snfpy 0.2.2

A Python toolbox for performing similarity network fusion (SNF)

SNFpy

This package provides a Python implementation of similarity network fusion (SNF), a technique for combining multiple data sources into a single graph representing sample relationships.

Table of Contents

If you know where you're going, feel free to jump ahead:

• Installation
• Purpose
• Example usage
• How to get involved
• Acknowlegments
• License information

Requirements and installation

This package requires Python version 3.5 or greater. Assuming you have the correct version of Python, you can install this package by opening a command terminal and running the following:

git clone https://github.com/rmarkello/snfpy.git
cd snfpy
python setup.py install

You can install the latest release from PyPi, with:

pip install snfpy

Purpose

Similarity network fusion is a technique originally proposed by Wang et al., 2014, Nature Methods to combine data from different sources for a shared group of samples. The procedure works by constructing networks of these samples for each data source that represent how similar each sample is to all the others, and then fusing the networks together. This figure from the original paper, which applied the method to genetics data, provides a nice demonstration:

The similarity network generation and fusion process use a K-nearest neighbors procedure to down-weight weaker relationships between samples. However, weak relationships that are consistent across data sources are retained via the fusion process. For more information on the math behind SNF you can read the original paper or take a look at the reference documentation.

Usage

There are ~three functions from which you can construct most SNF workflows. To demonstrate, we can use one of the example datasets provided with the snfpy distribution:

>>> from snf import datasets
>>> digits = datasets.load_digits()
>>> digits.keys()
dict_keys(['data', 'labels'])

The digits dataset is comprised of 600 samples profiled across four data types which have 76, 240, 216, and 47 features each; these data can be accessed via digits.data:

>>> for arr in digits.data:
...     print(arr.shape)
(600, 76)
(600, 240)
(600, 216)
(600, 47)

The dataset also comes with a set of labels grouping the samples into one of three categories (0, 1, or 2); these labels can be accessed via digits.labels. We can see that there are 200 samples per group:

import numpy as np
>>> groups, samples = np.unique(digits.labels, return_counts=True)
>>> for grp, count in zip(groups, samples):
...     print('Group {:.0f}: {} samples'.format(grp, count))
Group 0: 200 samples
Group 1: 200 samples
Group 2: 200 samples

The first step in SNF is converting these data arrays into similarity (or "affinity") networks. To do so, we provide the data arrays to the snf.make_affinity() function:

>>> import snf
>>> affinity_networks = snf.make_affinity(digits.data, metric='euclidean', K=20, mu=0.5)

The arguments provided to this function (metric, K, and mu) all play a role in how the similarity network is constructed. The metric argument controls the distance function used when constructing the network. Distance networks and similarity networks are inverses of one another, however, so we convert from one to the another. To do so, we apply a mu-weighted K-nearest neighbors kernel to the distance array (for more math, see the snf.make_affinity() docstring).

Once we have our similarity networks we can fuse them together with SNF:

>>> fused_network = snf.snf(affinity_networks, K=20)

The fused network is then ready for other analyses (like clustering!). If we want to cluster the network we can try and determine the "optimal" number of clusters to form using snf.get_n_clusters(). This functions returns the top two "optimal" number of clusters (estimated via an eigengap approach):

>>> best, second = snf.get_n_clusters(fused_network)
>>> best, second
(3, 4)

Then, we can cluster the network using, for example, spectral clustering and compare the resulting labels to the "true" labels provided with the test dataset:

>>> from sklearn.cluster import spectral_clustering
>>> from sklearn.metrics import v_measure_score

>>> labels = spectral_clustering(fused_network, n_clusters=best)
>>> v_measure_score(labels, digits.labels)
0.9734300455833589

The metric (v_measure_score) used here ranges from 0 to 1, where 1 indicates perfect overlap between the derived and true labels and 0 indicates no overlap. We see that 0.97 indicates that the SNF fused network clustering results were highly accurate!

Of course, your mileage may (will) vary for other datasets, but this should be sufficient to get you started! For more detailed examples and alternative uses check out our documentation.

How to get involved

We're thrilled to welcome new contributors! If you're interesting in getting involved, you should start by reading our contributing guidelines and code of conduct. Once you're done with that, take a look at our issues to see if there is anything you might like to work on. Alternatively, if you've found a bug, are experiencing a problem, or have a question, create a new issue with some information about it!

Acknowledgments

This code is a translation of the original similarity network fusion code implemented in R and Matlab. As such, if you use this code please (1) provide a link back to the snfpy GitHub repository with the version of the code used, and (2) cite the original similarity network fusion paper:

Wang, B., Mezlini, A. M., Demir, F., Fiume, M., Tu, Z., Brudno, M., Haibe-Kains, B., &
Goldenberg, A. (2014). Similarity network fusion for aggregating data types on a genomic scale.
Nature Methods, 11(3), 333.

License information

This code is partially translated from the original SNF code and is therefore released as a derivative under the LGPLv3. The full license may be found in the LICENSE file in the snfpy distribution.