Quest for the optimal algorithm

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Quest for the optimal algorithm

  1. 1. Quest for the Optimal Algorithm Melvin Zhang melvin@melvinzhang.net
  2. 2. CS5234 Projects by Students (Spring 2007) (as of 27-March-2007) ========================================================= Student | Type | Project ========================================================= CAO YU | B/C | Set bipartite matching CHENG WEI | B | Hierarchical Knapsack Problem DAI BINGDIAN | B/C | Set bipartitle matching DO HUY HOANG | C | Dynamic Graph Problems NGO THANH SON | B | Least Common Ancestor PATEL DHAVAL... | B | Mining on Graphs REN YUAN | B | XML Filtering TAN YEE FAN | C | Complexity of Sudoku ZHANG ... MELVIN | B | Finding Gene Teams ZHENG XUN | C | Airport Gate Allocation 9 students | A | BAP Partitioning =========================================================
  3. 3. CS5234 Projects by Students (Spring 2007) (as of 27-March-2007) ========================================================= Student | Type | Project ========================================================= CAO YU | B/C | Set bipartite matching CHENG WEI | B | Hierarchical Knapsack Problem DAI BINGDIAN | B/C | Set bipartitle matching DO HUY HOANG | C | Dynamic Graph Problems NGO THANH SON | B | Least Common Ancestor PATEL DHAVAL... | B | Mining on Graphs REN YUAN | B | XML Filtering TAN YEE FAN | C | Complexity of Sudoku ZHANG ... MELVIN | B | Finding Gene Teams ZHENG XUN | C | Airport Gate Allocation 9 students | A | BAP Partitioning =========================================================
  4. 4. A conserved gene cluster is a set of genes which are located close to one another in multiple genomes.
  5. 5. A conserved gene cluster is a set of genes which are located close to one another in multiple genomes.
  6. 6. A conserved gene cluster is a set of genes which are located close to one another in multiple genomes.
  7. 7. A δ gene team is a maximal set of genes where the distance between adjacent genes is at most δ
  8. 8. A δ gene team is a maximal set of genes where the distance between adjacent genes is at most δ
  9. 9. A δ gene team is a maximal set of genes where the distance between adjacent genes is at most δ
  10. 10. A δ gene team is a maximal set of genes where the distance between adjacent genes is at most δ
  11. 11. FindTeams algorithm for computing δ gene team of two permutations in O(n lg2 n)
  12. 12. 2007
  13. 13. 2007
  14. 14. 2007
  15. 15. Date: Mon, 9 Jun 2008 09:33:51 +0800 From: "Melvin Zhang" To: "Leong Hon Wai" Subject: Re: ISMB 2008 Late-breaking Posters ... we can squeeze all the additional bookkeeping to compute the GTT for permutations into work done by the parameterized algorithm, which means it would have O(n lg^2 n) complexity in the worst case. Regards, Melvin
  16. 16. 2008
  17. 17. 2009
  18. 18. Date: Monday, September 14, 2009 5:52 PM From: "Biing-Feng Wang" To: "Melvin Zhang", "Leong Hon Wai" Subject: Re: a request Dear Prof. Leong and Melvin, Many thanks for sending me the JCB paper. (I had read its conference version and I enjoyed the reading very much.) Now, we are working on a paper which gives improved algorithms for the problems of finding gene teams and constructing gene team trees. I will send you a copy once it is ready. Best Regards, Biing-Feng
  19. 19. 2011
  20. 20. An O(n lg n) algorithm for finding gene teams
  21. 21. Formulate the Maximum Gap problem delete(p) p
  22. 22. Formulate the Maximum Gap problem delete(p) p Proposed a data structure that supports n delete operations in O(n lg lg n) time
  23. 23. 2013
  24. 24. 2013 Proposed a data structure that supports n delete operations in O(n α(n)) time
  25. 25. 2014 Constructing a Gene Team Tree in O(n lg n) time?

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