Related papers: A Fixed-Parameter Algorithm for Minimum Common Str…
Consider two or more strings $\mathbf{x}^1,\mathbf{x}^2,\ldots,$ that are concatenated to form $\mathbf{x}=\langle \mathbf{x}^1,\mathbf{x}^2,\ldots \rangle$. Suppose that up to $\delta$ deletions occur in each of the concatenated strings.…
We consider the following multi-component sparse PCA problem: given a set of data points, we seek to extract a small number of sparse components with disjoint supports that jointly capture the maximum possible variance. These components can…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
Cardinality-constrained diameter partitioning asks for a partition of $n$ items into two classes of prescribed sizes that minimizes the larger of the two class diameters. We give an $O(n^2)$ algorithm and a matching $\Omega(n^2)$ lower…
In group testing, the goal is to identify a subset of defective items within a larger set of items based on tests whose outcomes indicate whether at least one defective item is present. This problem is relevant in areas such as medical…
We investigate the number of nested string replacements required to reduce a string of identical characters to one character.
We formulate low-level malware detection using algorithms based on feature matching as Order-based Malware Detection with Critical Instructions (General-OMDCI): given a pattern in the form of a sequence \(M\) of colored blocks, where each…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Binary size reduction is an increasingly important optimization objective for compilers. One emerging technique is function merging, where multiple similar functions are merged into one, thereby eliminating redundancy. The SOTA approach to…
We consider so-called $N$-fold integer programs (IPs) of the form $\max\{c^T x : Ax = b, \ell \leq x \leq u, x \in \mathbb Z^{nt}\}, where $A \in \mathbb Z^{(r+sn)\times nt} consists of $n$ arbitrary matrices $A^{(i)} \in \mathbb Z^{r\times…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
We study two optimization problems on simplicial complexes with homology over $\mathbb{Z}_2$, the minimum bounded chain problem: given a $d$-dimensional complex $\mathcal{K}$ embedded in $\mathbb{R}^{d+1}$ and a null-homologous…
Consistent hashing is a technique for distributing data across a network of nodes in a way that minimizes reorganization when nodes join or leave the network. It is extensively applied in modern distributed systems as a fundamental…
In the trace reconstruction problem our goal is to learn an unknown string $x\in \{0,1\}^n$ given independent traces of $x$. A trace is obtained by independently deleting each bit of $x$ with some probability $\delta$ and concatenating the…
Linear nested codes, where two or more sub-codes are nested in a global code, have been proposed as candidates for reliable multi-terminal communication. In this paper, we consider nested array-based spatially coupled low-density…
Minimum $k$-Section denotes the NP-hard problem to partition the vertex set of a graph into $k$ sets of sizes as equal as possible while minimizing the cut width, which is the number of edges between these sets. When $k$ is an input…
Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e. random graphs…
The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing,…
We study the optimization version of the equal cardinality set partition problem (where the absolute difference between the equal sized partitions' sums are minimized). While this problem is NP-hard and requires exponential complexity to…
Puncturing is a well-known coding technique widely used for constructing rate-compatible codes. In this paper, we consider the problem of puncturing low-density parity-check codes and propose a new algorithm for intentional puncturing. The…