Skip to main content

Processing Natural Language with Biomolecules: Where Linguistics, Biology and Computation Meet

  • Conference paper
  • First Online:
Revolutions and Revelations in Computability (CiE 2022)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 13359))

Included in the following conference series:

  • 355 Accesses

Abstract

The explanation, formal modelling and processing of language remain a challenge. Natural language is a hard problem not only for linguistics that has not yet provided universal accepted theories about how language is acquired and processed, but also for computer science that has not found a satisfactory computational model for processing natural language. The interplay between linguistics, biology and computation can provide a new paradigm where challenges in the area of natural language can be afforded in a different way and where new models can be devised. In this paper, we present the challenges and opportunities of applying computing with biomolecules to natural language processing. We present a state-of-the-art of the interchange of methods between linguistics, biology and computation and show how computer science can provide the theoretical tools and formalisms to transfer biological concepts to natural language in order to improve language processing.

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 54.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 69.99
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. Adleman, L.: Molecular computation of solutions to combinatorial problems. Science 226, 1021–1024 (1994)

    Article  Google Scholar 

  2. Asimov, I.: Il Codice Genetico. Einaudi, Torino (1968)

    Google Scholar 

  3. Bayley, R., Cameron, R., Lucas, C.: The Oxford Handbook of Sociolinguistics. Oxford University Press, Oxford (2013)

    Book  Google Scholar 

  4. Bel-Enguix, G., Jiménez-López, M.D.: Byosyntax. an overview. Fundam. Inform. 64, 1–12 (2005)

    MATH  Google Scholar 

  5. Enguix, G.B., Jiménez-López, M.D.: Linguistic membrane systems and applications. In: Ciobanu, G., Păun, G., Pérez-Jiménez, M.J. (eds.) Applications of Membrane Computing, pp. 347–388. Springer, Berlin (2005). https://doi.org/10.1007/3-540-29937-8_13

  6. Bel-Enguix, G., Jiménez-López, M.D., Mercas, R., Perekrestenko, A.: Networks of evolutionary processors as natural language parsers. In: Proceedings of the First International Conference on Agents and Artificial Intelligence, pp. 619–625. INSTICC, Oporto (2009)

    Google Scholar 

  7. Blache, P., Balfourier, J.: Property grammars: a flexible constraint-based approach to parsing. In: Proceedings of Seventh International Workshop on Parsing Technologies. Tsinghua University Press, Beijing (2001)

    Google Scholar 

  8. Castellanos, J., Martín-Vide, C., Mitrana, V., Sempere, J.: Networks of evolutionary processors. Acta Informatica 39, 517–529 (2003). https://doi.org/10.1007/s00236-003-0114-y

    Article  MathSciNet  MATH  Google Scholar 

  9. Clark, A., Giorgolo, G., Lappin, S.: Towards a statistical model of grammaticality. In: Proceedings of the 35th Annual Conference of the Cognitive Science Society (2013)

    Google Scholar 

  10. Collado-Vides, J.: Towards a grammatical paradigm for the study of the regulation of gene expression. In: Theoretical Biology. Epigenetic and Evolutionary Order from Complex Systems. Edinburgh University Press, Edinburgh (1989)

    Google Scholar 

  11. Croft, W.: Explaining Language Change: An Evolutionary Approach. Longman, Singapore (2000)

    Google Scholar 

  12. Dorigo, M., Stützle, T.: Ant Colony Optimization. MIT Press/Bradford Books, Cambridge, MA (2004)

    Book  Google Scholar 

  13. Duchier, D., Prost, J.-P., Dao, T.-B.-H.: A model-theoretic framework for grammaticality judgements. In: de Groote, P., Egg, M., Kallmeyer, L. (eds.) FG 2009. LNCS (LNAI), vol. 5591, pp. 17–30. Springer, Heidelberg (2011). https://doi.org/10.1007/978-3-642-20169-1_2

    Chapter  Google Scholar 

  14. Fetzer, A.: Recontextualizing Context: Grammaticality Meets Appropriateness. John Benjamins, Amsterdam (2004)

    Book  Google Scholar 

  15. Fetzer, A.: Context and Appropriateness: Micro Meets Macro. John Benjamins, Amsterdam (2007)

    Book  Google Scholar 

  16. Forster, P.: Network analysis of word lists. In: Third International Conference on Quantitative Linguistics, pp. 184–186. Research Institute for the Languages of Finland, Helsinki (1997)

    Google Scholar 

  17. Geeraerts, D., Cuyckens, H.: The Oxford Handbook of Cognitive Linguistics. Oxford University Press, Oxford (2010)

    Book  Google Scholar 

  18. Gong, T., Shuai, L., Zhang, M.: Modelling language evolution: examples and predictions. Phys. Life Rev. 11(2), 280–302 (2014)

    Article  Google Scholar 

  19. Head, T.: Formal language theory and DNA: an analysis of the generative capacity of specific recombination behaviors. Bull. Math. Biol. 49, 737–759 (1987). https://doi.org/10.1007/BF02481771

    Article  MathSciNet  MATH  Google Scholar 

  20. Holland, J.: Adaptation in Natural and Artificial Systems. University of Michigan Press, Michigan (1975)

    Google Scholar 

  21. Hopfiel, H.: Neural networks and physical systems with emergent collective computational abilities. In: Proceedings of the National Academy of Sciences-USA, vol. 79, p. 2554. National Academy of Sciences (1982)

    Google Scholar 

  22. Horn, L., Ward, G.: The Handbook of Pragmatics. Blackwell, Oxford (2005)

    Book  Google Scholar 

  23. Jakobson, R.: Linguistics. In: Main Trends of Research in the Social and Human Sciences, pp. 419–463. Mouton, Paris (1970)

    Google Scholar 

  24. Jakobson, R.: Essais de Linguistique Générale. 2, Rapports Internes et Externes du Language. Les Éditions de Minuit, Paris (1973)

    Google Scholar 

  25. Ji, S.: Microsemiotics of DNA. Semiotica 138(1/4), 15–42 (2002)

    Google Scholar 

  26. Keller, F.: Gradience in grammar: experimental and computational aspects of degrees of grammaticality. Ph.D. thesis, University of Edinburgh (2000)

    Google Scholar 

  27. Kornai, A.: Speech and handwriting. In: Mathematical Linguistics. AIKP, pp. 219–246. Springer, London (2008). https://doi.org/10.1007/978-1-84628-986-6_9

    Chapter  MATH  Google Scholar 

  28. Lappin, S.: The Handbook of Contemporary Semantic Theory. Blackwell, Oxford (1997)

    Book  Google Scholar 

  29. Levelt, W.: Formal Grammars in Linguistics and Psycholinguistics. Jonh Benjamins, Amsterdam (2008)

    Book  Google Scholar 

  30. Manning, C.: Probabilistic approaches to syntax. In: Probability Theory in Linguistics, pp. 289–342. MIT Press, Cambridge (2003)

    Google Scholar 

  31. Marcus, S.: Language at the Crossroad of Computation and Biology. In: Computing with Bio-Molecules, pp. 1–35. Springer, Singapore (1998)

    Google Scholar 

  32. Martín-Vide, C., Pazos, J., Păun, G., Rodríguez-Patón, A.: A new class of symbolic abstract neural nets: tissue P systems. In: Ibarra, O.H., Zhang, L. (eds.) COCOON 2002. LNCS, vol. 2387, pp. 290–299. Springer, Heidelberg (2002). https://doi.org/10.1007/3-540-45655-4_32

    Chapter  Google Scholar 

  33. Melinger, A., Branigan, H., Pickering, M.: Parallel processing in language production. Lang. Cogn. Neurosci. 29(6), 663–683 (2014)

    Article  Google Scholar 

  34. von Neumann, J.: The Theory of Self-Reproducing Automata. University of Illinois Press, Urbana, IL (1968)

    Google Scholar 

  35. Newmeyer, F.: Generative Linguistics: An Historical Perspective. Routledge, London (1997)

    Google Scholar 

  36. Partee, B., ter Meulen, A., Wall, R.: Mathematical Methods in Linguistics. Kluwer, Drodrecht (1993)

    Book  Google Scholar 

  37. Pawlak, Z.: Gramatyka i Matematika. Panstwowe Zakady Wydawnietw Szkolnych, Warzsawa (1998)

    Google Scholar 

  38. Post, E.: Finite combinatory processes-formulation. J. Symbolic Logic 1, 103–105 (1936)

    Article  Google Scholar 

  39. Prince, A., Smolensky, P.: Optimality theory: constraint interaction in generative grammar. Technical report, Rutgers University (1993)

    Google Scholar 

  40. Păun, G.: Computing with membranes. J. Comput. Syst. Sci. 61, 108–143 (2000)

    Article  MathSciNet  Google Scholar 

  41. Păun, G., Rozenberg, G., Salomaa, A.: DNA Computing. New Computing Paradigms. Springer, Berlin (1998)

    Google Scholar 

  42. Ramchand, G., Reiss, C.: The Oxford Handbook of Linguistic Interfaces. Oxford University Press, Oxford (2007)

    Book  Google Scholar 

  43. Sadock, J.: Autolexical Syntax. A Theory of Parallel Grammatical Representations. University of Chicago Press, Chicago (1991)

    Google Scholar 

  44. Sakakibara, Y., Brown, M., Underwood, R., Mian, I.S., Haussler, D.: Stochastic context-free grammars for modeling RNA. In: Proceedings of the 27th Hawaii International Conference on System Sciences, pp. 284–293. IEEE Computer Society Press, Honolulu (1994)

    Google Scholar 

  45. Schleicher, A.: Die Darwinsche Theorie Und Die Sprachwissenschaft. Böhlau, Weimar (1863)

    Google Scholar 

  46. Schmidt, J.: Die Verwantschaftsverhältnisse Der Indogermanischen Sprachen. Böhlau, Weimar (1872)

    Google Scholar 

  47. Searls, D.: Investigating the linguistics of DNA with definite clause grammars. In: Logic Programming: Proceedings of the North American Conference on Logic Programming, vol. 1. Association for Logic Programming (1989)

    Google Scholar 

  48. Smith, A.: Models of language evolution and change. Wiley Interdisc. Rev.: Cogn. Sci. 5(3), 281–293 (2014)

    Article  Google Scholar 

  49. Smolensky, P., Legendre, G.: The Harmonic Mind: From Neural Computation to Optimality-Theoretic Grammar. MIT Press, Cambridge (2006)

    MATH  Google Scholar 

  50. Tateisi, Y., Ohta, T., Tsujii, J.: Annotation of predicate-argument structure on molecular biology text. In: Proceedings of the Workshop on the 1st International Joint Conference on Natural Language Processing (IJCNLP) (2004)

    Google Scholar 

  51. Thue, A.: Über unendliche zeichenreihen. Norske Vid. Selsk. Skr., I Mat. Nat. Kl., Kristiania vol. 7, pp. 1–22 (1906)

    Google Scholar 

  52. Thue, A.: Über die gegenseitige lage gleicher teile gewisser zeichenreihen. Norske Vid. Selsk. Skr., I Mat. Nat. Kl., Kristiania, vol. 1, pp. 1–67 (1912)

    Google Scholar 

  53. Turing, A.M.: On computable numbers with an application to the entscheidungsproblem. In: Proceedings London Mathematical Society, vol. 2/42 (1937)

    Google Scholar 

  54. Uemura, Y., Hasegawa, A., Kobayashi, S., Yokomori, T.: Tree adjoining grammars for RNA structure prediction. Theor. Comput. Sci. 210(2), 277–303 (1999)

    Article  MathSciNet  Google Scholar 

  55. Watson, J.: Biologie Moléculaire du Gène. Ediscience, Paris (1968)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to M. Dolores Jiménez López .

Editor information

Editors and Affiliations

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

Jiménez López, M.D. (2022). Processing Natural Language with Biomolecules: Where Linguistics, Biology and Computation Meet. In: Berger, U., Franklin, J.N.Y., Manea, F., Pauly, A. (eds) Revolutions and Revelations in Computability. CiE 2022. Lecture Notes in Computer Science, vol 13359. Springer, Cham. https://doi.org/10.1007/978-3-031-08740-0_12

Download citation

  • DOI: https://doi.org/10.1007/978-3-031-08740-0_12

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-031-08739-4

  • Online ISBN: 978-3-031-08740-0

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics