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Longest common subsequence INPUT: two strings OUTPUT: longest common subsequence ACTGAACTCTGTGCACT TGACTCAGCACAAAAAC Travelling Salesman Problem if S={u,v} then K[S,u ...

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Fast Subsequence Matching in Time-Series Databases Christos Faloutsos M. Ranganathan Yannis Manolopoulos Department of Computer Science and ISR University of Maryland ...

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Protein: linear sequence of amino acids. Protein subcellular localization ... Sequence information alone (no additional data) Class imbalance ...

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Fast Subsequence Matching in Time-Series Databases. Author: Christos Faloutsos etc. ... False alarm: non-qualified sequence not discarded, Not so bad. Discrete ...

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Not discrete symbols. Applications for time-series databases. 5. Financial data. Astrological data. Weather data. Sociological data ...many more. Example database ...

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Dynamic programming algorithms for all-pairs shortest path and ... min(dij(k-1),dik(k-1)+dkj(k-1 ... Figure 3 Comparison of two strings Longest common ...

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Longest Common Subsequence (LCS) Dr. Nancy Warter-Perez Outline Longest Common Subsequence (LCS) Problem Definition Scoring Algorithm Printing Algorithm Longest ...

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Whole Matching (Previous Work) ... The structure of a leaf node and a non-leaf node. Proposed Method (cont.) Two questions ... time series matching by wavelets ...

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Brute force solution. Writing a recurrence equation. The ... Brute force solution. Solution: For every subsequence of x, check if it is a subsequence of y. ...

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George Liu / Luis L. Perez. Time series? Definition. Applications. Financial markets ... Given a database S with n sequences, all of them equally long, and a query ...

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on Management of Data, pages 419--429, Minneapolis, May 1994. presented by ... find companies whose stock prices move similarly ...

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Create two matrices with n 1 rows and m 1 columns (superimpose into 1 matrix for ... if vi == wj. si,j = si-1,j-1 1; bi,j = DIAG. else if si-1,j = si,j-1. si, ...

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Longest Common Rigid Subsequence Bin Ma and Kaizhong Zhang Department of Computer Science University of Western Ontario Ontario, Canada. (Rigid) Subsequence ...

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Longest Increasing Subsequences in Windows. Based on Canonical ... An O(n log log n) algorithm is possible by using van Emde Boas tree on a permutation. ...

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Title: Longest Common Subsequences and Its Variants Author: Last modified by: ynag Created Date: 11/11/2008 7:29:26 AM Document presentation format

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Longest Common Subsequence (LCS) Dr. Nancy Warter-Perez. June 22, 2005. June 22, 2005 ... Longest Common Subsequence. 5. Indels insertions and deletions (e.g., gaps) ...

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Sentiment Classification. using Word Sub-Sequences. and ... Document sentiment classification ... Positive( ) weight shows positive sentiment polarity ...

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LIS(A)= length of longest increasing subsequence of sequence A ... existing deterministic algorithms for quantile approximation in all intervals [LLXY, ICDE04] ...

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aracari: IBM cluster, 64 2-way SMP Pentium3 1.4 GHz/128 GB of memory ... aracari 0.00055 ns/op 1.8 G op/s. May 09/2006 ... aracari/MPI 32 Processors. May 09/2006 ...

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Finding a sequence of greatest possible length that can be obtained ... O(min(pm, mLgm p(n-p)]) Goeman, Clausen. 1999. contours. 3. O(pm) Apostolico, et al. ...

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Problem: Given a sequence of (possibly negative) integers find ... which is slicker but perhaps harder to understand.) 2/13/06. Lecture Notes 8. 15. Program 4 ...

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Some say 'Nobody really Knows!' MS Visual C Express Edition Why? ... has all the necessary tool to write, debug, test, and compile parallel programs. ...

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Title: The Communication and Streaming Complexity of Computing the Longest Common and Increasing Subsequences Author: David Woodruff Last modified by

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Hydrophobicity Sliding Window Program Using Functions (1) #include iostream #include string ... program will compute the hydrophobicity of an sequence of ...

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Computational Molecular Biology An Algorithmic Approach, Pavel Pevzner. June 25, 2003 ... Longest Common Subsequence (LCS) Problem ...

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Brenda S. Baker, Raffaele Giancarlo. Journal of Algorithms, Vol. 42, 2002, pp. 231-254 ... We provide a new sparse dynamic programming technique that extends the Hunt ...

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Arc-annotated sequence usage. The secondary and tertiary structure of RNA ... Alas, I know little about dynamic programming -but I know divide-and- conquer ...

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A Linear Time Algorithm for Finding All Maximal Subsequences. Walter L. Ruzzo and Martin Tompa ... A subsequence S is a maximal subsequence of A if. P1.all ...

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Longest common subsequence (LCS) Problem. Notation: let Xk be the sequence: x1,x2,..., xk ... subsequence common to them: Elements in the common subsequence ...

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Dynamic Programming Longest Common Subsequence

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Dynamic Programming Longest Common Subsequence

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Longest Common Subsequence (LCS) Application: comparison of two DNA strings ... Longest Common Subsequence: X = A B C B D A B. Y = B D C A B A ...

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????? BIG O ??? loop ????? (???) ?????????????? Nested loop ?????????? ... Maximum Subsequence Sum, ???????????????? code ?????? Big O ???????? ...

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Lecture 8: Dynamic Programming Shang-Hua Teng Longest Common Subsequence Biologists need to measure how similar strands of DNA are to determine how closely related an ...

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Longest Increasing Subsequence. Anna Gal UT Austin. Parikshit Gopalan U. Washington ... LIS( ): Length of Longest Increasing Subsequence. 5 7 8 1 4 2 10 3 6 9 ...

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Inexact Matching Charles Yan 2008 Longest Common Subsequence Given two strings, find a longest subsequence that they share substring vs. subsequence of a string ...

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Example : Longest Uprising Subsequence ... Example : Longest Uprising Subsequence. But it is not yet done! ... of the longest uprising sequence terminating at ...

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Merging of relaxed Subsequences adds another level of freedom to test compaction. ... A relaxed test set facilitates Subsequence Merging and State Traversal. ...

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The longest common subsequence problem. Dynamic programming algorithms for alignment ... one, check to see if it is a subsequence of v and w. Very expensive...

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Microcode. An other type of CU is Hardwire. Subsequence of Instruction ... Instruction Decoder ?????????????? CU ??????????????????? Microcode ?????? Sequencer ...

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Divide recursively into smaller subsequences. Quicksort. n elements stored in A[1...n] ... C = subsequence received along ith dimension. Merge B1 and C into B. else ...

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Longest common subsequence. A subsequence is formed from a list by deleting zero or more elements (the ... an initial sublist of a list. If x = (a1,a2,a3, ...

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Hamming distance. Lifshits (2007) #P-complete ... Hamming distance. Longest common subsequence. Longest common substring #P-comprete [Lifshits 07] ...

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Split the TS into subsequences and symbolize them ... Random Projection symbolization. Applies PAA (Piecewise Aggregate Approximation) Input TS: ...

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Basic algorithm returns length of longest common subsequence: 6. Can return trace of subsequence if desired: GTCCAG. GATCCAGT. GTACACTGAG ...

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(1977) Hunt, Szymanski - A fast algorithm for computing longest common subsequence. ... (1992) Eppstein, Galil, Giancarlo, Italiano - Sparse dynamic programming I: ...

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... LIS (Longest Increasing Subsequences), Smith-Waterman alignment algorithm ... Use the Smith-Waterman alignments ( short gaps) 13. MUMmer Output. 14. Observations ...

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Basic objective: find a pair of subsequences within S with maximum similarity ... Specification: the two sequences must be consecutive (tandem repeat) ...

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Let D(i, j) refer to the dynamic time warping distance between the subsequences. x1, x2, ..., xi ... Project the query Q in the same feature space ...

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Calcuate fitness score of each position of out sequence ... Fitness Score. Ax = Qx / Px. Qx: probability of generating subsequence x from current motif ...

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(Presence of Long Subsequence and its Reverse Complement Lead to Stabilization ) ... Hamming, Reverse Complement Hamming Distance at Least d. Longest Length ...

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Conquer the sub-problems by solving ... Conquer: Sort the two subsequences recursively ... Conquer: solving 2 sub-problem takes 2T(n/2) Combine: merging ...

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Mining sequence patterns in transactional databases. Mining ... Y. Moon, K. Whang, W. Loh. Duality Based Subsequence Matching in Time-Series Databases, ICDE'02 ...

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There are, however, reasons to use objects in place of primitives, and the Java ... CharSequence subSequence(int beginIndex, int endIndex) ...

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Chunks are non-recursive. Chunk parsing can be implemented with a finite state machine ... If matching subsequences overlap, the first one gets priority ...

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Smith and Waterman approach: Aligns subsequences of given sequences ... Smith-Waterman. Time. Implementation. CMSC 838T Presentation. Evaluation ...

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