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Node2Vec

Node2Vec is a vertex embedding algorithm proposed in node2vec: Scalable Feature Learning for Networks. TigerGraph splits the computation into two parts: the random walk process and the embedding training process. Assuming that you are using version 3.6 or greater of the TigerGraph database, ignore the UDF install instructions.

TigerGraph Node2Vec Documentation

Instructions

Random Walk Process Install

There are two different random walk processes to choose from. The first is regular random walks, implemented in tg_random_walk.gsql. This is equivalent to setting p and q parameters of Node2Vec both to 1, which is also equivalent to the DeepWalk paper. This version is more performant than tg_weighted_random_walk.gsql, due to the less computation that is needed. If the graph is large, you may want to batch the random walk process to reduce memory consumption. Use tg_random_walk_batch.gsql if this is desired.

The second option is weighted random walk, as described in the Node2Vec paper. This is implemented in the tg_weighted_random_walk_sub.gsql and tg_weighted_random_walk.gsql. If your TigerGraph database version is below 3.6, see the UDF installation instructions below. If the graph is large, you may want to batch the random walk process to reduce memory consumption. Use tg_weighted_random_walk_batch.gsql with tg_weighted_random_walk_sub.gsql if desired.

To install the un-weighted random walk: copy the algorithm from tg_random_walk.gsql and install it on the database using the standard query install process.

To install the weighted random walk: copy tg_weighted_random_walk_sub.gsql and install. Then copy and install tg_weighted_random_walk.gsql.

Node2Vec Embedding Install

Once the random walks have been generated, we can use the output to train the Node2Vec model. To install, make sure the proper UDFs are installed. If you are using a TigerGraph database of version 3.6 or greater, the UDFs are pre-installed.

To install Node2Vec query: copy the query from tg_node2vec.gsql and install on the database.

Preliminary Notes

Vim is the text editor of choice in this README, any other text editors such as Emacs or Nano will suffice in the commands listed below
<TGversion> should be replaced with your current Tigergraph version number

UDF installation

Weighted Random Walk UDF install

If you are using tg_weighted_random_walk_sub.gsql, then you will need to install the tg_random_udf.cpp. **The code defined in tg_random_udf.cpp should be pasted inside the UDIMPLf namespace inside of ExprFunctions.hpp.

# open file and paste code

$ vim ~/tigergraph/app/<TGversion>/dev/gdk/gsql/src/QueryUdf/ExprFunctions.hpp

Node2Vec UDF install

tg_node2vec_sub() is a UDF that is called in tg_node2vec.gsql.
**The code defined in tg_node2vec_sub.cpp should be pasted inside the UDIMPL namespace inside of ExprFunctions.hpp

# open file and paste code

$ vim ~/tigergraph/app/<TGversion>/dev/gdk/gsql/src/QueryUdf/ExprFunctions.hpp
Getting Word2vec file

There are multiple options to get word2vec.h

  1. Download/Copy word2vec.h file into ~/tigergraph/app/<TGversion>/dev/gdk/gsdk/include directory
  2. Create the file and copy the code from word2vec.h and paste it into the newly created file (steps shown below)
# Go to correct directory
$ cd ~/tigergraph/app/<TGversion>/dev/gdk/gsdk/include/

# create file and paste code
$ vim word2vec.h
Including word2vec

The newly created word2vec.h needs to be included in the ExprUtil.hpp file

$ vim ~/tigergraph/app/<TGversion>/dev/gdk/gsql/src/QueryUdf/ExprUtil.hpp

Once inside the text editor, paste the following line of C++ code into under the other include statements

#include "/home/tigergraph/tigergraph/app/<TGversion>/dev/gdk/gsdk/include/word2vec.h"

Multiple machines(cluster) or Single Machine?

If you are working on a single machine, remove the Distributed GSQL keyword from the header of the random_walk query

# Change first header to the second header

CREATE DISTRIBUTED QUERY random_walk(...) {...}         
CREATE QUERY random_walk(...) {...}

After doing this, proceed to the next section(Running Queries)

If you are on multiple machines or a cluster

# For every machine in cluster  

$ gssh <machine>
$ PUT ExprFunctions from "/home/tigergraph/tigergraph/app/<TGversion>/dev/gdk/gsql/src/QueryUdf/ExprFunctions.hpp"

Running Queries

** The following instructions can be done with GraphStudio or GSQL terminal

  1. Install the random_walk query
  2. Run query random_walk with desired parameters. Visit https://docs.tigergraph.com/graph-ml/current/node-embeddings/node2vec for a description of the random walk query parameters. Make sure that TigerGraph has the correct permissions to write to the output directory you specify.
  3. (optional) Inspect output of random_walk query 
    # For the default filepath parameter

$ cat ~/path.csv
  4. Run node2vec_query with desired parameters. Dimension denotes the embedding dimension size
  5. (optional) Inspect Embeddings 
    # For the default filepath parameter

$ cat ~/embedding.csv