Related papers: Genome assembly, from practice to theory: safe, co…
A "genome structure" is a labeled directed graph with vertices of degree 1 or 2. A set of operations over such graphs is fixed, and each of the operations has a certain cost, a strictly positive number. The transformation problem consists…
In recent years, Graph Neural Networks (GNNs) have achieved remarkable success in many graph mining tasks. However, scaling them to large graphs is challenging due to the high computational and storage costs of repeated feature propagation…
We consider the optimization problem of constructing a binary orthogonal array (OA) starting from a bigger one, by removing a specified amount of lines. In particular, we develop a genetic algorithm (GA) where the underlying chromosomes are…
An algorithm is developed for finding a close to optimal junction tree of a given graph G. The algorithm has a worst case complexity O(c^k n^a) where a and c are constants, n is the number of vertices, and k is the size of the largest…
In this paper, we provide a novel enumeration algorithm for the set of all walks of a given length within a directed graph. Our algorithm has worst-case constant delay between outputting succinct representations of such walks, after a…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
Let G be a directed graph with n vertices and non-negative weights in its directed edges, embedded on a surface of genus g, and let f be an arbitrary face of G. We describe a randomized algorithm to preprocess the graph in O(gn log n) time…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
We study the following problem: given an integer $k \ge 3$ and a simple graph $G$, sample a connected induced $k$-node subgraph of $G$ uniformly at random. This is a fundamental graph mining primitive with applications in social network…
The question to enumerate all inclusion-minimal connected dominating sets in a graph of order $n$ in time significantly less than $2^n$ is an open question that was asked in many places. We answer this question affirmatively, by providing…
In graph theory, the longest path problem is the problem of finding a simple path of maximum length in a given graph. For some small classes of graphs, the problem can be solved in polynomial time [2, 4], but it remains NP-hard on general…
We study the problems of finding a minimum cycle basis (a minimum weight set of cycles that form a basis for the cycle space) and a minimum homology basis (a minimum weight set of cycles that generates the $1$-dimensional…
An assembly is a large population of neurons whose synchronous firing is hypothesized to represent a memory, concept, word, and other cognitive categories. Assemblies are believed to provide a bridge between high-level cognitive phenomena…
In this work, we generalize the recently-introduced graph composition framework to the non-boolean setting. A quantum algorithm in this framework is represented by a hypergraph, where each hyperedge is adjacent to multiple vertices. The…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
We study the complexity of finding communication trees with the lowest possible completion time for rooted, irregular gather and scatter collective communication operations in fully connected, $k$-ported communication networks under a…
In network tomography, one goal is to identify a small set of failed links in a network, by sending a few packets through the network and seeing which reach their destination. This problem can be seen as a variant of combinatorial group…
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…