The longest common subsequence (LCS) problem is a classic and well-studied problem in computer science with extensive applications in diverse areas ranging from spelling error corrections to molecular biology. This paper focuses on LCS for fixed alphabet size and fixed run-lengths (i.e., maximum number of consecutive occurrences of the same symbol). We show that LCS is NP-complete even when restricted to (i) alphabets of size 3 and run-length at most 1, and (ii) alphabets of size 2 and run-length at most 2 (both results are tight). For the latter case, we show that the problem is approximable within ratio 3/5.

We present a method for extracting contours from digital images, using techniques from computational geometry. Our approach is different from traditional pixel-based methods in image processing. Instead of working directly with pixels, we extract a set of oriented feature points from the input digital images, then apply classical geometric techniques, such as clustering, linking, and simplification, to find contours among these points. Experiments on synthetic and natural images show that our method can effectively extract contours, even from images with considerable noise; moreover, the extracted contours have a very compact representation.(176 pages) iv Acknowledgments Many thanks to my advisor, Dr. Minghui Jiang, for his encouragement and support, and for getting me interested in the field of computational geometry. His concern for me as a student and his advice have been a great help. He introduced me to the practice of doing research, and his many comments have helped me become a better researcher.

RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots. An RNA secondary structure is k-partite if it is the union of k pseudoknot-free sub-structures. Most known RNA secondary structures are either bipartite or tripartite. We show that there exists a constant number k such that any secondary structure can be modified into a k-partite secondary structure with approximately the same free energy. This offers a partial explanation of the prevalence of k-partite secondary structures with small k. We give a complete characterization of the computational complexities of recognizing k-partite secondary structures for all k ! 2, and show that this recognition problem is essentially the same as the k-colorability problem on circle graphs. We present two simple heuristics, iterated peeling and first-fit packing, for finding k-partite RNA secondary structures. For maximizing the number of base pair stackings, our iterated peeling heuristic achieves a constant approximation ratio of at most k for 2 k 5, and at most 6 1 À (1 À 6=k) k 6 1 À e À 6 56:01491 for k ! 6. Experiment on sequences from PseudoBase shows that our first-fit packing heuristic outperforms the leading method HotKnots in predicting RNA secondary structures with pseudoknots. Supplementary Material can be found at www.libertonline.com.

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Given k labelings of a finite d-dimensional grid, define the combined distance between two labels to be the sum of the ℓ 1 -distance between the two labels in each labeling. We present asymptotically optimal constructions of k labelings of cubical d-dimensional grids which maximize the minimum combined distance.