Related papers: Constructing $k$-ary Orientable Sequences with Asy…
Sequence organizations are viewed from two points: one is from informational redundancy or informational correlation (IC) and another is from k-mer frequency statistics. Two problems are investigated. The first is how the ICs exceed the…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…
Binary cyclic codes are worth studying due to their applications and theoretical importance. It is an important problem to construct an infinite family of cyclic codes with large minimum distance $d$ and dual distance $d^{\perp}$. In recent…
Given a clique-width $k$-expression of a graph $G$, we provide $2^{O(k)}\cdot n$ time algorithms for connectivity constraints on locally checkable properties such as Node-Weighted Steiner Tree, Connected Dominating Set, or Connected Vertex…
We revisit the \textsc{$k$-Secluded Tree} problem. Given a vertex-weighted undirected graph $G$, its objective is to find a maximum-weight induced subtree $T$ whose open neighborhood has size at most $k$. We present a fixed-parameter…
Randomly sampling an acyclic orientation on the complete bipartite graph $K_{n,k}$ with parts of size $n$ and $k$, we investigate the length of the longest path. We provide a probability generating function for the distribution of the…
The $k$-mismatch problem consists in computing the Hamming distance between a pattern $P$ of length $m$ and every length-$m$ substring of a text $T$ of length $n$, if this distance is no more than $k$. In many real-world applications, any…
A (v,k,t) covering design, or covering, is a family of k-subsets, called blocks, chosen from a v-set, such that each t-subset is contained in at least one of the blocks. The number of blocks is the covering's size}, and the minimum size of…
Datasets from several domains, such as life-sciences, semantic web, machine learning, natural language processing, etc. are naturally structured as acyclic graphs. These datasets, particularly those in bio-informatics and computational…
In this paper we consider a variant of population protocols in which agents are allowed to be connected by edges, known as the constructors model. During an interaction between two agents the relevant connecting edge can be formed,…
We explore labeled chip-firing on undirected $k$-ary trees, trees where every vertex has degree $k+1$. First, we extend known results for binary trees from Musiker and Nguyen, including the endgame and the locations of the smallest and…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Karloff? and Shirley recently proposed summary trees as a new way to visualize large rooted trees (Eurovis 2013) and gave algorithms for generating a maximum-entropy k-node summary tree of an input n-node rooted tree. However, the algorithm…
Consider a finite set of sources, each producing i.i.d. observations that follow a unique probability distribution on a finite alphabet. We study the problem of matching a finite set of observed sequences to the set of sources under the…
Let $r$ and $d$ be positive integers with $r<d$. Consider a random $d$-ary tree constructed as follows. Start with a single vertex, and in each time-step choose a uniformly random leaf and give it $d$ newly created offspring. Let ${\mathcal…
Subspace codes, and in particular cyclic subspace codes, have gained significant attention in recent years due to their applications in error correction for random network coding. In this paper, we introduce a new technique for constructing…
This paper investigates the approximability of the Longest Common Subsequence (LCS) problem. The fastest algorithm for solving the LCS problem exactly runs in essentially quadratic time in the length of the input, and it is known that under…
The traditional k nearest neighbor (kNN) approach uses a distance formula within a spherical region to determine the k closest training observations to a test sample point. However, this approach may not work well when test point is located…
We describe a data structure that supports access, rank and select queries, as well as symbol insertions and deletions, on a string $S[1,n]$ over alphabet $[1..\sigma]$ in time $O(\lg n/\lg\lg n)$, which is optimal even on binary sequences…
Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…