mlsanityData to 7 Oct 2026

Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations

arXiv 1802.00864 ↗First posted 31 Jan 2018q-bio.QM cs.AIcited by 18

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Abstract (arXiv)

We propose the Onto2Vec method, an approach to learn feature vectors for biological entities based on their annotations to biomedical ontologies. Our method can be applied to a wide range of bioinformatics research problems such as similarity-based prediction of interactions between proteins, classification of interaction types using supervised learning, or clustering.

Key facts. Cited by 18 papers in the map (data through 7 Oct 2026). First posted on arXiv 31 Jan 2018.

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Citing papers per year: 2021: 5; 2022: 5; 2023: 2; 2024: 4; 2025: 1; 2026: 1.

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  1. 2022OntoProtein: Protein Pretraining With Gene Ontology Embeddingcited by 70
  2. 2022Contextual Semantic Embeddings for Ontology Subsumption Predictioncited by 31
  3. 2022Faithiful Embeddings for EL++ Knowledge Basescited by 25
  4. 2024Ontology Embedding: A Survey of Methods, Applications and Resourcescited by 12
  5. 2021Predicting Gene-Disease Associations with Knowledge Graph Embeddings over Multiple Ontologiescited by 6
  6. 2021Bio-JOIE: Joint Representation Learning of Biological Knowledge Basescited by 4
  7. 2024Ontology Completion with Natural Language Inference and Concept Embeddings: An Analysiscited by 4
  8. 2022FALCON: Scalable Reasoning over Inconsistent ALC Ontologiescited by 2
  9. 2024Embedding Ontologies via Incorporating Extensional and Intensional Knowledgecited by 2
  10. 2024A Self-matching Training Method with Annotation Embedding Models for Ontology Subsumption Predictioncited by 2
  11. 2021Network representation learning systematic review: ancestors and current development statecited by 1
  12. 2021Why Settle for Just One? Extending EL++ Ontology Embeddings with Many-to-Many Relationshipscited by 1
6 more
  1. 2021Link Analysis meets Ontologies: Are Embeddings the Answer?cited by 1
  2. 2022Differentiable Fuzzy ALC: A Neural-Symbolic Representation Language for Symbol Groundingcited by 1
  3. 2023Neuro-Symbolic RDF and Description Logic Reasoners: The State-Of-The-Art and Challengescited by 1
  4. 2025T-TExTS (Teaching Text Expansion for Teacher Scaffolding): Enhancing Text Selection in High School Literature through Knowledge Graph-Based Recommendationcited by 1
  5. 2023Lattice-preserving ALC ontology embeddings with saturationcited by 0
  6. 2026Extending Ontologies: From Dense Embeddings to Hybrid Quantum-Fuzzy Systemscited by 0