arXiv subjects

Shihyen Chen

Publications and source records attributed to Shihyen Chen.

2 recordsLinked to original sources

arXiv2015

A Review on the Tree Edit Distance Problem and Related Path-Decomposition Algorithms

An ordered labeled tree is a tree in which the nodes are labeled and the left-to-right order among siblings is relevant. The edit distance between two ordered labeled trees is the minimum cost of changing one tree into the other through a sequence of edit steps. In the literature, there are a class of algorithms based on different yet closely related path-decomposition schemes. This article reviews the principles of these algorithms, and studies the concepts related to the algorithmic complexities as a consequence of the decomposition schemes.

cs.DS↗

arXiv2015

Pattern Matching and Local Alignment for RNA Structures

The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between A-U and G-C. For secondary structures, these bonds have been traditionally assumed to be one-to-one and non-crossing. This paper considers pattern matching as well as local alignment between two RNA structures. For pattern matching, we present two algorithms, one for obtaining an exact match, the other for approximate match. We then present an algorithm for RNA local structural alignment.

cs.DS↗