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Applications of Answer Set Programming in Phylogenetic Systematics

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Logic Programming, Knowledge Representation, and Nonmonotonic Reasoning

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 6565))

Abstract

We summarize some applications of Answer Set Programming (ASP) in phylogenetics systematics, focusing on the challenges, how they are handled using computational methods of ASP, the usefulness of the ASP-based methods/tools both from the point of view of phylogenetic systematics and from the point of view of ASP.

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References

  1. Bodenreider, O., Çoban, Z.H., Doğanay, M.C., Erdem, E., Koşucu, H.: A preliminary report on answering complex queries related to drug discovery using answer set programming. In: Proc. of ALPSWS (2008)

    Google Scholar 

  2. Bodlaender, H.L., Fellows, M.R., Warnow, T.J.: Two strikes against perfect phylogeny. In: Proc. of 19th International Colloquidum on Automata Languages and Programming, pp. 273–283. Springer, Heidelberg (1992)

    Chapter  Google Scholar 

  3. Brooks, D.R., Erdem, E., Erdoğan, S.T., Minett, J.W., Ringe, D.: Inferring phylogenetic trees using answer set programming. Journal of Automated Reasoning 39(4), 471–511 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  4. Brooks, D.R., Erdem, E., Minett, J.W., Ringe, D.: Character-based cladistics and answer set programming. In: Hermenegildo, M.V., Cabeza, D. (eds.) PADL 2004. LNCS, vol. 3350, pp. 37–51. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  5. Cakmak, D.: Reconstructing weighted phylogenetic trees and weighted phylogenetic networks using answer set programming, M.S. Thesis, Sabancı University (2010)

    Google Scholar 

  6. Cakmak, D., Erdem, E., Erdogan, H.: Computing weighted solutions in answer set programming. In: Erdem, E., Lin, F., Schaub, T. (eds.) LPNMR 2009. LNCS, vol. 5753, pp. 416–422. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  7. Cakmak, D., Erdogan, H., Erdem, E.: Computing weighted solutions in ASP: Representation-based method vs. search-based method. In: Proc. of RCRA Workshop on Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion (2010)

    Google Scholar 

  8. Davis, M., Logemann, G., Loveland, D.: A machine program for theorem-proving. Communications of the ACM 5, 394–397 (1962)

    Article  MathSciNet  MATH  Google Scholar 

  9. Day, W.H.E., Sankoff, D.: Computational complexity of inferring phylogenies by compatibility. Systematic Zoology 35(2), 224–229 (1986)

    Article  MATH  Google Scholar 

  10. Dworschak, S., Grell, S., Nikiforova, V.J., Schaub, T., Selbig, J.: Modeling biological networks by action languages via answer set programming. Constraints 13(1-2), 21–65 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  11. Eiter, T., Erdem, E., Erdogan, H., Fink, M.: Finding similar or diverse solutions in answer set programming. In: Hill, P.M., Warren, D.S. (eds.) ICLP 2009. LNCS, vol. 5649, pp. 342–356. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  12. Eiter, T., Ianni, G., Schindlauer, R., Tompits, H.: A uniform integration of higher-order reasoning and external evaluations in answer-set programming. In: Proc. of IJCAI, pp. 90–96 (2005)

    Google Scholar 

  13. Eiter, T., Leone, N., Mateis, C., Pfeifer, G., Scarcello, F.: A deductive system for non-monotonic reasoning. In: Fuhrbach, U., Dix, J., Nerode, A. (eds.) LPNMR 1997. LNCS, vol. 1265, pp. 364–375. Springer, Heidelberg (1997)

    Google Scholar 

  14. Erdem, E., Erdem, O., Ture, F.: HAPLO-ASP: Haplotype inference using answer set programming. In: Erdem, E., Lin, F., Schaub, T. (eds.) LPNMR 2009. LNCS, vol. 5753, pp. 573–578. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  15. Erdem, E., Lifschitz, V., Nakhleh, L., Ringe, D.: Reconstructing the evolutionary history of indo-european languages using answer set programming. In: Dahl, V. (ed.) PADL 2003. LNCS, vol. 2562, pp. 160–176. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  16. Erdem, E., Lifschitz, V., Ringe, D.: Temporal phylogenetic networks and logic programming. Theory and Practice of Logic Programming 6(5), 539–558 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  17. Erdem, E., Ture, F.: Efficient haplotype inference with answer set programming. In: Proc. of AAAI, pp. 436–441 (2008)

    Google Scholar 

  18. Erdem, E., Wang, F.: Reconstructing the evolutionary history of Chinese dialects (2006) (accepted for presentation at the 39th International Conference on Sino-Tibetan Languages and Linguistics, ICSTLL 2006)

    Google Scholar 

  19. Erdem, E., Yeniterzi, R.: Transforming controlled natural language biomedical queries into answer set programs. In: Proc. of BioNLP, pp. 117–124 (2009)

    Google Scholar 

  20. Erdogan, H., Bodenreider, O., Erdem, E.: Finding semantic inconsistencies in UMLS using answer set programming. In: Proc. of AAAI (2010)

    Google Scholar 

  21. Erdogan, H., Erdem, E., Bodenreider, O.: Exploiting umls semantics for checking semantic consistency among umls concepts. In: Proc. of MedInfo (2010)

    Google Scholar 

  22. Gebser, M., Kaufmann, B., Neumann, A., Schaub, T.: Conflict-driven answer set solving. In: Proc. of IJCAI, pp. 386–392 (2007)

    Google Scholar 

  23. Gebser, M., Guziolowski, C., Ivanchev, M., Schaub, T., Siegel, A., Thiele, S., Veber, P.: Repair and prediction (under inconsistency) in large biological networks with answer set programming. In: Proc. of KR (2010)

    Google Scholar 

  24. Gebser, M., Schaub, T., Thiele, S., Usadel, B., Veber, P.: Detecting inconsistencies in large biological networks with answer set programming. In: Garcia de la Banda, M., Pontelli, E. (eds.) ICLP 2008. LNCS, vol. 5366, pp. 130–144. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  25. Gelfond, M., Lifschitz, V.: The stable model semantics for logic programming. In: Kowalski, R., Bowen, K. (eds.) Logic Programming: Proceedings of the Fifth International Conference and Symposium, pp. 1070–1080 (1988)

    Google Scholar 

  26. Grell, S., Schaub, T., Selbig, J.: Modelling biological networks by action languages via answer set programming. In: Etalle, S., Truszczyński, M. (eds.) ICLP 2006. LNCS, vol. 4079, pp. 285–299. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  27. Hennig, W.: Phylogenetic Systematics. University of Illinois Press, Urbana (1966); translated from: Davis, D. D., Zangerl, R.: Grundzuege einer Theorie der phylogenetischen Systematik (1950)

    Google Scholar 

  28. Leone, N., Pfeifer, G., Faber, W., Eiter, T., Gottlob, G., Perri, S., Scarcello, F.: The dlv system for knowledge representation and reasoning. ACM Trans. Comput. Log. 7(3), 499–562 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  29. Lierler, Y., Maratea, M.: Cmodels-2: SAT-based answer set solver enhanced to non-tight programs. In: Lifschitz, V., Niemelä, I. (eds.) LPNMR 2004. LNCS (LNAI), vol. 2923, pp. 346–350. Springer, Heidelberg (2004)

    Chapter  Google Scholar 

  30. Lifschitz, V.: Answer set programming and plan generation. Artificial Intelligence 138, 39–54 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  31. Lifschitz, V.: What is answer set programming? In: Proc. of AAAI (2008)

    Google Scholar 

  32. Marek, V., Truszczyński, M.: Stable models and an alternative logic programming paradigm. In: The Logic Programming Paradigm: a 25-Year Perspective, pp. 375–398. Springer, Heidelberg (1999)

    Chapter  Google Scholar 

  33. Marques-Silva, J., Sakallah, K.: Grasp: A search algorithm for propositional satisfiability. IEEE Trans. Computers 5, 506–521 (1999)

    Article  MathSciNet  Google Scholar 

  34. Nakhleh, L.: Phylogenetic Networks. Ph.D. thesis, The university of Texas at Austin (2004)

    Google Scholar 

  35. Niemelä, I., Simons, P.: Smodels - an implementation of the stable model and well-founded semantics for normal lp. In: Fuhrbach, U., Dix, J., Nerode, A. (eds.) LPNMR 1997. LNCS, vol. 1265, pp. 421–430. Springer, Heidelberg (1997)

    Chapter  Google Scholar 

  36. Schaub, T., Thiele, S.: Metabolic network expansion with answer set programming. In: Hill, P.M., Warren, D.S. (eds.) ICLP 2009. LNCS, vol. 5649, pp. 312–326. Springer, Heidelberg (2009)

    Chapter  Google Scholar 

  37. Simons, P., Niemelä, I., Soininen, T.: Extending and implementing the stable model semantics. Artificial Intelligence 138, 181–234 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  38. Tari, L., Anwar, S., Liang, S., Hakenberg, J., Baral, C.: Synthesis of pharmacokinetic pathways through knowledge acquisition and automated reasoning. In: Proc. of PSB, pp. 465–476 (2010)

    Google Scholar 

  39. Tran, N., Baral, C.: Reasoning about triggered actions in ansprolog and its application to molecular interactions in cells. In: Proc. of KR, pp. 554–564 (2004)

    Google Scholar 

  40. Tran, N., Baral, C.: Hypothesizing about signaling networks. J. Applied Logic 7(3), 253–274 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  41. Ture, F., Erdem, E.: Efficient haplotype inference with answer set programming. In: Proc. of AAAI, pp. 1834–1835 (2008)

    Google Scholar 

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Author information

Authors and Affiliations

  1. Faculty of Engineering and Natural Sciences, Sabancı University, Orhanlı, Tuzla, İstanbul, 34956, Turkey

    Esra Erdem

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  1. Esra Erdem
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Editors and Affiliations

  1. Eastman Kodak Company, Rochester, NY, USA

    Marcello Balduccini

  2. Department of Computer Science, New Mexico State University, 88003, Las Cruces, NM, USA

    Tran Cao Son

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Erdem, E. (2011). Applications of Answer Set Programming in Phylogenetic Systematics. In: Balduccini, M., Son, T.C. (eds) Logic Programming, Knowledge Representation, and Nonmonotonic Reasoning. Lecture Notes in Computer Science(), vol 6565. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-20832-4_26

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  • DOI: https://doi.org/10.1007/978-3-642-20832-4_26

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-20831-7

  • Online ISBN: 978-3-642-20832-4

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