pygrank 0.2.1

Recommendation algorithms for large graphs

Fast recommendation algorithms for large graphs based on link analysis.

License: Apache Software License
Author: Emmanouil (Manios) Krasanakis
Dependencies: networkx, numpy, scipy, sklearn, tqdm

:hammer_and_wrench: Installation

pygrank is meant to work with Python 3.6 or later. It can be installed with pip per:

pip install pygrank

Parts of the documentation are still under construction.

To use machine learning backends (e.g. to integrate the package in machine learning projects), such as tensorflow, manually change the automatically created configuration file whose path is displayed in the error console. If you want others to run your code that depends on pygrank with a specific backend, add the following recipe at your code's entry point to override other configurations:

from pygrank import backend
backend.load_backend(`tensorflow`)

:zap: Quickstart

As a quick start, let us construct a networkx graph G and a set of nodes seeds.

>>> import networkx as nx
>>> G = nx.Graph()
>>> G.add_edge("A", "B")
>>> G.add_edge("B", "C")
>>> G.add_edge("C", "D")
>>> G.add_edge("D", "E")
>>> G.add_edge("A", "C")
>>> G.add_edge("C", "E")
>>> G.add_edge("B", "E")
>>> seeds = {"A", "B"}

We run a personalized PageRank graph filter to score the structural relatedness of graph nodes to the ones of the given set. For instructional purposes, we show the default values of some parameters: the graph diffusion rate alpha required by the algorithm, a numerical tolerance tol at the convergence point and a graph preprocessing strategy "auto" normalization of the garph adjacency matrix to determine between column-based and symmetric normalization depending on whether the graph is undirected (as in this example) or not respectively.

>>> from pygrank.algorithms.adhoc import PageRank
>>> ranker = PageRank(alpha=0.85, tol=1.E-6, normalization="auto")
>>> ranks = ranker.rank(G, {v: 1 for v in seeds})

Node ranking output is always organized into graph signals which can be used like dictionaries. For example, we can print the scores of some nodes per:

>>> print(ranks["B"], ranks["D"], ranks["E"])
0.25865456609095644 0.12484722044728883 0.17079023174039495

We alter this outcome so that it outputs node order, where higher node scores are assigned lower order. This is achieved by wrapping a postprocessor around the algorithm. There are various postprocessors, including ones to make scores fairness-aware.

>>> from pygrank.algorithms.postprocess import Ordinals
>>> ordinals = Ordinals(ranker).rank(G, {v: 1 for v in seeds})
>>> print(ordinals["B"], ordinals["D"], ordinals["E"])
1 5 4

How much time did it take for the base ranker to converge? (Depends on backend and device characteristics.)

>>> print(ranker.convergence)
19 iterations (0.001831000000009908 sec)

Since only the node order is important, we can use a different way to specify convergence:

>>> from pygrank.algorithms.utils.convergence import RankOrderConvergenceManager
>>> convergence = RankOrderConvergenceManager(pagerank_alpha=0.85, confidence=0.98) 
>>> early_stop_ranker = PageRank(alpha=0.85, convergence=convergence)
>>> ordinals = Ordinals(early_stop_ranker).rank(G, {v: 1 for v in seeds})
>>> print(early_stop_ranker.convergence)
2 iterations (0.0006313000000091051 sec)
>>> print(ordinals["B"], ordinals["D"], ordinals["E"])
1 5 4

Close to the previous results at a fraction of the time!! Note that convergence time measurements do not take into account the time needed to preprocess graphs.

:brain: Overview

Analyzing graph edges (links) between nodes can help rank/score graph nodes based on their structural proximity to structural or attribute-based communities of nodes. With the introduction of graph signal processing and decoupled graph neural networks the importance of node ranking has drastically increased, as its ability to perform inductive learning by quickly spreading node information through edges has been theoretically and experimentally corroborated. For example, it can be used to make predictions based on few known node attributes or base predictions outputted by low-quality feature-based machine learning models.

pygrank is a collection of node ranking algorithms and practices that support real-world conditions, such as large graphs and heterogeneous preprocessing and postprocessing requiremenets. Thus, it provides ready-to-use tools that simplify deployment of theoretical advancements and testing of new algorithms.

Some of the library's advantages are:

1. Compatibility with networkx and tensorflow.
2. Datacentric programming interfaces that do not require transformations to identifiers.
3. Large graph support with sparse representations.
4. Seamless pipelines, from graph preprocessing up to evaluation.
5. Modular combination of components.

:link: Material

Documentation

:fire: Features

• Graph filters
• Community detection
• Graph normalization
• Convergence criteria
• Postprocessing (e.g. fairness awareness)
• Evaluation measures
• Benchmarks

:thumbsup: Contributing

Feel free to contribute in any way, for example through the issue tracker or by participating in discussions. Please check out the contribution guidelines to bring modifications to the code base. If so, make sure to follow the pull checklist described in the guidelines.

:notebook: Citation

If pygrank has been useful in your research and you would like to cite it in a scientific publication, please refer to the following paper:

TBD

To publish research that uses provided methods, please cite the appropriate paper(s) listed here.