Embeddings only for selected nodes.

[Kronossos]

Let me quickly describe me graph.

I have a graph that links every species by its taxon for mammals. See below small example for Hominoidea:

There are five organisms (HSA, PPS, PTR, GGO, PON) at the end of this lineage. Only organisms that are at the end of the lineage have the property of kegg=kegg_genome_id. Each of these nodes has relationships to a different node type labelled as KO (functional orthologs). See the example below just for two organisms. The same KO nodes can link to many mammalian organisms like elephant, human or a mouse (or even to all mammals),

This results in a network with 337 (111 are organisms) taxa nodes and 12142 Ko nodes and over 1,200,000 relations.

Now i want to build a model that would predict based on KO whenever a given species belongs toEuarchontoglires. Every organism node that is linked to Euarchontoglires has a property category=1. The rest of the organisms have the property category=0. 

This was just an introduction.

What I want to know is how I can calculate node2vec ONLY for these organism nodes. We do not want to have embeddings for KO nodes.

I have a projected graph:

graph.run("""

CALL gds.graph.project(

  'graph_info',

    { 

      taxa: { 

                label: 'Taxa', 

                properties: ['category']

                },

      ko: { 

                label: 'Ko'

                } 

    },

    {

        RELS: {

            type: 'HAS_KO',

            orientation: 'UNDIRECTED'

        }

    }

)

""")

I do not know how to write gds.beta.node2vec.write only for the nodes that I will later use for ML.

MATCH (n:Taxa) WHERE n.kegg is not null RETURN n.name, n.category, n.n2v_all_nodes

Can u guide me?

[michael_hunger]

You can probably rather use cypher-projection where you can use arbitrary filters and pattern matches to determine the nodes and relationships to be projected into the in-memory graph.

https://neo4j.com/docs/graph-data-science/current/graph-project-cypher/

https://neo4j.com/docs/graph-data-science/current/graph-project-cypher-aggregation/