Skip to main content

Improving the Quality of Semantic Retrieval in DNA-Based Memories with Learning

  • Conference paper
Knowledge-Based Intelligent Information and Engineering Systems (KES 2004)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 3213))

Abstract

At least three types of associative memories based on DNA-affinity have been proposed. Previously, we have quantified the quality of retrieval of genomic information in simulation by comparison to state-of-the-art symbolic methods available, such as LSA (Latent Semantic Analysis.) Their ability is poor when performed without a proper compaction procedure. Here, we use a different compaction procedure that uses learning to improve the ability of DNA-based memories to store abiotic data. We evaluate and compare the quality of the retrieval of semantic information. Their performance is much closer to that of LSA, according to human expert ratings, and slightly better than the previous method using a summarization procedure. These results are expected to improve and feasibly scale up with actual DNA molecules in real test tubes.

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 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adleman, L.M.: Molecular Computation of Solutions to Combinatorial Problems. Science 266, 1021–1024 (1994)

    Article  Google Scholar 

  2. Baum, E.: Building an Associative Memory Vastly Larger Than the Brain. Science 268, 583–585 (1995)

    Article  Google Scholar 

  3. Chen, J., Deaton, R., Wang, Y.Z.: A DNA-based Memory with in vitro Learning and Associative Recall. In: Chen, J., Reif, J.H. (eds.) DAN 2003. LNCS, vol. 2943, pp. 145–156. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  4. Deaton, R., Chen, J., Bi, H., Garzon, M., Rubin, H., Wood, D.H.: A PCR-Based Protocol for In-Vitro Selection of Non-cross hybridizing Oligonucleotides.  10, 105–114

    Google Scholar 

  5. Deaton, R.J., Chen, J., Bi, H., Rose, J.A.: A Software Tool for Generating Non-cross hybridizing Libraries of DNA Oligonucleotides.   In: [10], pp. 211–220

    Google Scholar 

  6. Garzon, G., Blain, D., Bobba, K., Neel, A., West, M.: Self-Assembly of DNA-like structures in silico. Journal of Genetic Programming and Evolvable Machines 4, 185–200 (2003)

    Article  Google Scholar 

  7. Garzon, M.H., Neel, A., Bobba, K.: Efficiency and Reliability of Semantic Retrieval in DNA-based Memories. In: Chen, J., Reif, J.H. (eds.) DAN 2003. LNCS, vol. 2943, pp. 157–169. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  8. Garzon, M.: Biomolecular Computing. silico. Bull. of the European Assoc. for Theoretical Computer Science EATCS 79, 129–145 (2003)

    MathSciNet  Google Scholar 

  9. Garzon, M.H., Oehmen, C.: Biomolecular Computation on Virtual Test Tubes. In: Jonoska, N., Seeman, N.C. (eds.) DNA 2001. LNCS, vol. 2340, pp. 117–128. Springer, Heidelberg (2002)

    Chapter  Google Scholar 

  10. Hagiya, M., Ohuchi, A. (eds.): DNA 2002. LNCS, vol. 2568. Springer, Heidelberg (2003)

    Google Scholar 

  11. Landauer, T.K., Dumais, S.T.: A Solution to Plato’s Problem: The Latent Semantic Analysis Theory of the Acquisition, Induction, and Representation of Knowledge. Psychological Review 104, 211–240 (1997)

    Article  Google Scholar 

  12. Neel, A., Garzon, M.: Efficiency and Reliability of Genomic Information Storage and Retrieval in DNA-based Memories with Compaction. Congress for Evolutionary Computation CEC, 2733–2739 (2003)

    Google Scholar 

  13. Neel, A., Garzon, M., Penumatsa, P.: Semantic Retrieval in DNA-based Memories with Abiotic Data. Congress for Evolutionary Computation (in press, 2004)

    Google Scholar 

  14. Reif, J.H., LaBean, T.: Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using Error-Correcting Codes and Vector Quantization. In: Condon, A., Rozenberg, G. (eds.) DNA 2000. LNCS, vol. 2054, pp. 145–172. Springer, Heidelberg (2001)

    Chapter  Google Scholar 

  15. Reif, J.H., LaBean, T., Pirrung, M., Rana, V.S., Guo, B., Kingsford, C., Wickham, G.S.: Experimental Construction of Very Large DNA Databases with Associative Search Capability. In: Jonoska, N., Seeman, N.C. (eds.) DNA 2001. LNCS, vol. 2340, Springer, Heidelberg (2002)

    Google Scholar 

  16. Test of English as a Foreign Language (TOEFL), Educational Testing Service, Princeton, New Jersey, http://www.ets.org/

  17. Landauer, T.K., Foltz, P.W., Laham, D.: Introduction to Latent Semantic Analysis. Discourse Processes 25, 259-284

    Google Scholar 

  18. http://www.autotutor.org

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Neel, A., Garzon, M., Penumatsa, P. (2004). Improving the Quality of Semantic Retrieval in DNA-Based Memories with Learning. In: Negoita, M.G., Howlett, R.J., Jain, L.C. (eds) Knowledge-Based Intelligent Information and Engineering Systems. KES 2004. Lecture Notes in Computer Science(), vol 3213. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-30132-5_7

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-30132-5_7

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-23318-3

  • Online ISBN: 978-3-540-30132-5

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics