, you can use feature vectors with only one “feature”, which is an index into a separate data structure, and supply a custom metric function that looks up the actual data in this data structure. E.g., to use DBSCAN with Levenshtein distances:

>>> from leven import levenshtein       
>>> import numpy as np
>>> from sklearn.cluster import dbscan
>>> data = ["ACCTCCTAGAAG", "ACCTACTAGAAGTT", "GAATATTAGGCCGA"]
>>> def lev_metric(x, y):
...     i, j = int(x[0]), int(y[0])     # extract indices
...     return levenshtein(data[i], data[j])
...
>>> X = np.arange(len(data)).reshape(-1, 1)
>>> X
array([[0],
       [1],
       [2]])
>>> dbscan(X, metric=lev_metric, eps=5, min_samples=2)  
([0, 1], array([ 0,  0, -1]))

(This uses the third-party edit distance package leven.)

Similar tricks can be used, with some care, for tree kernels, graph kernels, etc.

Why do I sometime get a crash/freeze with n_jobs > 1 under OSX or Linux?¶

Several scikit-learn tools such as GridSearchCV and cross_val_score rely internally on Python’s multiprocessing module to parallelize execution onto several Python processes by passing n_jobs > 1 as argument.

The problem is that Python multiprocessing does a fork system call without following it with an exec system call for performance reasons. Many libraries like (some versions of) Accelerate / vecLib under OSX, (some versions of) MKL, the OpenMP runtime of GCC, nvidia’s Cuda (and probably many others), manage their own internal thread pool. Upon a call to fork, the thread pool state in the child process is corrupted: the thread pool believes it has many threads while only the main thread state has been forked. It is possible to change the libraries to make them detect when a fork happens and reinitialize the thread pool in that case: we did that for OpenBLAS (merged upstream in master since 0.2.10) and we contributed a patch to GCC’s OpenMP runtime (not yet reviewed).

But in the end the real culprit is Python’s multiprocessing that does fork without exec to reduce the overhead of starting and using new Python processes for parallel computing. Unfortunately this is a violation of the POSIX standard and therefore some software editors like Apple refuse to consider the lack of fork-safety in Accelerate / vecLib as a bug.

In Python 3.4+ it is now possible to configure multiprocessing to use the ‘forkserver’ or ‘spawn’ start methods (instead of the default ‘fork’) to manage the process pools. This makes it possible to not be subject to this issue anymore. The version of joblib shipped with scikit-learn automatically uses that setting by default (under Python 3.4 and later).

If you have custom code that uses multiprocessing directly instead of using it via joblib you can enable the the ‘forkserver’ mode globally for your program: Insert the following instructions in your main script:

import multiprocessing

# other imports, custom code, load data, define model...

if __name__ == '__main__':
    multiprocessing.set_start_method('forkserver')

    # call scikit-learn utils with n_jobs > 1 here

You can find more default on the new start methods in the multiprocessing documentation.