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 were 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.

What’s the best way to get help on scikit-learn usage?¶

For general machine learning questions, please use Cross Validated with the [machine-learning] tag.

For scikit-learn usage questions, please use Stack Overflow with the [scikit-learn] and [python] tags. You can alternatively use the mailing list.

Please make sure to include a minimal reproduction code snippet (ideally shorter than 10 lines) that highlights your problem on a toy dataset (for instance from sklearn.datasets or randomly generated with functions of numpy.random with a fixed random seed). Please remove any line of code that is not necessary to reproduce your problem.

The problem should be reproducible by simply copy-pasting your code snippet in a Python shell with scikit-learn installed. Do not forget to include the import statements.

More guidance to write good reproduction code snippets can be found at:

http://stackoverflow.com/help/mcve

If your problem raises an exception that you do not understand (even after googling it), please make sure to include the full traceback that you obtain when running the reproduction script.

For bug reports or feature requests, please make use of the issue tracker on Github.

There is also a scikit-learn Gitter channel where some users and developers might be found.

Please do not email any authors directly to ask for assistance, report bugs, or for any other issue related to scikit-learn.

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.

What are the inclusion criteria for new algorithms ?¶

We only consider well-established algorithms for inclusion. A rule of thumb is at least 3 years since publication, 200+ citations and wide use and usefulness. A technique that provides a clear-cut improvement (e.g. an enhanced data structure or a more efficient approximation technique) on a widely-used method will also be considered for inclusion.

From the algorithms or techniques that meet the above criteria, only those which fit well within the current API of scikit-learn, that is a fit, predict/transform interface and ordinarily having input/output that is a numpy array or sparse matrix, are accepted.

The contributor should support the importance of the proposed addition with research papers and/or implementations in other similar packages, demonstrate its usefulness via common use-cases/applications and corroborate performance improvements, if any, with benchmarks and/or plots. It is expected that the proposed algorithm should outperform the methods that are already implemented in scikit-learn at least in some areas.

Also note that your implementation need not be in scikit-learn to be used together with scikit-learn tools. You can implement your favorite algorithm in a scikit-learn compatible way, upload it to github and let us know. We will list it under Related Projects.

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.

If you have custom code that uses multiprocessing directly instead of using it via joblib you can enable 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.

Why is there no support for deep or reinforcement learning / Will there be support for deep or reinforcement learning in scikit-learn?¶

Deep learning and reinforcement learning both require a rich vocabulary to define an architecture, with deep learning additionally requiring GPUs for efficient computing. However, neither of these fit within the design constraints of scikit-learn; as a result, deep learning and reinforcement learning are currently out of scope for what scikit-learn seeks to achieve.

Why is my pull request not getting any attention?¶

The scikit-learn review process takes a significant amount of time, and contributors should not be discouraged by a lack of activity or review on their pull request. We care a lot about getting things right the first time, as maintenance and later change comes at a high cost. We rarely release any “experimental” code, so all of our contributions will be subject to high use immediately and should be of the highest quality possible initially.

Beyond that, scikit-learn is limited in its reviewing bandwidth; many of the reviewers and core developers are working on scikit-learn on their own time. If a review of your pull request comes slowly, it is likely because the reviewers are busy. We ask for your understanding and request that you not close your pull request or discontinue your work solely because of this reason.

How do I set a `random_state` for an entire execution?¶

For testing and replicability, it is often important to have the entire execution controlled by a single seed for the pseudo-random number generator used in algorithms that have a randomized component. Scikit-learn does not use its own global random state; whenever a RandomState instance or an integer random seed is not provided as an argument, it relies on the numpy global random state, which can be set using numpy.random.seed. For example, to set an execution’s numpy global random state to 42, one could execute the following in his or her script:

import numpy as np
np.random.seed(42)

However, a global random state is prone to modification by other code during execution. Thus, the only way to ensure replicability is to pass RandomState instances everywhere and ensure that both estimators and cross-validation splitters have their random_state parameter set.