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MUSAE

The reference implementation of Multi-Scale Attributed Node Embedding. (Journal of Complex Networks 2021)

Abstract

We present network embedding algorithms that capture information about a node from the local distribution over node attributes around it, as observed over random walks following an approach similar to Skip-gram. Observations from neighborhoods of different sizes are either pooled (AE) or encoded distinctly in a multi-scale approach (MUSAE). Capturing attribute-neighborhood relationships over multiple scales is useful for a diverse range of applications, including latent feature identification across disconnected networks with similar attributes. We prove theoretically that matrices of node-feature pointwise mutual information are implicitly factorized by the embeddings. Experiments show that our algorithms are robust, computationally efficient and outperform comparable models on social, web and citation network datasets.

The second-order random walks sampling methods were taken from the reference implementation of Node2Vec.

The datasets are also available on SNAP.

The model is now also available in the package Karate Club.

This repository provides the reference implementations for MUSAE and AE as described in the paper:

Multi-Scale Attributed Node Embedding. Benedek Rozemberczki, Carl Allen, and Rik Sarkar. Journal of Complex Networks 2021

Citing
Requirements
Datasets
Logging
Options
Examples

Citing

If you find MUSAE useful in your research, please consider citing the following paper:

>@article{musae,
          author = {Rozemberczki, Benedek and Allen, Carl and Sarkar, Rik},
          title = {{Multi-Scale Attributed Node Embedding}},
          journal = {Journal of Complex Networks},
          volume = {9},
          number = {2},
          year = {2021},
}

Requirements

The codebase is implemented in Python 3.5.2. package versions used for development are just below.

networkx          2.4
tqdm              4.28.1
numpy             1.15.4
pandas            0.23.4
texttable         1.5.0
scipy             1.1.0
argparse          1.1.0
gensim            3.6.0

Datasets

Logging

The models are defined in a way that parameter settings and runtimes are logged. Specifically we log the followings:

1. Hyperparameter settings.     We save each hyperparameter used in the experiment.
2. Optimization runtime.        We measure the time needed for optimization - measured by seconds.
3. Sampling runtime.            We measure the time needed for sampling - measured by seconds.

Options

Learning the embedding is handled by the src/main.py script which provides the following command line arguments.

Input and output options

  --graph-input      STR   Input edge list csv.     Default is `input/edges/chameleon_edges.csv`.
  --features-input   STR   Input features json.     Default is `input/features/chameleon_features.json`.
  --output           STR   Embedding output path.   Default is `output/chameleon_embedding.csv`.
  --log              STR   Log output path.         Default is `logs/chameleon.json`.

Random walk options

  --sampling      STR       Random walker order (first/second).              Default is `first`.
  --P             FLOAT     Return hyperparameter for second-order walk.     Default is 1.0
  --Q             FLOAT     In-out hyperparameter for second-order walk.     Default is 1.0.
  --walk-number   INT       Walks per source node.                           Default is 5.
  --walk-length   INT       Truncated random walk length.                    Default is 80.

Model options

  --model                 STR        Pooled or multi-scale model (AE/MUSAE).      Default is `musae`.
  --base-model            STR        Use of Doc2Vec base model.                   Default is `null`.
  --approximation-order   INT        Matrix powers approximated.                  Default is 3.
  --dimensions            INT        Number of dimensions.                        Default is 32.
  --down-sampling         FLOAT      Length of random walk per source.            Default is 0.001.
  --exponent              FLOAT      Downsampling exponent of frequency.          Default is 0.75.
  --alpha                 FLOAT      Initial learning rate.                       Default is 0.05.
  --min-alpha             FLOAT      Final learning rate.                         Default is 0.025.
  --min-count             INT        Minimal occurence of features.               Default is 1.
  --negative-samples      INT        Number of negative samples per node.         Default is 5.
  --workers               INT        Number of cores used for optimization.       Default is 4.
  --epochs                INT        Gradient descent epochs.                     Default is 5.

Examples

Training a MUSAE model for a 10 epochs.

$ python src/main.py --epochs 10

Changing the dimension size.

$ python src/main.py --dimensions 32

License