Related papers: A Fixed-Parameter Algorithm for Minimum Common Str…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
In this paper, the problem of the minimal description of the structure of a vector function f(x) over an $N$-dimensional interval is studied. Methods adaptively subdividing the original interval in smaller subintervals and evaluating f(x)…
In this work, we consider a restricted case of the well studied Sorting by Block Interchanges problem. We put an upper bound k on the length of the blocks (substrings) to be interchanged at each step. We call the problem Sorting by k-Block…
In this paper, we consider how to partition the parity-check matrices (PCMs) to reduce the hardware complexity and computation delay for the row layered decoding of quasi-cyclic low-density parity-check (QC-LDPC) codes. First, we formulate…
Given $n$ length-$\ell$ strings $S =\{s_1, ..., s_n\}$ over a constant size alphabet $\Sigma$ together with parameters $d$ and $k$, the objective in the {\em Consensus String with Outliers} problem is to find a subset $S^*$ of $S$ of size…
In this work, a graph partitioning problem in a fixed number of connected components is considered. Given an undirected graph with costs on the edges, the problem consists of partitioning the set of nodes into a fixed number of subsets with…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
A string $S[1,n]$ is a power (or tandem repeat) of order $k$ and period $n/k$ if it can decomposed into $k$ consecutive equal-length blocks of letters. Powers and periods are fundamental to string processing, and algorithms for their…
Finding the common subsequences of $L$ multiple strings has many applications in the area of bioinformatics, computational linguistics, and information retrieval. A well-known result states that finding a Longest Common Subsequence (LCS)…
String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge. In this paper, we…
In the classic Minimum Bisection problem we are given as input a graph $G$ and an integer $k$. The task is to determine whether there is a partition of $V(G)$ into two parts $A$ and $B$ such that $||A|-|B|| \leq 1$ and there are at most $k$…
Gibbons and Korach studied a fundamental problem in 1997: given an observed sequence of reads and writes of a multi-threaded program, does there exist an interleaving which is sequentially consistent? Apart from applications in testing…
Balanced partitioning is often a crucial first step in solving large-scale graph optimization problems, e.g., in some cases, a big graph can be chopped into pieces that fit on one machine to be processed independently before stitching the…
We extend a primal-dual fixed point algorithm (PDFP) proposed in [5] to solve two kinds of separable multi-block minimization problems, arising in signal processing and imaging science. This work shows the flexibility of applying PDFP…
Longest Common Subsequence ($LCS$) deals with the problem of measuring similarity of two strings. While this problem has been analyzed for decades, the recent interest stems from a practical observation that considering single characters is…
In this work, we consider a variant of the classical Longest Common Subsequence problem called Doubly-Constrained Longest Common Subsequence (DC-LCS). Given two strings s1 and s2 over an alphabet A, a set C_s of strings, and a function Co…
Consider two independent random strings having same length and taking values uniformly in a common finite alphabet. We study the order of the variance of the length of the longest common subsequences (LCS) of these strings when long blocks,…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for both unique string…
Our research deals with the optimization version of the set partition problem, where the objective is to minimize the absolute difference between the sums of the two disjoint partitions. Although this problem is known to be NP-hard and…
Our goal in this paper is to automatically extract a set of decision rules (rule set) that best explains a classification data set. First, a large set of decision rules is extracted from a set of decision trees trained on the data set. The…