Skip to main content

Faithful Embeddings for \(\mathcal{E}\mathcal{L}^{++}\) Knowledge Bases

  • Conference paper
  • First Online:
The Semantic Web – ISWC 2022 (ISWC 2022)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 13489))

Included in the following conference series:

Abstract

Recently, increasing efforts are put into learning continual representations for symbolic knowledge bases (KBs). However, these approaches either only embed the data-level knowledge (ABox) or suffer from inherent limitations when dealing with concept-level knowledge (TBox), i.e., they cannot faithfully model the logical structure present in the KBs. We present BoxEL, a geometric KB embedding approach that allows for better capturing the logical structure (i.e., ABox and TBox axioms) in the description logic \(\mathcal{E}\mathcal{L}^{++}\). BoxEL models concepts in a KB as axis-parallel boxes that are suitable for modeling concept intersection, entities as points inside boxes, and relations between concepts/entities as affine transformations. We show theoretical guarantees (soundness) of BoxEL for preserving logical structure. Namely, the learned model of BoxEL embedding with loss 0 is a (logical) model of the KB. Experimental results on (plausible) subsumption reasonings and a real-world application–protein-protein prediction show that BoxEL outperforms traditional knowledge graph embedding methods as well as state-of-the-art \(\mathcal{E}\mathcal{L}^{++}\) embedding approaches.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Notes

  1. 1.

    Under the translation setting, the embeddings will simply become \(\textsf {Parent} \equiv \textsf {Person}\), which is obviously not what we want as we can express \(\textsf {Parent} \not \equiv \textsf {Person}\) with \(\mathcal{E}\mathcal{L}^{++}\) by propositions like \(\textsf {Children} \sqcap \textsf {Parent} \sqsubseteq \bot \), \(\textsf {Children} \sqsubseteq \textsf {Person}\) and \(\textsf {Children}(a)\).

  2. 2.

    Compared with the example given in [15], we add additional concept assertion statements that distinguish entities and concepts:.

  3. 3.

    https://github.com/bio-ontology-research-group/machine-learning-with-ontologies.

  4. 4.

    https://github.com/Box-EL/BoxEL.

  5. 5.

    https://arxiv.org/abs/2201.09919.

References

  1. Abboud, R., Ceylan, İ.İ., Lukasiewicz, T., Salvatori, T.: Boxe: A box embedding model for knowledge base completion. In: NeurIPS (2020)

    Google Scholar 

  2. Baader, F., Brandt, S., Lutz, C.: Pushing the el envelope. In: IJCAI. vol. 5, pp. 364–369 (2005)

    Google Scholar 

  3. Baader, F., Calvanese, D., McGuinness, D., Patel-Schneider, P., Nardi, D., et al.: The description logic handbook: Theory, implementation and applications. Cambridge University Press (2003)

    Google Scholar 

  4. Bordes, A., Usunier, N., García-Durán, A., Weston, J., Yakhnenko, O.: Translating embeddings for modeling multi-relational data. In: NIPS. pp. 2787–2795 (2013)

    Google Scholar 

  5. Consortium, G.O.: Gene ontology consortium: going forward. Nucleic acids research 43(D1), D1049–D1056 (2015)

    Google Scholar 

  6. Dasgupta, S.S., Boratko, M., Zhang, D., Vilnis, L., Li, X., McCallum, A.: Improving local identifiability in probabilistic box embeddings. In: NeurIPS (2020)

    Google Scholar 

  7. Dettmers, T., Minervini, P., Stenetorp, P., Riedel, S.: Convolutional 2d knowledge graph embeddings. In: AAAI, pp. 1811–1818. AAAI Press (2018)

    Google Scholar 

  8. Gärdenfors, P.: Conceptual spaces - the geometry of thought. MIT Press (2000)

    Google Scholar 

  9. Garg, D., Ikbal, S., Srivastava, S.K., Vishwakarma, H., Karanam, H.P., Subramaniam, L.V.: Quantum embedding of knowledge for reasoning. In: NeurIPS, pp. 5595–5605 (2019)

    Google Scholar 

  10. Graua, B.C., Horrocksa, I., Motika, B., Parsiab, B., Patel-Schneiderc, P., Sattlerb, U.: Web semantics: science, services and agents on the world wide web. Web Semantics: Sci. Serv. Agents World Wide Web 6, 309–322 (2008)

    Google Scholar 

  11. Gutiérrez-Basulto, V., Schockaert, S.: From knowledge graph embedding to ontology embedding? an analysis of the compatibility between vector space representations and rules. In: KR, pp. 379–388. AAAI Press (2018)

    Google Scholar 

  12. Harris, M., et al.: The gene ontology (go) database and informatics resource nucleic acids research, 32. D258–D261 (2004)

    Google Scholar 

  13. Kazakov, Y., Krötzsch, M., Simancik, F.: The incredible ELK - from polynomial procedures to efficient reasoning with el ontologies. J. Autom. Reason. 53(1), 1–61 (2014)

    Article  MathSciNet  Google Scholar 

  14. Kingma, D.P., Ba, J.: Adam: A method for stochastic optimization. In: ICLR (Poster) (2015)

    Google Scholar 

  15. Kulmanov, M., Liu-Wei, W., Yan, Y., Hoehndorf, R.: EL embeddings: Geometric construction of models for the description logic EL++. In: IJCAI, pp. 6103–6109. ijcai.org (2019)

    Google Scholar 

  16. Kulmanov, M., Smaili, F.Z., Gao, X., Hoehndorf, R.: Semantic similarity and machine learning with ontologies. Briefings Bioinform. 22(4) (2021)

    Google Scholar 

  17. Li, X., Vilnis, L., Zhang, D., Boratko, M., McCallum, A.: Smoothing the geometry of probabilistic box embeddings. In: ICLR. OpenReview.net (2019)

    Google Scholar 

  18. Lin, Y., Liu, Z., Sun, M., Liu, Y., Zhu, X.: Learning entity and relation embeddings for knowledge graph completion. In: AAAI, pp. 2181–2187. AAAI Press (2015)

    Google Scholar 

  19. Liu, H., Wu, Y., Yang, Y.: Analogical inference for multi-relational embeddings. In: ICML. Proceedings of Machine Learning Research, vol. 70, pp. 2168–2178. PMLR (2017)

    Google Scholar 

  20. Mondal, S., Bhatia, S., Mutharaju, R.: Emel++: Embeddings for EL++ description logic. In: AAAI Spring Symposium: Combining Machine Learning with Knowledge Engineering. CEUR Workshop Proceedings, vol. 2846. CEUR-WS.org (2021)

    Google Scholar 

  21. Mungall, C.J., Torniai, C., Gkoutos, G.V., Lewis, S.E., Haendel, M.A.: Uberon, an integrative multi-species anatomy ontology. Genome Biol. 13(1), 1–20 (2012)

    Article  Google Scholar 

  22. Nickel, M., Tresp, V., Kriegel, H.: A three-way model for collective learning on multi-relational data. In: ICML, pp. 809–816. Omnipress (2011)

    Google Scholar 

  23. Özçep, Ö.L., Leemhuis, M., Wolter, D.: Cone semantics for logics with negation. In: IJCAI, pp. 1820–1826. ijcai.org (2020)

    Google Scholar 

  24. Patel, D., Dasgupta, S.S., Boratko, M., Li, X., Vilnis, L., McCallum, A.: Representing joint hierarchies with box embeddings. In: Automated Knowledge Base Construction (2020). https://openreview.net/forum?id=J246NSqR_l

  25. Rector, A.L., Rogers, J.E., Pole, P.: The galen high level ontology. In: Medical Informatics Europe’96, pp. 174–178. IOS Press (1996)

    Google Scholar 

  26. Ren, H., Hu, W., Leskovec, J.: Query2box: Reasoning over knowledge graphs in vector space using box embeddings. In: ICLR, OpenReview.net (2020)

    Google Scholar 

  27. Ren, H., Leskovec, J.: Beta embeddings for multi-hop logical reasoning in knowledge graphs. In: Neurips (2020)

    Google Scholar 

  28. Smaili, F.Z., Gao, X., Hoehndorf, R.: Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations. Bioinformatics 34(13), i52–i60 (2018)

    Article  Google Scholar 

  29. Smaili, F.Z., Gao, X., Hoehndorf, R.: Opa2vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction. Bioinformatics 35(12), 2133–2140 (2019)

    Article  Google Scholar 

  30. Steigmiller, A., Liebig, T., Glimm, B.: Konclude: system description. J. Web Semant. 27–28, 78–85 (2014)

    Article  Google Scholar 

  31. Trouillon, T., Welbl, J., Riedel, S., Gaussier, É., Bouchard, G.: Complex embeddings for simple link prediction. In: ICML. JMLR Workshop and Conference Proceedings, vol. 48, pp. 2071–2080. JMLR.org (2016)

    Google Scholar 

  32. Vilnis, L., Li, X., Murty, S., McCallum, A.: Probabilistic embedding of knowledge graphs with box lattice measures. In: ACL (1), pp. 263–272. Association for Computational Linguistics (2018)

    Google Scholar 

  33. Wang, Q., Mao, Z., Wang, B., Guo, L.: Knowledge graph embedding: a survey of approaches and applications. IEEE Trans. Knowl. Data Eng. 29(12), 2724–2743 (2017)

    Article  Google Scholar 

  34. Wang, Z., Zhang, J., Feng, J., Chen, Z.: Knowledge graph embedding by translating on hyperplanes. In: AAAI, pp. 1112–1119. AAAI Press (2014)

    Google Scholar 

  35. Yang, B., Yih, W., He, X., Gao, J., Deng, L.: Embedding entities and relations for learning and inference in knowledge bases. In: ICLR (Poster) (2015)

    Google Scholar 

Download references

Acknowledgments

The authors thank the International Max Planck Research School for Intelligent Systems (IMPRS-IS) for supporting Bo Xiong. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No: 860801. Nico Potyka was partially funded by DFG projects Evowipe/COFFEE.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Bo Xiong .

Editor information

Editors and Affiliations

1 Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (pdf 149 KB)

Rights and permissions

Reprints and permissions

Copyright information

© 2022 The Author(s), under exclusive license to Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Xiong, B., Potyka, N., Tran, TK., Nayyeri, M., Staab, S. (2022). Faithful Embeddings for \(\mathcal{E}\mathcal{L}^{++}\) Knowledge Bases. In: Sattler, U., et al. The Semantic Web – ISWC 2022. ISWC 2022. Lecture Notes in Computer Science, vol 13489. Springer, Cham. https://doi.org/10.1007/978-3-031-19433-7_2

Download citation

  • DOI: https://doi.org/10.1007/978-3-031-19433-7_2

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-19432-0

  • Online ISBN: 978-3-031-19433-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics