{"id":104,"date":"2014-06-12T12:30:45","date_gmt":"2014-06-12T16:30:45","guid":{"rendered":"https:\/\/sites.bu.edu\/phenogeno\/?page_id=104"},"modified":"2014-07-17T12:39:47","modified_gmt":"2014-07-17T16:39:47","slug":"high-performance-algorithms","status":"publish","type":"page","link":"https:\/\/sites.bu.edu\/phenogeno\/research\/high-performance-algorithms\/","title":{"rendered":"High Performance Algorithms"},"content":{"rendered":"

<\/h4>\n

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Selected Publications<\/p>\n

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Journal Publications<\/strong><\/p>\n

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    \n
  1. Alon N, Asodi V, Cantor C, Kasif S, Rachlin J.\u00a0Multi-node graphs: a framework for multiplexed biological assays<\/a>. J Comput Biol. 2006 Dec;13(10):1659-72. PMID: 17238837<\/li>\n
  2. Formula dissection: A parallel algorithm for constraint satisfaction<\/a>. Reif, J. H., Kasif, S., and Sherlekar, D.\u00a0 Comput. Math. Appl. 55, 6 (Mar. 2008), 1170- 1177 (republished from a 1987 conference version).<\/li>\n
  3. Noga Alon, Richard Beigel and Simon\u00a0Kasif and Steven Rudich and Benny Sudakov, “Learning a Hidden Matching<\/a>“, SIAM Journal of Computing, 2004.<\/li>\n
  4. Wu CJ, Fu Y, Murali TM, Kasif S. \u00a0Gene expression module discovery using Gibbs sampling<\/a>. Genome Inform. 2004;15(1):239-48. PMID: 15712126<\/li>\n
  5. Letovsky S, Kasif S.\u00a0\u00a0Predicting protein function from protein\/protein interaction data: a probabilistic approach<\/a>.\u00a0 Bioinformatics. 2003;19 Suppl 1:i197-204. PMID: 12855458<\/li>\n
  6. Kasif S, Weng Z, Derti A, Beigel R, DeLisi C.\u00a0A computational framework for optimal masking in the synthesis of oligonucleotide microarrays<\/a>. Nucleic Acids Res. 2002 Oct 15;30(20):e106. PMID: 12384608<\/li>\n
  7. Tettelin H, Radune D, Kasif S, Khouri H, Salzberg SL.\u00a0\u00a0Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project<\/a>. Genomics. 1999 Dec 15;62(3):500-7. PMID: 10644449<\/li>\n
  8. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL.\u00a0Improved microbial gene identification with GLIMMER<\/a>. Nucleic Acids Res. 1999 Dec 1;27(23):4636-41. PMID: 10556321<\/li>\n
  9. Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL.\u00a0Alignment of whole genomes<\/a>. Nucleic Acids Res. 1999 Jun 1;27(11):2369-76. PMID: 10325427<\/li>\n
  10. Kasif, S.,\u00a0 \u201cDatascope: Mining Biological Sequences\u201d, special issue on Data Mining, IEEE Intelligent Systems,\u00a0 pp. 38–45, 1999.<\/li>\n
  11. Kasif, S., Salzberg, S., Waltz, D., J. Rachlin, and Aha, D., \u201cTowards of a Framework for Memory-Based Reasoning\u201d, Artificial Intelligence, pp. 287–311, 1998.<\/li>\n
  12. Kasif, S., \u201cTowards a Constraint-Based Engineering Framework for Algorithm Design and Application<\/a>\u201d, Journal of Constraints, 1997.<\/li>\n
  13. Delcher, A, A. Grove, S. Kasif and J. Pearl, \u201cLogarithmic Time Queries and Updates in Probabilistic Networks<\/a>\u201d, Journal of Artificial Intelligence Research, Vol. 4., pp. 37–59, 1996.<\/li>\n
  14. Waltz, D. and S. Kasif, \u201cOn Reasoning from Data<\/a>\u201d, Computing Surveys, 1996.<\/li>\n
  15. Delcher, A. and S. Kasif, \u201cTerm Matching on a Mesh-Connected Array of Processors\u201d, Annals of Mathematics and Artificial Intelligence, Volume 14, pp.177–186, 1995.<\/li>\n
  16. Murthy, S., S. Kasif and S. Salzberg, \u201c\u00a0System for Induction of Oblique Decision Trees<\/a>\u201d, Journal of Artificial Intelligence Research, 2:1, pp.1–33, 1994.<\/li>\n
  17. Heath, D., S. Kasif, S. R. Kosaraju, S. Salzberg and G. Sullivan, \u201cLearning Nested Concept Classes with Limited Memory<\/a>\u201d, Journal of Experimental and Theoretical AI, 1996.<\/li>\n
  18. Kasif, S., \u201cOptimal Parallel Algorithms for Quad-Tree Problems<\/a>\u201d, Journal of Computer Vision and Image Processing, pp.281–285, May 1994.<\/li>\n
  19. Kasif, S. and A. Delcher, \u201cAnalysis of Local Consistency in Parallel Constraint Networks\u201d, Artificial Intelligence, 69, pp.307–327, 1994.<\/li>\n
  20. Heath, D. and S. Kasif, \u201cOn Voronoi Covers with Applications to Machine Learning<\/a>\u201d, Computational Geometry: Theory and Applications, pp. 289-305, Nov. 1993.<\/li>\n
  21. Kasif, S., S. Banerjee, A. Delcher and G. Sullivan, \u201cSome Results on the Complexity of Symmetric Connectionist Networks<\/a>\u201d, Annals of Mathematics and Artificial Intelligence, pp.327-344, Nov. 1993.<\/li>\n
  22. Delcher, A. and S. Kasif,\u00a0 \u201cEfficient Parallel Term Matching and Anti-Unification”, Journal of Automated Reasoning, pp.\u00a0 391–406, 1992.<\/li>\n
  23. Kasif, S., \u201cOn the Parallel Complexity of Discrete Relaxation in Constraint Networks\u201d, Artificial Intelligence, pp. 275-286, October 1990.<\/li>\n
  24. Delcher, A. and S. Kasif, \u201cSome Results On the Complexity of Maintaining Data Flow Dependencies in Parallel Logic Programs\u201d, Journal of Logic Programming, pp.229–241, April 1989.<\/li>\n
  25. Kasif, S., \u201cControl and Data Driven Execution of Logic Programs: A Comparison\u201d, Journal of Parallel Programming.Vol.15, No.1, pp.73–100, February 1987.<\/li>\n
  26. Kasif, S., L. Kitchen and A. Rosenfeld, \u201cA Hough Transform Technique for Subgraph Isomorphism\u201d, Pattern Recognition Letters. Vol.2, pp.83–88, December 1983.<\/li>\n
  27. Kasif, S. and A. Rosenfeld, \u201cPyramid Linking as a Special Case of Isodata\u201d, IEEE Transactions on Systems, Man and Cybernetics, Vol.SMC-13, No.1, January 1983.<\/li>\n<\/ol>\n

     <\/p>\n

    Books, Books Chapters and Special Reports<\/b><\/p>\n

     <\/p>\n

      \n
    1. \u00a0S. Kasif and A. Delcher, \u201cAnalysis of Local Consistency in Parallel Constraint Networks\u201d, Principle and Practice of Constraint Programming, published by MIT press, editors Pascal van Henteryck and V.J. Saraswat, 1994.<\/li>\n
    2. Heath, D., S. Kasif and S. Salzberg, \u201cCommittees of Decision Trees\u201d, Cognitive Technology, North Holland Publishers, 1995<\/li>\n
    3. Simon Kasif and Stuart Russell (Eds.), Proceedings of the AAAI Fall Symposium on Learning Complex Behaviors, AAAI Press, 1996.<\/li>\n
    4. J. Flannagan, T. Huang, P. Jones, and S. Kasif, \u201cHuman Centered Systems: Information, Interactivity and Intelligence<\/a>\u201d, Executive NSF Steering Committee Report, July, 1997.<\/li>\n
    5. R. Grossman, S. Kasif, J. Ullman, et al,\u00a0 \u201cData Mining<\/a>\u201d, Executive Committee NSF Report, 1998.<\/li>\n
    6. Kasif, S. and A. Delcher, \u201cBiological Data Modeling using Probabilistic Networks\u201d, in Salzberg, S., D. Searls, and S. Kasif, \u201cComputational Methods in Molecular Biology\u201d, Elsevier, Publ. 1998.<\/li>\n
    7. S. Salzberg, D. Searls and S. Kasif, eds, \u201cComputational Methods in Molecular Biology<\/a>\u201d, Elsevier Publ. 1998. (2nd<\/sup>\u00a0Printing, February 1999).<\/li>\n
    8. Rich Roberts, Peter Karp, Simon Kasif and Stuart Linn, \u201cAn Experimental Approach to Gene Function<\/a>\u201d, Executive Report, American Academy for Microbiology.<\/li>\n
    9. Satoru Miyano Jill Mesirov, Simon Kasif, Sorin Istrail Pavel Pevzner, Michael Waterman,\u00a0Research in Computational Molecular Biology: 9th Annual International Conference, RECOMB 2005<\/a>, Cambridge, MA, USA, May 14-18, 2005, Proceedings Lecture Notes in Bioinformatics.<\/li>\n<\/ol>\n

       <\/p>\n

       <\/p>\n

      Papers in Peer-Reviewed Conferences<\/b><\/p>\n

      Publications in very selective conferences with acceptance rates of 25% or less are marked with asterisks *. These papers are typically considered equal to a journal publication in Computer Science.<\/p>\n

       <\/p>\n

        \n
      1. *Eisinger, N., S. Kasif and J. Minker, \u201cLogic Programming: A Parallel Approach\u201d, First International Logic Programming Conf., Faculte des Sciences de Luminy Marseille, France, pp.71–77, September 1982.<\/li>\n
      2. Kasif, S., M. Kohli and J. Minker, \u201cPRISM—A Parallel Inference System Based on Logic\u201d, Logic Programming Workshop, pp.123–152, Portugal, June 1983.<\/li>\n
      3. *Kasif, S., M. Kohli and J. Minker, \u201cControl Facilities of PRISM—A Parallel Inference System Based on Logic\u201d, International Joint Conf. on Artificial Intelligence, August 1983.<\/li>\n
      4. \u00a0Chakravarthy, U. S., S. Kasif, M. Kohli, J. Minker and D. Cao, \u201cLogic Programming on ZMOB: A Highly Parallel Machine\u201d, Proc. 1982 International Conf. on Parallel Processing, IEEE Press, pp.347\u2014349 New York, 1982.<\/li>\n
      5. *Kasif, S. and A. Rosenfeld, \u201cThe Fixpoints of Images and Scenes\u201d, Conf. on Computer Vision and Pattern Recognition, pp.454-456, June 1983.<\/li>\n
      6. *Kasif, S. and J. Minker, \u201cThe Intelligent Channel:\u00a0 A Scheme for Result Sharing in Parallel Logic Programs\u201d, International Joint Conf. on Artificial Intelligence, pp.29-31, August 1985.<\/li>\n
      7. *Kasif, S., \u201cOn the Parallel Complexity of Some Constraint Satisfaction Problems\u201d, National Conf. on Artificial Intelligence (AAAI-86), pp.349-353, August 1986.<\/li>\n
      8. Kasif, S., J. Reif and D. Sherlekar, \u201cFormula Dissection: A Parallel Algorithm for Constraint Satisfaction\u201d<\/a>, IEEE Workshop on Computer Architecture for Pattern Analysis and Machine Intelligence, pp.51-57, October 1987.<\/li>\n
      9. Delcher, A. and S. Kasif, \u201cOn the Complexity of Incremental Parallel Computations in Artificial Intelligence\u201d, IEEE Workshop on Computer Architecture for Pattern Analysis and Machine Intelligence, pp.59-64, October 1987.<\/li>\n
      10. Kasif, S., \u201cEfficient Parallel Quad-Tree Algorithms\u201d, Proc. of 1988 ICAI, Tel Aviv, Israel, pp.353-363, December 1988.<\/li>\n
      11. Delcher, A. and S. Kasif, \u201cParallel Term Matching on Mesh Connected Computers\u201d, Proc. of 1988 ICAI, Tel Aviv, Israel, pp.~441-452, December 1988.<\/li>\n
      12. *Kasif, S., \u201cParallel Solutions to Constraint Satisfaction Problems\u201d, IEEE Conf. on Principles of Knowledge Representation and Reasoning, pp. 180-187, May 1989.<\/li>\n
      13. *Delcher, A. and S. Kasif, \u201cParallel Term Matching and Anti-Unification<\/a>\u201d, International Conf. on Logic Programming, pp.355–369, June 1990.<\/li>\n
      14. *Heath, D., S. Kasif, S. R. Kosaraju, S. Salzberg and G. Sullivan, \u201cLearning Nested Concept Classes with Limited Storage<\/a>\u201d, Proceedings of the International Joint Conference on Artificial Intelligence(IJCAI-91), pp. 777-782, 1991.<\/li>\n
      15. *Salzberg, S., D. Heath, A. Delcher and S. Kasif, \u201cLearning with a Helpful Teacher\u201d, Proceedings of the International Joint Conference on Artificial Intelligence, (IJCAI-91), pp. 705-711, 1991.<\/li>\n
      16. *S. Kasif and A. Delcher, \u201cImproved Decision Making in Game Trees: Recovering from Pathology\u201d, Proceedings of the National Conference on Artificial Intelligence (AAAI-92), pp. 513-518, July 1992.<\/li>\n
      17. D. Heath, S. Kasif and S. Salzberg, \u201cLearning Oblique Decision Trees\u201d, Computational Learning Theory and Natural Learning Systems, 1992.<\/li>\n
      18. Kasif, S. and A. Delcher, \u201cAnalysis of Local Consistency in Parallel Constraint Networks\u201d, International Conference on Artificial Intelligence and Vision, pp. 217-231, 1992.<\/li>\n
      19. S. Kasif, \u201cIterative Focusing and Hashing: An Alternative to Alpha-Beta\u201d, International Conference on Artificial Intelligence and Vision, pp. 59-72, 1992.<\/li>\n
      20. *D. Heath, S. Kasif and S. Salzberg, \u201cLearning Oblique Decision Trees\u201d, Proceedings of the International Joint Conference on Artificial Intelligence, (IJCAI 93), pp. 1002–1007, August 1993.<\/li>\n
      21. *Murthy, S., S. Kasif, S. Salzberg and R. Beigel, \u201cOC1: A Randomized Algorithm for Building Oblique Decision Trees<\/a>\u201d, Proceedings of the National Conference on Artificial Intelligence, (AAAI-93), pp. 322–327, July 93.<\/li>\n
      22. Heath, D., S. Kasif and S. Salzberg, \u201ck-DT: A Multi-Tree Learning Method\u201d, Proceedings of the Second International Workshop on Multi-strategy Learning (pp. 138–149), Harpers Ferry, West Virginia, 1993.<\/li>\n
      23. *Delcher, A., S. Kasif, H. Goldberg and W. Xsu, \u201cProtein Secondary-Structure Modeling with Probabilistic Networks<\/a>\u201d, International Conference on Intelligent Systems and Molecular Biology, pp. 109–117, 1993.<\/li>\n
      24. *Delcher, A., S. Kasif, H. Goldberg and W. Xsu, \u201cApplication of Probabilistic Causal Trees to Analysis of Protein Secondary Structure\u201d, Proceedings of the National Conference on Artificial Intelligence, pp. 316–321, July 1993.<\/li>\n
      25. *Bright, J., Kasif, L. Stiller, \u201cExploiting Algebraic Structure in Parallel State-Space Search<\/a>\u201d, Proc. of the 11-th National Conf. on Artificial Intelligence, July 1994, (AAAI-94), pp. 1341-1346, preliminary version presented in the AAAI Symposium on Massively Parallel AI”, March 1993.<\/li>\n
      26. *Rachlin, J., S. Kasif, S. Salzberg and D. Aha, \u201cToward of a better understanding of Memory-Based Classifiers\u201d,\u00a0 (plenary talk), Proceeding of the 11-th Intern. Conf. on Machine Learning, pp. 242–250, July 1994.<\/li>\n
      27. *Fulton, T., S. Kasif and S. Salzberg, \u201cEfficient Algorithms for Finding Multi-Way Splits for Decision Trees\u201d, JHU TR, December 1993, Proceeding of the 12-th Intern. Conf. on Machine Learning, July 1995.<\/li>\n
      28. *Delcher, A, A. Grove, S. Kasif and J. Pearl, \u201cLogarithmic Time Queries and Updates in Probabilistic Networks<\/a>\u201d, Proceedings of the 1995 Conference on Uncertainty in AI, August 1995.<\/li>\n
      29. D. Dobkin, D. Gunopoulous,\u00a0 S. Kasif, \u201cInduction of Low-Depth Decision Trees\u201d, International Conference on Mathematics and Artificial Intelligence, 1996,<\/li>\n
      30. S. Weiss, S. Kasif, and E. Brill, \u201cTowards a Framework for Adaptive Information Retrieval\u201d, AAAI Spring Symposium on Information Retrieval (1996).<\/li>\n
      31. *T. Fulton, S., Kasif, S. Salzberg, and D. Waltz, \u201cLocal Induction of Decision Trees<\/a>”, Proceedings of the 1996 Conference of Knowledge Discovery in Databases\u201d, August 1996.<\/li>\n
      32. R. Grossman, S. Bailey, S. Kasif, \u201cPapyrous: A System for Distributed Data Mining\u201d, Workshop on Distributed Data Mining, NYC, 1998.<\/li>\n
      33. *Beigel, R., N. Alon, S. Apaydin, L. Fortnow, and S. Kasif, \u201cAn Optimal Multiplex PCR Protocol for Closing Gaps in Whole Genomes\u201d, RECOMB, April 2001.<\/li>\n
      34. * Noga Alon, Richard Beigel and Simon Kasif and Steven Rudich and Benny Sudakov, \u201cLearning a Hidden Matching\u201d, Foundations of Computer Science, FOCS 2002.<\/li>\n
      35. T.M. Murali and S. Kasif, \u201cExtracting Conserved Gene Expression Motifs from from Microarray Data<\/a>\u201d, Pacific Symposium on Biocomputing, January 2003.<\/li>\n
      36. B. Logan, P. Moreno, B. Suzek, Z. Weng, and S. Kasif, \u201cRemote Homology Detection Using Feature Vectors Formed Using Alignments of Small Motifs\u201d, RECOMB 2002 (poster and patent 2000).<\/li>\n
      37. D. Pervouchine, J. Graber, and S. Kasif, \u201cStable RNA Secondary Structure of Human Donor Splice Sites\u201d, RECOMB 2002 (poster)<\/li>\n
      38. M. Walker, V. Pavlovic, and S. Kasif, \u201cA Comparative Genomic Method for Computational Identification of Prokaryotic Translation Initiation Sites\u201d, RECOMB 2002 (poster)<\/li>\n
      39. Y. Zheng, R. J. Roberts, and S. Kasif, \u201cComputational Identification of Operons in Microbial Genomes\u201d, RECOMB 2002 (poster).<\/li>\n
      40. Murali TM, Kasif S. \u00a0Extracting conserved gene expression motifs from gene expression data<\/a>. Pac Symp Biocomput. 2003;:77-88. PMID: 12603019<\/li>\n
      41. *S. Letovsky and S. Kasif, “A Probabilistic Approach to Gene Function Assignment and Propagation in Protein Interaction Networks”, June 2003, ISMB 2003.<\/li>\n<\/ol>\n

         <\/p>\n

        <\/strong><\/p>\n

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          Selected Publications   Journal Publications   Alon N, Asodi V, Cantor C, Kasif S, Rachlin J.\u00a0Multi-node graphs: a framework for multiplexed biological assays. J Comput Biol. 2006 Dec;13(10):1659-72. PMID: 17238837 Formula dissection: A parallel algorithm for constraint satisfaction. Reif, J. H., Kasif, S., and Sherlekar, D.\u00a0 Comput. Math. Appl. 55, 6 (Mar. 2008), 1170- […]<\/p>\n","protected":false},"author":8738,"featured_media":0,"parent":11,"menu_order":8,"comment_status":"closed","ping_status":"closed","template":"profiles.php","meta":[],"_links":{"self":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/104"}],"collection":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/users\/8738"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/comments?post=104"}],"version-history":[{"count":7,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/104\/revisions"}],"predecessor-version":[{"id":491,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/104\/revisions\/491"}],"up":[{"embeddable":true,"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/pages\/11"}],"wp:attachment":[{"href":"https:\/\/sites.bu.edu\/phenogeno\/wp-json\/wp\/v2\/media?parent=104"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}