Related papers: Prefix Block-Interchanges on Binary and Ternary St…
In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, $n$ nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and…
Quadratic Unconstrained Binary Optimization (QUBO) is a standard NP-hard optimization problem. Recently, it has gained renewed interest through quantum computing, as QUBOs directly reduce to the Ising model, on which quantum annealing…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
A novel adaptive binary decoding algorithm for LDPC codes is proposed, which reduces the decoding complexity while having a comparable or even better performance than corresponding non-adaptive alternatives. In each iteration the variable…
Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…
We study systems of String Equations where block variables need to be assigned strings so that their concatenation gives a specified target string. We investigate this problem under a multivariate complexity framework, searching for…
We explore the hypothesis that poor compositional generalization in neural networks is caused by difficulties with learning effective routing. To solve this problem, we propose the concept of block-operations, which is based on splitting…
This paper provides simple lower bounds on the number of iterations which is required for successful message-passing decoding of some important families of graph-based code ensembles (including low-density parity-check codes and variations…
We propose an efficient encoding algorithm for the binary and non-binary low-density parity-check codes. This algorithm transforms the parity part of the parity-check matrix into a block triangular matrix with low weight diagonal…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…
The orbit problem is at the heart of symmetry reduction methods for model checking concurrent systems. It asks whether two given configurations in a concurrent system (represented as finite strings over some finite alphabet) are in the same…
Pairwise sequence comparison is one of the most fundamental problems in string processing. The most common metric to quantify the similarity between sequences S and T is edit distance, d(S,T), which corresponds to the number of characters…
We study the problems of finding a shortest synchronizing word and its length for a given prefix code. This is done in two different settings: when the code is defined by an arbitrary decoder recognizing its star and when the code is…
The Priority Inheritance Protocol (PIP) is arguably the best-known protocol for resource sharing under real-time constraints. Its importance in modern applications is undisputed. Nevertheless, because jobs may be blocked under PIP for a…
In this work, we study the problem of scheduling a maximal set of transmitters subjected to an interference constraint across all the nodes. Given a set of nodes, the problem reduces to finding the maximum cardinality of a subset of nodes…
In distributed computing, the renaming problem requires $n$ nodes with unique identities from a large namespace $[N]$ to acquire new, distinct identities from a smaller target namespace $[M]$. A solution is strong if $M=n$, and is…
Motivated by applications in polymer-based data storage, we study the problem of reconstructing a string from part of its composition multiset. We give a full description of the structure of the strings that cannot be uniquely reconstructed…
This paper considers the task of performing binary search under noisy decisions, focusing on the application of target area localization. In the presence of noise, the classical partitioning approach of binary search is prone to error…
This manuscript describes the notions of blocker and interdiction applied to well-known optimization problems. The main interest of these two concepts is the capability to analyze the existence of a combinatorial structure after some…