Related papers: Expected Density of Random Minimizers
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
We address a fundamental problem arising from analysis of biomolecular sequences. The input consists of two numbers $w_{\min}$ and $w_{\max}$ and a sequence $S$ of $n$ number pairs $(a_i,w_i)$ with $w_i>0$. Let {\em segment} $S(i,j)$ of $S$…
For positive integers $s$ and $k_1, k_2, ..., k_s$, let $w(k_1,k_2,...,k_s)$ be the minimum integer $n$ such that any $s$-coloring $\{1,2,...,n\} \to \{1,2,...,s\}$ admits a $k_i$-term arithmetic progression of color $i$ for some $i$, $1…
We consider the minimal k-grouping problem: given a graph G=(V,E) and a constant k, partition G into subgraphs of diameter no greater than k, such that the union of any two subgraphs has diameter greater than k. We give a silent…
We consider a connected undirected graph $G(n,m)$ with $n$ nodes and $m$ edges. A $k$-dominating set $D$ in $G$ is a set of nodes having the property that every node in $G$ is at most $k$ edges away from at least one node in $D$. Finding a…
Clustering is an important technique for identifying structural information in large-scale data analysis, where the underlying dataset may be too large to store. In many applications, recent data can provide more accurate information and…
Kosaraju in ``Computation of squares in a string'' briefly described a linear-time algorithm for computing the minimal squares starting at each position in a word. Using the same construction of suffix trees, we generalize his result and…
Given a stream of items each associated with a numerical value, its edit distance to monotonicity is the minimum number of items to remove so that the remaining items are non-decreasing with respect to the numerical value. The space…
Clustering is a fundamental problem in unsupervised machine learning with many applications in data analysis. Popular clustering algorithms such as Lloyd's algorithm and $k$-means++ can take $\Omega(ndk)$ time when clustering $n$ points in…
A word $x$ that is absent from a word $y$ is called minimal if all its proper factors occur in $y$. Given a collection of $k$ words $y_1,y_2,\ldots,y_k$ over an alphabet $\Sigma$, we are asked to compute the set…
The size $b$ of the smallest bidirectional macro scheme, which is arguably the most general copy-paste scheme to generate a given sequence, is considered to be the strictest reachable measure of repetitiveness. It is strictly lower-bounded…
Space efficient algorithms play a central role in dealing with large amount of data. In such settings, one would like to analyse the large data using small amount of "working space". One of the key steps in many algorithms for analysing…
A collection of $K$ random variables are called $(K,n)$-MDS if any $n$ of the $K$ variables are independent and determine all remaining variables. In the MDS variable generation problem, $K$ users wish to generate variables that are…
A string $w$ is called a minimal absent word (MAW) for another string $T$ if $w$ does not occur in $T$ but the proper substrings of $w$ occur in $T$. For example, let $\Sigma = \{\mathtt{a, b, c}\}$ be the alphabet. Then, the set of MAWs…
The sum of radii problem ($k$-MSR) asks, given a metric space on $n$ points, to place $k$ balls covering all points so as to minimize the sum of their radii. Despite extensive study from the perspectives of approximation and parameterized…
This paper defines multidimensional sequential optimization numbers and prove that the unsigned Stirling numbers of first kind are 1-dimensional sequential optimization numbers. This paper gives a recurrence formula and an upper bound of…
Given a string $w$ over a finite alphabet $\Sigma$ and an integer $K$, can $w$ be partitioned into strings of length at most $K$, such that there are no \emph{collisions}? We refer to this question as the \emph{string partition} problem and…
Clustering is a popular form of unsupervised learning for geometric data. Unfortunately, many clustering algorithms lead to cluster assignments that are hard to explain, partially because they depend on all the features of the data in a…
We study explicit constructions of min-wise hash families and their extension to $k$-min-wise hash families. Informally, a min-wise hash family guarantees that for any fixed subset $X\subseteq[N]$, every element in $X$ has an equal chance…
The notion of \emph{string attractor} has recently been introduced in [Prezza, 2017] and studied in [Kempa and Prezza, 2018] to provide a unifying framework for known dictionary-based compressors. A string attractor for a word…