Question: Is it possible get the embedding of the relations and entities separately using Ontoprotein ?

zjunlp / OntoProtein

[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding

MIT License

141 stars 22 forks source link

Question: Is it possible get the embedding of the relations and entities separately using Ontoprotein ? #33

Open anonimoustt opened 4 months ago

anonimoustt commented 4 months ago

Hi,

I am just curious is it possible to get the embedding of proteins and relations in https://www.zjukg.org/project/ProteinKG25/ separately using huggingface ontoprotein model ( https://huggingface.co/zjunlp/OntoProtein)? Let us say,

Protein_1 Enables Protein_2 is triple in the knowledge graph.

Is it to get the embedding of Protein_1, Enables, Protein_2 separately using https://huggingface.co/zjunlp/OntoProtein

Alexzhuan commented 4 months ago

You can obtain the embedding of a protein sequence by applying mean pooling to the hidden states from last layer. However, the relation embedding is not available.

anonimoustt commented 3 months ago

Hi, I see the protein knowledge graph https://www.zjukg.org/project/ProteinKG25/ in your github which is really interesting. Do you have more knowledge graphs on full protein relations? If there are more knowledge graph like ProteinKG25 would you please share?