Abstract
Associative memories based on DNA-affinity have been proposed. Here, the efficiency, reliability, and semantic capability for associative retrieval of three models of a DNA-based memory are quantified and compared to current conventional methods. In affinity-based memories[1], retrievals and deletions under stringent conditions occur reliably (98%) within very short times (100 milliseconds), regardless of the degree of stringency of the recall or the number of simultaneous queries in the input. In a more sophisticated type of DNA-based memory B proposed and experimentally verified by Chen et al. [2] with three genomes, the sensitivity of the discrimination ability remains unchanged when used on a library of 18 plasmids in the range of 1-4kbps and does appear to grow exponentially with the number of library strands used, even under simultaneous multiple queries in the same input. Finally, using a new type of memory compaction mechanism for data mining in vitro, DNA-based semantic retrieval compares favorably with statistically-based Latent Semantic Analysis (LSA), one of the best performers for semantic associative-based retrieval on text corpora.
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References
Baum, E.: Building An Associative Memory Vastly Larger Than The Brain. Science 268, 583–585 (1995)
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.) DNA 2003. LNCS, vol. 2943, Springer, Heidelberg (2004)
Deaton, R., Chen, J., Bi, H., Garzon, M., Rubin, H., Wood, D.H.: A PCR-Based Protocol for In-Vitro Selection of Non-Crosshybridizing Oligonucleotides. In: [8], pp. 196–204
Deaton, R.J., Chen, J., Bi, H., Rose, J.A.: A Software Tool for Generating Non- crosshybridizing Libraries of DNA Oligonucleotides. In: [8], pp. 252–261
Garzon, M., 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)
Garzon, M.: Biomolecular Computation in silico. Bull. of the European Assoc. For Theoretical Computer Science EATCS 19, 128–144 (2003)
Garzon, M., 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)
Hagiya, M., Ohuchi, A. (eds.): DNA 2002. LNCS, vol. 2568. Springer, Heidelberg (2003)
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)
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, pp. 231–247. Springer, Heidelberg (2002)
Schmidt, K.A., Henkel, C.V., Rozenberg, G.: DNA computing with single molecule detection. In: Proc. of DNA7, Hokkaido U, p. 336 (2001)
Landauer, T.K., Foltz, P.W., Laham, D.: Introduction to Latent Semantic Analysis. Discourse Processes 25, 259–284 (1998)
Wetmur, J.G.: Physical Chemistry of Nucleic Acid Hybridization. In: Proceedings of the 3rd DIMACS Meeting on DNA Based Computers, University of Pennsylvania (June 1997)
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Garzon, M.H., Bobba, K., Neel, A. (2004). Efficiency and Reliability of Semantic Retrieval in DNA-Based Memories. In: Chen, J., Reif, J. (eds) DNA Computing. DNA 2003. Lecture Notes in Computer Science, vol 2943. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24628-2_15
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DOI: https://doi.org/10.1007/978-3-540-24628-2_15
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