Skip to main content

An Unsupervised Approach for Cause-Effect Relation Extraction from Biomedical Text

  • Conference paper
  • First Online:
Natural Language Processing and Information Systems (NLDB 2018)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 10859))

Abstract

Identification of Cause-effect (CE) relation mentions, along with the arguments, are crucial for creating a scientific knowledge-base. Linguistically complex constructs are used to express CE relations in text, mainly using generic causative (causal) verbs (cause, lead, result etc). We observe that some generic verbs have a domain-specific causative sense (inhibit, express) and some domains have altogether new causative verbs (down-regulate). Not every mention of a generic causative verb (e.g., lead) indicates a CE relation mention. We propose a linguistically-oriented unsupervised iterative co-discovery approach to identify domain-specific causative verbs, starting from a small set of seed causative verbs and an unlabeled corpus. We use known causative verbs to extract CE arguments, and use known CE arguments to discover causative verbs (hence co-discovery). Since causes and effects are typically agents, events, actions, or conditions, we use WordNet hypernym categories to identify suitable CE arguments. PMI is used to measure linguistic associations between a causative verb and its argument. Once we have a list of domain-specific causative verbs, we use it to extract CE relation mentions from a given corpus in an unsupervised manner, filtering out non-causative use of a causative verb using WordNet hypernym check of its arguments. Our approach extracts 256 domain-specific causative verbs from 10, 000 PubMed abstracts of Leukemia papers, and outperforms several baselines for extracting intra-sentence CE relation mentions.

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 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
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

Similar content being viewed by others

References

  1. Joskowicz, L., Ksiezyck, T., Grishman, R.: Deep domain models for discourse analysis. In: Proceedings of the Annual AI Systems in Government Conference, 1989, pp. 195–200. IEEE (1989)

    Google Scholar 

  2. Khoo, C.S., Kornfilt, J., Oddy, R.N., Myaeng, S.H.: Automatic extraction of cause-effect information from newspaper text without knowledge-based inferencing. Lit. Linguist. Comput. 13(4), 177–186 (1998)

    Article  Google Scholar 

  3. Girju, R.: Automatic detection of causal relations for question answering. In: Proceedings of the ACL 2003 workshop on Multilingual Summarization and Question Answering, vol. 12, pp. 76–83. Association for Computational Linguistics (2003)

    Google Scholar 

  4. Radinsky, K., Davidovich, S., Markovitch, S.: Learning causality from textual data. In: Proceedings of Learning by Reading for Intelligent Question Answering Conference (2011)

    Google Scholar 

  5. Kim, H.D., Zhai, C., Rietz, T.A., Diermeier, D., Hsu, M., Castellanos, M., Ceja Limon, C.A.: Incatomi: integrative causal topic miner between textual and non-textual time series data. In: Proceedings of the 21st ACM International Conference on Information and Knowledge Management, pp. 2689–2691. ACM (2012)

    Google Scholar 

  6. Chang, D.-S., Choi, K.-S.: Causal relation extraction using cue phrase and lexical pair probabilities. In: Su, K.-Y., Tsujii, J., Lee, J.-H., Kwong, O.Y. (eds.) IJCNLP 2004. LNCS (LNAI), vol. 3248, pp. 61–70. Springer, Heidelberg (2005). https://doi.org/10.1007/978-3-540-30211-7_7

    Chapter  Google Scholar 

  7. Do, Q.X., Chan, Y.S., Roth, D.: Minimally supervised event causality identification. In: Proceedings of the Conference on Empirical Methods in Natural Language Processing, pp. 294–303. Association for Computational Linguistics (2011)

    Google Scholar 

  8. Bouma, G.: Normalized (pointwise) mutual information in collocation extraction. In: Proceedings of GSCL, pp. 31–40 (2009)

    Google Scholar 

  9. Recchia, G., Jones, M.N.: More data trumps smarter algorithms: comparing pointwise mutual information with latent semantic analysis. Behav. Res. Methods 41(3), 647–656 (2009)

    Article  Google Scholar 

  10. Schuster, S., Manning, C.D.: Enhanced english universal dependencies: an improved representation for natural language understanding tasks. In: LREC (2016)

    Google Scholar 

  11. Pawar, S., Bhattacharyya, P., Palshikar, G.: End-to-end relation extraction using neural networks and markov logic networks. In: Proceedings 15th Meeting of the European Chapter of the Association for Computational Linguistics (EACL 2017), vol. 1, pp. 818–827 (2017)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Raksha Sharma .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Sharma, R., Palshikar, G., Pawar, S. (2018). An Unsupervised Approach for Cause-Effect Relation Extraction from Biomedical Text. In: Silberztein, M., Atigui, F., Kornyshova, E., Métais, E., Meziane, F. (eds) Natural Language Processing and Information Systems. NLDB 2018. Lecture Notes in Computer Science(), vol 10859. Springer, Cham. https://doi.org/10.1007/978-3-319-91947-8_43

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-91947-8_43

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-91946-1

  • Online ISBN: 978-3-319-91947-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics