# A Self-matching Training Method with Annotation Embedding Models for Ontology Subsumption Prediction

arXiv: https://arxiv.org/abs/2402.16278 · HTML: https://mlsanity.com/paper/2402.16278/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 47 references that are in the map.
- First posted on arXiv 26 Feb 2024.

## Builds on (most cited first, 18 of 18)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [Embedding Entities and Relations for Learning and Inference in Knowledge Bases](https://mlsanity.com/paper/1412.6575/) (2014)
- [Complex Embeddings for Simple Link Prediction](https://mlsanity.com/paper/1606.06357/) (2016)
- [RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space](https://mlsanity.com/paper/1902.10197/) (2019)
- [Holographic Embeddings of Knowledge Graphs](https://mlsanity.com/paper/1510.04935/) (2015)
- [Learning Hierarchy-Aware Knowledge Graph Embeddings for Link Prediction](https://mlsanity.com/paper/1911.09419/) (2019)
- [OWL2Vec*: Embedding of OWL Ontologies](https://mlsanity.com/paper/2009.14654/) (2020)
- [EL Embeddings: Geometric construction of models for the Description Logic EL ++](https://mlsanity.com/paper/1902.10499/) (2019)
- [Making Large Language Models Perform Better in Knowledge Graph Completion](https://mlsanity.com/paper/2310.06671/) (2023)
- [Exploring Large Language Models for Knowledge Graph Completion](https://mlsanity.com/paper/2308.13916/) (2023)
- [Modeling Heterogeneous Hierarchies with Relation-specific Hyperbolic Cones](https://mlsanity.com/paper/2110.14923/) (2021)
- [Contextual Semantic Embeddings for Ontology Subsumption Prediction](https://mlsanity.com/paper/2202.09791/) (2022)
- [OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction](https://mlsanity.com/paper/1804.10922/) (2018)
- [Faithiful Embeddings for EL++ Knowledge Bases](https://mlsanity.com/paper/2201.09919/) (2022)
- [Dual Box Embeddings for the Description Logic EL++](https://mlsanity.com/paper/2301.11118/) (2023)
- [Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations](https://mlsanity.com/paper/1802.00864/) (2018)

## Built on by (most cited first, 2 of 2)

- [Enhancing Geometric Ontology Embeddings for EL++ with Negative Sampling and Deductive Closure Filtering](https://mlsanity.com/paper/2405.04868/) (2024)
- [DELE: Deductive EL++ Embeddings for Knowledge Base Completion](https://mlsanity.com/paper/2411.01574/) (2024)

## Abstract (arXiv)

Recently, ontology embeddings representing entities in a low-dimensional space have been proposed for ontology completion. However, the ontology embeddings for concept subsumption prediction do not address the difficulties of similar and isolated entities and fail to extract the global information of annotation axioms from an ontology. In this paper, we propose a self-matching training method for the two ontology embedding models: Inverted-index Matrix Embedding (InME) and Co-occurrence Matrix Embedding (CoME). The two embeddings capture the global and local information in annotation axioms by means of the occurring locations of each word in a set of axioms and the co-occurrences of words in each axiom. The self-matching training method increases the robustness of the concept subsumption prediction when predicted superclasses are similar to subclasses and are isolated to other entities in an ontology. Our evaluation experiments show that the self-matching training method with InME outperforms the existing ontology embeddings for the GO and FoodOn ontologies and that the method with the concatenation of CoME and OWL2Vec* outperforms them for the HeLiS ontology.