Related papers: Approximating Weighted Duo-Preservation in Compara…

String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…

We consider the maximum vertex-weighted matching problem (MVM), in which non-negative weights are assigned to the vertices of a graph, the weight of a matching is the sum of the weights of the matched vertices, and we are required to…

Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…

Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…

In this paper, we introduce a novel iterative algorithm for the problem of phase-retrieval where the measurements consist of only the magnitude of linear function of the unknown signal, and the noise in the measurements follow Poisson…

Permutation Pattern Matching (or PPM) is a decision problem whose input is a pair of permutations $\pi$ and $\tau$, represented as sequences of integers, and the task is to determine whether $\tau$ contains a subsequence order-isomorphic to…

We study the problem of supervised learning a metric space under discriminative constraints. Given a universe $X$ and sets ${\cal S}, {\cal D}\subset {X \choose 2}$ of similar and dissimilar pairs, we seek to find a mapping $f:X\to Y$, into…

Joint distribution matching (JDM) problem, which aims to learn bidirectional mappings to match joint distributions of two domains, occurs in many machine learning and computer vision applications. This problem, however, is very difficult…

Recently, due to the genomic sequence analysis in several types of cancer, the genomic data based on {\em copy number profiles} ({\em CNP} for short) are getting more and more popular. A CNP is a vector where each component is a…

Submodular functions have many applications. Matchings have many applications. The bitext word alignment problem can be modeled as the problem of maximizing a nonnegative, monotone, submodular function constrained to matchings in a complete…

Given an indeterminate string pattern $p$ and an indeterminate string text $t$, the problem of order-preserving pattern matching with character uncertainties ($\mu$OPPM) is to find all substrings of $t$ that satisfy one of the possible…

In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…

An instance $I$ of the Stable Matching Problem (SMP) is given by a bipartite graph with a preference list of neighbors for every vertex. A swap in $I$ is the exchange of two consecutive vertices in a preference list. A swap can be viewed as…

We study variants of the mean problem under the $p$-Dynamic Time Warping ($p$-DTW) distance, a popular and robust distance measure for sequential data. In our setting we are given a set of finite point sequences over an arbitrary metric…

We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…

In this article we propose a Weighted Stochastic Mesh (WSM) Algorithm for approximating the value of a discrete and continuous time optimal stopping problem. We prove that in the discrete case the WSM algorithm leads to semi-tractability of…

Consider a set of labels $L$ and a set of trees ${\mathcal T} = \{{\mathcal T}^{(1), {\mathcal T}^{(2), ..., {\mathcal T}^{(k) \$ where each tree ${\mathcal T}^{(i)$ is distinctly leaf-labeled by some subset of $L$. One fundamental problem…

We study a weighted generalization of the fractional cut-covering problem, which we relate to the maximum cut problem via antiblocker and gauge duality. This relationship allows us to introduce a semidefinite programming (SDP) relaxation…

In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…

In the Strip Packing problem (SP), we are given a vertical half-strip $[0,W]\times[0,\infty)$ and a set of $n$ axis-aligned rectangles of width at most $W$. The goal is to find a non-overlapping packing of all rectangles into the strip such…