PecanPy: a fast, efficient and parallelized Python implementation of node2vec

Abstract

Learning low-dimensional representations (embeddings) of nodes in large graphs is key to applying machine learning on massive biological networks. Node2vec is the most widely used method for node embedding. However, its original Python and C++ implementations scale poorly with network density, failing for dense biological networks with hundreds of millions of edges. We have developed PecanPy, a new Python implementation of node2vec that uses cache-optimized compact graph data structures and precomputing/parallelization to result in fast, high-quality node embeddings for biological networks of all sizes and densities.